diff --git a/.github/workflows/pylint_on_pull_request.yml b/.github/workflows/pylint_on_pull_request.yml index d6b5e73213..dfb9bf6f68 100644 --- a/.github/workflows/pylint_on_pull_request.yml +++ b/.github/workflows/pylint_on_pull_request.yml @@ -22,7 +22,7 @@ jobs: BASE_REF: ${{ github.event.pull_request.base.ref }} - name: Get Base Lint Score run: | - echo ::set-env name=BASE_LINT::$(git diff --name-only --diff-filter=M $HEAD_REF | grep -E "\.py" | xargs pylint | grep -E -o "at [0-9.-]+" | grep -E -o [0-9.-]+) + echo BASE_LINT=$(git diff --name-only --diff-filter=M $HEAD_REF | grep -E "\.py" | xargs pylint | grep -E -o "at [0-9.-]+" | grep -E -o [0-9.-]+) >> $GITHUB_ENV env: HEAD_REF: ${{ github.event.pull_request.head.ref }} if: always() @@ -31,17 +31,20 @@ jobs: env: HEAD_REF: ${{ github.event.pull_request.head.ref }} - name: Get Lint Delta Sign (+/-) - run: echo ::set-env name=PASSING_SCORE::$(git diff --name-only --diff-filter=M $BASE_REF | grep -E "\.py" | xargs pylint | grep -Eo "10, [+-]" | grep -Eo [+-] ) + run: | + echo PASSING_SCORE=$(git diff --name-only --diff-filter=M $BASE_REF | grep -E "\.py" | xargs pylint | grep -Eo "10, [+-]" | grep -Eo [+-] ) >> $GITHUB_ENV env: BASE_REF: ${{ github.event.pull_request.base.ref }} if: always() - name: Get Head Lint Score - run: echo ::set-env name=HEAD_LINT::$(git diff --name-only --diff-filter=M $BASE_REF | grep -E "\.py" | xargs pylint | grep -E -o "at [0-9.-]+" | grep -E -o [0-9.-]+) + run: | + echo HEAD_LINT=$(git diff --name-only --diff-filter=M $BASE_REF | grep -E "\.py" | xargs pylint | grep -E -o "at [0-9.-]+" | grep -E -o [0-9.-]+) >> $GITHUB_ENV env: BASE_REF: ${{ github.event.pull_request.base.ref }} if: always() - name: Get Added Files Lint Score - run: echo ::set-env name=ADDED_LINT::$(git diff --name-only --diff-filter=A $BASE_REF | grep -E "\.py" | xargs pylint | grep -E -o "at [0-9.-]+" | grep -E -o [0-9.-]+) + run: | + echo ADDED_LINT=$(git diff --name-only --diff-filter=A $BASE_REF | grep -E "\.py" | xargs pylint | grep -E -o "at [0-9.-]+" | grep -E -o [0-9.-]+) >> $GITHUB_ENV env: BASE_REF: ${{ github.event.pull_request.base.ref }} if: always() diff --git a/.gitignore b/.gitignore index 17adea81b3..f425602443 100644 --- a/.gitignore +++ b/.gitignore @@ -8,6 +8,12 @@ stochss-model-editor.html stochss-workflow-manager.html stochss-workflow-selection.html stochss-project-manager.html +multiple-plots-page.html +stochss-domain-editor.html +stochss-loading-page.html +stochss-project-browser.html +stochss-quick-start.html +stochss-user-home.html *.swp *.swo package-lock.json diff --git a/__version__.py b/__version__.py index 29e0d89856..03724dc3d0 100644 --- a/__version__.py +++ b/__version__.py @@ -5,7 +5,7 @@ # @website https://github.com/stochss/stochss # ============================================================================= -__version__ = '2.1.6' +__version__ = '2.3.2' __title__ = 'StochSS' __description__ = 'StochSS is an integrated development environment (IDE) \ for simulation of biochemical networks.' diff --git a/client/app.js b/client/app.js index 27868bb188..9aac1d1023 100644 --- a/client/app.js +++ b/client/app.js @@ -17,7 +17,11 @@ along with this program. If not, see . */ //var config = require('./config.js')(process.env.NODE_ENV); +let xhr = require('xhr'); +let $ = require('jquery'); let path = require('path'); +//support files +let modals = require('./modals'); let routePrefix = 'stochss'; let apiPrefix = path.join(routePrefix, 'api'); @@ -77,14 +81,128 @@ var BrowserDetect = { ] }; +let changeCollapseButtonText = (view, e) => { + let source = e.target.dataset.hook; + let isBtn = $(view.queryByHook(source)).attr("class").includes("btn"); + let collapseContainer = $(view.queryByHook(source).dataset.target); + if(isBtn && !collapseContainer.attr("class").includes("collapsing")) { + let collapseBtn = $(view.queryByHook(source)); + let text = collapseBtn.text(); + text === '+' ? collapseBtn.text('-') : collapseBtn.text('+'); + } +}; + +let registerRenderSubview = (parent, view, hook) => { + parent.registerSubview(view); + parent.renderSubview(view, parent.queryByHook(hook)); +}; + +let getXHR = (endpoint, { + always = function (err, response, body) {}, success = function (err, response, body) {}, + error = function (err, response, body) {}}={}) => { + xhr({uri: endpoint, json: true}, function (err, response, body) { + if(response.statusCode < 400) { + success(err, response, body); + }else if(response.statusCode < 500) { + error(err, response, body); + }else{ + console.log("Critical Error Detected"); + } + always(err, response, body); + }); +}; + +let postXHR = (endpoint, data, { + always = function (err, response, body) {}, success = function (err, response, body) {}, + error = function (err, response, body) {}}={}, isJSON) => { + xhr({uri: endpoint, json: isJSON !== undefined ? isJSON : true, method: "post", body: data}, function (err, response, body) { + if(response.statusCode < 400) { + success(err, response, body); + }else if(response.statusCode < 500) { + error(err, response, body); + }else{ + console.log("Critical Error Detected"); + } + always(err, response, body); + }); +}; + let getBrowser = () => { BrowserDetect.init(); return {"name":BrowserDetect.browser,"version":BrowserDetect.version}; } +let validateName = (input, rename = false) => { + var error = "" + if(input.endsWith('/')) { + error = 'forward' + } + var invalidChars = "`~!@#$%^&*=+[{]}\"|:;'<,>?\\" + if(rename) { + invalidChars += "/" + } + for(var i = 0; i < input.length; i++) { + if(invalidChars.includes(input.charAt(i))) { + error = error === "" || error === "special" ? "special" : "both" + } + } + return error +} + +let newWorkflow = (parent, mdlPath, isSpatial, type) => { + if(document.querySelector('#newWorkflowModal')) { + document.querySelector('#newWorkflowModal').remove() + } + let self = parent; + let ext = isSpatial ? /.smdl/g : /.mdl/g + let name = mdlPath.split('/').pop().replace(ext, "") + let modal = $(modals.newWorkflowHtml(name, type)).modal(); + let okBtn = document.querySelector('#newWorkflowModal .ok-model-btn'); + let input = document.querySelector('#newWorkflowModal #workflowNameInput'); + okBtn.disabled = false; + input.addEventListener("keyup", function (event) { + if(event.keyCode === 13){ + event.preventDefault(); + okBtn.click(); + } + }); + input.addEventListener("input", function (e) { + let endErrMsg = document.querySelector('#newWorkflowModal #workflowNameInputEndCharError') + let charErrMsg = document.querySelector('#newWorkflowModal #workflowNameInputSpecCharError') + let error = validateName(input.value) + okBtn.disabled = error !== "" || input.value.trim() === "" + charErrMsg.style.display = error === "both" || error === "special" ? "block" : "none" + endErrMsg.style.display = error === "both" || error === "forward" ? "block" : "none" + }); + okBtn.addEventListener('click', function (e) { + modal.modal("hide"); + let typeCode = type === "Ensemble Simulation" ? "_ES" : "_PS"; + let wkflFile = input.value.trim() + typeCode + ".wkfl"; + if(mdlPath.includes(".proj") && !mdlPath.includes(".wkgp")){ + var wkflPath = path.join(path.dirname(mdlPath), "WorkflowGroup1.wkgp", wkflFile); + }else{ + var wkflPath = path.join(path.dirname(mdlPath), wkflFile); + } + let queryString = "?path=" + wkflPath + "&model=" + mdlPath + "&type=" + type; + let endpoint = path.join(getApiPath(), "workflow/new") + queryString; + getXHR(endpoint, { + success: function (err, response, body) { + window.location.href = path.join(getBasePath(), "stochss/workflow/edit") + "?path=" + body.path; + } + }); + }); +} + module.exports = { routePrefix: routePrefix, getApiPath: getApiPath, getBasePath: getBasePath, - getBrowser: getBrowser + getBrowser: getBrowser, + registerRenderSubview: registerRenderSubview, + changeCollapseButtonText: changeCollapseButtonText, + newWorkflow: newWorkflow, + getXHR: getXHR, + postXHR: postXHR }; + + diff --git a/client/modals.js b/client/modals.js index bcef01879e..c55db1f6b8 100644 --- a/client/modals.js +++ b/client/modals.js @@ -190,6 +190,39 @@ let templates = { ` + }, + fileSelect : (modalID, fileID, locationID, title, label, files) => { + return ` + ` } } @@ -200,10 +233,14 @@ module.exports = { return templates.confirmation(modalID, title) }, - moveToTrashConfirmHtml : (fileType) => { + moveToTrashConfirmHtml : (fileType, newProjectFormat=false) => { let modalID = "moveToTrashConfirmModal" let title = `Move this ${fileType} to trash?` + if(newProjectFormat) { + let message = "The workflows for this model will be archived" + return templates.confirmation_with_message(modalID, title, message); + } return templates.confirmation(modalID, title) }, emptyTrashConfirmHtml : () => { @@ -237,17 +274,19 @@ module.exports = { return templates.input(modalID, inputID, title, label, value) }, - newProjectModelHtml : (options) => { + newProjectModelHtml : (files) => { let modalID = "newProjectModelModal" - let selectID = "modelPathInput" + let fileID = "modelFileInput" + let locationID = "modelPathInput" let title = "Add Existing Model to Project" - let label = "Path to the Model" - options = options.map(function (name) { - return `` + let label = "Models: " + files = files.map(function (file) { + return `` }) - options = options.join(" ") + files.unshift(``) + files = files.join(" ") - return templates.select(modalID, selectID, title, label, options) + return templates.fileSelect(modalID, fileID, locationID, title, label, files) }, newProjectModelSuccessHtml : (message) => { let modalID = "newProjectModelSuccessModal" @@ -428,6 +467,28 @@ module.exports = { return templates.message(modalID, title, message) }, + newWorkflowHtml: (name, type) => { + let modalID = "newWorkflowModal" + let inputID = "workflowNameInput" + let title = `New ${type} Workflow` + let label = "Name:" + let value = name + + return templates.input(modalID, inputID, title, label, value); + }, + updateFormatHtml: (fileType) => { + let modalID = `update${fileType}FormatModal` + let title = `Update ${fileType} Format` + if(fileType === "Project") { + fileType += "s and Workflow"; + var target = "project and its workflows"; + }else{ + var target = "workflow"; + } + let message = `StochSS ${fileType}s have a new format. Would you like to update this ${target} to the new format?` + + return templates.confirmation_with_message(modalID, title, message); + }, renderDefaultModeModalHtml : () => { let concentrationDesciption = `Variables will only be represented using continuous (floating point) values.`; let populationDescription = `Population - Variables will only be represented using discrete (integer count) values.`; diff --git a/client/models/creator.js b/client/models/creator.js index 103eec1764..ee9d3be24d 100644 --- a/client/models/creator.js +++ b/client/models/creator.js @@ -24,7 +24,8 @@ module.exports = State.extend({ fname: 'string', lname: 'string', email: 'string', - organization: 'string' + organization: 'string', + elementID: 'string' }, initialize: function(attrs, options) { State.prototype.initialize.apply(this, arguments) diff --git a/client/models/models.js b/client/models/creators.js similarity index 58% rename from client/models/models.js rename to client/models/creators.js index d35fba09e9..df67172530 100644 --- a/client/models/models.js +++ b/client/models/creators.js @@ -16,11 +16,24 @@ You should have received a copy of the GNU General Public License along with this program. If not, see . */ -var app = require('ampersand-app'); -var RestCollection = require('ampersand-rest-collection'); -var Model = require('./model'); -var path = require('path'); +//collections +let Collection = require('ampersand-collection'); +//models +let Creator = require('./creator'); -module.exports = RestCollection.extend({ - model: Model +module.exports = Collection.extend({ + model: Creator, + indexes: ["elementID"], + addCreator: function (creatorInfo) { + let elementID = "C" + (this.length + 1); + let creator = new Creator({ + fname: creatorInfo.fname, + lname: creatorInfo.lname, + email: creatorInfo.email, + organization: creatorInfo.organization, + elementID: elementID + }); + this.add(creator); + return creator; + } }); diff --git a/client/models/domain.js b/client/models/domain.js index 7d802531f5..73c34cbe6a 100644 --- a/client/models/domain.js +++ b/client/models/domain.js @@ -32,7 +32,8 @@ module.exports = State.extend({ size: 'number', x_lim: 'object', y_lim: 'object', - z_lim: 'object' + z_lim: 'object', + static: 'boolean' }, collections: { types: Types, diff --git a/client/models/job.js b/client/models/job.js new file mode 100644 index 0000000000..d519da4f3c --- /dev/null +++ b/client/models/job.js @@ -0,0 +1,78 @@ +/* +StochSS is a platform for simulating biochemical systems +Copyright (C) 2019-2020 StochSS developers. + +This program is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with this program. If not, see . +*/ + +//models +let Model = require('./model'); +let Settings = require('./settings'); +let State = require('ampersand-state'); + +module.exports = State.extend({ + children: { + model: Model, + settings: Settings + }, + session: { + directory: 'string', + logs: 'string', + startTime: 'string', + status: 'string' + }, + derived: { + elementID: { + deps: ["collection"], + fn: function () { + if(this.collection) { + return this.collection.parent.elementID + "J" + (this.collection.indexOf(this) + 1); + } + return "J-"; + } + }, + name: { + deps: ["directory"], + fn: function () { + return this.directory.split("/").pop(); + } + }, + fmtStartTime: { + deps: ["startTime"], + fn: function () { + let date = new Date(this.startTime); + let months = ['Jan.', 'Feb.', 'Mar.', 'Apr.', 'May', 'Jun.', 'Jul.', 'Aug.', 'Sept.', 'Oct.', 'Nov.', 'Dec.']; + var stamp = months[date.getMonth()] + " "; + stamp += date.getDate() + ", "; + stamp += date.getFullYear() + " "; + let hours = date.getHours(); + let ampm = hours >= 12 ? 'PM' : 'AM'; // get AM or PM based on hours + hours = hours%12; // format hours to 12 hour time format + hours = hours ? hours : 12; // replace 0 with 12 + let minutes = date.getMinutes(); + minutes = minutes < 10 ? '0' + minutes : minutes; // format minutes to always have two chars + let timeZone = date.toString().split('(').pop().split(')').shift(); // get the timezone from the date + if(timeZone.includes(" ")){ + tzparts = timeZone.split(" "); + tzparts = tzparts.map(function (element) { + return element.charAt(0); + }) + timeZone = tzparts.join(""); + } + // timeZone = timeZone.replace('(', '').replace(')', '') // remove the '()' from the timezone + return stamp + hours + ":" + minutes + " " + ampm + " " + timeZone; + } + } + } +}); \ No newline at end of file diff --git a/client/views/view-parameter.js b/client/models/jobs.js similarity index 79% rename from client/views/view-parameter.js rename to client/models/jobs.js index a5ba33c0a4..01ecde1afb 100644 --- a/client/views/view-parameter.js +++ b/client/models/jobs.js @@ -16,11 +16,11 @@ You should have received a copy of the GNU General Public License along with this program. If not, see . */ -//views -var View = require('ampersand-view'); -//templates -var template = require('../templates/includes/viewParameters.pug'); +//collections +let Collection = require('ampersand-collection'); +//models +let Job = require('./job'); -module.exports = View.extend({ - template: template, -}); \ No newline at end of file +module.exports = Collection.extend({ + model: Job +}); diff --git a/client/models/plots.js b/client/models/metadata.js similarity index 82% rename from client/models/plots.js rename to client/models/metadata.js index bd6a22cbaf..2a80da336c 100644 --- a/client/models/plots.js +++ b/client/models/metadata.js @@ -17,15 +17,11 @@ along with this program. If not, see . */ //models -var State = require('ampersand-state'); +let State = require('ampersand-state'); module.exports = State.extend({ props: { - key: 'string', - title: 'string', - xaxis: 'string', - yaxis: 'string', - stamp: 'number', - species: 'object' + description: 'string', + creators: 'object' } -}); \ No newline at end of file +}); diff --git a/client/models/model.js b/client/models/model.js index 64915fe68c..b8b59ab441 100644 --- a/client/models/model.js +++ b/client/models/model.js @@ -18,10 +18,9 @@ along with this program. If not, see . var app = require('../app'); var path = require('path'); -var xhr = require('xhr'); //models var Model = require('ampersand-model'); -var ModelSettings = require('./model-settings'); +var TimespanSettings = require('./timespan-settings'); var Domain = require('./domain'); //collections var Species = require('./species'); @@ -53,7 +52,7 @@ module.exports = Model.extend({ functionDefinitions: FunctionDefinitions }, children: { - modelSettings: ModelSettings, + modelSettings: TimespanSettings, domain: Domain }, session: { @@ -65,6 +64,24 @@ module.exports = Model.extend({ valid: 'boolean', error: 'object' }, + derived: { + elementID: { + deps: ["collection"], + fn: function () { + if(this.collection) { + return "M" + (this.collection.indexOf(this) + 1); + } + return "M-"; + } + }, + open: { + deps: ["directory"], + fn: function () { + let queryStr = "?path=" + this.directory; + return path.join(app.getBasePath(), "stochss/models/edit") + queryStr; + } + } + }, initialize: function (attrs, options){ Model.prototype.initialize.apply(this, arguments); this.species.on('add change remove', this.updateValid, this); @@ -119,9 +136,9 @@ module.exports = Model.extend({ self.parameters.trigger('update-parameters', parameter.compID, parameter); }); if(cb) { - this.save({success: cb}); + app.postXHR(this.url(), this.toJSON(), { success: cb }); }else{ - this.save() + app.postXHR(this.url(), this.toJSON()); } }, }); diff --git a/client/models/parameter-sweep-settings.js b/client/models/parameter-sweep-settings.js index f4a5609836..1b746a5b2e 100644 --- a/client/models/parameter-sweep-settings.js +++ b/client/models/parameter-sweep-settings.js @@ -16,27 +16,32 @@ You should have received a copy of the GNU General Public License along with this program. If not, see . */ +//collections +let SweepParameters = require('./sweep-parameters'); //models -var State = require('ampersand-state'); -var Parameter = require('./parameter'); -var Species = require('./specie'); +let State = require('ampersand-state'); +let Species = require('./specie'); module.exports = State.extend({ - props: { - is1D: 'boolean', - p1Min: 'number', - p1Max: 'number', - p1Steps: 'number', - p2Min: 'number', - p2Max: 'number', - p2Steps: 'number' - }, children: { - parameterOne: Parameter, - parameterTwo: Parameter, speciesOfInterest: Species }, + collections: { + parameters: SweepParameters + }, initialize: function(attrs, options) { State.prototype.initialize.apply(this, arguments); + }, + updateVariables: function (parameters) { + this.parameters.forEach(function (variable) { + let parameter = parameters.filter(function (parameter) { + return parameter.compID === variable.paramID; + })[0]; + if(parameter === undefined) { + this.removeVariable(variable); + }else{ + variable.updateVariable(variable); + } + }); } }); \ No newline at end of file diff --git a/client/models/project.js b/client/models/project.js index 568ae61861..404e84bc9f 100644 --- a/client/models/project.js +++ b/client/models/project.js @@ -16,27 +16,59 @@ You should have received a copy of the GNU General Public License along with this program. If not, see . */ -var path = require('path'); +let path = require('path'); //Support Files -var app = require('../app.js'); +let app = require('../app.js'); //Collections -var ModelsCollection = require('./models'); -var WorkflowGroupsCollection = require('./workflow-groups'); +let Creators = require('./creators'); +let WorkflowGroups = require('./workflow-groups'); //Models -var Model = require('ampersand-model'); +let Metadata = require('./metadata'); +let Model = require('ampersand-model'); module.exports = Model.extend({ url: function () { return path.join(app.getApiPath(), "project/load-project")+"?path="+this.directory; }, + children: { + metadata: Metadata + }, collections: { - models: ModelsCollection, - workflowGroups: WorkflowGroupsCollection + workflowGroups: WorkflowGroups, + archive: WorkflowGroups, + creators: Creators }, session: { + annotation: 'string', directory: 'string', - parentDir: 'string', - plot: 'object', - annotation: 'string' + dirname: 'string', + name: 'string', + newFormat: 'boolean' + }, + derived: { + elementID: { + deps: ["collection"], + fn: function () { + if(this.collection) { + return "P" + (this.collection.indexOf(this) + 1); + } + return "P-"; + } + }, + location: { + deps: ["dirname"], + fn: function () { + if(this.dirname) { + return "Location: " + this.dirname; + } + return ""; + } + }, + open: { + deps: ["directory"], + fn: function () { + return path.join(app.getBasePath(), "stochss/project/manager")+"?path="+this.directory + } + } } -}) \ No newline at end of file +}); \ No newline at end of file diff --git a/client/models/settings.js b/client/models/settings.js index 7b80a1271c..fe6911dcaa 100644 --- a/client/models/settings.js +++ b/client/models/settings.js @@ -18,12 +18,14 @@ along with this program. If not, see . //models var State = require('ampersand-state'); +let TimespanSettings = require('./timespan-settings'); var SimulationSettings = require('./simulation-settings'); var ParameterSweepSettings = require('./parameter-sweep-settings'); var ResultsSettings = require('./results-settings'); module.exports = State.extend({ children: { + timespanSettings: TimespanSettings, simulationSettings: SimulationSettings, parameterSweepSettings: ParameterSweepSettings, resultsSettings: ResultsSettings diff --git a/client/models/simulation-settings.js b/client/models/simulation-settings.js index 92a36fd970..a67ede077b 100644 --- a/client/models/simulation-settings.js +++ b/client/models/simulation-settings.js @@ -31,32 +31,5 @@ module.exports = State.extend({ }, initialize: function (attrs, options) { State.prototype.initialize.apply(this, arguments); - }, - letUsChooseForYou: function (model) { - if(model.rules.length || model.eventsCollection.length || model.functionDefinitions.length){ - this.algorithm = "Hybrid-Tau-Leaping" - return - } - - var mode = model.defaultMode - - if(mode === "dynamic"){ - let isDiscrete = Boolean(model.species.filter(specie => specie.mode !== "discrete")) - let isContinuous = Boolean(model.species.filter(specie => specie.mode !== "continuous")) - - if(isDiscrete){ - mode = "discrete" - }else if(isContinuous){ - mode = "continuous" - } - } - - if(mode === "dynamic"){ - this.algorithm = "Hybrid-Tau-Leaping" - }else if(mode === "discrete"){ - this.algorithm = "SSA" - }else{ - this.algorithm = "ODE" - } - }, + } }); \ No newline at end of file diff --git a/client/models/sweep-parameter.js b/client/models/sweep-parameter.js new file mode 100644 index 0000000000..e9efdf0a38 --- /dev/null +++ b/client/models/sweep-parameter.js @@ -0,0 +1,55 @@ +/* +StochSS is a platform for simulating biochemical systems +Copyright (C) 2019-2020 StochSS developers. + +This program is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with this program. If not, see . +*/ + +//models +var State = require('ampersand-state'); + +module.exports = State.extend({ + props: { + paramID: 'number', + min: 'any', + max: 'any', + name: 'string', + range: 'object', + steps: 'any', + hasChangedRange: 'boolean' + }, + derived: { + elementID: { + deps: ["collection"], + fn: function () { + if(this.collection) { + return "ST" + (this.collection.indexOf(this) + 1); + } + return "ST-" + } + } + }, + initialize: function(attrs, options) { + State.prototype.initialize.apply(this, arguments); + }, + updateVariable: function (parameter) { + let value = parameter.expression; + if(this.min <= 0 || !this.hasChangedRange) { + this.min = value * 0.5; + } + if(this.max <= 0 || !this.hasChangedRange) { + this.max = value * 1.5; + } + } +}); diff --git a/client/models/ssa-settings.js b/client/models/sweep-parameters.js similarity index 61% rename from client/models/ssa-settings.js rename to client/models/sweep-parameters.js index 79b4f7ff0b..eb60b7f7c0 100644 --- a/client/models/ssa-settings.js +++ b/client/models/sweep-parameters.js @@ -17,16 +17,23 @@ along with this program. If not, see . */ //models -var State = require('ampersand-state'); +let SweepParameter = require('./sweep-parameter'); +//collections +let Collection = require('ampersand-collection'); -module.exports = State.extend({ - props: { - seed: { - type: 'number', - default: -1, - }, - }, - initialize: function (attrs, options) { - State.prototype.initialize.apply(this, arguments); +module.exports = Collection.extend({ + model: SweepParameter, + addSweepParameter: function (paramID, name) { + let variable = this.add({ + paramID: paramID, + min: 0, + max: 0, + name: name, + steps: 11, + hasChangedRange: false + }); }, + removeSweepParameter: function (variable) { + this.remove(variable); + } }); \ No newline at end of file diff --git a/client/models/model-settings.js b/client/models/timespan-settings.js similarity index 100% rename from client/models/model-settings.js rename to client/models/timespan-settings.js diff --git a/client/models/workflow-group.js b/client/models/workflow-group.js index 689b7e6262..2ba66cc014 100644 --- a/client/models/workflow-group.js +++ b/client/models/workflow-group.js @@ -16,16 +16,47 @@ You should have received a copy of the GNU General Public License along with this program. If not, see . */ +let path = require('path'); +//Support Files +let app = require('../app.js'); //collections -var WorkflowCollection = require('./workflows'); +let Workflows = require('./workflows'); //models -var State = require('ampersand-state'); +let Model = require('./model'); +let Metadata = require('./metadata'); +let State = require('ampersand-state'); module.exports = State.extend({ + children: { + model: Model, + metadata: Metadata + }, collections: { - workflows: WorkflowCollection + workflows: Workflows }, session: { name: 'string' + }, + derived: { + elementID: { + deps: ["collection"], + fn: function () { + let identifier = !this.model || Boolean(this.model.name) ? "WG" : "AW" + if(this.collection) { + return this.collection.parent.elementID + identifier + (this.collection.indexOf(this) + 1) + } + return identifier + "-" + } + }, + open: { + deps: ["model"], + fn: function () { + if(this.model.directory){ + let queryStr = "?path=" + this.model.directory; + return path.join(app.getBasePath(), "stochss/models/edit") + queryStr; + } + return null + } + } } }); \ No newline at end of file diff --git a/client/models/workflow-groups.js b/client/models/workflow-groups.js index c8a1e49d2f..a33b2dce18 100644 --- a/client/models/workflow-groups.js +++ b/client/models/workflow-groups.js @@ -23,4 +23,4 @@ var WorkflowGroup = require('./workflow-group'); module.exports = Collection.extend({ model: WorkflowGroup -}); \ No newline at end of file +}); diff --git a/client/models/workflow.js b/client/models/workflow.js index c847ce18b8..36427fdfd9 100644 --- a/client/models/workflow.js +++ b/client/models/workflow.js @@ -16,19 +16,57 @@ You should have received a copy of the GNU General Public License along with this program. If not, see . */ +let path = require('path'); +//Support Files +let app = require('../app.js'); //collections +let Jobs = require('./jobs'); //models -var State = require('ampersand-state'); +let Job = require('./job'); +let Model = require('ampersand-model'); +let Settings = require('./settings'); -module.exports = State.extend({ +module.exports = Model.extend({ + url: function () { + return path.join(app.getApiPath(), "workflow/load-workflow") + "?path=" + this.directory; + }, props: { - path: 'string', - annotation: 'string', - outputs: 'object', - type: 'string' + model: 'string' + }, + children: { + settings: Settings, + activeJob: Job + }, + collections: { + jobs: Jobs }, session: { + annotation: 'string', + directory: 'string', name: 'string', - status: 'string' + status: 'string', + type: 'string', + newFormat: 'boolean' + }, + derived: { + elementID: { + deps: ["collection"], + fn: function () { + if(this.collection) { + return this.collection.parent.elementID + "W" + (this.collection.indexOf(this) + 1) + } + return "W-" + } + }, + open: { + deps: ["directory", "type"], + fn: function () { + if(this.type === "Notebook") { + return path.join(app.getBasePath(), "notebooks", this.directory) + } + let queryStr = "?path=" + this.directory + "&type=none" + return path.join(app.getBasePath(), "stochss/workflow/edit") + queryStr + } + } } -}); \ No newline at end of file +}); diff --git a/client/models/workflows.js b/client/models/workflows.js index 1073cd8037..194fe9b0da 100644 --- a/client/models/workflows.js +++ b/client/models/workflows.js @@ -23,4 +23,4 @@ var Workflow = require('./workflow'); module.exports = Collection.extend({ model: Workflow -}); \ No newline at end of file +}); diff --git a/client/pages/domain-editor.js b/client/pages/domain-editor.js index a2d13c03a9..4160ab3d44 100644 --- a/client/pages/domain-editor.js +++ b/client/pages/domain-editor.js @@ -16,7 +16,6 @@ You should have received a copy of the GNU General Public License along with this program. If not, see . */ -var xhr = require('xhr'); var $ = require('jquery'); let path = require('path'); var _ = require('underscore'); @@ -55,6 +54,7 @@ let DomainEditor = PageView.extend({ 'click [data-hook=save-to-file]' : 'handleSaveToFile', 'click [data-hook=import-particles-btn]' : 'handleImportMesh', 'click [data-hook=set-particle-types-btn]' : 'getTypesFromFile', + 'change [data-hook=static-domain]' : 'setStaticDomain', 'change [data-hook=density]' : 'setDensity', 'change [data-target=gravity]' : 'setGravity', 'change [data-hook=pressure]' : 'setPressure', @@ -88,44 +88,50 @@ let DomainEditor = PageView.extend({ importMesh: function (data) { let self = this; let file = $("#meshfile").prop("files")[0]; + let typeFiles = $("#typefile").prop("files") let formData = new FormData(); formData.append("datafile", file); formData.append("particleData", JSON.stringify(data)); + if(typeFiles.length) { + formData.append("typefile", typeFiles[0]); + } let endpoint = path.join(app.getApiPath(), 'spatial-model/import-mesh'); - let req = new XMLHttpRequest(); - req.open("POST", endpoint); - req.onload = function (e) { - var resp = JSON.parse(req.response); - if(req.status < 400) { - self.addParticles(resp.particles); - if(self.domain.x_lim[0] > resp.limits.x_lim[0]) { - self.domain.x_lim[0] = resp.limits.x_lim[0] + app.postXHR(endpoint, formData, { + success: function (err, response, body) { + body = JSON.parse(body); + if(body.types) { + self.addMissingTypes(body.types) + } + self.addParticles(body.particles); + if(self.domain.x_lim[0] > body.limits.x_lim[0]) { + self.domain.x_lim[0] = body.limits.x_lim[0] } - if(self.domain.y_lim[0] > resp.limits.y_lim[0]) { - self.domain.y_lim[0] = resp.limits.y_lim[0] + if(self.domain.y_lim[0] > body.limits.y_lim[0]) { + self.domain.y_lim[0] = body.limits.y_lim[0] } - if(self.domain.z_lim[0] > resp.limits.z_lim[0]) { - self.domain.z_lim[0] = resp.limits.z_lim[0] + if(self.domain.z_lim[0] > body.limits.z_lim[0]) { + self.domain.z_lim[0] = body.limits.z_lim[0] } - if(self.domain.x_lim[1] < resp.limits.x_lim[1]) { - self.domain.x_lim[1] = resp.limits.x_lim[1] + if(self.domain.x_lim[1] < body.limits.x_lim[1]) { + self.domain.x_lim[1] = body.limits.x_lim[1] } - if(self.domain.y_lim[1] < resp.limits.y_lim[1]) { - self.domain.y_lim[1] = resp.limits.y_lim[1] + if(self.domain.y_lim[1] < body.limits.y_lim[1]) { + self.domain.y_lim[1] = body.limits.y_lim[1] } - if(self.domain.z_lim[1] < resp.limits.z_lim[1]) { - self.domain.z_lim[1] = resp.limits.z_lim[1] + if(self.domain.z_lim[1] < body.limits.z_lim[1]) { + self.domain.z_lim[1] = body.limits.z_lim[1] } self.renderDomainLimitations(); self.completeAction("Mesh successfully imported", "im") $('html, body').animate({ scrollTop: $("#domain-plot").offset().top }, 20); - }else{ - self.errorAction(resp.Message, "im") + }, + error: function (err, response, body) { + body = JSON.parse(body); + self.errorAction(body.Message, "im") } - } - req.send(formData) + }, false) }, handleSetDefaults: function (e) { let mass = Number($(this.queryByHook("td-mass")).find('input')[0].value); @@ -209,7 +215,6 @@ let DomainEditor = PageView.extend({ $(this.queryByHook("type-location-container")).css("display", "none"); var disabled = true; } - console.log(disabled) $(this.queryByHook("set-particle-types-btn")).prop("disabled", disabled); }, handleSelectTypeLocation: function (e) { @@ -240,13 +245,15 @@ let DomainEditor = PageView.extend({ this.queryStr += "domain_path=" + domainPath } let endpoint = path.join(app.getApiPath(), "spatial-model/load-domain") + this.queryStr - xhr({uri: endpoint, json: true}, function (err, resp, body) { - self.domain = new Domain(body.domain); - self.domain.directory = domainPath - self.domain.dirname = newDomain && !modelPath ? domainPath : null - self.model = self.buildModel(body.model, modelPath); - self.actPart = {"part":null, "tn":0, "pn":0}; - self.renderSubviews(); + app.getXHR(endpoint, { + success: function (err, response, body) { + self.domain = new Domain(body.domain); + self.domain.directory = domainPath + self.domain.dirname = newDomain && !modelPath ? domainPath : null + self.model = self.buildModel(body.model, modelPath); + self.actPart = {"part":null, "tn":0, "pn":0}; + self.renderSubviews(); + } }); $(document).on('shown.bs.modal', function (e) { $('[autofocus]', e.target).focus(); @@ -265,8 +272,6 @@ let DomainEditor = PageView.extend({ if(!fromImport) { this.renderDomainTypes(); this.updatePlot(); - }else{ - console.log("From Imports") } if(cb) { cb(); @@ -313,13 +318,7 @@ let DomainEditor = PageView.extend({ return model; }, changeCollapseButtonText: function (e) { - let source = e.target.dataset.hook - let collapseContainer = $(this.queryByHook(source).dataset.target) - if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) { - let collapseBtn = $(this.queryByHook(source)) - let text = collapseBtn.text(); - text === '+' ? collapseBtn.text('-') : collapseBtn.text('+'); - } + app.changeCollapseButtonText(this, e); }, changeParticleLocation: function (x, y, z) { this.domain.particles.get(this.actPart.part.particle_id, "particle_id").point = [x, y, z]; @@ -429,6 +428,9 @@ let DomainEditor = PageView.extend({ if(this.model) { data.model = {"name":this.model.name, "href":mdlEP + this.model.directory}; let dirname = path.dirname(this.model.directory); + if(dirname.includes(".wkgp")) { + dirname = path.dirname(dirname); + } if(dirname.endsWith(".proj")) { let name = dirname.split("/").pop().split(".proj")[0]; data.project = {"name":name, "href":projEP + dirname}; @@ -464,14 +466,15 @@ let DomainEditor = PageView.extend({ let self = this; let queryStr = "?path=" + this.typeDescriptionsFile; let endpoint = path.join(app.getApiPath(), "spatial-model/particle-types") + queryStr; - xhr({uri: endpoint, json: true}, function (err, resp, body) { - if(resp.statusCode < 400) { - self.addMissingTypes(body.names) - self.changeParticleTypes(body.types) - self.completeAction("Types set", "st") - }else{ - self.errorAction(body.Message, "st") - console.log(err) + app.getXHR(endpoint, { + success: function (err, response, body) { + self.addMissingTypes(body.names); + self.changeParticleTypes(body.types); + self.completeAction("Types set", "st"); + }, + error: function (err, response, body) { + self.errorAction(body.Message, "st"); + console.log(err); } }); }, @@ -492,7 +495,7 @@ let DomainEditor = PageView.extend({ parent: this, model: this.domain }); - this.registerRenderSubview(this.create3DDomainView, "add-3d-domain"); + app.registerRenderSubview(this, this.create3DDomainView, "add-3d-domain"); }, renderDomainLimitations: function () { if(this.xLimMinView) { @@ -506,53 +509,54 @@ let DomainEditor = PageView.extend({ this.xLimMinView = new InputView({parent: this, required: true, name: 'x-lim-min', valueType: 'number', value: this.domain.x_lim[0] || 0}); - this.registerRenderSubview(this.xLimMinView, "x_lim-min"); + app.registerRenderSubview(this, this.xLimMinView, "x_lim-min"); this.yLimMinView = new InputView({parent: this, required: true, name: 'y-lim-min', valueType: 'number', value: this.domain.y_lim[0] || 0}); - this.registerRenderSubview(this.yLimMinView, "y_lim-min"); + app.registerRenderSubview(this, this.yLimMinView, "y_lim-min"); this.zLimMinView = new InputView({parent: this, required: true, name: 'z-lim-min', valueType: 'number', value: this.domain.z_lim[0] || 0}); - this.registerRenderSubview(this.zLimMinView, "z_lim-min"); + app.registerRenderSubview(this, this.zLimMinView, "z_lim-min"); this.xLimMaxView = new InputView({parent: this, required: true, name: 'x-lim-max', valueType: 'number', value: this.domain.x_lim[1] || 0}); - this.registerRenderSubview(this.xLimMaxView, "x_lim-max"); + app.registerRenderSubview(this, this.xLimMaxView, "x_lim-max"); this.yLimMaxView = new InputView({parent: this, required: true, name: 'y-lim-max', valueType: 'number', value: this.domain.y_lim[1] || 0}); - this.registerRenderSubview(this.yLimMaxView, "y_lim-max"); + app.registerRenderSubview(this, this.yLimMaxView, "y_lim-max"); this.zLimMaxView = new InputView({parent: this, required: true, name: 'z-lim-max', valueType: 'number', value: this.domain.z_lim[1] || 0}); - this.registerRenderSubview(this.zLimMaxView, "z_lim-max"); + app.registerRenderSubview(this, this.zLimMaxView, "z_lim-max"); }, renderDomainProperties: function () { + $(this.queryByHook("static-domain")).prop("checked", this.domain.static); let densityView = new InputView({parent: this, required: true, name: 'density', valueType: 'number', value: this.domain.rho_0 || 1}); - this.registerRenderSubview(densityView, "density"); + app.registerRenderSubview(this, densityView, "density"); let gravityXView = new InputView({parent: this, required: true, name: 'gravity-x', valueType: 'number', value: this.domain.gravity[0], label: "X: "}); - this.registerRenderSubview(gravityXView, "gravity-x"); + app.registerRenderSubview(this, gravityXView, "gravity-x"); let gravityYView = new InputView({parent: this, required: true, name: 'gravity-y', valueType: 'number', value: this.domain.gravity[1], label: "Y: "}); - this.registerRenderSubview(gravityYView, "gravity-y"); + app.registerRenderSubview(this, gravityYView, "gravity-y"); let gravityZView = new InputView({parent: this, required: true, name: 'gravity-z', valueType: 'number', value: this.domain.gravity[2], label: "Z: "}); - this.registerRenderSubview(gravityZView, "gravity-z"); + app.registerRenderSubview(this, gravityZView, "gravity-z"); let pressureView = new InputView({parent: this, required: true, name: 'pressure', valueType: 'number', value: this.domain.p_0 || 0}); - this.registerRenderSubview(pressureView, "pressure"); + app.registerRenderSubview(this, pressureView, "pressure"); let speedView = new InputView({parent: this, required: true, name: 'speed', valueType: 'number', value: this.domain.c_0 || 0}); - this.registerRenderSubview(speedView, "speed"); + app.registerRenderSubview(this, speedView, "speed"); }, renderDomainTypes: function () { if(this.domainTypesView) { @@ -599,15 +603,15 @@ let DomainEditor = PageView.extend({ this.massView = new InputView({parent: this, required: true, name: 'mass', valueType: 'number', value: type.mass}); - this.registerRenderSubview(this.massView, "td-mass"); + app.registerRenderSubview(this, this.massView, "td-mass"); this.volView = new InputView({parent: this, required: true, name: 'volume', valueType: 'number', value: type.volume}); - this.registerRenderSubview(this.volView, "td-vol"); + app.registerRenderSubview(this, this.volView, "td-vol"); this.nuView = new InputView({parent: this, required: true, name: 'viscosity', valueType: 'number', value: type.nu}); - this.registerRenderSubview(this.nuView, "td-nu"); + app.registerRenderSubview(this, this.nuView, "td-nu"); $(this.queryByHook("td-fixed")).prop("checked", type.fixed); $(this.queryByHook("edit-defaults")).css("display", "block"); }, @@ -624,21 +628,21 @@ let DomainEditor = PageView.extend({ model: particle, newParticle: false, }); - this.registerRenderSubview(this.editParticleView, "edit-particle"); + app.registerRenderSubview(this, this.editParticleView, "edit-particle"); }, renderMeshTransformations: function () { let xtrans = new InputView({parent: this, required: true, name: 'x-transformation', valueType: 'number', value: 0}); - this.registerRenderSubview(xtrans, "mesh-x-trans"); + app.registerRenderSubview(this, xtrans, "mesh-x-trans"); let ytrans = new InputView({parent: this, required: true, name: 'y-transformation', valueType: 'number', value: 0}); - this.registerRenderSubview(ytrans, "mesh-y-trans"); + app.registerRenderSubview(this, ytrans, "mesh-y-trans"); let ztrans = new InputView({parent: this, required: true, name: 'z-transformation', valueType: 'number', value: 0}); - this.registerRenderSubview(ztrans, "mesh-z-trans"); + app.registerRenderSubview(this, ztrans, "mesh-z-trans"); }, renderMeshTypeDefaults: function (id) { let type = this.domain.types.get(id, "typeID") @@ -656,11 +660,7 @@ let DomainEditor = PageView.extend({ model: particle, newParticle: true, }); - this.registerRenderSubview(this.newParticleView, "new-particle"); - }, - registerRenderSubview: function (view, hook) { - this.registerSubview(view); - return this.renderSubview(view, this.queryByHook(hook)); + app.registerRenderSubview(this, this.newParticleView, "new-particle"); }, renderSubviews: function () { let breadData = this.getBreadcrumbData(); @@ -669,19 +669,28 @@ let DomainEditor = PageView.extend({ let projBC = $(this.queryByHook("grandparent-breadcrumb")); projBC.text(breadData.project.name); projBC.prop("href", breadData.project.href); + $(this.queryByHook("return-to-project")).prop("href", breadData.project.href); let mdlBC = $(this.queryByHook("parent-two-breadcrumb")); mdlBC.text(breadData.model.name); mdlBC.prop("href", breadData.model.href); + $(this.queryByHook("return-to-model")).prop("href", breadData.model.href); }else if(breadData.model || breadData.project) { $(this.queryByHook("one-parent-breadcrumb-links")).css("display", "block"); let breadcrumb = $(this.queryByHook("parent-one-breadcrumb")); if(breadData.project) { breadcrumb.text(breadData.project.name) breadcrumb.prop("href", breadData.project.href); + $(this.queryByHook("return-to-project")).prop("href", breadData.project.href); + $(this.queryByHook("return-to-model")).css("display", "none"); }else { breadcrumb.text(breadData.model.name) breadcrumb.prop("href", breadData.model.href); + $(this.queryByHook("return-to-project")).css("display", "none"); + $(this.queryByHook("return-to-model")).prop("href", breadData.model.href); } + }else{ + $(this.queryByHook("return-to-model")).css("display", "none"); + $(this.queryByHook("return-to-project")).css("display", "none"); } this.renderDomainProperties(); this.renderDomainLimitations(); @@ -698,9 +707,11 @@ let DomainEditor = PageView.extend({ this.renderCreate3DDomain(); let self = this; let endpoint = path.join(app.getApiPath(), "spatial-model/domain-plot") + this.queryStr; - xhr({uri: endpoint, json: true}, function (err, resp, body) { - self.plot = body.fig; - self.displayDomain(); + app.getXHR(endpoint, { + success: function (err, response, body) { + self.plot = body.fig; + self.displayDomain(); + } }); $(document).ready(function () { $('[data-toggle="tooltip"]').tooltip(); @@ -717,17 +728,19 @@ let DomainEditor = PageView.extend({ renderTypesFileSelect: function () { let self = this; let endpoint = path.join(app.getApiPath(), "spatial-model/types-list"); - xhr({uri: endpoint, json:true}, function (err, resp, body) { - self.typeDescriptions = body.paths; - var typesSelectView = new SelectView({ - label: '', - name: 'type-files', - required: false, - idAttributes: 'cid', - options: body.files, - unselectedText: "-- Select Type File --", - }); - self.registerRenderSubview(typesSelectView, "types-file-select") + app.getXHR(endpoint, { + success: function (err, response, body) { + self.typeDescriptions = body.paths; + var typesSelectView = new SelectView({ + label: '', + name: 'type-files', + required: false, + idAttributes: 'cid', + options: body.files, + unselectedText: "-- Select Type File --", + }); + app.registerRenderSubview(self, typesSelectView, "types-file-select"); + } }); }, renderTypesLocationSelect: function (options) { @@ -742,7 +755,7 @@ let DomainEditor = PageView.extend({ options: options, unselectedText: "-- Select Location --" }); - this.registerRenderSubview(this.typesLocationSelectView, "types-file-location-select") + app.registerRenderSubview(this, this.typesLocationSelectView, "types-file-location-select") }, renderTypeSelectView: function () { if(this.typeView) { @@ -758,7 +771,7 @@ let DomainEditor = PageView.extend({ options: this.domain.types, value: this.domain.types.get(0, "typeID") }); - this.registerRenderSubview(this.typeView, "mesh-type-select") + app.registerRenderSubview(this, this.typeView, "mesh-type-select") }, saveDomain: function (name=null) { let domain = this.domain.toJSON(); @@ -771,12 +784,13 @@ let DomainEditor = PageView.extend({ } let self = this; let endpoint = path.join(app.getApiPath(), "file/json-data") + "?path=" + domainPath; - xhr({uri: endpoint, method: "post", json: true, body: domain}, function (err, response, body) { - if(response.statusCode >= 400) { - self.errorAction(body.Message, "sd"); - console.log(body.message) - }else{ + app.postXHR(endpoint, domain, { + success: function (err, response, body) { self.completeAction("Domain save to file (.domn)", "sd"); + }, + error: function (err, response, body) { + self.errorAction(body.Message, "sd"); + console.log(body.message); } }); }, @@ -821,6 +835,10 @@ let DomainEditor = PageView.extend({ let value = Number(e.target.value) this.domain.c_0 = value; }, + setStaticDomain: function (e) { + let value = e.target.checked; + this.domain.statis = value; + }, startAction: function (action, src) { $(this.queryByHook(src + "-complete")).css("display", "none"); $(this.queryByHook(src + "-action-in-progress")).text(action); diff --git a/client/pages/file-browser.js b/client/pages/file-browser.js index 13c882d997..94dc7d5c75 100644 --- a/client/pages/file-browser.js +++ b/client/pages/file-browser.js @@ -18,7 +18,6 @@ along with this program. If not, see . let jstree = require('jstree'); let path = require('path'); -let xhr = require('xhr'); let $ = require('jquery'); let _ = require('underscore'); //support files @@ -45,6 +44,7 @@ let FileBrowser = PageView.extend({ 'click [data-hook=file-browser-help]' : function () { let modal = $(modals.operationInfoModalHtml('file-browser')).modal(); }, + 'click [data-hook=empty-trash]' : 'emptyTrash' }, initialize: function (attrs, options) { PageView.prototype.initialize.apply(this, arguments) @@ -79,7 +79,10 @@ let FileBrowser = PageView.extend({ if(op === 'move_node' && more && more.ref && more.ref.type && !(more.ref.type == 'folder' || more.ref.type == 'root')){ return false } - if(op === 'move_node' && more && more.ref && more.ref.type && more.ref.type === 'folder'){ + if(op === 'move_node' && more && more.ref && more.ref.original && path.dirname(more.ref.original._path).split("/").includes("trash")){ + return false + } + if(op === 'move_node' && more && more.ref && more.ref.type && more.ref.type === 'folder' && more.ref.text !== "trash"){ if(!more.ref.state.loaded){ return false } @@ -106,15 +109,21 @@ let FileBrowser = PageView.extend({ var oldPath = node.original._path let queryStr = "?srcPath="+oldPath+"&dstPath="+path.join(newDir, file) var endpoint = path.join(app.getApiPath(), "file/move")+queryStr - xhr({uri: endpoint}, function(err, response, body) { - if(response.statusCode < 400) { - node.original._path = path.join(newDir, file) + app.getXHR(endpoint, { + success: function (err, response, body) { + node.original._path = path.join(newDir, file); if(node.type === "folder") { $('#models-jstree').jstree().refresh_node(node); + }else if(newDir.endsWith("trash")) { + $(self.queryByHook('empty-trash')).prop('disabled', false); + $('#models-jstree').jstree().refresh_node(par); + }else if(oldPath.split("/").includes("trash")) { + $('#models-jstree').jstree().refresh_node(par); } - }else{ - body = JSON.parse(body) - $('#models-jstree').jstree().refresh() + }, + error: function (err, response, body) { + body = JSON.parse(body); + $('#models-jstree').jstree().refresh(); } }); } @@ -262,11 +271,9 @@ let FileBrowser = PageView.extend({ formData.append("datafile", file) formData.append("fileinfo", JSON.stringify(fileinfo)) let endpoint = path.join(app.getApiPath(), 'file/upload'); - let req = new XMLHttpRequest(); - req.open("POST", endpoint) - req.onload = function (e) { - var resp = JSON.parse(req.response) - if(req.status < 400) { + app.postXHR(endpoint, formData, { + success: function (err, response, body) { + body = JSON.parse(body); if(o){ var node = $('#models-jstree').jstree().get_node(o.parent); if(node.type === "root" || node.type === "#"){ @@ -277,16 +284,17 @@ let FileBrowser = PageView.extend({ }else{ self.refreshJSTree(); } - if(resp.errors.length > 0){ - let errorModal = $(modals.uploadFileErrorsHtml(file.name, type, resp.message, resp.errors)).modal(); + if(body.errors.length > 0){ + let errorModal = $(modals.uploadFileErrorsHtml(file.name, type, body.message, body.errors)).modal(); } - }else{ - let zipErrorModal = $(modals.projectExportErrorHtml(resp.Reason, resp.Message)).modal() + }, + error: function (err, response, body) { + body = JSON.parse(body); + let zipErrorModal = $(modals.projectExportErrorHtml(resp.Reason, resp.Message)).modal(); } - } - req.send(formData) + }, false); modal.modal('hide') - }) + }); }, deleteFile: function (o) { var fileType = o.type @@ -306,24 +314,25 @@ let FileBrowser = PageView.extend({ let yesBtn = document.querySelector('#deleteFileModal .yes-modal-btn'); yesBtn.addEventListener('click', function (e) { var endpoint = path.join(app.getApiPath(), "file/delete")+"?path="+o.original._path - xhr({uri: endpoint}, function(err, response, body) { - if(response.statusCode < 400) { + app.getXHR(endpoint, { + success: function (err, response, body) { var node = $('#models-jstree').jstree().get_node(o.parent); if(node.type === "root"){ self.refreshJSTree(); - let actionsBtn = $(self.queryByHook("options-for-node")) + let actionsBtn = $(self.queryByHook("options-for-node")); if(actionsBtn.text().endsWith(o.text)) { - actionsBtn.text("Actions") - actionsBtn.prop("disabled", true) - self.nodeForContextMenu = "" + actionsBtn.text("Actions"); + actionsBtn.prop("disabled", true); + self.nodeForContextMenu = ""; } }else{ $('#models-jstree').jstree().refresh_node(node); } - }else{ - body = JSON.parse(body) + }, + error: function (err, response, body) { + body = JSON.parse(body); } - }) + }); modal.modal('hide') }); }, @@ -348,27 +357,26 @@ let FileBrowser = PageView.extend({ var identifier = "file/duplicate" } var endpoint = path.join(app.getApiPath(), identifier)+queryStr - xhr({uri: endpoint, json: true}, function (err, response, body) { - if(response.statusCode < 400) { - var node = $('#models-jstree').jstree().get_node(parentID); - if(node.type === "root"){ - self.refreshJSTree() - }else{ - $('#models-jstree').jstree().refresh_node(node); - } - if(type === "workflow"){ - var message = "" - if(body.error){ - message = body.error - }else{ - message = "The model for "+body.File+" is located here: "+body.mdlPath+"" - } - let modal = $(modals.duplicateWorkflowHtml(body.File, message)).modal() + app.getXHR(endpoint, { + success: function (err, response, body) { + var node = $('#models-jstree').jstree().get_node(parentID); + if(node.type === "root"){ + self.refreshJSTree(); + }else{ + $('#models-jstree').jstree().refresh_node(node); + } + if(type === "workflow"){ + var message = "" + if(body.error){ + message = body.error; + }else{ + message = "The model for "+body.File+" is located here: "+body.mdlPath+""; } - self.selectNode(node, body.File) + let modal = $(modals.duplicateWorkflowHtml(body.File, message)).modal(); } + self.selectNode(node, body.File); } - ); + }); }, getTimeStamp: function () { var date = new Date(); @@ -399,19 +407,17 @@ let FileBrowser = PageView.extend({ var self = this; var parentID = o.parent; var endpoint = path.join(app.getApiPath(), "model/to-spatial")+"?path="+o.original._path; - xhr({uri: endpoint, json: true}, - function (err, response, body) { - if(response.statusCode < 400) { - var node = $('#models-jstree').jstree().get_node(parentID); - if(node.type === "root"){ - self.refreshJSTree() - }else{ - $('#models-jstree').jstree().refresh_node(node); - } - self.selectNode(node, body.File) + app.getXHR(endpoint, { + success: function (err, response, body) { + var node = $('#models-jstree').jstree().get_node(parentID); + if(node.type === "root"){ + self.refreshJSTree(); + }else{ + $('#models-jstree').jstree().refresh_node(node); } + self.selectNode(node, body.File); } - ); + }); }, toModel: function (o, from) { var self = this; @@ -422,24 +428,23 @@ let FileBrowser = PageView.extend({ var identifier = "sbml/to-model" } let endpoint = path.join(app.getApiPath(), identifier)+"?path="+o.original._path; - xhr({uri: endpoint, json: true}, function (err, response, body) { - if(response.statusCode < 400) { - var node = $('#models-jstree').jstree().get_node(parentID); - if(node.type === "root"){ - self.refreshJSTree() - }else{ - $('#models-jstree').jstree().refresh_node(node); - } - self.selectNode(node, body.File) - if(from === "SBML" && body.errors.length > 0){ - var title = "" - var msg = body.message - var errors = body.errors - let modal = $(modals.sbmlToModelHtml(msg, errors)).modal(); - } + app.getXHR(endpoint, { + success: function (err, response, body) { + var node = $('#models-jstree').jstree().get_node(parentID); + if(node.type === "root"){ + self.refreshJSTree(); + }else{ + $('#models-jstree').jstree().refresh_node(node); + } + self.selectNode(node, body.File); + if(from === "SBML" && body.errors.length > 0){ + var title = ""; + var msg = body.message; + var errors = body.errors; + let modal = $(modals.sbmlToModelHtml(msg, errors)).modal(); } } - ); + }); }, toNotebook: function (o, type) { let self = this @@ -449,19 +454,17 @@ let FileBrowser = PageView.extend({ }else{ endpoint = path.join(app.getApiPath(), "workflow/notebook")+"?type=none&path="+o.original._path } - xhr({ uri: endpoint, json: true}, function (err, response, body) { - if(response.statusCode < 400){ - var node = $('#models-jstree').jstree().get_node(o.parent) + app.getXHR(endpoint, { + success: function (err, response, body) { + var node = $('#models-jstree').jstree().get_node(o.parent); if(node.type === 'root'){ self.refreshJSTree(); }else{ $('#models-jstree').jstree().refresh_node(node); } - var notebookPath = path.join(app.getBasePath(), "notebooks", body.FilePath) - self.selectNode(node, body.File) - console.log(notebookPath) - window.open(notebookPath) - console.log("Opened new window") + var notebookPath = path.join(app.getBasePath(), "notebooks", body.FilePath); + self.selectNode(node, body.File); + window.open(notebookPath); } }); }, @@ -469,15 +472,15 @@ let FileBrowser = PageView.extend({ var self = this; var parentID = o.parent; var endpoint = path.join(app.getApiPath(), "model/to-sbml")+"?path="+o.original._path; - xhr({uri: endpoint, json: true}, function (err, response, body) { - if(response.statusCode < 400) { + app.getXHR(endpoint, { + success: function (err, response, body) { var node = $('#models-jstree').jstree().get_node(parentID); if(node.type === "root"){ - self.refreshJSTree() + self.refreshJSTree(); }else{ $('#models-jstree').jstree().refresh_node(node); } - self.selectNode(node, body.File) + self.selectNode(node, body.File); } }); }, @@ -491,24 +494,24 @@ let FileBrowser = PageView.extend({ $('#models-jstree').jstree().edit(o, null, function(node, status) { if(text != node.text){ var endpoint = path.join(app.getApiPath(), "file/rename")+"?path="+ o.original._path+"&name="+node.text - xhr({uri: endpoint, json: true}, function (err, response, body){ - if(response.statusCode < 400) { - if(body.changed) { - nameWarning.text(body.message) - nameWarning.collapse('show'); - window.scrollTo(0,0) - setTimeout(_.bind(self.hideNameWarning, self), 10000); - } - node.original._path = body._path - } - if(text.split('.').pop() != node.text.split('.').pop()){ + app.getXHR(endpoint, { + always: function (err, response, body) { if(parent.type === "root"){ - self.refreshJSTree() + self.refreshJSTree(); }else{ $('#models-jstree').jstree().refresh_node(parent); } + }, + success: function (err, response, body) { + if(body.changed) { + nameWarning.text(body.message); + nameWarning.collapse('show'); + window.scrollTo(0,0); + setTimeout(_.bind(self.hideNameWarning, self), 10000); + } + node.original._path = body._path; } - }) + }); } extensionWarning.collapse('hide'); nameWarning.collapse('hide'); @@ -545,10 +548,10 @@ let FileBrowser = PageView.extend({ } } var endpoint = path.join(app.getApiPath(), identifier)+queryStr - xhr({uri: endpoint, json: isJSON}, function (err, response, body) { - if(response.statusCode < 400) { + app.getXHR(endpoint, { + success: function (err, response, body) { if(dataType === "json") { - let data = nodeType === "domain" ? body.domain : body + let data = nodeType === "domain" ? body.domain : body; self.exportToJsonFile(data, o.original.text); }else if(dataType === "zip") { var node = $('#models-jstree').jstree().get_node(o.parent); @@ -557,13 +560,14 @@ let FileBrowser = PageView.extend({ }else{ $('#models-jstree').jstree().refresh_node(node); } - self.exportToZipFile(body.Path) + self.exportToZipFile(body.Path); }else{ self.exportToFile(body, o.original.text); } - }else{ + }, + error: function (err, response, body) { if(dataType === "plain-text") { - body = JSON.parse(body) + body = JSON.parse(body); } } }); @@ -594,7 +598,7 @@ let FileBrowser = PageView.extend({ var endpoint = path.join(app.getBasePath(), "/files", targetPath); window.open(endpoint) }, - validateName(input, rename = false) { + validateName: function (input, rename = false) { var error = "" if(input.endsWith('/')) { error = 'forward' @@ -615,21 +619,9 @@ let FileBrowser = PageView.extend({ if(document.querySelector("#newProjectModal")) { document.querySelector("#newProjectModal").remove() } - if(document.querySelector("#newWorkflowGroupModal")) { - document.querySelector("#newWorkflowGroupModal").remove() - } - var modal = "" - var okBtn = "" - var input = "" - if(isProject) { - modal = $(modals.newProjectModalHtml()).modal(); - okBtn = document.querySelector('#newProjectModal .ok-model-btn'); - input = document.querySelector('#newProjectModal #projectNameInput'); - }else{ - modal = $(modals.newWorkflowGroupModalHtml()).modal(); - okBtn = document.querySelector('#newWorkflowGroupModal .ok-model-btn'); - input = document.querySelector('#newWorkflowGroupModal #workflowGroupNameInput'); - } + var modal = $(modals.newProjectModalHtml()).modal(); + var okBtn = document.querySelector('#newProjectModal .ok-model-btn'); + var input = document.querySelector('#newProjectModal #projectNameInput'); input.addEventListener("keyup", function (event) { if(event.keyCode === 13){ event.preventDefault(); @@ -637,15 +629,8 @@ let FileBrowser = PageView.extend({ } }); input.addEventListener("input", function (e) { - var endErrMsg = "" - var charErrMsg = "" - if(isProject){ - endErrMsg = document.querySelector('#newProjectModal #projectNameInputEndCharError') - charErrMsg = document.querySelector('#newProjectModal #projectNameInputSpecCharError') - }else{ - endErrMsg = document.querySelector('#newWorkflowGroupModal #workflowGroupNameInputEndCharError') - charErrMsg = document.querySelector('#newWorkflowGroupModal #workflowGroupNameInputSpecCharError') - } + var endErrMsg = document.querySelector('#newProjectModal #projectNameInputEndCharError') + var charErrMsg = document.querySelector('#newProjectModal #projectNameInputSpecCharError') let error = self.validateName(input.value) okBtn.disabled = error !== "" || input.value.trim() === "" charErrMsg.style.display = error === "both" || error === "special" ? "block" : "none" @@ -653,43 +638,29 @@ let FileBrowser = PageView.extend({ }); okBtn.addEventListener("click", function (e) { if(Boolean(input.value)) { + modal.modal('hide') var parentPath = "" if(o && o.original && o.original.type !== "root") { parentPath = o.original._path } - var endpoint = "" - if(isProject){ - var projectName = input.value.trim() + ".proj" - var projectPath = path.join(parentPath, projectName) - endpoint = path.join(app.getApiPath(), "project/new-project")+"?path="+projectPath - }else{ - var workflowGroupName = input.value.trim() + ".wkgp" - var workflowGroupPath = path.join(parentPath, workflowGroupName) - endpoint = path.join(app.getApiPath(), "project/new-workflow-group")+"?path="+workflowGroupPath - } - xhr({uri: endpoint,json: true}, function (err, response, body) { - if(response.statusCode < 400) { - if(isProject) { - if(o){//directory was created with context menu option - var node = $('#models-jstree').jstree().get_node(o); - if(node.type === "root"){ - self.refreshJSTree() - }else{ - $('#models-jstree').jstree().refresh_node(node); - } - }else{//directory was created with create directory button - self.refreshJSTree() - } - }else{ - let successModal = $(modals.newWorkflowGroupSuccessHtml(body.message)).modal() - } - }else{ - let errorModel = $(modals.newProjectOrWorkflowGroupErrorHtml(body.Reason, body.Message)).modal() + var projectName = input.value.trim() + ".proj" + var projectPath = path.join(parentPath, projectName) + var endpoint = path.join(app.getApiPath(), "project/new-project")+"?path="+projectPath + app.getXHR(endpoint, { + success: function (err, response, body) { + let queryStr = "?path=" + body.path; + let endpoint = path.join(app.getBasePath(), 'stochss/project/manager') + queryStr; + window.location.href = endpoint; + }, + error: function (err, response, body) { + let errorModel = $(modals.newProjectOrWorkflowGroupErrorHtml(body.Reason, body.Message)).modal(); } - modal.modal('hide') - }) + }); } - }) + }); + }, + newWorkflow: function (o, type) { + app.newWorkflow(this, o.original._path, o.type === "spatial", type); }, addExistingModel: function (o) { var self = this @@ -697,23 +668,80 @@ let FileBrowser = PageView.extend({ document.querySelector('#newProjectModelModal').remove() } let mdlListEP = path.join(app.getApiPath(), 'project/add-existing-model') + "?path="+o.original._path - xhr({uri:mdlListEP, json:true}, function (err, response, body) { - let modal = $(modals.newProjectModelHtml(body.models)).modal() - let okBtn = document.querySelector('#newProjectModelModal .ok-model-btn') - let select = document.querySelector('#newProjectModelModal #modelPathInput') - okBtn.addEventListener("click", function (e) { - let queryString = "?path="+o.original._path+"&mdlPath="+select.value - let endpoint = path.join(app.getApiPath(), 'project/add-existing-model') + queryString - xhr({uri:endpoint, json:true, method:"post"}, function (err, response, body) { - if(response.statusCode < 400) { - let successModal = $(modals.newProjectModelSuccessHtml(body.message)).modal() + app.getXHR(mdlListEP, { + always: function (err, response, body) { + let modal = $(modals.newProjectModelHtml(body.files)).modal(); + let okBtn = document.querySelector('#newProjectModelModal .ok-model-btn'); + let select = document.querySelector('#newProjectModelModal #modelFileInput'); + let location = document.querySelector('#newProjectModelModal #modelPathInput'); + select.addEventListener("change", function (e) { + okBtn.disabled = e.target.value && body.paths[e.target.value].length >= 2; + if(body.paths[e.target.value].length >= 2) { + var locations = body.paths[e.target.value].map(function (path) { + return ``; + }); + locations.unshift(``); + locations = locations.join(" "); + $("#modelPathInput").find('option').remove().end().append(locations); + $("#location-container").css("display", "block"); }else{ - let errorModal = $(modals.newProjectModelErrorHtml(body.Reason, body.Message)).modal() + $("#location-container").css("display", "none"); + $("#modelPathInput").find('option').remove().end(); } }); - modal.modal('hide') + location.addEventListener("change", function (e) { + okBtn.disabled = !Boolean(e.target.value); + }); + okBtn.addEventListener("click", function (e) { + let mdlPath = body.paths[select.value].length < 2 ? body.paths[select.value][0] : location.value; + let queryString = "?path="+o.original._path+"&mdlPath="+mdlPath; + let endpoint = path.join(app.getApiPath(), 'project/add-existing-model') + queryString; + app.postXHR(endpoint, null, { + success: function (err, response, body) { + let successModal = $(modals.newProjectModelSuccessHtml(body.message)).modal(); + }, + error: function (err, response, body) { + let errorModal = $(modals.newProjectModelErrorHtml(body.Reason, body.Message)).modal(); + } + }); + modal.modal('hide'); + }); + } + }); + }, + addModel: function (parentPath, modelName, message) { + var endpoint = path.join(app.getBasePath(), "stochss/models/edit") + if(parentPath.endsWith(".proj")) { + let queryString = "?path=" + parentPath + "&mdlFile=" + modelName + let newMdlEP = path.join(app.getApiPath(), "project/new-model") + queryString + app.getXHR(newMdlEP, { + success: function (err, response, body) { + endpoint += "?path="+body.path; + window.location.href = endpoint; + }, + error: function (err, response, body) { + let title = "Model Already Exists"; + let message = "A model already exists with that name"; + let errorModel = $(modals.newProjectOrWorkflowGroupErrorHtml(title, message)).modal(); + } }); - }) + }else{ + let modelPath = path.join(parentPath, modelName) + let queryString = "?path="+modelPath+"&message="+message; + endpoint += queryString + let existEP = path.join(app.getApiPath(), "model/exists")+queryString + app.getXHR(existEP, { + always: function (err, response, body) { + if(body.exists) { + let title = "Model Already Exists"; + let message = "A model already exists with that name"; + let errorModel = $(modals.newProjectOrWorkflowGroupErrorHtml(title, message)).modal(); + }else{ + window.location.href = endpoint; + } + } + }); + } }, newModelOrDirectory: function (o, isModel, isSpatial) { var self = this @@ -749,54 +777,35 @@ let FileBrowser = PageView.extend({ let modelName = o && o.type === "project" ? input.value.trim().split("/").pop() + ext : input.value.trim() + ext; let message = modelName !== input.value.trim() + ext? "Warning: Models are saved directly in StochSS Projects and cannot be saved to the "+input.value.trim().split("/")[0]+" directory in the project.

Do you wish to save your model directly in your project?

" : "" - let modelPath = path.join(parentPath, modelName) - let queryString = "?path="+modelPath+"&message="+message; - let endpoint = path.join(app.getBasePath(), "stochss/models/edit")+queryString - let existEP = path.join(app.getApiPath(), "model/exists")+queryString if(message){ let warningModal = $(modals.newProjectModelWarningHtml(message)).modal() let yesBtn = document.querySelector('#newProjectModelWarningModal .yes-modal-btn'); yesBtn.addEventListener('click', function (e) { warningModal.modal('hide') - xhr({uri: existEP, json: true}, function (err, response, body) { - if(body.exists) { - let title = "Model Already Exists" - let message = "A model already exists with that name" - let errorModel = $(modals.newProjectOrWorkflowGroupErrorHtml(title, message)).modal() - }else{ - window.location.href = endpoint - } - }) - }) + self.addModel(parentPath, modelName, message); + }); }else{ - xhr({uri: existEP, json: true}, function (err, response, body) { - if(body.exists) { - let title = "Model Already Exists" - let message = "A model already exists with that name" - let errorModel = $(modals.newProjectOrWorkflowGroupErrorHtml(title, message)).modal() - }else{ - window.location.href = endpoint - } - }) + self.addModel(parentPath, modelName, message); } }else{ let dirName = input.value.trim(); let endpoint = path.join(app.getApiPath(), "directory/create")+"?path="+path.join(parentPath, dirName); - xhr({uri:endpoint}, function (err, response, body) { - if(response.statusCode < 400){ + app.getXHR(endpoint, { + success: function (err, response, body) { if(o){//directory was created with context menu option var node = $('#models-jstree').jstree().get_node(o); if(node.type === "root"){ - self.refreshJSTree() + self.refreshJSTree(); }else{ $('#models-jstree').jstree().refresh_node(node); } }else{//directory was created with create directory button - self.refreshJSTree() + self.refreshJSTree(); } - }else{//new directory not created no need to refresh - body = JSON.parse(body) - let errorModal = $(modals.newDirectoryErrorHtml(body.Reason, body.Message)).modal() + }, + error: function (err, response, body) { + body = JSON.parse(body); + let errorModal = $(modals.newDirectoryErrorHtml(body.Reason, body.Message)).modal(); } }); } @@ -822,18 +831,73 @@ let FileBrowser = PageView.extend({ }, editWorkflowModel: function (o) { let endpoint = path.join(app.getApiPath(), "workflow/edit-model")+"?path="+o.original._path - xhr({uri: endpoint, json: true}, function (err, response, body) { - if(response.statusCode < 400) { + app.getXHR(endpoint, { + success: function (err, response, body) { if(body.error){ - let title = o.text + " Not Found" - let message = body.error - let modal = $(modals.duplicateWorkflowHtml(title, message)).modal() + let title = o.text + " Not Found"; + let message = body.error; + let modal = $(modals.duplicateWorkflowHtml(title, message)).modal(); }else{ - window.location.href = path.join(app.routePrefix, "models/edit")+"?path="+body.file + window.location.href = path.join(app.routePrefix, "models/edit")+"?path="+body.file; + } + } + }); + }, + extractAll: function (o) { + let self = this; + let queryStr = "?path=" + o.original._path; + let endpoint = path.join(app.getApiPath(), "file/unzip") + queryStr; + app.getXHR(endpoint, { + success: function (err, response, body) { + let node = $('#models-jstree').jstree().get_node(o.parent); + if(node.type === "root"){ + self.refreshJSTree(); + }else{ + $('#models-jstree').jstree().refresh_node(node); } + }, + error: function (err, response, body) { + let modal = $(modals.newProjectModelErrorHtml(body.Reason, body.message)).modal(); } }); }, + moveToTrash: function (o) { + if(document.querySelector('#moveToTrashConfirmModal')) { + document.querySelector('#moveToTrashConfirmModal').remove(); + } + let self = this; + let modal = $(modals.moveToTrashConfirmHtml("model")).modal(); + let yesBtn = document.querySelector('#moveToTrashConfirmModal .yes-modal-btn'); + yesBtn.addEventListener('click', function (e) { + modal.modal('hide'); + let queryStr = "?srcPath=" + o.original._path + "&dstPath=" + path.join("trash", o.text) + let endpoint = path.join(app.getApiPath(), "file/move") + queryStr + app.getXHR(endpoint, { + always: function (err, response, body) { + $(self.queryByHook('empty-trash')).prop('disabled', false); + $('#models-jstree').jstree().refresh(); + } + }); + }); + }, + emptyTrash: function (e) { + if(document.querySelector("#emptyTrashConfirmModal")) { + document.querySelector("#emptyTrashConfirmModal").remove() + } + let self = this; + let modal = $(modals.emptyTrashConfirmHtml()).modal(); + let yesBtn = document.querySelector('#emptyTrashConfirmModal .yes-modal-btn'); + yesBtn.addEventListener('click', function (e) { + modal.modal('hide'); + let endpoint = path.join(app.getApiPath(), "file/empty-trash") + "?path=trash"; + app.getXHR(endpoint, { + success: function (err, response, body) { + self.refreshJSTree(); + $(self.queryByHook('empty-trash')).prop('disabled', true); + } + }); + }); + }, setupJstree: function () { var self = this; $.jstree.defaults.contextmenu.items = (o, cb) => { @@ -879,6 +943,17 @@ let FileBrowser = PageView.extend({ self.duplicateFileOrDirectory(o, null) } }, + "MoveToTrash" : { + "label" : "Move To Trash", + "_disabled" : false, + "separator_before" : false, + "separator_after" : false, + "action" : function (data) { + self.moveToTrash(o); + } + } + } + let delete_node = { "Delete" : { "label" : "Delete", "_disabled" : false, @@ -996,6 +1071,35 @@ let FileBrowser = PageView.extend({ } } // common to both spatial and non-spatial models + let newWorkflow = { + "ensembleSimulation" : { + "label" : "Ensemble Simulation", + "_disabled" : false, + "separator_before" : false, + "separator_after" : false, + "action" : function (data) { + self.newWorkflow(o, "Ensemble Simulation") + } + }, + "parameterSweep" : { + "label" : "Parameter Sweep", + "_disabled" : false, + "separator_before" : false, + "separator_after" : false, + "action" : function (data) { + self.newWorkflow(o, "Parameter Sweep") + } + }, + "jupyterNotebook" : { + "label" : "Jupyter Notebook", + "_disabled" : false, + "separator_before" : false, + "separator_after" : false, + "action" : function (data) { + window.location.href = path.join(app.getBasePath(), "stochss/workflow/selection")+"?path="+o.original._path; + } + } + } let model = { "Edit" : { "label" : "Edit", @@ -1012,9 +1116,7 @@ let FileBrowser = PageView.extend({ "_disabled" : false, "separator_before" : false, "separator_after" : false, - "action" : function (data) { - window.location.href = path.join(app.getBasePath(), "stochss/workflow/selection")+"?path="+o.original._path; - } + "submenu" : o.type === "nonspatial" ? newWorkflow : {"jupyterNotebook":newWorkflow.jupyterNotebook} } } // convert options for spatial models @@ -1135,15 +1237,6 @@ let FileBrowser = PageView.extend({ } // specific to workflows let workflow = { - "Convert to Notebook" : { - "label" : "To Notebook", - "_disabled" : false, - "separator_before" : false, - "separator_after" : false, - "action" : function (data) { - self.toNotebook(o, "workflow") - } - }, "Start/Restart Workflow" : { "label" : (o.original._status === "ready") ? "Start Workflow" : "Restart Workflow", "_disabled" : true, @@ -1170,7 +1263,7 @@ let FileBrowser = PageView.extend({ "submenu" : { "Edit" : { "label" : " Edit", - "_disabled" : !(o.original._status === "ready"), + "_disabled" : (!o.original._newFormat && o.original._status !== "ready"), "separator_before" : false, "separator_after" : false, "action" : function (data) { @@ -1179,7 +1272,7 @@ let FileBrowser = PageView.extend({ }, "Extract" : { "label" : "Extract", - "_disabled" : false, + "_disabled" : (o.original._newFormat && !o.original._hasJobs), "separator_before" : false, "separator_after" : false, "action" : function (data) { @@ -1209,9 +1302,27 @@ let FileBrowser = PageView.extend({ } } } + //Specific to zip archives + let extractAll = { + "extractAll" : { + "label" : "Extract All", + "_disabled" : false, + "separator_before" : false, + "separator_after" : false, + "action" : function (data) { + self.extractAll(o); + } + } + } if (o.type === 'root'){ return folder } + if (o.text === "trash") { + return {"Refresh": folder.Refresh} + } + if (o.original._path.split("/")[0] === "trash") { + return delete_node + } if (o.type === 'folder') { return $.extend(folder, common) } @@ -1227,6 +1338,9 @@ let FileBrowser = PageView.extend({ if (o.type === 'workflow') { return $.extend(open, workflow, common) } + if (o.text.endsWith(".zip")) { + return $.extend(open, extractAll, common) + } if (o.type === 'notebook' || o.type === "other") { return $.extend(open, common) } @@ -1267,26 +1381,28 @@ let FileBrowser = PageView.extend({ var file = e.target.text var node = $('#models-jstree').jstree().get_node(e.target) var _path = node.original._path; - if(file.endsWith('.mdl') || file.endsWith('.smdl')){ - window.location.href = path.join(app.getBasePath(), "stochss/models/edit")+"?path="+_path; - }else if(file.endsWith('.ipynb')){ - var notebookPath = path.join(app.getBasePath(), "notebooks", _path) - window.open(notebookPath, '_blank') - }else if(file.endsWith('.sbml')){ - var openPath = path.join(app.getBasePath(), "edit", _path) - window.open(openPath, '_blank') - }else if(file.endsWith('.proj')){ - window.location.href = path.join(app.getBasePath(), "stochss/project/manager")+"?path="+_path; - }else if(file.endsWith('.wkfl')){ - window.location.href = path.join(app.getBasePath(), "stochss/workflow/edit")+"?path="+_path+"&type=none"; - }else if(file.endsWith('.domn')) { - let queryStr = "?domainPath=" + _path - window.location.href = path.join(app.getBasePath(), "stochss/domain/edit") + queryStr - }else if(node.type === "folder" && $('#models-jstree').jstree().is_open(node) && $('#models-jstree').jstree().is_loaded(node)){ - $('#models-jstree').jstree().refresh_node(node) - }else if(node.type === "other"){ - var openPath = path.join(app.getBasePath(), "view", _path); - window.open(openPath, "_blank"); + if(!(_path.split("/")[0] === "trash")) { + if(file.endsWith('.mdl') || file.endsWith('.smdl')){ + window.location.href = path.join(app.getBasePath(), "stochss/models/edit")+"?path="+_path; + }else if(file.endsWith('.ipynb')){ + var notebookPath = path.join(app.getBasePath(), "notebooks", _path) + window.open(notebookPath, '_blank') + }else if(file.endsWith('.sbml')){ + var openPath = path.join(app.getBasePath(), "edit", _path) + window.open(openPath, '_blank') + }else if(file.endsWith('.proj')){ + window.location.href = path.join(app.getBasePath(), "stochss/project/manager")+"?path="+_path; + }else if(file.endsWith('.wkfl')){ + window.location.href = path.join(app.getBasePath(), "stochss/workflow/edit")+"?path="+_path+"&type=none"; + }else if(file.endsWith('.domn')) { + let queryStr = "?domainPath=" + _path + window.location.href = path.join(app.getBasePath(), "stochss/domain/edit") + queryStr + }else if(node.type === "folder" && $('#models-jstree').jstree().is_open(node) && $('#models-jstree').jstree().is_loaded(node)){ + $('#models-jstree').jstree().refresh_node(node) + }else if(node.type === "other"){ + var openPath = path.join(app.getBasePath(), "view", _path); + window.open(openPath, "_blank"); + } } }); } diff --git a/client/pages/loading-page.js b/client/pages/loading-page.js new file mode 100644 index 0000000000..f6ba556d4f --- /dev/null +++ b/client/pages/loading-page.js @@ -0,0 +1,144 @@ +/* +StochSS is a platform for simulating biochemical systems +Copyright (C) 2019-2020 StochSS developers. + +This program is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with this program. If not, see . +*/ + +let $ = require('jquery'); +let path = require('path'); +//support files +let app = require('../app'); +let modals = require('../modals'); +// views +var PageView = require('./base'); +// templates +var template = require('../templates/pages/loadingPage.pug'); + +import initPage from './page.js'; + +let LoadingPage = PageView.extend({ + template: template, + initialize: function (attrs, options) { + PageView.prototype.initialize.apply(this, arguments); + let urlParams = new URLSearchParams(window.location.search) + this.filePath = urlParams.get("path"); + this.action = urlParams.get("action"); + }, + render: function (attrs, options) { + PageView.prototype.render.apply(this, arguments); + $(document.querySelector("div[data-hook=side-navbar]")).css("display", "none"); + $(document.querySelector("main[data-hook=page-main]")).removeClass().addClass("col-md-12 body"); + $(this.queryByHook("loading-spinner")).css("display", "block"); + if(this.action === "open") { + this.uploadFileFromLink(this.filePath); + }else if(this.action === "update-workflow") { + this.updateWorkflowFormat(this.filePath); + }else if(this.action === "update-project") { + this.updateProjectFormat(this.filePath); + } + }, + getUploadResponse: function () { + let self = this; + setTimeout(function () { + let queryStr = "?path=" + self.responsePath + "&cmd=read"; + let endpoint = path.join(app.getApiPath(), 'file/upload-from-link') + queryStr; + let errorCB = function (err, response, body) { + $(this.queryByHook("loading-spinner")).css("display", "none"); + let model = $(modals.projectExportErrorHtml(body.reason, body.message)).modal(); + let close = document.querySelector("button[data-dismiss=modal]"); + close.addEventListener("click", function (e) { + window.history.back(); + }); + } + app.getXHR(endpoint, { + success: function (err, response, body) { + if(Object.keys(body).includes("reason")) { + errorCB(err, response, body); + }else if(body.done) { + if(body.file_path.endsWith(".proj")){ + self.openStochSSPage("stochss/project/manager", body.file_path); + }else if(body.file_path.endsWith(".wkfl")){ + self.openStochSSPage("stochss/workflow/edit", body.file_path); + }else if(body.file_path.endsWith(".mdl")){ + self.openStochSSPage("stochss/models/edit", body.file_path); + }else if(body.file_path.endsWith(".domn")){ + self.openStochSSPage("stochss/domain/edit", body.file_path); + }else if(body.file_path.endsWith(".ipynb")){ + self.openNotebookFile(body.file_path); + }else{ + self.openStochSSPage('stochss/files'); + } + }else{ + self.getUploadResponse(); + } + }, + error: errorCB + }); + }, 1000); + }, + openNotebookFile: function (filePath) { + window.open(path.join(app.getBasePath(), "notebooks", filePath)); + window.history.back(); + }, + openStochSSPage: function (identifier, filePath) { + var endpoint = path.join(app.getBasePath(), identifier); + if(filePath) { + let query = identifier.includes("domain") ? "?domainPath=" : "?path="; + endpoint += query + filePath; + } + window.location.href = endpoint; + }, + updateFormat: function (filePath, message, target, identifier) { + $(this.queryByHook("loading-header")).html("Updating Format"); + $(this.queryByHook("loading-target")).html(filePath.split('/').pop()); + $(this.queryByHook("loading-message")).html(message); + let self = this; + let queryStr = "?path=" + filePath; + let endpoint = path.join(app.getApiPath(), target, "update-format") + queryStr; + app.getXHR(endpoint, { + success: function (err, response, body) { + let dst = target === "workflow" ? body : filePath; + self.openStochSSPage(identifier, dst); + } + }); + }, + updateProjectFormat: function (filePath) { + let message = `You can update the format of any project and its workflows by opening the project and clicking yes when prompted to update the format.`; + let identifier = "stochss/project/manager" + this.updateFormat(filePath, message, "project", identifier); + }, + updateWorkflowFormat: function (filePath) { + let message = `You can update the format of any workflow by opening the workflow and clicking yes when prompted to update the format.`; + let identifier = "stochss/workflow/edit" + this.updateFormat(filePath, message, "workflow", identifier); + }, + uploadFileFromLink: function (filePath) { + $(this.queryByHook("loading-header")).html("Uploading file"); + $(this.queryByHook("loading-target")).html(filePath.split('/').pop()); + let message = `If the file is a Project, Workflow, Model, Domain, or Notebook it will be opened when the upload has completed.`; + $(this.queryByHook("loading-message")).html(message); + let self = this; + let queryStr = "?path=" + filePath; + let endpoint = path.join(app.getApiPath(), 'file/upload-from-link') + queryStr; + app.getXHR(endpoint, { + success: function (err, response, body) { + self.responsePath = body.responsePath; + self.getUploadResponse(); + } + }); + } +}); + +initPage(LoadingPage); diff --git a/client/pages/model-editor.js b/client/pages/model-editor.js index 7deaff4ef5..bdb85123e5 100644 --- a/client/pages/model-editor.js +++ b/client/pages/model-editor.js @@ -16,7 +16,6 @@ You should have received a copy of the GNU General Public License along with this program. If not, see . */ -var xhr = require('xhr'); var _ = require('underscore'); var $ = require('jquery'); let path = require('path'); @@ -33,7 +32,6 @@ var SpeciesViewer = require('../views/species-viewer'); var InitialConditionsEditorView = require('../views/initial-conditions-editor'); var InitialConditionsViewer = require('../views/initial-conditions-viewer'); var ParametersEditorView = require('../views/parameters-editor'); -var ParameterViewer = require('../views/parameters-viewer'); var ParticleViewer = require('../views/view-particle'); var ReactionsEditorView = require('../views/reactions-editor'); var ReactionsViewer = require('../views/reactions-viewer'); @@ -42,7 +40,7 @@ var EventsViewer = require('../views/events-viewer'); var RulesEditorView = require('../views/rules-editor'); var RulesViewer = require('../views/rules-viewer'); var SBMLComponentView = require('../views/sbml-component-editor'); -var ModelSettingsView = require('../views/model-settings'); +var TimespanSettingsView = require('../views/timespan-settings'); var ModelStateButtonsView = require('../views/model-state-buttons'); var QuickviewDomainTypes = require('../views/quickview-domain-types'); //models @@ -83,10 +81,14 @@ let ModelEditor = PageView.extend({ }); if(directory.includes('.proj')) { this.projectPath = path.dirname(directory) + if(this.projectPath.endsWith(".wkgp")) { + this.projectPath = path.dirname(this.projectPath) + } this.projectName = this.getFileName(this.projectPath) } - this.model.fetch({ - success: function (model, response, options) { + app.getXHR(this.model.url(), { + success: function (err, response, body) { + self.model.set(body) if(directory.includes('.proj')) { self.queryByHook("project-breadcrumb-links").style.display = "block" self.queryByHook("model-name-header").style.display = "none" @@ -94,7 +96,7 @@ let ModelEditor = PageView.extend({ self.renderSubviews(); self.model.updateValid() } - }); + }) this.model.reactions.on("change", function (reactions) { this.updateSpeciesInUse(); this.updateParametersInUse(); @@ -205,7 +207,7 @@ let ModelEditor = PageView.extend({ this.particleViewer = new ParticleViewer({ model: particle }); - this.registerRenderSubview(this.particleViewer, "me-particle-viewer") + app.registerRenderSubview(this, this.particleViewer, "me-particle-viewer") }else{ $(this.queryByHook("me-select-particle")).css("display", "block") this.typeQuickViewer = this.renderCollection( @@ -213,11 +215,10 @@ let ModelEditor = PageView.extend({ QuickviewDomainTypes, this.queryByHook("me-types-quick-view") ); - console.log(this.domainViewer.model.types.models) } }, renderSubviews: function () { - this.modelSettings = new ModelSettingsView({ + this.modelSettings = new TimespanSettingsView({ parent: this, model: this.model.modelSettings, }); @@ -227,8 +228,8 @@ let ModelEditor = PageView.extend({ this.renderSpeciesView(); this.renderParametersView(); this.renderReactionsView(); - this.registerRenderSubview(this.modelSettings, 'model-settings-container'); - this.registerRenderSubview(this.modelStateButtons, 'model-state-buttons-container'); + app.registerRenderSubview(this, this.modelSettings, 'model-settings-container'); + app.registerRenderSubview(this, this.modelStateButtons, 'model-state-buttons-container'); if(this.model.is_spatial) { $(this.queryByHook("model-editor-advanced-container")).css("display", "none"); $(this.queryByHook("spatial-beta-message")).css("display", "block"); @@ -242,8 +243,9 @@ let ModelEditor = PageView.extend({ if(this.model.functionDefinitions.length) { var sbmlComponentView = new SBMLComponentView({ functionDefinitions: this.model.functionDefinitions, + viewModel: false }); - this.registerRenderSubview(sbmlComponentView, 'sbml-component-container'); + app.registerRenderSubview(this, sbmlComponentView, 'sbml-component-container'); } this.renderSystemVolumeView(); } @@ -257,10 +259,6 @@ let ModelEditor = PageView.extend({ e.target.remove() }); }, - registerRenderSubview: function (view, hook) { - this.registerSubview(view); - this.renderSubview(view, this.queryByHook(hook)); - }, renderDomainViewer: function(domainPath=null) { if(this.domainViewer) { this.domainViewer.remove() @@ -269,14 +267,16 @@ let ModelEditor = PageView.extend({ let self = this; let queryStr = "?path=" + this.model.directory + "&domain_path=" + domainPath let endpoint = path.join(app.getApiPath(), "spatial-model/load-domain") + queryStr - xhr({uri: endpoint, json: true}, function (err, resp, body) { - let domain = new Domain(body.domain); - self.domainViewer = new DomainViewer({ - parent: self, - model: domain, - domainPath: domainPath - }); - self.registerRenderSubview(self.domainViewer, 'domain-viewer-container'); + app.getXHR(endpoint, { + always: function (err, response, body) { + let domain = new Domain(body.domain); + self.domainViewer = new DomainViewer({ + parent: self, + model: domain, + domainPath: domainPath + }); + app.registerRenderSubview(self, self.domainViewer, 'domain-viewer-container'); + } }); }else{ this.domainViewer = new DomainViewer({ @@ -284,7 +284,7 @@ let ModelEditor = PageView.extend({ model: this.model.domain, domainPath: domainPath }); - this.registerRenderSubview(this.domainViewer, 'domain-viewer-container'); + app.registerRenderSubview(this, this.domainViewer, 'domain-viewer-container'); } }, renderSpeciesView: function (mode="edit") { @@ -296,7 +296,7 @@ let ModelEditor = PageView.extend({ }else{ this.speciesEditor = new SpeciesViewer({collection: this.model.species}); } - this.registerRenderSubview(this.speciesEditor, 'species-editor-container'); + app.registerRenderSubview(this, this.speciesEditor, 'species-editor-container'); }, renderInitialConditions: function (mode="edit", opened=false) { if(this.initialConditionsEditor) { @@ -312,18 +312,14 @@ let ModelEditor = PageView.extend({ collection: this.model.initialConditions }); } - this.registerRenderSubview(this.initialConditionsEditor, 'initial-conditions-editor-container'); + app.registerRenderSubview(this, this.initialConditionsEditor, 'initial-conditions-editor-container'); }, - renderParametersView: function (mode="edit", opened=false) { + renderParametersView: function () { if(this.parametersEditor) { this.parametersEditor.remove() } - if(mode === "edit") { - this.parametersEditor = new ParametersEditorView({collection: this.model.parameters, opened: opened}); - }else{ - this.parametersEditor = new ParameterViewer({collection: this.model.parameters}); - } - this.registerRenderSubview(this.parametersEditor, 'parameters-editor-container'); + this.parametersEditor = new ParametersEditorView({collection: this.model.parameters}); + app.registerRenderSubview(this, this.parametersEditor, 'parameters-editor-container'); }, renderReactionsView: function (mode="edit", opened=false) { if(this.reactionsEditor) { @@ -334,7 +330,7 @@ let ModelEditor = PageView.extend({ }else{ this.reactionsEditor = new ReactionsViewer({collection: this.model.reactions}); } - this.registerRenderSubview(this.reactionsEditor, 'reactions-editor-container'); + app.registerRenderSubview(this, this.reactionsEditor, 'reactions-editor-container'); }, renderEventsView: function (mode="edit", opened=false) { if(this.eventsEditor){ @@ -345,7 +341,7 @@ let ModelEditor = PageView.extend({ }else{ this.eventsEditor = new EventsViewer({collection: this.model.eventsCollection}); } - this.registerRenderSubview(this.eventsEditor, 'events-editor-container'); + app.registerRenderSubview(this, this.eventsEditor, 'events-editor-container'); }, renderRulesView: function (mode="edit", opened=false) { if(this.rulesEditor){ @@ -356,7 +352,7 @@ let ModelEditor = PageView.extend({ }else{ this.rulesEditor = new RulesViewer({collection: this.model.rules}) } - this.registerRenderSubview(this.rulesEditor, 'rules-editor-container'); + app.registerRenderSubview(this, this.rulesEditor, 'rules-editor-container'); }, renderSystemVolumeView: function () { if(this.systemVolumeView) { @@ -372,19 +368,13 @@ let ModelEditor = PageView.extend({ valueType: 'number', value: this.model.volume, }); - this.registerRenderSubview(this.systemVolumeView, 'volume') + app.registerRenderSubview(this, this.systemVolumeView, 'volume') if(this.model.defaultMode === "continuous") { $(this.queryByHook("system-volume-container")).collapse("hide") } }, changeCollapseButtonText: function (e) { - let source = e.target.dataset.hook - let collapseContainer = $(this.queryByHook(source).dataset.target) - if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) { - let collapseBtn = $(this.queryByHook(source)) - let text = collapseBtn.text(); - text === '+' ? collapseBtn.text('-') : collapseBtn.text('+'); - } + app.changeCollapseButtonText(this, e); }, togglePreviewPlot: function (e) { let action = e.target.innerText diff --git a/client/pages/multiple-plots.js b/client/pages/multiple-plots.js new file mode 100644 index 0000000000..ad54c5b373 --- /dev/null +++ b/client/pages/multiple-plots.js @@ -0,0 +1,61 @@ +/* +StochSS is a platform for simulating biochemical systems +Copyright (C) 2019-2020 StochSS developers. + +This program is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with this program. If not, see . +*/ + +let path = require('path'); +//support files +let app = require('../app'); +let Plotly = require('../lib/plotly'); +//views +var PageView = require('../pages/base'); +//templates +let template = require("../templates/pages/multiplePlots.pug"); + +import initPage from './page.js'; + +let ModelEditor = PageView.extend({ + template: template, + initialize: function (attrs, options) { + PageView.prototype.initialize.apply(this, arguments); + let urlParams = new URLSearchParams(window.location.search); + this.workflow = urlParams.get("wkfl"); + this.job = urlParams.get("job"); + this.path = urlParams.get("path"); + this.data = urlParams.get("data"); + }, + render: function (attrs, options) { + PageView.prototype.render.apply(this, arguments); + let queryStr = "?path=" + this.path + "&data=" + this.data; + let endpoint = path.join(app.getApiPath(), "workflow/plot-results") + queryStr; + let self = this; + app.getXHR(endpoint, { + success: function (err, response, body) { + self.plotFigure(body); + }, + error: function (err, response, body) { + console.log(body) + } + }); + }, + plotFigure: function (figure) { + let el = this.queryByHook("figures"); + let config = {"responsive":true}; + Plotly.newPlot(el, figure, config); + } +}); + +initPage(ModelEditor); \ No newline at end of file diff --git a/client/pages/project-browser.js b/client/pages/project-browser.js index 051fc554c8..1b65377b8d 100644 --- a/client/pages/project-browser.js +++ b/client/pages/project-browser.js @@ -18,7 +18,6 @@ along with this program. If not, see . let $ = require('jquery'); let path = require('path'); -let xhr = require('xhr'); //support files let app = require('../app'); let modals = require('../modals'); @@ -27,10 +26,10 @@ let Project = require('../models/project'); //collections let Collection = require('ampersand-collection'); //views -var PageView = require('./base'); +let PageView = require('./base'); let EditProjectView = require('../views/edit-project'); //templates -var template = require('../templates/pages/projectBrowser.pug'); +let template = require('../templates/pages/projectBrowser.pug'); import initPage from './page.js'; @@ -40,13 +39,13 @@ let projectBrowser = PageView.extend({ 'click [data-hook=new-project-btn]' : 'handleNewProjectClick' }, initialize: function (attrs, options) { - PageView.prototype.initialize.apply(this, arguments) - let self = this - let endpoint = path.join(app.getApiPath(), "project/load-browser") - xhr({uri:endpoint, json:true}, function (err, response, body) { - if(response.statusCode < 400) { - self.projects = body.projects - self.renderProjectsView() + PageView.prototype.initialize.apply(this, arguments); + let self = this; + let endpoint = path.join(app.getApiPath(), "project/load-browser"); + app.getXHR(endpoint, { + success: function (err, response, body) { + self.projects = body.projects; + self.renderProjectsView(); } }); }, @@ -56,35 +55,15 @@ let projectBrowser = PageView.extend({ e.target.remove() }); }, - renderProjectsView: function () { - if(this.projectsView) { - this.projectsView.remove() - } - let projects = new Collection(this.projects, {model: Project, comparator: 'parentDir'}) - this.projectsView = this.renderCollection(projects, EditProjectView, this.queryByHook("projects-view-container")) - }, - validateName(input) { - var error = "" - if(input.endsWith('/')) { - error = 'forward' - } - let invalidChars = "`~!@#$%^&*=+[{]}\"|:;'<,>?\\" - for(var i = 0; i < input.length; i++) { - if(invalidChars.includes(input.charAt(i))) { - error = error === "" || error === "special" ? "special" : "both" - } - } - return error - }, handleNewProjectClick: function (e) { - let self = this + let self = this; if(document.querySelector("#newProjectModal")) { - document.querySelector("#newProjectModal").remove() + document.querySelector("#newProjectModal").remove(); } - let modal = $(modals.newProjectModalHtml()).modal() - let input = document.querySelector("#newProjectModal #projectNameInput") - input.focus() - let okBtn = document.querySelector("#newProjectModal .ok-model-btn") + let modal = $(modals.newProjectModalHtml()).modal(); + let input = document.querySelector("#newProjectModal #projectNameInput"); + input.focus(); + let okBtn = document.querySelector("#newProjectModal .ok-model-btn"); input.addEventListener("keyup", function (event) { if(event.keyCode === 13){ event.preventDefault(); @@ -92,28 +71,49 @@ let projectBrowser = PageView.extend({ } }); input.addEventListener("input", function (e) { - var endErrMsg = document.querySelector('#newProjectModal #projectNameInputEndCharError') - var charErrMsg = document.querySelector('#newProjectModal #projectNameInputSpecCharError') - let error = self.validateName(input.value) - okBtn.disabled = error !== "" - charErrMsg.style.display = error === "both" || error === "special" ? "block" : "none" - endErrMsg.style.display = error === "both" || error === "forward" ? "block" : "none" + var endErrMsg = document.querySelector('#newProjectModal #projectNameInputEndCharError'); + var charErrMsg = document.querySelector('#newProjectModal #projectNameInputSpecCharError'); + let error = self.validateName(input.value); + okBtn.disabled = error !== ""; + charErrMsg.style.display = error === "both" || error === "special" ? "block" : "none"; + endErrMsg.style.display = error === "both" || error === "forward" ? "block" : "none"; }); okBtn.addEventListener("click", function (e) { if(Boolean(input.value)) { - modal.modal('hide') - let projectPath = input.value.trim() + ".proj" - let endpoint = path.join(app.getApiPath(), "project/new-project")+"?path="+projectPath - xhr({uri:endpoint, json:true}, function (err, response, body) { - if(response.statusCode < 400) { - window.location.href = path.join(app.getBasePath(), "stochss/project/manager")+"?path="+body.path - }else{ - let errorModel = $(modals.newProjectOrWorkflowGroupErrorHtml(body.Reason, body.Message)).modal() + modal.modal('hide'); + let projectPath = input.value.trim() + ".proj"; + let endpoint = path.join(app.getApiPath(), "project/new-project") + "?path=" + projectPath; + app.getXHR(endpoint, { + success: function (err, response, body) { + window.location.href = path.join(app.getBasePath(), "stochss/project/manager")+"?path="+body.path; + }, + error: function (err, response, body) { + let errorModel = $(modals.newProjectOrWorkflowGroupErrorHtml(body.Reason, body.Message)).modal(); } - }) + }); } }); + }, + renderProjectsView: function () { + if(this.projectsView) { + this.projectsView.remove() + } + let projects = new Collection(this.projects, {model: Project, comparator: 'parentDir'}) + this.projectsView = this.renderCollection(projects, EditProjectView, this.queryByHook("projects-view-container")) + }, + validateName(input) { + var error = ""; + if(input.endsWith('/')) { + error = 'forward'; + } + let invalidChars = "`~!@#$%^&*=+[{]}\"|:;'<,>?\\"; + for(var i = 0; i < input.length; i++) { + if(invalidChars.includes(input.charAt(i))) { + error = error === "" || error === "special" ? "special" : "both"; + } + } + return error; } }); -initPage(projectBrowser); \ No newline at end of file +initPage(projectBrowser); diff --git a/client/pages/project-manager.js b/client/pages/project-manager.js index 5db3e27a68..67f45073ba 100644 --- a/client/pages/project-manager.js +++ b/client/pages/project-manager.js @@ -16,304 +16,177 @@ You should have received a copy of the GNU General Public License along with this program. If not, see . */ -var $ = require('jquery'); -var xhr = require('xhr'); -var path = require('path'); +let $ = require('jquery'); +let path = require('path'); //support files -var app = require('../app'); -var modals = require('../modals'); -//views -var PageView = require('./base'); -var PlotsView = require('../views/plots-view'); -var EditModelsView = require('../views/edit-models-view'); -var EditWorkflowGroupsView = require('../views/edit-workflow-groups-view'); -var ProjectViewer = require('../views/project-viewer'); -var FileBrowser = require('../views/file-browser-view'); -var MetaDataView = require('../views/meta-data'); +let app = require('../app'); +let modals = require('../modals'); +//collection +let Collection = require('ampersand-collection'); //models -var Project = require('../models/project'); -var Plot = require('../models/plots'); +let Model = require('../models/model'); +let Project = require('../models/project'); +//views +let PageView = require('./base'); +let MetaDataView = require('../views/meta-data'); +let ModelListing = require('../views/model-listing'); +let FileBrowser = require('../views/file-browser-view'); +let ArchiveListing = require('../views/archive-listing'); +let WorkflowListing = require('../views/workflow-listing'); +let WorkflowGroupListing = require('../views/workflow-group-listing'); //templates -var template = require('../templates/pages/projectManager.pug'); +let template = require('../templates/pages/projectManager.pug'); import initPage from './page.js' let ProjectManager = PageView.extend({ template: template, events: { + 'change [data-hook=annotation-text-container]' : 'updateAnnotation', + 'click [data-hook=edit-annotation-btn]' : 'handleEditAnnotationClick', + 'click [data-hook=collapse-annotation-text]' : 'changeCollapseButtonText', 'click [data-hook=new-model]' : 'handleNewModelClick', - 'click [data-hook=new-workflow-group]' : 'handleNewWorkflowGroupClick', 'click [data-hook=existing-model]' : 'handleExistingModelClick', - 'click [data-hook=export-project-as-zip]' : 'handleExportZipClick', - // 'click [data-hook=export-project-as-combine]' : 'handleExportCombineClick', - 'click [data-hook=empty-project-trash]' : 'handleEmptyTrashClick', - 'click [data-hook=collapse-most-recent-plot-btn]' : 'changeCollapseButtonText', - 'click [data-hook=project-manager-advanced-btn]' : 'changeCollapseButtonText', - 'click [data-hook=collapse-annotation-container]' : 'changeCollapseButtonText', - 'change [data-hook=annotation-text-container]' : 'updateAnnotation', 'click [data-hook=upload-file-btn]' : 'handleUploadModelClick', - 'click [data-hook=edit-annotation-btn]' : 'handleEditAnnotationClick' + 'click [data-hook=new-ensemble-simulation]' : 'handleNewWorkflowClick', + 'click [data-hook=new-parameter-sweep]' : 'handleNewWorkflowClick', + 'click [data-hook=new-jupyter-notebook]' : 'handleNewWorkflowClick', + 'click [data-hook=project-manager-advanced-btn]' : 'changeCollapseButtonText', + 'click [data-hook=archive-btn]' : 'changeCollapseButtonText', + 'click [data-hook=export-project-as-zip]' : 'handleExportZipClick', + 'click [data-hook=export-project-as-combine]' : 'handleExportCombineClick', + 'click [data-hook=empty-project-trash]' : 'handleEmptyTrashClick' }, initialize: function (attrs, options) { PageView.prototype.initialize.apply(this, arguments) - let self = this - this.url = decodeURI(document.URL) - let urlParams = new URLSearchParams(window.location.search) - this.projectPath = urlParams.get('path') - this.projectName = this.getFileName(this.projectPath) + let self = this; + let urlParams = new URLSearchParams(window.location.search); this.model = new Project({ - directory: self.projectPath + directory: urlParams.get('path') }); - this.model.fetch({ - success: function (model, response, options) { - if(response.trash_empty) { - $(self.queryByHook('empty-project-trash')).prop('disabled', true) + app.getXHR(this.model.url(), { + success: function (err, response, body) { + self.model.set(body) + self.models = new Collection(body.models, {model: Model}); + if(!self.model.newFormat) { + self.model.workflowGroups.models[0].model = null; } - self.renderSubviews() + self.renderSubviews(body.trash_empty); } }); - }, - update: function (target) { - let self = this - this.model.fetch({ - success: function (model, response, options) { - self.renderProjectViewer() - $(self.queryByHook('empty-project-trash')).prop('disabled', response.trash_empty) - if(target === "model-editor" || target === "workflows-editor" || target === "trash") { - self.projectFileBrowser.refreshJSTree() - }else if(target === "workflow-group-editor"){ - self.projectFileBrowser.refreshJSTree() - self.renderEditModelsView() - }else if(target === "file-browser") { - self.renderEditModelsView() - self.renderEditWorkflowGroupsView() - }else{ - self.renderEditModelsView() - self.renderEditWorkflowGroupsView() - self.projectFileBrowser.refreshJSTree() - } + window.addEventListener("pageshow", function (event) { + var navType = window.performance.navigation.type + if(navType === 2){ + window.location.reload() } }); }, - getFileName: function (file) { - if(file.endsWith('/')) { - file.slice(0, -1) - } - if(file.includes('/')) { - file = file.split('/').pop() - } - if(!file.includes('.')) { - return file - } - return file.split('.').slice(0, -1).join('.') - }, - renderSubviews: function () { - this.renderProjectViewer(); - this.renderProjectFileBrowser(); - this.renderRecentPlotView(); - this.renderEditModelsView(); - this.renderEditWorkflowGroupsView(); - if(this.model.annotation){ - $(this.queryByHook('annotation-text-container')).text(this.model.annotation) - $(this.queryByHook("collapse-annotation-container")).collapse('show') - }else{ - $(this.queryByHook('edit-annotation-btn')).text('Add Notes') + addExistingModel: function () { + if(document.querySelector('#newProjectModelModal')){ + document.querySelector('#newProjectModelModal').remove(); } - $(document).on('hide.bs.modal', '.modal', function (e) { - e.target.remove() + let self = this + let mdlListEP = path.join(app.getApiPath(), 'project/add-existing-model') + "?path=" + self.model.directory; + app.getXHR(mdlListEP, { + always: function (err, response, body) { + let modal = $(modals.newProjectModelHtml(body.files)).modal(); + let okBtn = document.querySelector('#newProjectModelModal .ok-model-btn'); + let select = document.querySelector('#newProjectModelModal #modelFileInput'); + let location = document.querySelector('#newProjectModelModal #modelPathInput'); + select.addEventListener("change", function (e) { + okBtn.disabled = e.target.value && body.paths[e.target.value].length >= 2; + if(body.paths[e.target.value].length >= 2) { + var locations = body.paths[e.target.value].map(function (path) { + return ``; + }); + locations.unshift(``); + locations = locations.join(" "); + $("#modelPathInput").find('option').remove().end().append(locations); + $("#location-container").css("display", "block"); + }else{ + $("#location-container").css("display", "none"); + $("#modelPathInput").find('option').remove().end(); + } + }); + location.addEventListener("change", function (e) { + okBtn.disabled = !Boolean(e.target.value); + }); + okBtn.addEventListener("click", function (e) { + modal.modal('hide'); + let mdlPath = body.paths[select.value].length < 2 ? body.paths[select.value][0] : location.value; + let queryString = "?path=" + self.model.directory + "&mdlPath=" + mdlPath; + let endpoint = path.join(app.getApiPath(), 'project/add-existing-model') + queryString + app.postXHR(endpoint, null, { + success: function (err, response, body) { + let successModal = $(modals.newProjectModelSuccessHtml(body.message)).modal(); + }, + error: function (err, response, body) { + let errorModal = $(modals.newProjectModelErrorHtml(body.Reason, body.Message)).modal(); + } + }); + self.update("Model"); + }); + } }); }, - renderRecentPlotView: function () { - if(this.recentPlotView) { - this.recentPlotView.remove() - } - if(this.model.plot) { - var plot = new Plot(this.model.plot.output) - var expName = path.dirname(this.model.plot.path).split('/').pop().split('.')[0] - var wkflName = this.model.plot.path.split('/').pop().split('.')[0] - this.recentPlotView = new PlotsView({ - model: plot, - path: this.model.plot.path, - heading: expName + " - " + wkflName + addModel: function (parentPath, modelName, message) { + var endpoint = path.join(app.getBasePath(), "stochss/models/edit"); + if(parentPath.endsWith(".proj")) { + let queryString = "?path=" + parentPath + "&mdlFile=" + modelName; + let newMdlEP = path.join(app.getApiPath(), "project/new-model") + queryString; + app.getXHR(newMdlEP, { + success: function (err, response, body) { + endpoint += "?path="+body.path; + window.location.href = endpoint; + }, + error: function (err, response, body) { + let title = "Model Already Exists"; + let message = "A model already exists with that name"; + let errorModel = $(modals.newProjectOrWorkflowGroupErrorHtml(title, message)).modal(); + } }); - this.registerRenderSubview(this.recentPlotView, "project-most-recent-plot"); }else{ - let message = "Their are no saved plots in the workflows of this project" - $(this.queryByHook("project-most-recent-plot")).text(message) - } - }, - renderEditModelsView: function () { - if(this.editModelsView) { - this.editModelsView.remove() - } - this.editModelsView = new EditModelsView({ - collection: this.model.models - }); - this.registerRenderSubview(this.editModelsView, "edit-models-container") - }, - renderEditWorkflowGroupsView: function () { - if(this.editWorkflowGroupsView) { - this.editWorkflowGroupsView.remove() - } - this.editWorkflowGroupsView = new EditWorkflowGroupsView({ - collection: this.model.workflowGroups - }); - this.registerRenderSubview(this.editWorkflowGroupsView, "edit-workflow-groups-container") - }, - renderProjectViewer: function () { - if(this.projectViewer) { - this.projectViewer.remove() - } - this.projectViewer = new ProjectViewer({ - model: this.model, - name: this.projectName - }); - this.registerRenderSubview(this.projectViewer, "project-viewer") - }, - renderProjectFileBrowser: function () { - let self = this - if(this.projectFileBrowser) { - this.projectFileBrowser.remove() - } - this.projectFileBrowser = new FileBrowser({ - root: self.projectPath - }) - this.registerRenderSubview(this.projectFileBrowser, "file-browser") - }, - renderMetaDataView: function (target, files, download) { - if(this.metaDataView) { - this.metaDataView.remove() - } - this.metaDataView = new MetaDataView({ - parent: this, - projectName: this.model.directory, - files: files, - path: target, - download: download - }); - this.registerRenderSubview(this.metaDataView, "project-meta-data-container") - $(this.queryByHook("project-meta-data-container")).collapse("show") - }, - registerRenderSubview: function (view, hook) { - this.registerSubview(view); - this.renderSubview(view, this.queryByHook(hook)); - }, - handleEditAnnotationClick: function (e) { - let buttonTxt = e.target.innerText; - if(buttonTxt.startsWith("Add")){ - $(this.queryByHook('collapse-annotation-container')).collapse('show') - $(this.queryByHook('edit-annotation-btn')).text('Edit Notes') - }else if(!$("#annotation-text").attr('class').includes('show')){ - $("#annotation-text").collapse('show') - $(this.queryByHook("collapse-annotation-text")).text('-') - } - document.querySelector("#annotation").focus() - }, - updateAnnotation: function (e) { - this.model.annotation = e.target.value.trim(); - if(this.model.annotation === ""){ - $(this.queryByHook('edit-annotation-btn')).text('Add Notes') - $(this.queryByHook("collapse-annotation-container")).collapse('hide') - } - let endpoint = path.join(app.getApiPath(), "project/save-annotation")+"?path="+this.model.directory - xhr({uri: endpoint, json: true, method: "post", data: {'annotation': this.model.annotation}}, function (err, response, body) { - console.log("Saved project notes") - }) - }, - handleNewModelClick: function (e) { - let isSpatial = e.target.dataset.type === "spatial" - this.addNewModel(isSpatial) - }, - handleNewWorkflowGroupClick: function () { - this.addNewWorkflowGroup() - }, - handleExistingModelClick: function () { - this.addExistingModel() - }, - handleExportZipClick: function () { - let self = this - let queryStr = "?path="+this.projectPath+"&action=generate" - let endpoint = path.join(app.getApiPath(), "file/download-zip")+queryStr - xhr({uri:endpoint, json:true}, function (err, response, body) { - if(response.statusCode < 400) { - var downloadEP = path.join(app.getBasePath(), "/files", body.Path); - window.open(downloadEP) - } - }) - }, - handleExportCombineClick: function () { - this.exportAsCombine(this.projectPath, true) - }, - handleEmptyTrashClick: function () { - let self = this; - if(document.querySelector("#emptyTrashConfirmModal")) { - document.querySelector("#emptyTrashConfirmModal").remove() - } - let modal = $(modals.emptyTrashConfirmHtml()).modal(); - let yesBtn = document.querySelector('#emptyTrashConfirmModal .yes-modal-btn'); - yesBtn.addEventListener('click', function (e) { - modal.modal('hide') - let endpoint = path.join(app.getApiPath(), "project/empty-trash")+"?path="+path.join(self.projectPath, "trash") - xhr({uri: endpoint, json: true}, function (err, response, body) { - if(response.statusCode < 400) { - $(self.queryByHook('empty-project-trash')).prop('disabled', true) - self.update("trash") - console.log(body) - }else{ - console.log(body) + let modelPath = path.join(parentPath, modelName); + let queryString = "?path="+modelPath+"&message="+message; + endpoint += queryString; + let existEP = path.join(app.getApiPath(), "model/exists")+queryString; + app.getXHR(existEP, { + always: function (err, response, body) { + if(body.exists) { + let title = "Model Already Exists"; + let message = "A model already exists with that name"; + let errorModel = $(modals.newProjectOrWorkflowGroupErrorHtml(title, message)).modal(); + }else{ + window.location.href = endpoint; + } } }); - }); - }, - handleUploadModelClick: function (e) { - let type = e.target.dataset.type - this.projectFileBrowser.uploadFile(undefined, type) + } }, addNewModel: function (isSpatial) { - let self = this - let isModel = true if(document.querySelector('#newModalModel')) { - document.querySelector('#newModalModel').remove() + document.querySelector('#newModalModel').remove(); } - let modal = $(modals.renderCreateModalHtml(isModel, isSpatial)).modal(); + let self = this; + let modal = $(modals.renderCreateModalHtml(true, isSpatial)).modal(); let okBtn = document.querySelector('#newModalModel .ok-model-btn'); let input = document.querySelector('#newModalModel #modelNameInput'); okBtn.addEventListener('click', function (e) { - modal.modal('hide') + modal.modal('hide'); if (Boolean(input.value)) { - let ext = isSpatial ? ".smdl" : ".mdl" + let ext = isSpatial ? ".smdl" : ".mdl"; let modelName = input.value.split("/").pop() + ext; let message = modelName.split(".")[0] !== input.value ? - "Warning: Models are saved directly in StochSS Projects and cannot be saved to the "+input.value.split("/")[0]+" directory in the project.

Your model will be saved directly in your project.

" : "" - let modelPath = path.join(self.projectPath, modelName) - let queryString = "?path="+modelPath+"&message="+message - let endpoint = path.join(app.getBasePath(), app.routePrefix, 'models/edit')+queryString - let existEP = path.join(app.getApiPath(), "model/exists")+queryString + "Warning: The save as feature is not available for models in projects." : ""; if(message){ - let warningModal = $(modals.newProjectModelWarningHtml(message)).modal() + let warningModal = $(modals.newProjectModelWarningHtml(message)).modal(); let yesBtn = document.querySelector('#newProjectModelWarningModal .yes-modal-btn'); yesBtn.addEventListener('click', function (e) { - warningModal.modal('hide') - xhr({uri: existEP, json: true}, function (err, response, body) { - if(body.exists) { - let title = "Model Already Exists" - let message = "A model already exists with that name" - let errorModel = $(modals.newProjectOrWorkflowGroupErrorHtml(title, message)).modal() - }else{ - window.location.href = endpoint - } - }) - }) - }else{ - xhr({uri: existEP, json: true}, function (err, response, body) { - if(body.exists) { - let title = "Model Already Exists" - let message = "A model already exists with that name" - let errorModel = $(modals.newProjectOrWorkflowGroupErrorHtml(title, message)).modal() - }else{ - window.location.href = endpoint - } + warningModal.modal('hide'); + self.addModel(self.model.directory, modelName, message); }); + }else{ + self.addModel(self.model.directory, modelName, message); } } }); @@ -332,131 +205,252 @@ let ProjectManager = PageView.extend({ } }); }, - validateName(input) { - var error = "" - if(input.endsWith('/')) { - error = 'forward' - } - let invalidChars = "`~!@#$%^&*=+[{]}\"|:;'<,>?\\" - for(var i = 0; i < input.length; i++) { - if(invalidChars.includes(input.charAt(i))) { - error = error === "" || error === "special" ? "special" : "both" - } + changeCollapseButtonText: function (e) { + app.changeCollapseButtonText(this, e); + }, + exportAsCombine: function () {}, + handleEditAnnotationClick: function (e) { + let buttonTxt = e.target.innerText; + if(buttonTxt.startsWith("Add")){ + $(this.queryByHook('collapse-annotation-container')).collapse('show'); + $(this.queryByHook('edit-annotation-btn')).text('Edit Notes'); + }else if(!$("#annotation-text").attr('class').includes('show')){ + $("#annotation-text").collapse('show'); + $(this.queryByHook("collapse-annotation-text")).text('-'); } - return error + document.querySelector("#annotation").focus(); }, - addNewWorkflowGroup: function (cb) { - let self = this - if(document.querySelector("#newWorkflowGroupModal")) { - document.querySelector("#newWorkflowGroupModal").remove() + handleEmptyTrashClick: function () { + if(document.querySelector("#emptyTrashConfirmModal")) { + document.querySelector("#emptyTrashConfirmModal").remove() } - let modal = $(modals.newWorkflowGroupModalHtml()).modal(); - let okBtn = document.querySelector('#newWorkflowGroupModal .ok-model-btn'); - let input = document.querySelector('#newWorkflowGroupModal #workflowGroupNameInput'); - input.addEventListener("keyup", function (event) { - if(event.keyCode === 13){ - event.preventDefault(); - okBtn.click(); + let self = this; + let modal = $(modals.emptyTrashConfirmHtml()).modal(); + let yesBtn = document.querySelector('#emptyTrashConfirmModal .yes-modal-btn'); + yesBtn.addEventListener('click', function (e) { + modal.modal('hide'); + let endpoint = path.join(app.getApiPath(), "file/empty-trash")+"?path="+path.join(self.model.directory, "trash"); + app.getXHR(endpoint, { + success: function (err, response, body) { + $(self.queryByHook('empty-project-trash')).prop('disabled', true); + self.update("trash"); + } + }); + }); + }, + handleExistingModelClick: function () { + this.addExistingModel() + }, + handleExportCombineClick: function () { + this.exportAsCombine(); + }, + handleExportZipClick: function () { + let self = this; + let queryStr = "?path="+this.model.directory+"&action=generate"; + let endpoint = path.join(app.getApiPath(), "file/download-zip")+queryStr; + app.getXHR(endpoint, { + success: function (err, response, body) { + var downloadEP = path.join(app.getBasePath(), "/files", body.Path); + window.open(downloadEP); } }); - input.addEventListener("input", function (e) { - var endErrMsg = document.querySelector('#newWorkflowGroupModal #workflowGroupNameInputEndCharError') - var charErrMsg = document.querySelector('#newWorkflowGroupModal #workflowGroupNameInputSpecCharError') - let error = self.validateName(input.value) - okBtn.disabled = error !== "" - charErrMsg.style.display = error === "both" || error === "special" ? "block" : "none" - endErrMsg.style.display = error === "both" || error === "forward" ? "block" : "none" + }, + handleNewModelClick: function (e) { + let isSpatial = e.target.dataset.type === "spatial"; + this.addNewModel(isSpatial); + }, + handleNewWorkflowClick: function (e) { + let type = e.target.dataset.type; + let models = type === "Jupyter Notebook" ? this.models : this.models.filter(function (model) { + return !model.is_spatial }); - okBtn.addEventListener("click", function (e) { - if(Boolean(input.value)) { - let workflowGroupName = input.value + ".wkgp" - let workflowGroupPath = path.join(self.projectPath, workflowGroupName) - let endpoint = path.join(app.getApiPath(), "project/new-workflow-group")+"?path="+workflowGroupPath - xhr({uri: endpoint,json: true}, function (err, response, body) { - if(response.statusCode < 400) { - if(cb) { - cb(workflowGroupName) - }else{ - self.update("workflow-group") - } - }else{ - let errorModel = $(modals.newProjectOrWorkflowGroupErrorHtml(body.Reason, body.Message)).modal() - } - modal.modal('hide') - }); + if(models && models.length > 0) { + let self = this; + if(document.querySelector("#newProjectWorkflowModal")) { + document.querySelector("#newProjectWorkflowModal").remove(); } + let options = models.map(function (model) { return model.name }); + let modal = $(modals.newProjectWorkflowHtml("Name of the model: ", options)).modal(); + let okBtn = document.querySelector("#newProjectWorkflowModal .ok-model-btn"); + let select = document.querySelector("#newProjectWorkflowModal #select"); + okBtn.addEventListener('click', function (e) { + modal.modal('hide'); + let mdl = models.filter(function (model) { + return model.name === select.value; + })[0]; + if(type === "Jupyter Notebook") { + let parentPath = path.join(path.dirname(mdl.directory), "WorkflowGroup1.wkgp"); + let queryString = "?path=" + mdl.directory + "&parentPath=" + parentPath; + let endpoint = path.join(app.getBasePath(), 'stochss/workflow/selection') + queryString; + window.location.href = endpoint; + }else { + app.newWorkflow(self, mdl.directory, mdl.is_spatial, type); + } + }); + }else{ + let title = "No Models Found for " + type + " Workflows"; + if(this.models.length > 0) { + var message = "Jupyter Notebook workflows are the only workflows available for spatial models."; + }else{ + var message = "You need to add a model before you can create a new workflow."; + } + let modal = $(modals.noModelsMessageHtml(title, message)).modal(); + } + }, + handleUploadModelClick: function (e) { + let type = e.target.dataset.type + this.projectFileBrowser.uploadFile(undefined, type) + }, + renderArchiveCollection: function () { + if(this.archiveCollectionView) { + this.archiveCollectionView.remove(); + } + this.archiveCollectionView = this.renderCollection( + this.model.archive, + ArchiveListing, + this.queryByHook("archive-listing") + ); + }, + renderMetaDataView: function () { + if(this.metaDataView) { + this.metaDataView.remove(); + } + this.metaDataView = new MetaDataView({ + model: this.model }); + app.registerRenderSubview(this, this.metaDataView, "project-meta-data-container"); }, - addExistingModel: function () { - let self = this - if(document.querySelector('#newProjectModelModal')){ - document.querySelector('#newProjectModelModal').remove() + renderModelsCollection: function () { + if(this.modelCollectionView){ + this.modelCollectionView.remove(); } - let mdlListEP = path.join(app.getApiPath(), 'project/add-existing-model') + "?path="+self.projectPath - xhr({uri:mdlListEP, json:true}, function (err, response, body) { - let modal = $(modals.newProjectModelHtml(body.models)).modal() - let okBtn = document.querySelector('#newProjectModelModal .ok-model-btn') - let select = document.querySelector('#newProjectModelModal #modelPathInput') - okBtn.addEventListener("click", function (e) { - let queryString = "?path="+self.projectPath+"&mdlPath="+select.value - let endpoint = path.join(app.getApiPath(), 'project/add-existing-model') + queryString - xhr({uri:endpoint, json:true, method:"post"}, function (err, response, body) { - if(response.statusCode < 400) { - let successModal = $(modals.newProjectModelSuccessHtml(body.message)).modal() - }else{ - let errorModal = $(modals.newProjectModelErrorHtml(body.Reason, body.Message)).modal() - } - }); - modal.modal('hide') - self.update("existing-model") - }); + this.modelCollectionView = this.renderCollection( + this.models, + ModelListing, + this.queryByHook("model-listing") + ); + }, + renderProjectFileBrowser: function () { + if(this.projectFileBrowser) { + this.projectFileBrowser.remove(); + } + let self = this; + this.projectFileBrowser = new FileBrowser({ + root: self.model.directory }); + app.registerRenderSubview(this, this.projectFileBrowser, "file-browser"); }, - exportAsCombine: function(target, download) { - let self = this - if(document.querySelector("#addMetaDataModal")) { - document.querySelector("#addMetaDataModal").remove() + renderSubviews: function (emptyTrash) { + PageView.prototype.render.apply(this, arguments); + if(!this.model.newFormat) { + let self = this; + let modal = $(modals.updateFormatHtml("Project")).modal(); + let yesBtn = document.querySelector("#updateProjectFormatModal .yes-modal-btn"); + yesBtn.addEventListener("click", function (e) { + modal.modal("hide"); + let queryStr = "?path=" + self.model.directory + "&action=update-project"; + let endpoint = path.join(app.getBasePath(), "stochss/loading-page") + queryStr; + window.location.href = endpoint; + }); } - let modal = $(modals.addMetaDataHtml("Do you wish to add/update the meta-data for this archive?")).modal() - let yesBtn = document.querySelector("#addMetaDataModal .yes-modal-btn") - let noBtn = document.querySelector("#addMetaDataModal .no-modal-btn") - yesBtn.addEventListener('click', function (e) { - modal.modal('hide') - var files = [] - if(target === self.projectPath){ - files = self.model.workflowGroups.map(function (workflowGroup) {return workflowGroup.name+".wkgp"}) - files.unshift(self.model.directory) - }else{ - files = [self.model.directory, target.split('/').pop()] - } - self.renderMetaDataView(target, files, download) + $("#page-title").text("Project: " + this.model.name); + if(this.model.annotation){ + $(this.queryByHook('edit-annotation-btn')).text('Edit Notes'); + $(this.queryByHook('annotation-text-container')).text(this.model.annotation); + $(this.queryByHook("collapse-annotation-container")).collapse('show'); + } + if(this.model.newFormat) { + $("#" + this.model.elementID + "-archive-section").css("display", "block"); + this.renderWorkflowGroupCollection(); + this.renderArchiveCollection(); + }else{ + $("#" + this.model.elementID + "-workflows-section").css("display", "block"); + this.renderModelsCollection(); + this.renderWorkflowsCollection(); + } + this.renderMetaDataView(); + this.renderProjectFileBrowser(); + $(this.queryByHook('empty-project-trash')).prop('disabled', emptyTrash); + $(document).on('hide.bs.modal', '.modal', function (e) { + e.target.remove() + }); + $(document).ready(function () { + $('[data-toggle="tooltip"]').tooltip(); + $('[data-toggle="tooltip"]').click(function () { + $('[data-toggle="tooltip"]').tooltip("hide"); + }); }); - noBtn.addEventListener('click', function (e) { - let queryString = "?path="+target+"&projectPath="+self.projectPath - let endpoint = path.join(app.getApiPath(), "project/export-combine")+queryString - xhr({uri:endpoint, json:true}, function (err, response, body) { - if(response.statusCode < 400) { - if(download) { - let downloadEP = path.join(app.getBasePath(), "/files", body.file_path); - window.open(downloadEP) + }, + renderWorkflowsCollection: function () { + if(this.workflowCollectionView) { + this.workflowCollectionView.remove(); + } + this.workflowCollectionView = this.renderCollection( + this.model.workflowGroups.models[0].workflows, + WorkflowListing, + this.queryByHook("workflow-listing") + ); + }, + renderWorkflowGroupCollection: function () { + if(this.workflowGroupCollection) { + this.workflowGroupCollection.remove(); + } + this.workflowGroupCollection = this.renderCollection( + this.model.workflowGroups, + WorkflowGroupListing, + this.queryByHook("model-listing") + ); + }, + update: function (target) { + this.projectFileBrowser.refreshJSTree(); + let fetchTypes = ["Model", "Workflow", "WorkflowGroup", "Archive"]; + if(fetchTypes.includes(target)) { + let self = this; + app.getXHR(this.model.url(), { + success: function (err, response, body) { + self.model.set(body) + if(self.model.newFormat) { + self.renderWorkflowGroupCollection(); }else{ - let modal = $(modals.projectExportSuccessHtml(body.file_type, body.message)).modal() + if(target === "Workflow"){ + self.renderWorkflowsCollection(); + } + if(target === "Model"){ + self.models = new Collection(body.models, {model: Model}); + self.renderModelsCollection(); + } } - }else{ - let modal = $(modals.projectExportErrorHtml(body.Reason, body.Message)) + $(self.queryByHook('empty-project-trash')).prop('disabled', body.trash_empty) } }); + } + }, + updateAnnotation: function (e) { + this.model.annotation = e.target.value.trim(); + if(this.model.annotation === ""){ + $(this.queryByHook('edit-annotation-btn')).text('Add Notes'); + $(this.queryByHook("collapse-annotation-container")).collapse('hide'); + } + let endpoint = path.join(app.getApiPath(), "project/save-annotation")+"?path="+this.model.directory; + let data = {'annotation': this.model.annotation}; + app.postXHR(endpoint, data, { + always: function (err, response, body) { + console.log(body); + } }); }, - changeCollapseButtonText: function (e) { - let source = e.target.dataset.hook - let isBtn = $(this.queryByHook(source)).attr("class").includes("btn") - let collapseContainer = $(this.queryByHook(source).dataset.target) - if(isBtn && !collapseContainer.attr("class").includes("collapsing")) { - let collapseBtn = $(this.queryByHook(source)) - let text = collapseBtn.text(); - text === '+' ? collapseBtn.text('-') : collapseBtn.text('+'); + validateName(input) { + var error = ""; + if(input.endsWith('/')) { + error = 'forward'; + } + let invalidChars = "`~!@#$%^&*=+[{]}\"|:;'<,>?\\"; + for(var i = 0; i < input.length; i++) { + if(invalidChars.includes(input.charAt(i))) { + error = error === "" || error === "special" ? "special" : "both"; + } } + return error; } }); diff --git a/client/pages/users-home.js b/client/pages/users-home.js index a85842f539..c5fa5b81c5 100644 --- a/client/pages/users-home.js +++ b/client/pages/users-home.js @@ -17,7 +17,6 @@ along with this program. If not, see . */ let $ = require('jquery'); -let xhr = require('xhr'); let path = require('path'); //support files let app = require('../app'); @@ -42,15 +41,9 @@ let usersHomePage = PageView.extend({ PageView.prototype.initialize.apply(this, arguments) let urlParams = new URLSearchParams(window.location.search) if(urlParams.has("open")){ - let uploadPath = urlParams.get("open") - let endpoint = path.join(app.getApiPath(), 'file/upload-from-link')+"?path="+uploadPath - let self = this - xhr({uri:endpoint, json:true}, function (err, response, body) { - if(response.statusCode < 400) { - self.responsePath = body.responsePath - self.getUploadResponse() - } - }) + let queryString = "?path=" + urlParams.get("open") + "&action=open"; + let endpoint = path.join(app.getBasePath(), 'stochss/loading-page') + queryString; + window.location.href = endpoint; } }, render: function (attrs, options) { @@ -59,27 +52,6 @@ let usersHomePage = PageView.extend({ e.target.remove() }); }, - getUploadResponse: function () { - let self = this - setTimeout(function () { - let endpoint = path.join(app.getApiPath(), 'file/upload-from-link')+"?path="+self.responsePath+"&cmd=read" - xhr({uri: endpoint, json: true}, function (err, response, body) { - if(response.statusCode >= 400 || Object.keys(body).includes("reason")) { - let model = $(modals.projectExportErrorHtml(body.reason, body.message)).modal() - }else if(body.done) { - if(body.file_path.endsWith(".proj")){ - window.location.href = path.join(app.getBasePath(), "stochss/project/manager")+"?path="+body.file_path - }else if(body.file_path.endsWith(".mdl")){ - window.location.href = path.join(app.getBasePath(), "stochss/models/edit")+"?path="+body.file_path - }else if(body.file_path.endsWith(".ipynb")){ - window.open(path.join(app.getBasePath(), "notebooks", body.file_path)) - } - }else{ - self.getUploadResponse() - } - }) - }, 1000) - }, validateName(input) { var error = "" if(input.endsWith('/')) { @@ -122,16 +94,18 @@ let usersHomePage = PageView.extend({ let modelPath = input.value + '.mdl' let queryString = "?path="+modelPath let existEP = path.join(app.getApiPath(), "model/exists")+queryString - xhr({uri: existEP, json: true}, function (err, response, body) { - if(body.exists) { - let title = "Model Already Exists" - let message = "A model already exists with that name" - let errorModel = $(modals.newProjectOrWorkflowGroupErrorHtml(title, message)).modal() - }else{ - let endpoint = path.join(app.getBasePath(), "stochss/models/edit")+queryString - self.navToPage(endpoint) + app.getXHR(existEP, { + always: function (err, response, body) { + if(body.exists) { + let title = "Model Already Exists"; + let message = "A model already exists with that name"; + let errorModel = $(modals.newProjectOrWorkflowGroupErrorHtml(title, message)).modal(); + }else{ + let endpoint = path.join(app.getBasePath(), "stochss/models/edit")+queryString; + self.navToPage(endpoint); + } } - }) + }); } }); }, @@ -164,13 +138,14 @@ let usersHomePage = PageView.extend({ let projectPath = input.value + ".proj" let queryString = "?path="+projectPath let endpoint = path.join(app.getApiPath(), "project/new-project")+queryString - xhr({uri:endpoint, json:true}, function (err, response, body) { - if(response.statusCode < 400) { - let projectQS = "?path="+body.path - let projectEP = path.join(app.getBasePath(), "stochss/project/manager")+projectQS - self.navToPage(projectEP) - }else{ - let errorModel = $(modals.newProjectOrWorkflowGroupErrorHtml(body.Reason, body.Message)).modal() + app.getXHR(endpoint, { + success: function (err, response, body) { + let projectQS = "?path="+body.path; + let projectEP = path.join(app.getBasePath(), "stochss/project/manager")+projectQS; + self.navToPage(projectEP); + }, + error: function (err, response, body) { + let errorModel = $(modals.newProjectOrWorkflowGroupErrorHtml(body.Reason, body.Message)).modal(); } }); } diff --git a/client/pages/workflow-manager.js b/client/pages/workflow-manager.js index 76687b5532..3dd79cdc2e 100644 --- a/client/pages/workflow-manager.js +++ b/client/pages/workflow-manager.js @@ -16,389 +16,290 @@ You should have received a copy of the GNU General Public License along with this program. If not, see . */ -var _ = require('underscore'); -var $ = require('jquery'); -var path = require('path'); -var xhr = require('xhr'); +let $ = require('jquery'); +let path = require('path'); +let _ = require('underscore'); //support files -var app = require('../app'); -var tests = require('../views/tests'); -var modals = require('../modals') -//views -var PageView = require('./base'); -var WorkflowEditorView = require('../views/workflow-editor'); -var WorkflowStatusView = require('../views/workflow-status'); -var WorkflowResultsView = require('../views/workflow-results'); -var ModelViewer = require('../views/model-viewer'); -var InfoView = require('../views/workflow-info'); -var InputView = require('../views/input'); -var SelectView = require('ampersand-select-view'); +let app = require('../app'); +let modals = require('../modals'); //models -var Model = require('../models/model') +let Workflow = require('../models/workflow'); +//views +let PageView = require('./base'); +let SettingsView = require('../views/settings'); +let LogsView = require('../views/workflow-info'); +let SelectView = require('ampersand-select-view'); +let StatusView = require('../views/workflow-status'); +let JobListingView = require('../views/job-listing'); +let ModelViewerView = require('../views/model-viewer'); +let ResultsView = require('../views/workflow-results'); +let SettingsViewerView = require('../views/settings-viewer'); //templates -var template = require('../templates/pages/workflowManager.pug'); +let template = require('../templates/pages/workflowManager.pug'); import initPage from './page.js'; let WorkflowManager = PageView.extend({ template: template, events: { - 'change [data-hook=workflow-name]' : 'setWorkflowName', - 'input [data-hook=workflow-name' : 'validateWorkflowName', - 'change [data-hook=model-path]' : 'updateWkflModel', - 'input [data-hook=model-path]' : 'validateModelPath', - 'click [data-hook=edit-workflow-help]' : function () { - let modal = $(modals.operationInfoModalHtml('wkfl-manager')).modal(); - }, - 'click [data-hook=project-breadcrumb]' : 'handleReturnToProjectClick', - 'click [data-hook=return-to-project-btn]' : 'handleReturnToProjectClick' + 'change [data-hook=model-file]' : 'handleModelSelect', + 'change [data-hook=model-location]' : 'handleLocationSelect', + 'click [data-hook=project-breadcrumb]' : 'handleReturnToProject', + 'click [data-hook=save-model]' : 'handleSaveWorkflow', + 'click [data-hook=collapse-jobs]' : 'changeCollapseButtonText', + 'click [data-hook=return-to-project-btn]' : 'handleReturnToProject' }, initialize: function (attrs, options) { PageView.prototype.initialize.apply(this, arguments); - var self = this; - $(document).on('hidden.bs.modal', function (e) { - if(e.target.id === "modelNotFoundModal") - $(self.queryByHook("model-path")).find('input').focus(); + let urlParams = new URLSearchParams(window.location.search); + this.model = new Workflow({ + directory: urlParams.get('path') }); - this.url = decodeURI(document.URL) - let urlParams = new URLSearchParams(window.location.search) - let type = urlParams.get('type'); - this.urlPathParam = urlParams.get('path'); - var stamp = this.getCurrentDate(); - this.titleType = "Loading ..."; - this.startLoadingDisplay(); - var queryStr = "?stamp="+stamp+"&type="+type+"&path="+this.urlPathParam - if(urlParams.has('parentPath')) { - queryStr += ("&parentPath=" + urlParams.get('parentPath')) - } - var endpoint = path.join(app.getApiPath(), "workflow/load-workflow")+queryStr - xhr({uri: endpoint, json: true}, function (err, resp, body) { - self.stopLoadingDisplay(); - if(resp.statusCode < 400) { - self.settings = body.settings - self.type = body.type - self.titleType = body.titleType - self.modelDirectory = body.mdlPath - self.wkflDirectory = body.wkflDir - self.workflowDate = body.timeStamp - self.workflowName = body.wkflName - self.status = body.status - self.startTime = body.startTime - self.wkflParPath = body.wkflParPath - self.wkflPath = path.join(self.wkflParPath, self.wkflDirectory) - self.buildWkflModel(body) + let self = this; + app.getXHR(this.model.url(), { + success: function (err, response, body) { + self.model.set(body) + $("#page-title").text("Workflow: " + self.model.name); + if(self.model.directory.includes('.proj')) { + let index = self.model.directory.indexOf('.proj') + 5; + self.projectPath = self.model.directory.slice(0, index); + $(self.queryByHook('project-breadcrumb')).text(self.projectPath.split('/').pop().split('.proj')[0]); + $(self.queryByHook('workflow-breadcrumb')).text(self.model.name); + self.queryByHook("project-breadcrumb-links").style.display = "block"; + self.queryByHook("return-to-project-btn").style.display = "inline-block"; + } + if(body.models){ + self.renderModelSelectView(body.models); + } self.renderSubviews(); - if(self.wkflPath.includes('.proj')) { - self.projectPath = path.dirname(self.wkflParPath) - $(self.queryByHook('project-breadcrumb')).text(self.projectPath.split('/').pop().split('.')[0]) - $(self.queryByHook('workflow-breadcrumb')).text(self.workflowName) - self.queryByHook("project-breadcrumb-links").style.display = "block" - self.queryByHook("return-to-project-btn").style.display = "inline-block" + if(!self.model.newFormat) { + let modal = $(modals.updateFormatHtml("Workflow")).modal(); + let yesBtn = document.querySelector("#updateWorkflowFormatModal .yes-modal-btn"); + yesBtn.addEventListener("click", function (e) { + modal.modal("hide"); + let queryStr = "?path=" + self.model.directory + "&action=update-workflow"; + let endpoint = path.join(app.getBasePath(), "stochss/loading-page") + queryStr; + window.location.href = endpoint; + }); } - }else{ - self.renderLoadError(resp.body); } }); }, - buildWkflModel: function (data) { - let model = data.model - this.model = new Model(model) - this.model.name = this.modelDirectory.split('/').pop().split('.')[0] - this.model.directory = this.modelDirectory - this.model.is_spatial = this.modelDirectory.endsWith(".smdl") - this.model.isPreview = false - this.model.for = "wkfl" - if(!model) { - this.modelLoadError = true - this.wkflModelNotFound(data.error) - }else{ - this.modelLoadError = false + changeCollapseButtonText: function (e) { + app.changeCollapseButtonText(this, e); + }, + handleLocationSelect: function (e) { + let value = e.srcElement.value; + if(value) { + this.model.model = value; } }, - wkflModelNotFound: function (error) { - let modal = $(modals.modelNotFoundHtml(error.Reason, error.Message)).modal() + handleModelSelect: function (e) { + let value = e.srcElement.value; + if(value) { + if(this.models.paths[value].length == 1) { + $("#model-location-info").css("display", "none"); + if(this.modelLocationSelectView) { + this.modelLocationSelectView.remove(); + } + this.model.model = this.models.paths[value][0]; + }else{ + $("#model-location-info").css("display", "block"); + this.renderModelLocationSelectView(value); + } + } }, - update: function () { + handleReturnToProject: function (e) { + if(this.model.activeJob.model.directory){ + this.handleSaveWorkflow(e, _.bind(function () { + let queryStr = "?path=" + this.projectPath; + let endpoint = path.join(app.getBasePath(), "stochss/project/manager") + queryStr; + window.location.href = endpoint; + }, this)); + }else{ + let queryStr = "?path=" + this.projectPath; + let endpoint = path.join(app.getBasePath(), "stochss/project/manager") + queryStr; + window.location.href = endpoint; + } }, - updateValid: function () { + handleSaveWorkflow: function (e, cb) { + let self = this; + let endpoint = this.model.url(); + app.postXHR(endpoint, this.model.toJSON(), { + success: function (err, response, body) { + if(cb) { + cb(); + }else{ + $(self.queryByHook("src-model")).css("display", "none"); + let oldFormRdyState = !self.model.newFormat && self.model.activeJob.status === "ready"; + if(oldFormRdyState || self.model.newFormat) { + self.renderSettingsView(); + } + } + } + }); }, - getCurrentDate: function () { - var date = new Date(); - var year = date.getFullYear(); - var month = date.getMonth() + 1; - if(month < 10){ - month = "0" + month - } - var day = date.getDate(); - if(day < 10){ - day = "0" + day + removeActiveJob: function () { + $(this.queryByHook("active-job-header-container")).css("display", "none"); + if(this.resultsView) { + this.resultsView.remove(); } - var hours = date.getHours(); - if(hours < 10){ - hours = "0" + hours + if(this.logsView) { + this.logsView.remove(); + this.modelViewerView.remove(); + this.settingsViewerView.remove(); } - var minutes = date.getMinutes(); - if(minutes < 10){ - minutes = "0" + minutes - } - var seconds = date.getSeconds(); - if(seconds < 10){ - seconds = "0" + seconds - } - return "_" + month + day + year + "_" + hours + minutes + seconds; - }, - startLoadingDisplay: function () { - }, - stopLoadingDisplay: function () { }, - renderLoadError: function (resp) { - $(this.queryByHook("page-title")).text("Workflow: Load Error") - $(this.queryByHook("load-wkfl-error")).css('display', 'block') - $(this.queryByHook("reason")).text(resp.Reason) - $(this.queryByHook("message")).text(resp.Message) - $(this.queryByHook("traceback")).text(resp.Traceback) - }, - renderSubviews: function () { - $(this.queryByHook("page-title")).text('Workflow: '+this.titleType) - this.renderWkflNameInputView(); - this.renderMdlPathInputView(); - this.renderWorkflowEditor(); - if(this.status !== "new" && this.status !== "ready") { - this.renderWorkflowStatusView(); - this.renderModelViewer(); + renderActiveJob: function () { + if(this.model.newFormat) { + $(this.queryByHook("active-job-header")).text("Job: " + this.model.activeJob.name); + $(this.queryByHook("active-job-header-container")).css("display", "block"); } - if(this.status === "error" || this.status === "complete") { + if(this.model.activeJob.status !== "error") { this.renderResultsView(); - this.renderInfoView(); } - if(this.status === 'running'){ - this.getWorkflowStatus(); - } - $(document).on('hide.bs.modal', '.modal', function (e) { - e.target.remove() - }); + this.renderLogsView(); + this.renderSettingsViewerView(); + this.renderModelViewerView(); }, - registerRenderSubview: function (view, hook) { - this.registerSubview(view); - return this.renderSubview(view, this.queryByHook(hook)); + renderJobListingView: function () { + if(this.jobListingView) { + this.jobListingView.remove(); + } + this.jobListingView = this.renderCollection( + this.model.jobs, + JobListingView, + this.queryByHook("job-listing") + ); }, - renderWkflNameInputView: function () { - let inputName = new InputView({ - parent: this, - required: true, - name: 'name', - label: 'Workflow Name: ', - tests: '', - modelKey: null, - valueType: 'string', - value: this.workflowName, - }); - this.registerRenderSubview(inputName, 'workflow-name'); - if(this.status !== "new") { - $(this.queryByHook('workflow-name')).find('input').prop('disabled', true); + renderLogsView: function () { + if(this.logsView) { + this.logsView.remove(); } + this.logsView = new LogsView({ + logs: this.model.activeJob.logs + }); + app.registerRenderSubview(this, this.logsView, "workflow-info-container"); }, - renderMdlPathInputView: function () { - let modelPathInput = new InputView({ - parent: this, + renderModelLocationSelectView: function (model) { + if(this.modelLocationSelectView) { + this.modelLocationSelectView.remove(); + } + this.modelLocationSelectView = new SelectView({ + label: 'Location: ', + name: 'source-model-location', required: true, - name: 'name', - label: 'Model Path: ', - tests: "", - modelKey: 'directory', - valueType: 'string', - value: this.model.directory, + idAttributes: 'cid', + options: this.models.paths[model], + unselectedText: "-- Select Location --" }); - this.registerRenderSubview(modelPathInput, "model-path"); - if(this.status !== "new" && this.status !== "ready") { - $(this.queryByHook('model-path')).find('input').prop('disabled', true); - } + app.registerRenderSubview(this, this.modelLocationSelectView, "model-location"); }, - renderWorkflowEditor: function () { - if(this.workflowEditorView){ - this.workflowEditorView.remove() - } - this.workflowEditor = new WorkflowEditorView({ - model: this.model, - settings: this.settings, - type: this.type, - status: this.status, + renderModelSelectView: function (models) { + this.models = models; + $(this.queryByHook("src-model")).css("display", "block"); + let modelSelectView = new SelectView({ + label: 'Model: ', + name: 'source-model', + required: true, + idAttributes: 'cid', + options: models.files, + unselectedText: "-- Select Model --" }); - this.workflowEditorView = this.registerRenderSubview(this.workflowEditor, 'workflow-editor-container'); + app.registerRenderSubview(this, modelSelectView, "model-file"); }, - renderWorkflowStatusView: function () { - if(this.workflowStatusView){ - this.workflowStatusView.remove(); + renderModelViewerView: function () { + if(this.modelViewerView) { + this.modelViewerView.remove(); } - var statusView = new WorkflowStatusView({ - startTime: this.startTime, - status: this.status, + this.modelViewerView = new ModelViewerView({ + model: this.model.activeJob.model }); - this.workflowStatusView = this.registerRenderSubview(statusView, 'workflow-status-container'); + app.registerRenderSubview(this, this.modelViewerView, "model-viewer-container"); }, renderResultsView: function () { - if(this.workflowResultsView){ - this.workflowResultsView.remove(); + if(this.resultsView) { + this.resultsView.remove(); } - var resultsView = new WorkflowResultsView({ - parent: this, - trajectories: this.settings.simulationSettings.realizations, - status: this.status, - species: this.model.species, - type: this.type, - speciesOfInterest: this.settings.parameterSweepSettings.speciesOfInterest.name + this.resultsView = new ResultsView({ + model: this.model.activeJob }); - this.workflowResultsView = this.registerRenderSubview(resultsView, 'workflow-results-container'); + app.registerRenderSubview(this, this.resultsView, "workflow-results-container"); }, - renderInfoView: function () { - if(this.infoView){ - this.infoView.remove(); + renderStatusView: function () { + if(this.statusView) { + this.statusView.remove(); } - this.infoView = new InfoView({ - status: this.status, - logsPath: path.join(this.wkflPath, "logs.txt") + this.statusView = new StatusView({ + model: this.model.activeJob }); - this.registerRenderSubview(this.infoView, 'workflow-info-container') + app.registerRenderSubview(this, this.statusView, "status-container"); }, - renderModelViewer: function (){ - if(this.modelViewer){ - this.modelViewer.remove(); + renderSettingsView: function () { + if(this.settingsView) { + this.settingsView.remove(); } - this.modelViewer = new ModelViewer({ - model: this.model, - status: this.status, - type: this.type + this.settingsView = new SettingsView({ + model: this.model.settings }); - this.registerRenderSubview(this.modelViewer, 'model-viewer-container') + app.registerRenderSubview(this, this.settingsView, "settings-container"); }, - getWorkflowStatus: function () { - var self = this; - var endpoint = path.join(app.getApiPath(), "workflow/workflow-status")+"?path="+this.wkflPath; - xhr({uri: endpoint}, function (err, response, body) { - if(self.status !== body ) - self.status = body; - if(self.status === 'running') - setTimeout(_.bind(self.getWorkflowStatus, self), 1000); - else{ - self.renderWorkflowStatusView() - self.renderInfoView(); - } - if(self.status === 'complete') { - self.renderWorkflowEditor(); - self.renderResultsView(); - self.renderModelViewer(); - } + renderSettingsViewerView: function () { + if(this.settingsViewerView) { + this.settingsViewerView.remove(); + } + this.settingsViewerView = new SettingsViewerView({ + model: this.model.activeJob.settings }); + app.registerRenderSubview(this, this.settingsViewerView, "settings-viewer-container"); }, - validateName(input, rename = false) { - var error = "" - if(input.endsWith('/')) { - error = 'forward' + renderSubviews: function () { + let oldFormRdyState = !this.model.newFormat && this.model.activeJob.status === "ready"; + let newFormNotArchive = this.model.newFormat && this.model.model; + if(!this.models && (oldFormRdyState || newFormNotArchive)) { + this.renderSettingsView(); + }else if(this.settingsView) { + this.settingsView.remove(); } - var invalidChars = "`~!@#$%^&*=+[{]}\"|:;'<,>?\\" - if(rename) { - invalidChars += "/" + if(this.model.newFormat) { + $(this.queryByHook("jobs-container")).css("display", "block"); + this.renderJobListingView(); + }else if(this.model.activeJob.status !== "ready") { + this.renderStatusView(); } - for(var i = 0; i < input.length; i++) { - if(invalidChars.includes(input.charAt(i))) { - error = error === "" || error === "special" ? "special" : "both" - } + let detailsStatus = ["error", "complete"] + if(this.model.activeJob && detailsStatus.includes(this.model.activeJob.status)) { + this.renderActiveJob(); } - return error }, - validateWorkflowName: function (e) { - if(this.validateName(e.target.value, true) !== ""){ - document.querySelector("#workflowNameSpecialCharError").style.display = "block" - }else{ - document.querySelector("#workflowNameSpecialCharError").style.display = "none" - } - }, - validateModelPath: function (e) { - if(this.validateName(e.target.value) !== ""){ - document.querySelector("#modelPathSpecialCharError").style.display = "block" - }else{ - document.querySelector("#modelPathSpecialCharError").style.display = "none" - } + setActiveJob: function (job) { + this.model.activeJob = job; + this.removeActiveJob(); + this.renderActiveJob(); }, - setWorkflowName: function(e) { - var newWorkflowName = e.target.value.trim(); - if(this.validateName(newWorkflowName) === "") { - if(newWorkflowName.endsWith(this.workflowDate)){ - this.workflowName = newWorkflowName - }else{ - this.workflowName = newWorkflowName + this.workflowDate - e.target.value = this.workflowName - } - $(this.queryByHook('workflow-breadcrumb')).text(this.workflowName) - this.wkflDirectory = this.workflowName + ".wkfl" - let queryStr = "?path=" + this.wkflPath + "&name=" + this.wkflDirectory; - this.wkflPath = path.join(this.wkflParPath, this.wkflDirectory) - let endpoint = path.join(app.getApiPath(), "file/rename") + queryStr - xhr({uri: endpoint, json: true}, function (err, resp, body) {}); - }else{ - e.target.value = this.workflowName - setTimeout(function (e) { - document.querySelector("#workflowNameSpecialCharError").style.display = "none" - }, 5000) - } - }, - updateWkflModel: function (e) { - if(this.validateName(e.target.value) === "") { - let self = this; - let parPath = path.dirname(self.modelDirectory) - if(parPath.endsWith(".proj") && parPath !== path.dirname(e.target.value)) { - self.model.directory = self.modelDirectory - $(self.queryByHook("model-path")).find('input').val(self.modelDirectory) - let mdlPathErr = $(modals.wkflModelPathErrorHtml()).modal() - }else{ - self.modelDirectory = e.target.value - this.model.directory = e.target.value - this.model.fetch({ - json: true, - success: function (model, response, options) { - self.modelLoadError = false - self.renderWorkflowEditor() - }, - error: function (model, response, options) { - self.modelLoadError = true - self.renderWorkflowEditor() - self.wkflModelNotFound(response.body) - } - }); - } - }else{ - e.target.value = this.modelDirectory - setTimeout(function (e) { - document.querySelector("#modelPathSpecialCharError").style.display = "none" - }, 5000) - } - }, - reloadWkfl: function () { + updateWorkflow: function (newJob) { let self = this; - if(self.status === 'new') { - // Need to refactor this - let mdlParPath = path.dirname(this.modelDirectory) - if(mdlParPath !== "."){ - let replaceText = this.wkflPath.split(mdlParPath+'/').slice(1).join(mdlParPath) - this.url = this.url.replace(this.modelDirectory.split('/').pop(), replaceText) - }else{ - this.url = this.url.replace(this.modelDirectory, this.wkflPath) - } - window.location.href = this.url - } - else - window.location.reload() - }, - handleReturnToProjectClick: function(e) { - let self = this - if((this.status === 'ready' || this.status === 'new') && !this.modelLoadError){ - this.workflowEditorView.workflowStateButtons.clickSaveHandler(e, function (e) { - window.location.href = path.join(app.getBasePath(), "stochss/project/manager")+"?path="+self.projectPath - }) - }else{ - window.location.href = path.join(app.getBasePath(), "stochss/project/manager")+"?path="+self.projectPath + if(this.model.newFormat) { + let hadActiveJob = Boolean(this.model.activeJob.status) + app.getXHR(this.model.url(), { + success: function (err, response, body) { + self.model.set(body); + if(!Boolean(self.model.activeJob.status)){ + self.removeActiveJob(); + }else if(!hadActiveJob && Boolean(self.model.activeJob.status)) { + self.renderActiveJob(); + } + } + }); + }else if(!this.model.newFormat){ + app.getXHR(this.model.url(), { + success: function (err, response, body) { + self.model.set(body) + self.renderSubviews(); + } + }); } } }); -initPage(WorkflowManager); +initPage(WorkflowManager); \ No newline at end of file diff --git a/client/pages/workflow-selection.js b/client/pages/workflow-selection.js index a5ec46567e..71846a1d2b 100644 --- a/client/pages/workflow-selection.js +++ b/client/pages/workflow-selection.js @@ -16,18 +16,16 @@ You should have received a copy of the GNU General Public License along with this program. If not, see . */ -var $ = require('jquery'); -var xhr = require('xhr'); -var path = require('path'); +let $ = require('jquery'); +let path = require('path'); //support files var app = require('../app'); -var Tooltips = require('../tooltips'); //models -var Model = require('../models/model'); +let Model = require('../models/model'); //views -var PageView = require('./base'); +let PageView = require('./base'); //templates -var template = require('../templates/pages/workflowSelection.pug'); +let template = require('../templates/pages/workflowSelection.pug'); import initPage from './page.js'; @@ -39,128 +37,76 @@ let workflowSelection = PageView.extend({ "click [data-hook=oned-parameter-sweep]" : "notebookWorkflow", "click [data-hook=twod-parameter-sweep]" : "notebookWorkflow", "click [data-hook=sciope-model-exploration]" : "notebookWorkflow", - "click [data-hook=model-inference]" : "notebookWorkflow", - "click [data-hook=stochss-es]" : "handleEnsembleSimulationClick", - "click [data-hook=stochss-ps]" : "handleParameterSweepClick" + "click [data-hook=model-inference]" : "notebookWorkflow" }, initialize: function (attrs, options) { PageView.prototype.initialize.apply(this, arguments); - var self = this - let urlParams = new URLSearchParams(window.location.search) + let self = this; + let urlParams = new URLSearchParams(window.location.search); this.modelDir = urlParams.get('path'); if(urlParams.has('parentPath')){ - this.parentPath = urlParams.get('parentPath') + this.parentPath = urlParams.get('parentPath'); }else{ - this.parentPath = path.dirname(this.modelDir) + this.parentPath = path.dirname(this.modelDir); } if(this.modelDir.includes(".proj")) { - this.projectPath = path.dirname(this.modelDir) - this.projectName = this.projectPath.split('/').pop().split('.')[0] - this.workflowGroupName = this.parentPath.split('/').pop().split('.')[0] + this.projectPath = path.dirname(this.modelDir); + if(this.modelDir.includes(".wkgp")) { + this.projectPath = path.dirname(this.projectPath); + } + this.projectName = this.projectPath.split('/').pop().split('.proj')[0]; + this.workflowGroupName = this.parentPath.split('/').pop().split('.wkgp')[0]; } - this.tooltips = Tooltips.workflowSelection - $(document).ready(function () { - $('[data-toggle="tooltip"]').tooltip(); - $('[data-toggle="tooltip"]').click(function () { - $('[data-toggle="tooltip"]').tooltip("hide"); - - }); - }); - this.modelFile = this.getFileName(this.modelDir) - var isSpatial = this.modelDir.endsWith('.smdl'); this.model = new Model({ - name: this.modelFile, directory: this.modelDir, - is_spatial: isSpatial, isPreview: false, for: "wkfl", }); - this.model.fetch({ - success: function (model, response, options) { + app.getXHR(this.model.url(), { + success: function (err, response, body) { + self.model.set(body) + $(self.queryByHook("wkfl-selection-header")).text("Workflow Selection for " + self.model.name); if(self.modelDir.includes(".proj")) { - self.queryByHook("workflow-selection-breadcrumb-links").style.display = "block" + self.queryByHook("workflow-selection-breadcrumb-links").style.display = "block"; } self.validateWorkflows() } }); }, - getFileName: function (file) { - if(file.endsWith('/')) { - file.slice(0, -1) - } - if(file.includes('/')) { - file = file.split('/').pop() - } - if(!file.includes('.')) { - return file - } - return file.split('.').slice(0, -1).join('.') - }, - validateWorkflows: function () { - let modelInvalid = this.checkForErrors() - if(this.model.species.length < 1 || (this.model.reactions.length < 1 && this.model.eventsCollection.length < 1 && this.model.rules.length < 1) || modelInvalid){ - $(this.queryByHook('stochss-es')).prop('disabled', true) - $(this.queryByHook('stochss-ps')).prop('disabled', true) - $(this.queryByHook('ensemble-simulation')).prop('disabled', true) - $(this.queryByHook('spatial-simulation')).prop('disabled', true) - $(this.queryByHook('model-inference')).prop('disabled', true) - $(this.queryByHook('oned-parameter-sweep')).prop('disabled', true) - $(this.queryByHook('twod-parameter-sweep')).prop('disabled', true) - $(this.queryByHook('sciope-model-exploration')).prop('disabled', true) - if(modelInvalid) { - let endpoint = path.join(app.getBasePath(), "stochss/models/edit")+'?path='+this.model.directory - $(this.queryByHook('invalid-model-message')).html('Errors were detected in you model click here to fix your model') - } - $(this.queryByHook('invalid-model-message')).css('display', 'block') - }else if(this.model.is_spatial){ - $(this.queryByHook('stochss-es')).prop('disabled', true) - $(this.queryByHook('stochss-ps')).prop('disabled', true) - $(this.queryByHook('ensemble-simulation')).prop('disabled', true) - $(this.queryByHook('model-inference')).prop('disabled', true) - $(this.queryByHook('oned-parameter-sweep')).prop('disabled', true) - $(this.queryByHook('twod-parameter-sweep')).prop('disabled', true) - $(this.queryByHook('sciope-model-exploration')).prop('disabled', true) - }else if(this.model.parameters.length < 1){ - $(this.queryByHook('oned-parameter-sweep')).prop('disabled', true) - $(this.queryByHook('twod-parameter-sweep')).prop('disabled', true) - $(this.queryByHook('stochss-ps')).prop('disabled', true) - $(this.queryByHook('psweep-workflow-message')).css('display', 'block') - }else if(this.model.parameters.length < 2){ - $(this.queryByHook('twod-parameter-sweep')).prop('disabled', true) - $(this.queryByHook('psweep-workflow-message')).text('2D Parameter Sweep workflows require at least two parameters') - $(this.queryByHook('psweep-workflow-message')).css('display', 'block') - } - }, - checkForErrors: function (e) { - let invalidParams = this.model.parameters.filter(function (parameter) { - if(typeof parameter.expression === "string") return true - }) - if(invalidParams.length) {return true} - }, notebookWorkflow: function (e) { - var type = e.target.dataset.type; - this.toNotebook(type); - }, - toNotebook: function (type) { - let queryString = "?type="+type+"&path="+this.modelDir+"&parentPath="+this.parentPath - var endpoint = path.join(app.getApiPath(), "workflow/notebook")+queryString - xhr({uri:endpoint, json:true}, function (err, response, body) { - if(response.statusCode < 400){ - var notebookPath = path.join(app.getBasePath(), "notebooks", body.FilePath) + let type = e.target.dataset.type; + let queryString = "?type=" + type + "&path=" + this.modelDir + "&parentPath=" + this.parentPath + let endpoint = path.join(app.getApiPath(), "workflow/notebook") + queryString + app.getXHR(endpoint, { + success: function (err, response, body) { + let notebookPath = path.join(app.getBasePath(), "notebooks", body.FilePath) window.open(notebookPath, "_blank") + window.history.back(); } - }); - }, - handleEnsembleSimulationClick: function (e) { - this.launchStochssWorkflow("gillespy") - }, - handleParameterSweepClick: function (e) { - this.launchStochssWorkflow("parameterSweep") + }) }, - launchStochssWorkflow: function (type) { - let queryString = "?type=" + type + "&path=" + this.modelDir + "&parentPath=" + this.parentPath - let endpoint = path.join(app.getBasePath(), "stochss/workflow/edit")+queryString - window.location.href = endpoint + validateWorkflows: function () { + this.model.updateValid(); + let invalid = !this.model.valid; + if(invalid) { + let endpoint = path.join(app.getBasePath(), "stochss/models/edit") + '?path=' + this.model.directory; + let message = 'Errors were detected in you model click here to fix your model'; + $(this.queryByHook('invalid-model-message')).html(message); + $(this.queryByHook('invalid-model-message')).css('display', 'block'); + } + let dimensions = this.model.parameters.length; + if(dimensions < 2) { + $(this.queryByHook('psweep-workflow-message')).css('display', 'block'); + if(dimensions === 1) { + $(this.queryByHook('psweep-workflow-message')).text('2D Parameter Sweep workflows require at least two parameters'); + } + } + $(this.queryByHook('ensemble-simulation')).prop('disabled', invalid || this.model.is_spatial); + $(this.queryByHook('spatial-simulation')).prop('disabled', invalid || !this.model.is_spatial); + $(this.queryByHook('model-inference')).prop('disabled', invalid || this.model.is_spatial); + $(this.queryByHook('oned-parameter-sweep')).prop('disabled', invalid || this.model.is_spatial || dimensions < 1); + $(this.queryByHook('twod-parameter-sweep')).prop('disabled', invalid || this.model.is_spatial || dimensions < 2); + $(this.queryByHook('sciope-model-exploration')).prop('disabled', invalid || this.model.is_spatial); } }); diff --git a/client/styles/styles.css b/client/styles/styles.css index b9db4e30cf..29403e2122 100644 --- a/client/styles/styles.css +++ b/client/styles/styles.css @@ -1,3 +1,21 @@ +/* +StochSS is a platform for simulating biochemical systems +Copyright (C) 2019-2020 StochSS developers. + +This program is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with this program. If not, see . +*/ + body { min-width: 650px } @@ -19,6 +37,30 @@ img.quickstart { padding-left: 10px } +.side-navbar { + z-index: 0; +} + +.user-logs { + white-space: nowrap; + max-height: 250px; + padding: 5px; + margin-top: 10px; + width: auto; +} + +#user-logs { + width: auto; + font-size: 0.875rem; + background-color: #000033; + color: white; + bottom: 0; +} + +#user-logs:not(.show) { + height: 0px; +} + [role="main"] { padding-top: 20px; } @@ -32,11 +74,23 @@ img.quickstart { } .sidebar-sticky { position: fixed; + flex: 0 0 11.5%; + max-width: 11.5%; } .nav-flex-column { -ms-flex-direction: column !important; flex-direction: column !important; } + #user-logs:not(.show) { + height: 100%; + font-size: 0.5rem; + } + .expand-logs { + position: fixed; + left: auto; + right: auto; + width: 60%; + } } @media (min-width: 1450px) { @@ -225,7 +279,8 @@ input[type="file"]::-ms-browse { } .body { - min-width: 500px !important; + min-width: 500px !important; + z-index: 0; } .plot-preview { margin: 10px; @@ -635,3 +690,10 @@ span.checkbox { word-break: break-word !important; overflow-wrap: break-word !important; } + +.horizontal-scroll { + display: block; + overflow-x: scroll; + overflow-y: hidden; + white-space: nowrap; +} diff --git a/client/templates/body.pug b/client/templates/body.pug index cb1641d077..52eafd363f 100644 --- a/client/templates/body.pug +++ b/client/templates/body.pug @@ -32,9 +32,9 @@ body div.container-fluid div.row - div.col-sm-12.col-md-2.col-xxl-1 + div.col-sm-12.col-md-2.col-xxl-1.side-navbar(data-hook="side-navbar") nav.sidebar.d-md-block - div.sidebar-sticky.tools + div.sidebar-sticky ul.nav.nav-flex-column li.nav-item: a.nav-link(href="stochss/home", title="Users Home Page") | Home @@ -51,4 +51,16 @@ body li.nav-item div: a.nav-link(href="stochss/quickstart", title="Quickstart") Tutorial - main.col-sm-12.col-md-10.col-xl-9.col-xxl-6.body(role="main"): div.container-fluid(data-hook="page-container") + div.user-logs.card.card-body + + div.head + + h6.my-0.inline User Logs + + button.my-0.btn.btn-outline-collapse.inline(data-hook="user-logs-collapse") + + + div.pl-1.overflow-auto(id="user-logs") + + main.col-sm-12.col-md-10.col-xl-9.col-xxl-6.body(role="main" data-hook="page-main") + + div.container-fluid(data-hook="page-container") diff --git a/client/templates/includes/archiveListing.pug b/client/templates/includes/archiveListing.pug new file mode 100644 index 0000000000..0e3838b49c --- /dev/null +++ b/client/templates/includes/archiveListing.pug @@ -0,0 +1,29 @@ +div + + div.row + + div.col-md-11 + + h5=this.model.name + + div.col-md-1 + + button.btn.btn-outline-secondary.box-shadow(data-hook=this.model.elementID + "-remove") + + div.ml-2 + + div + + ul.nav.nav-tabs + + li.nav-item + + a.nav-link.tab.active(data-toggle="tab" href="#" + this.model.elementID + "-workflows-tab") Workflows + + button.btn.btn-outline-collapse(data-toggle="collapse" data-target="#" + this.model.elementID + "-tab-container" data-hook=this.model.elementID + "-tab-btn") - + + div.card.card-body.tab-content.collapse.show(id=this.model.elementID + "-tab-container") + + div.tab-pane.active(id=this.model.elementID + "-workflows-tab") + + div(id=this.model.elementID + "-workflow-listing" data-hook=this.model.elementID + "-workflow-listing") diff --git a/client/templates/includes/creatorList.pug b/client/templates/includes/creatorListing.pug similarity index 100% rename from client/templates/includes/creatorList.pug rename to client/templates/includes/creatorListing.pug diff --git a/client/templates/includes/domainViewer.pug b/client/templates/includes/domainViewer.pug index d01375fefc..296b7a0d7f 100644 --- a/client/templates/includes/domainViewer.pug +++ b/client/templates/includes/domainViewer.pug @@ -35,6 +35,9 @@ div#domain-viewer.card.card-body table.table tbody + tr + th(scope="row") Static Domain + td: input(type="checkbox" id="static-domain" data-hook="static-domain" checked=this.model.static disabled) tr th(scope="row") Density td=this.model.rho_0 diff --git a/client/templates/includes/edit3DDomain.pug b/client/templates/includes/edit3DDomain.pug index 5f17d4a75d..4a6e55b090 100644 --- a/client/templates/includes/edit3DDomain.pug +++ b/client/templates/includes/edit3DDomain.pug @@ -1,4 +1,4 @@ -div +div.card.card-body div diff --git a/client/templates/includes/editFunctionDefinition.pug b/client/templates/includes/editFunctionDefinition.pug index bb21886b08..1e9f7f5a54 100644 --- a/client/templates/includes/editFunctionDefinition.pug +++ b/client/templates/includes/editFunctionDefinition.pug @@ -6,6 +6,8 @@ tr div.tooltip-icon-large(data-hook="annotation-tooltip" data-html="true" data-toggle="tooltip" title=this.model.annotation || "Click 'Add' to add an annotation") - button.btn.btn-outline-secondary.btn-sm(data-hook="edit-annotation-btn") Edit + if(!this.parent.viewMode) + button.btn.btn-outline-secondary.btn-sm(data-hook="edit-annotation-btn") Edit - td: button.btn.btn-outline-secondary(data-hook="remove") X \ No newline at end of file + if(!this.parent.viewMode) + td: button.btn.btn-outline-secondary(data-hook="remove") X \ No newline at end of file diff --git a/client/templates/includes/editModelView.pug b/client/templates/includes/editModelView.pug deleted file mode 100644 index 402d814ed7..0000000000 --- a/client/templates/includes/editModelView.pug +++ /dev/null @@ -1,36 +0,0 @@ -- var workflowGroups = this.workflowGroupOptions; -div - - div.ml-1.row - - div.col-md-5: button.btn.btn-outline-secondary.box-shadow.text-break(data-hook="project-model-edit" style="width: 100%;")=this.model.name - - div.col-md-4 - - button.btn.btn-outline-secondary.inline.box-shadow( - id="new-workflow-btn", - data-hook="new-workflow-btn", - type="button", - ) New Workflow Using Model - - div.col-md-2 - - button.btn.btn-outline-secondary.btn-sm.box-shadow(data-hook="edit-model-annotation-btn") Edit Notes - - div.col-md-1: button.btn.btn-outline-secondary.box-shadow(data-hook="project-model-remove") - - div.mx-5.mt-4.collapse(data-hook="collapse-annotation-container"+this.model.name.replace(/ /g,"")) - - div.col-md-2.inline.align-top - - div - - div.inline: h5="Notes: " - - div.inline: button.btn.btn-outline-collapse(data-toggle="collapse" data-target="#annotation-text"+this.model.name.replace(/ /g,"") data-hook="collapse-annotation-text") + - - div.collapse.col-md-10.inline(id="annotation-text"+this.model.name.replace(/ /g,"")) - - div: textarea(id="annotation"+this.model.name.replace(/ /g,"") data-hook="annotation" rows="7" style="width: 100%;")=this.model.annotation - - hr \ No newline at end of file diff --git a/client/templates/includes/editModelsView.pug b/client/templates/includes/editModelsView.pug deleted file mode 100644 index c96de731c0..0000000000 --- a/client/templates/includes/editModelsView.pug +++ /dev/null @@ -1,9 +0,0 @@ -div#edit-project-models - - div - - h3.inline Models - - div.mx-1.row.head - - div.mt-3(id="project-models-list" data-hook="project-models-list") \ No newline at end of file diff --git a/client/templates/includes/editParameter.pug b/client/templates/includes/editParameter.pug new file mode 100644 index 0000000000..87c84fa80e --- /dev/null +++ b/client/templates/includes/editParameter.pug @@ -0,0 +1,24 @@ +div.mx-1 + + if(this.model.collection.indexOf(this.model) !== 0) + hr + + div.row + + div.col-sm-3 + + div.pl-2(data-hook="input-name-container") + + div.col-sm-5 + + div(data-hook="input-value-container") + + div.col-sm-2 + + div.tooltip-icon-large(data-hook="annotation-tooltip" data-html="true" data-toggle="tooltip" title=this.model.annotation || "Click 'Add' to add an annotation") + + button.btn.btn-outline-secondary.btn-sm.box-shadow(data-hook="edit-annotation-btn") Edit + + div.col-sm-2 + + button.btn.btn-outline-secondary.box-shadow(data-hook="remove") X diff --git a/client/templates/includes/editProject.pug b/client/templates/includes/editProject.pug index de5a7934bc..4104a043ca 100644 --- a/client/templates/includes/editProject.pug +++ b/client/templates/includes/editProject.pug @@ -1,7 +1,18 @@ tr - td: button.btn.btn-outline-secondary.box-shadow.name(id="open-project-btn" data-hook="open-project-btn")=this.projectName + td + a.btn.btn-outline-secondary.box-shadow.name( + id=this.model.elementID+"-open-btn" + href=this.model.open + role="button" + style="width: 100%" + )=this.model.name - td: div=this.location + td + div=this.model.location - td: button.btn.btn-outline-secondary.box-shadow(id="remove-project-btn" data-hook="remove-project-btn") \ No newline at end of file + td + button.btn.btn-outline-secondary.box-shadow( + id=this.model.elementID+"-remove-btn" + data-hook="remove-project-btn" + ) \ No newline at end of file diff --git a/client/templates/includes/editWorkflowGroupView.pug b/client/templates/includes/editWorkflowGroupView.pug deleted file mode 100644 index a968850cca..0000000000 --- a/client/templates/includes/editWorkflowGroupView.pug +++ /dev/null @@ -1,20 +0,0 @@ -div - - div.ml-1.row.verticle-space(style="display: none;") - - div.col-md-11 - - h4.inline=this.model.name - - button.btn.btn-outline-collapse(data-hook="project-workflow-group-view") + - - div.col-md-1: button.btn.btn-outline-secondary.box-shadow(data-hook="project-workflow-group-remove") - - div - - if(this.model.name === "WorkflowGroup1") - div.verticle-space(data-hook="project-workflows-container") - else - div.verticle-space(data-hook="project-workflows-container" style="display: none;") - - hr(style="display: none;") \ No newline at end of file diff --git a/client/templates/includes/editWorkflowGroupsView.pug b/client/templates/includes/editWorkflowGroupsView.pug deleted file mode 100644 index b77400e518..0000000000 --- a/client/templates/includes/editWorkflowGroupsView.pug +++ /dev/null @@ -1,9 +0,0 @@ -div#edit-project-workflow-groups - - div - - h3.inline Workflows - - div.mx-1.row - - div(id="project-workflow-groups-list" data-hook="project-workflow-groups-list") \ No newline at end of file diff --git a/client/templates/includes/editWorkflowView.pug b/client/templates/includes/editWorkflowView.pug deleted file mode 100644 index aa74ce5768..0000000000 --- a/client/templates/includes/editWorkflowView.pug +++ /dev/null @@ -1,35 +0,0 @@ -div - - div.ml-1.row - - div.col-md-5: button.btn.btn-outline-secondary.box-shadow.text-break(data-hook="project-workflow-open" style="width: 100%")=this.model.name - - div.col-md-4 - - div(data-hook="project-workflow-type")="Type: "+this.model.type - - div(data-hook="project-workflow-status")="Status: "+this.model.status - - div.col-md-2 - - div(data-hook="annotation-container") - - button.btn.btn-outline-secondary.btn-sm.box-shadow(data-hook="edit-workflow-annotation-btn") Edit Notes - - div.col-md-1: button.btn.btn-outline-secondary.box-shadow(data-hook="project-workflow-remove") - - div.mx-5.mt-2.collapse(data-hook="collapse-annotation-container"+this.model.name.replace(/ /g,"")) - - div.col-md-1.inline.align-top - - div.row - - div: h5="Notes: " - - div: button.btn.btn-outline-collapse(data-toggle="collapse" data-target="#annotation-text"+this.model.name.replace(/ /g,"") data-hook="collapse-annotation-text") + - - div.collapse.col-md-11.inline(id="annotation-text"+this.model.name.replace(/ /g,"")) - - div: textarea(id="annotation"+this.model.name.replace(/ /g,"") data-hook="annotation" rows="7" style="width: 100%;")=this.model.annotation - - hr \ No newline at end of file diff --git a/client/templates/includes/editWorkflowsView.pug b/client/templates/includes/editWorkflowsView.pug deleted file mode 100644 index f9acde56df..0000000000 --- a/client/templates/includes/editWorkflowsView.pug +++ /dev/null @@ -1,12 +0,0 @@ -div#edit-project-workflows - - div.mx-1.row.head - - div.mt-3(id="project-workflows-list" data-hook="project-workflows-list") - - div - - button.btn.btn-outline-primary.box-shadow( - id="project-workflow-group-new-workflow", - data-hook="project-workflow-group-new-workflow" - ) Add New Workflow diff --git a/client/templates/includes/gillespyResults.pug b/client/templates/includes/gillespyResults.pug index 18798bfb5c..354ec74d2a 100644 --- a/client/templates/includes/gillespyResults.pug +++ b/client/templates/includes/gillespyResults.pug @@ -3,9 +3,10 @@ div#workflow-results.card.card-body div h3.inline Results - button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-results", id="collapse" data-hook="collapse", disabled) + - div.collapse(id="collapse-results", data-hook="workflow-results") + button.btn.btn-outline-collapse(data-toggle="collapse" data-target="#collapse-results" data-hook="collapse-results-btn") - + + div.collapse.show(id="collapse-results" data-hook="workflow-results") div.collapse(id="edit-plot-args" data-hook="edit-plot-args") @@ -21,20 +22,44 @@ div#workflow-results.card.card-body td: div(id="title" data-hook="title") td: div(id="xaxis" data-hook="xaxis") td: div(id="yaxis" data-hook="yaxis") + div.card.card-body + div h5.inline Plot Trajectories - button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-trajectories", id="collapse-trajectories-btn" data-hook="collapse-trajectories") - - div.collapse(class="show", id="collapse-trajectories") + button.btn.btn-outline-collapse( + data-toggle="collapse" + data-target="#collapse-trajectories" + id="collapse-trajectories-btn" + data-hook="collapse-trajectories-btn" + data-trigger="collapse-plot-container" + data-type="trajectories" + ) - + + div.collapse.show(id="collapse-trajectories") + + div(data-hook="trajectories-plot") + + div.spinner-border.workflow-plot(data-hook="trajectories-plot-spinner") + + button.btn.btn-primary.box-shadow(data-hook="trajectories-edit-plot" data-target="edit-plot" disabled) Edit Plot + + button.btn.btn-primary.box-shadow( + data-hook="trajectories-download-png-custom" + data-target="download-png-custom" + data-type="trajectories" + disabled + ) Download PNG + + button.btn.btn-primary.box-shadow( + data-hook="trajectories-download-json" + data-target="download-json" + data-type="trajectories" + disabled + ) Download JSON - div(id="trajectories" data-hook="trajectories") - div.spinner-border.workflow-plot(id="trajectories" data-hook="plot-spinner") - button.btn.btn-primary.box-shadow(id="trajectories" data-hook="plot") Edit Plot - button.btn.btn-primary.box-shadow(id="trajectories" data-hook="save-plot" disabled) Save Plot to Project Viewer - button.btn.btn-primary.box-shadow(id="trajectories" data-hook="download-png-custom" disabled) Download PNG - button.btn.btn-primary.box-shadow(id="trajectories" data-hook="download-json" disabled) Download JSON + button.btn.btn-primary.box-shadow(id="convert-to-notebook" data-hook="convert-to-notebook") Convert to Notebook button.btn.btn-primary.box-shadow(id="download-results-csv" data-hook="download-results-csv") Download Results as .csv - \ No newline at end of file diff --git a/client/templates/includes/gillespyResultsEnsemble.pug b/client/templates/includes/gillespyResultsEnsemble.pug index 0ef1e9fe04..48186f5fb7 100644 --- a/client/templates/includes/gillespyResultsEnsemble.pug +++ b/client/templates/includes/gillespyResultsEnsemble.pug @@ -1,11 +1,12 @@ -div#workflow-results-ensemble.card.card-body +div#workflow-results.card.card-body div h3.inline Results - button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-results", id="collapse" data-hook="collapse", disabled) + - div.collapse(id="collapse-results", data-hook="workflow-results") + button.btn.btn-outline-collapse(data-toggle="collapse" data-target="#collapse-results" data-hook="collapse-results-btn") - + + div.collapse.show(id="collapse-results" data-hook="workflow-results") div.collapse(id="edit-plot-args" data-hook="edit-plot-args") @@ -23,64 +24,155 @@ div#workflow-results-ensemble.card.card-body td: div(id="yaxis" data-hook="yaxis") div.card.card-body + div - h5.inline Plot Standard Deviation Range - button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-stddevrange", id="collapse-stddevrange-btn" data-hook="collapse-stddevrange") - + h5.inline Plot Mean and Standard Deviation + + button.btn.btn-outline-collapse( + data-toggle="collapse" + data-target="#collapse-stddevrange" + id="collapse-stddevrange-btn" + data-hook="collapse-stddevrange-btn" + data-trigger="collapse-plot-container" + data-type="stddevran" + ) - + + div.collapse.show(id="collapse-stddevrange") - div.collapse(class="show", id="collapse-stddevrange") + div(data-hook="stddevran-plot") - div(id="stddevran" data-hook="stddevran") - div.spinner-border.workflow-plot(id="stddevran" data-hook="plot-spinner") - button.btn.btn-primary.box-shadow(id="stddevran" data-hook="plot") Edit Plot - button.btn.btn-primary.box-shadow(id="stddevran" data-hook="save-plot") Save Plot to Project Viewer - button.btn.btn-primary.box-shadow(id="stddevran" data-hook="download-png-custom" disabled) Download PNG - button.btn.btn-primary.box-shadow(id="stddevran" data-hook="download-json" disabled) Download JSON + div.spinner-border.workflow-plot(data-hook="stddevran-plot-spinner") + + button.btn.btn-primary.box-shadow(data-hook="stddevran-edit-plot" data-target="edit-plot" disabled) Edit Plot + + button.btn.btn-primary.box-shadow( + data-hook="stddevran-download-png-custom" + data-target="download-png-custom" + data-type="stddevran" + disabled + ) Download PNG + + button.btn.btn-primary.box-shadow( + data-hook="stddevran-download-json" + data-target="download-json" + data-type="stddevran" + disabled + ) Download JSON div.card.card-body + div h5.inline Plot Trajectories - button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-trajectories", id="collapse-trajectories-btn" data-hook="collapse-trajectories") + + + button.btn.btn-outline-collapse( + data-toggle="collapse" + data-target="#collapse-trajectories" + id="collapse-trajectories-btn" + data-hook="collapse-trajectories-btn" + data-trigger="collapse-plot-container" + data-type="trajectories" + ) + div.collapse(id="collapse-trajectories") - div(id="trajectories" data-hook="trajectories") - div.spinner-border.workflow-plot(id="trajectories" data-hook="plot-spinner") - button.btn.btn-primary.box-shadow(id="trajectories" data-hook="plot") Edit Plot - button.btn.btn-primary.box-shadow(id="trajectories" data-hook="save-plot" disabled) Save Plot to Project Viewer - button.btn.btn-primary.box-shadow(id="plot-multiple" data-hook="plot-multiple", disabled) Multiple Plots - button.btn.btn-primary.box-shadow(id="trajectories" data-hook="download-png-custom" disabled) Download PNG - button.btn.btn-primary.box-shadow(id="trajectories" data-hook="download-json" disabled) Download JSON + div(data-hook="trajectories-plot") + + div.spinner-border.workflow-plot(data-hook="trajectories-plot-spinner") + + button.btn.btn-primary.box-shadow(data-hook="trajectories-edit-plot" data-target="edit-plot" disabled) Edit Plot + + button.btn.btn-primary.box-shadow(data-hook="multiple-plots", data-type="mltplplt" disabled) Multiple Plots + + button.btn.btn-primary.box-shadow( + data-hook="trajectories-download-png-custom" + data-target="download-png-custom" + data-type="trajectories" + disabled + ) Download PNG + + button.btn.btn-primary.box-shadow( + data-hook="trajectories-download-json" + data-target="download-json" + data-type="trajectories" + disabled + ) Download JSON div.card.card-body + div h5.inline Plot Standard Deviation - button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-stddev", id="collapse-stddev-btn" data-hook="collapse-stddev") + + + button.btn.btn-outline-collapse( + data-toggle="collapse" + data-target="#collapse-stddev" + id="collapse-stddev-btn" + data-hook="collapse-stddev-btn" + data-trigger="collapse-plot-container" + data-type="stddev" + ) + div.collapse(id="collapse-stddev") - div(id="stddev" data-hook="stddev") - div.spinner-border.workflow-plot(id="stddev" data-hook="plot-spinner") - button.btn.btn-primary.box-shadow(id="stddev" data-hook="plot") Edit Plot - button.btn.btn-primary.box-shadow(id="stddev" data-hook="save-plot" disabled) Save Plot to Project Viewer - button.btn.btn-primary.box-shadow(id="stddev" data-hook="download-png-custom" disabled) Download PNG - button.btn.btn-primary.box-shadow(id="stddev" data-hook="download-json" disabled) Download JSON + div(data-hook="stddev-plot") + + div.spinner-border.workflow-plot(data-hook="stddev-plot-spinner") + + button.btn.btn-primary.box-shadow(data-hook="stddev-edit-plot" data-target="edit-plot" disabled) Edit Plot + + button.btn.btn-primary.box-shadow( + data-hook="stddev-download-png-custom" + data-target="download-png-custom" + data-type="stddev" + disabled + ) Download PNG + + button.btn.btn-primary.box-shadow( + data-hook="stddev-download-json" + data-target="download-json" + data-type="stddev" + disabled + ) Download JSON div.card.card-body + div h5.inline Plot Trajectory Mean - button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-trajmean", id="collapse-trajmean-btn" data-hook="collapse-trajmean") + + + button.btn.btn-outline-collapse( + data-toggle="collapse" + data-target="#collapse-trajmean" + id="collapse-trajmean-btn" + data-hook="collapse-trajmean-btn" + data-trigger="collapse-plot-container" + data-type="avg" + ) + div.collapse(id="collapse-trajmean") - div(id="avg" data-hook="avg") - div.spinner-border.workflow-plot(id="avg" data-hook="plot-spinner") - button.btn.btn-primary.box-shadow(id="avg" data-hook="plot") Edit Plot - button.btn.btn-primary.box-shadow(id="avg" data-hook="save-plot" disabled) Save Plot to Project Viewer - button.btn.btn-primary.box-shadow(id="avg" data-hook="download-png-custom" disabled) Download PNG - button.btn.btn-primary.box-shadow(id="avg" data-hook="download-json" disabled) Download JSON + div(data-hook="avg-plot") + + div.spinner-border.workflow-plot(data-hook="avg-plot-spinner") + + button.btn.btn-primary.box-shadow(data-hook="avg-edit-plot" data-target="edit-plot" disabled) Edit Plot + + button.btn.btn-primary.box-shadow( + data-hook="avg-download-png-custom" + data-target="download-png-custom" + data-type="avg" + disabled + ) Download PNG + + button.btn.btn-primary.box-shadow( + data-hook="avg-download-json" + data-target="download-json" + data-type="avg" + disabled + ) Download JSON + + button.btn.btn-primary.box-shadow(id="convert-to-notebook" data-hook="convert-to-notebook") Convert to Notebook - button.btn.btn-primary.box-shadow(id="download-results-csv" data-hook="download-results-csv") Download Results as .csv \ No newline at end of file + button.btn.btn-primary.box-shadow(id="download-results-csv" data-hook="download-results-csv") Download Results as .csv diff --git a/client/templates/includes/jobListing.pug b/client/templates/includes/jobListing.pug new file mode 100644 index 0000000000..c99fc04970 --- /dev/null +++ b/client/templates/includes/jobListing.pug @@ -0,0 +1,26 @@ +div(data-hook=this.model.elementID) + + if(this.model.collection.indexOf(this.model) !== 0) + hr + + div.row + + div.col-md-3 + + button.btn.btn-outline-secondary.box-shadow(data-hook=this.model.elementID + "-open" style="width: 100%")=this.model.name + + div.col-md-4 + + div.py-2=this.model.fmtStartTime + + div.col-md-3 + + div.py-2 + + div.inline(data-hook=this.model.elementID + "-status")=this.model.status + + div.inline.spinner-border.status(data-hook=this.model.elementID + "-running-spinner") + + div.col-md-2 + + button.btn.btn-outline-secondary.box-shadow(data-hook=this.model.elementID + "-remove") X \ No newline at end of file diff --git a/client/templates/includes/metaData.pug b/client/templates/includes/metaData.pug index ce6f62be4f..9519cf16c3 100644 --- a/client/templates/includes/metaData.pug +++ b/client/templates/includes/metaData.pug @@ -1,57 +1,73 @@ div#project-meta-data.card.card-body - h3 Metadata + div - div(id="file-select-view" data-hook="file-select-view") + h3.inline Metadata - div + div.inline - span(for="description-input-view") Description: + button.btn.btn-outline-collapse(data-toggle="collapse" data-target="#metadata-section" id="metadata-collapse-btn" data-hook="metadata-collapse-btn") + - textarea(id="description-input-view" data-hook="description-input-view" rows="5" style="width: 100%;") + div.collapse(id="metadata-section") - table.table + div(id="file-select-view" data-hook="file-select-view") - thead + div - tr + span(for="description-input-view") Description: - th(scope="col") Given Name + textarea(id="description-input-view" data-hook="description-input-view" rows="5" style="width: 100%;") - th(scope="col") Family Name + table.table - th(scope="col") E-Mail + thead - th(scope="col") Organization + tr - th(scpoe="col") Remove + th(scope="col") Given Name - tbody(id="list-of-creators" data-hook="list-of-creators") + th(scope="col") Family Name - hr + th(scope="col") E-Mail - p Add a new creator or update an existing creators information by selecting the appropriate 'creator' option and entering their information below. + th(scope="col") Organization - div(id="creator-select-view" data-hook="creator-select-view") + th(scpoe="col") Remove - div.inline + tbody(id="list-of-creators" data-hook="list-of-creators") - div.inline(id="given-name-input-view" data-hook="given-name-input-view") + hr - div.inline(id="family-name-input-view" data-hook="family-name-input-view") + p Add a new creator or update an existing creators information by selecting the appropriate 'creator' option and entering their information below. - div.inline(id="email-input-view" data-hook="email-input-view") + div(id="creator-select-view" data-hook="creator-select-view") - div.inline(id="organization-input-view" data-hook="organization-input-view") + div.inline - div + div.inline(id="given-name-input-view" data-hook="given-name-input-view") + + div.inline(id="family-name-input-view" data-hook="family-name-input-view") + + div.inline(id="email-input-view" data-hook="email-input-view") + + div.inline(id="organization-input-view" data-hook="organization-input-view") + + div + + button.btn.btn-outline-secondary.box-shadow(id="add-creator-btn" data-hook="add-creator-btn" disabled) Add + + hr + + div.inline + + button.btn.btn-primary.box-shadow(id="save-meta-data-button" data-hook="save-meta-data-button") Save - button.btn.btn-outline-secondary.box-shadow(id="add-creator-btn" data-hook="add-creator-btn" disabled) Add + div.mdl-edit-btn.saving-status.inline(data-hook="md-in-progress") - hr + div.spinner-grow.mr-2 - div.inline + span(data-hook="sd-action-in-progress") Saving - button.btn.btn-primary.box-shadow(id="save-meta-data-button" data-hook="save-meta-data-button") Save + div.mdl-edit-btn.saved-status.inline(data-hook="md-complete") - button.btn.btn-primary.box-shadow(id="submit-meta-data-button" data-hook="submit-meta-data-button") Submit \ No newline at end of file + span(data-hook="md-action-complete") Saved diff --git a/client/templates/includes/modelListing.pug b/client/templates/includes/modelListing.pug new file mode 100644 index 0000000000..418f283396 --- /dev/null +++ b/client/templates/includes/modelListing.pug @@ -0,0 +1,52 @@ +div + + div.ml-1.row + + div.col-md-5 + + a.btn.btn-outline-secondary.box-shadow.text-break(href=this.model.open role="button" style="width: 100%;")=this.model.name + + div.col-md-4 + + button.btn.btn-outline-secondary.inline.dropdown-toggle.box-shadow( + id=this.model.elementID + "-workflow-btn", + data-hook=this.model.elementID + "-workflow-btn", + data-toggle="dropdown", + aria-haspopup="true", + aria-expanded="false", + type="button" + ) New Workflow Using Model + + ul.dropdown-menu(aria-labelledby=this.model.elementID + "-workflow-btn") + if(!this.model.is_spatial) + li.dropdown-item(id=this.model.elementID + "-ensemble-simulation") Ensemble Simulation + li.dropdown-item(id=this.model.elementID + "-parameter-sweep") Parameter Sweep + li.dropdown-item + + a.btn(id=this.model.elementID + "-jupyter-notebook" data-hook=this.model.elementID + "-jupyter-notebook" style="padding: 0;") Jupyter Notebook + + div.col-md-2 + + button.btn.btn-outline-secondary.btn-sm.box-shadow(data-hook=this.model.elementID + "-notes-btn") Edit Notes + + div.col-md-1 + + button.btn.btn-outline-secondary.box-shadow(data-hook=this.model.elementID + "-remove") + + div.mx-5.mt-4.collapse(data-hook=this.model.elementID + "-notes-container") + + div.col-md-2.inline.align-top + + div.inline + + h5 Notes: + + div.inline + + button.btn.btn-outline-collapse(data-toggle="collapse" data-target="#" + this.model.elementID + "-annotation-container" data-hook=this.model.elementID + "-annotation-btn") + + + div.collapse.col-md-10.inline(id=this.model.elementID + "-annotation-container") + + div: textarea(id=this.model.elementID + "-annotation" data-hook=this.model.elementID + "-annotation" rows="7" style="width: 100%;")=this.model.annotation + + hr \ No newline at end of file diff --git a/client/templates/includes/modelSettingsViewer.pug b/client/templates/includes/modelSettingsViewer.pug deleted file mode 100644 index 22fc72168c..0000000000 --- a/client/templates/includes/modelSettingsViewer.pug +++ /dev/null @@ -1,26 +0,0 @@ -div#model-settings-viewer.card.card-body - - div - - h3.inline Model Settings - button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-model-settings-viewer", data-hook="collapse") - - - div.row.collapse(class="show", id="collapse-model-settings-viewer") - - table.table - - thead - - tr - - th(scope="col") End Simulation - - th(scope="col") Sample Frequency - - tbody - - tr - - td=this.model.endSim - - td=this.model.timeStep diff --git a/client/templates/includes/modelViewer.pug b/client/templates/includes/modelViewer.pug index d4e117dcf8..9559e2a1f8 100644 --- a/client/templates/includes/modelViewer.pug +++ b/client/templates/includes/modelViewer.pug @@ -3,9 +3,10 @@ div.card.card-body div(id="model-viewer-header") h3.inline="Review Model: "+this.model.name - button.btn.btn-outline-collapse(id=this.model.name, data-toggle="collapse", data-target="#collapse-model"+this.model.name.replace(/ /g, ''), data-hook="collapse-model") + - div.collapse(id="collapse-model"+this.model.name.replace(/ /g, '')) + button.btn.btn-outline-collapse(data-toggle="collapse" data-target="#collapse-model" data-hook="collapse-model") + + + div.collapse(id="collapse-model") div(data-hook="species-viewer-container") @@ -17,6 +18,6 @@ div.card.card-body div(data-hook="rules-viewer-container") - div.card.card-body="System Volume: "+this.model.volume + div(data-hook="sbml-components-viewer-container") - div(data-hook="model-settings-viewer-container") \ No newline at end of file + div.card.card-body="System Volume: "+this.model.volume diff --git a/client/templates/includes/modelsViewer.pug b/client/templates/includes/modelsViewer.pug deleted file mode 100644 index 3946f4979b..0000000000 --- a/client/templates/includes/modelsViewer.pug +++ /dev/null @@ -1,10 +0,0 @@ -div#models-viewer.card.card-body - - div - - h3.inline Models - button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-models", id="collapse-models-btn" data-hook="collapse-models") + - - div.collapse(id="collapse-models") - - div(id="model-container" data-hook="model-container") \ No newline at end of file diff --git a/client/templates/includes/parameterScanResults.pug b/client/templates/includes/parameterScanResults.pug new file mode 100644 index 0000000000..2f6efea14b --- /dev/null +++ b/client/templates/includes/parameterScanResults.pug @@ -0,0 +1,82 @@ +div#workflow-results.card.card-body + + div.head + + h3.inline.mr-2 Results + + button.btn.btn-outline-collapse.mb-1(data-toggle="collapse" data-target="#collapse-results" data-hook="collapse-results-btn") - + + div.collapse.show(id="collapse-results" data-hook="workflow-results") + + div.collapse(id="edit-plot-args" data-hook="edit-plot-args") + + table.table + thead + tr + th(scope="col") Title + th(scope="col") X-axis Label + th(scope="col") Y-axis Label + + tbody + tr + td: div(id="title" data-hook="title") + td: div(id="xaxis" data-hook="xaxis") + td: div(id="yaxis" data-hook="yaxis") + + div.card.card-body + + div + + h5.inline Parameter Sweep + + button.btn.btn-outline-collapse( + data-toggle="collapse" + data-target="#collapse-ts-psweep" + id="collapse-ts-psweep-btn" + data-hook="collapse-ts-psweep-btn" + data-trigger="collapse-plot-container" + data-type="ts-psweep" + ) - + + div.collapse.show(id="collapse-ts-psweep") + + div.row + + div.col-md-9 + + div(data-hook="ts-psweep-plot") + + div.spinner-border.workflow-plot(data-hook="ts-psweep-plot-spinner") + + button.btn.btn-primary.box-shadow(data-hook="ts-psweep-edit-plot" data-target="edit-plot" disabled) Edit Plot + + button.btn.btn-primary.box-shadow(data-hook="multiple-plots" data-type="ts-psweep-mp" style="display: none;" disabled) Multiple Plots + + button.btn.btn-primary.box-shadow( + data-hook="ts-psweep-download-png-custom" + data-target="download-png-custom" + data-type="ts-psweep" + disabled + ) Download PNG + + button.btn.btn-primary.box-shadow( + data-hook="ts-psweep-download-json" + data-target="download-json" + data-type="ts-psweep" + disabled + ) Download JSON + + div.col-md-3 + + div.head(data-hook="plot-type-header") + + h6 Plot Type + + div.mt-2(data-hook="plot-type-select") + + div.head + + h6 Parameters + + div.mt-2(data-hook="parameter-ranges") + diff --git a/client/templates/includes/parameterSettings.pug b/client/templates/includes/parameterSettings.pug new file mode 100644 index 0000000000..a64be2313f --- /dev/null +++ b/client/templates/includes/parameterSettings.pug @@ -0,0 +1,60 @@ +div#parameter-settings.card.card-body + + div + + h3.inline Parameter Settings + + button.btn.btn-outline-collapse(data-toggle="collapse" data-target="#collapse-psweep-settings" data-hook="collapse") - + + div.collapse(class="show", id="collapse-psweep-settings") + + div.verticle-space + + span.inline(for="variable-of-interest") Variable of Interest: + + div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.species) + + div.inline(id="variable-of-interest" data-hook="variable-of-interest-list") + + div + + h5 Configure Parameter(s) + + table.table + thead + tr + th(scope="col") + div + div.inline Sweep Target + + div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.variable) + + th(scope="col") + div + div.inline Current Value + + div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.value) + + th(scope="col") + div + div.inline Minimum Value + + div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.min) + + th(scope="col") + div + div.inline Maximum Value + + div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.max) + + th(scope="col") + div + div.inline Steps + + div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.steps) + + th(scope="col") Remove + + tbody(data-hook="ps-parameter-collection") + + button.btn.btn-outline-secondary.box-shadow(data-hook="add-ps-parameter") Add Parameter \ No newline at end of file diff --git a/client/templates/includes/parameterSweepResults.pug b/client/templates/includes/parameterSweepResults.pug index 9b6a7df031..3df6edbb08 100644 --- a/client/templates/includes/parameterSweepResults.pug +++ b/client/templates/includes/parameterSweepResults.pug @@ -1,11 +1,24 @@ div#workflow-results.card.card-body - div + div.head - h3.inline Results - button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-results", id="collapse" data-hook="collapse", disabled) + + h3.inline.mr-2 Results - div.collapse(id="collapse-results", data-hook="workflow-results") + div.inline + + ul.nav.nav-tabs + + li.nav-item + + a.nav-link.tab(data-toggle="tab" href="#time-series") Time Series + + li.nav-item + + a.nav-link.tab.active(data-toggle="tab" href="#sweep") Sweep + + button.btn.btn-outline-collapse.mb-1(data-toggle="collapse" data-target="#collapse-results" data-hook="collapse-results-btn") - + + div.collapse.show(id="collapse-results" data-hook="workflow-results") div.collapse(id="edit-plot-args" data-hook="edit-plot-args") @@ -22,45 +35,128 @@ div#workflow-results.card.card-body td: div(id="xaxis" data-hook="xaxis") td: div(id="yaxis" data-hook="yaxis") - div + div.tab-content + + div.tab-pane.card.card-body(id="time-series" data-hook="time-series") + + div + + h5.inline Parameter Sweep + + button.btn.btn-outline-collapse( + data-toggle="collapse" + data-target="#collapse-ts-psweep" + id="collapse-ts-psweep-btn" + data-hook="collapse-ts-psweep-btn" + data-trigger="collapse-plot-container" + data-type="ts-psweep" + ) - + + div.collapse.show(id="collapse-ts-psweep") + + div.row + + div.col-md-9 + + div(data-hook="ts-psweep-plot") + + div.spinner-border.workflow-plot(data-hook="ts-psweep-plot-spinner") + + button.btn.btn-primary.box-shadow(data-hook="ts-psweep-edit-plot" data-target="edit-plot" disabled) Edit Plot + + button.btn.btn-primary.box-shadow(data-hook="multiple-plots" data-type="ts-psweep-mp" style="display: none;" disabled) Multiple Plots + + button.btn.btn-primary.box-shadow( + data-hook="ts-psweep-download-png-custom" + data-target="download-png-custom" + data-type="ts-psweep" + disabled + ) Download PNG + + button.btn.btn-primary.box-shadow( + data-hook="ts-psweep-download-json" + data-target="download-json" + data-type="ts-psweep" + disabled + ) Download JSON + + div.col-md-3 + + div.head(data-hook="plot-type-header") + + h6 Plot Type + + div.mt-2(data-hook="plot-type-select") + + div.head + + h6 Parameters + + div.mt-2(data-hook="parameter-ranges") + + div.tab-pane.active.mt-3(id="sweep" data-hook="sweep") + + div.inline.horizontal-space + + span.inline(for="species-of-interest") Variable of Interest: + + div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.species) + + div.inline(id="species-of-interest" data-hook="specie-of-interest-list") + + div.inline.horizontal-space - div.inline.horizontal-space + span.inline(for="feature-extractor") Feature Extraction: - span.inline(for="species-of-interest") Variable of Interest: + div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.mapper) - div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.species) + div.inline(id="feature-extractor" data-hook="feature-extraction-list") - div.inline(id="species-of-interest" data-hook="specie-of-interest-list") + div.inline.horizontal-space(id="ensemble-aggragator-container" data-hook="ensemble-aggragator-container") - div.inline.horizontal-space + span.inline(for="ensemble-aggragator") Ensemble Aggragator: - span.inline(for="feature-extractor") Feature Extraction: + div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.reducer) + + div.inline(id="ensemble-aggragator" data-hook="ensemble-aggragator-list") - div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.mapper) + div.card.card-body - div.inline(id="feature-extractor" data-hook="feature-extraction-list") + div - div.horizontal-space.collapse(class="show" id="ensemble-aggragator-container" data-hook="ensemble-aggragator-container") + h5.inline Parameter Sweep - span.inline(for="ensemble-aggragator") Ensemble Aggragator: + button.btn.btn-outline-collapse( + data-toggle="collapse" + data-target="#collapse-psweep" + id="collapse-psweep-btn" + data-hook="collapse-psweep-btn" + data-trigger="collapse-plot-container" + data-type="psweep" + ) - + + div.collapse.show(id="collapse-psweep") - div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.reducer) - - div.inline(id="ensemble-aggragator" data-hook="ensemble-aggragator-list") + div(data-hook="psweep-plot") - div.card.card-body - div + div.spinner-border.workflow-plot(data-hook="psweep-plot-spinner") - h5.inline Parameter Sweep - button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-psweep", id="collapse-psweep-btn" data-hook="collapse-psweep") - + button.btn.btn-primary.box-shadow(data-hook="psweep-edit-plot" data-target="edit-plot" disabled) Edit Plot - div.collapse(class="show", id="collapse-psweep") + button.btn.btn-primary.box-shadow( + data-hook="psweep-download-png-custom" + data-target="download-png-custom" + data-type="psweep" + disabled + ) Download PNG - div(id="psweep" data-hook="psweep") - div.spinner-border.workflow-plot(id="psweep" data-hook="plot-spinner") - button.btn.btn-primary.box-shadow(id="psweep" data-hook="plot") Edit Plot - button.btn.btn-primary.box-shadow(id="psweep" data-hook="save-plot" disabled) Save Plot to Project Viewer - button.btn.btn-primary.box-shadow(id="psweep" data-hook="download-png-custom" disabled) Download PNG - button.btn.btn-primary.box-shadow(id="psweep" data-hook="download-json" disabled) Download JSON + button.btn.btn-primary.box-shadow( + data-hook="psweep-download-json" + data-target="download-json" + data-type="psweep" + disabled + ) Download JSON + + button.btn.btn-primary.box-shadow(id="convert-to-notebook" data-hook="convert-to-notebook") Convert to Notebook - button.btn.btn-primary.box-shadow(id="download-results-csv" data-hook="download-results-csv") Download Results as .csv \ No newline at end of file + button.btn.btn-primary.box-shadow(id="download-results-csv" data-hook="download-results-csv") Download Results as .csv diff --git a/client/templates/includes/parameterSweepSettings.pug b/client/templates/includes/parameterSweepSettings.pug deleted file mode 100644 index c9570ab557..0000000000 --- a/client/templates/includes/parameterSweepSettings.pug +++ /dev/null @@ -1,73 +0,0 @@ -div#parameter-sweep-settings.card.card-body - - div - - h3.inline Parameter Sweep Settings - button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-psweep-settings", data-hook="collapse") - - - div.collapse(class="show", id="collapse-psweep-settings") - div.row - div.col-md-6.verticle-space - span.inline Sweep Type: - - div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.sweepType) - - div.inline.horizontal-space - input(type="radio", name="sweepType", data-hook="one-parameter", data-name="1D" checked) - | One Parameter - div.inline.horizontal-space - input(type="radio", name="sweepType", data-hook="two-parameter", data-name="2D" disabled) - | Two Parameters - div.col-md-6.verticle-space - span.inline(for="species-of-interest") Variable of Interest: - - div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.species) - - div.inline(id="species-of-interest" data-hook="specie-of-interest-list") - h5 Configure Variable(s) - table.table - thead - tr - th(scope="col") - div - div.inline Sweep Variable - - div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.variable) - - th(scope="col") - div - div.inline Current Value - - div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.value) - - th(scope="col") - div - div.inline Minimum Value - - div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.min) - - th(scope="col") - div - div.inline Maximum Value - - div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.max) - - th(scope="col") - div - div.inline Steps - - div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.steps) - - tbody - tr - td: div(data-hook="sweep-variable-one-select") - td: div(data-hook="current-value-one-input") - td: div(data-hook="minimum-value-one-input") - td: div(data-hook="maximum-value-one-input") - td: div(data-hook="step-one-input") - tr.collapse(data-hook="parameter-two-row") - td: div(data-hook="sweep-variable-two-select") - td: div(data-hook="current-value-two-input") - td: div(data-hook="minimum-value-two-input") - td: div(data-hook="maximum-value-two-input") - td: div(data-hook="step-two-input") \ No newline at end of file diff --git a/client/templates/includes/parameterSweepSettingsViewer.pug b/client/templates/includes/parameterSweepSettingsViewer.pug deleted file mode 100644 index a045813a6e..0000000000 --- a/client/templates/includes/parameterSweepSettingsViewer.pug +++ /dev/null @@ -1,35 +0,0 @@ -div#parameter-sweep-settings-viewer.card.card-body - - div - - h3.inline Parameter Sweep Settings - button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-psweep-settings-viewer", data-hook="collapse") - - - div.collapse(class="show", id="collapse-psweep-settings-viewer") - - div(style="margin-bottom: 0.75rem;" data-hook="sweep-type-viewer") - - h5.inline Sweep Variables - - table.table - thead - tr - th(scope="col") Variable - th(scope="col") Current Value - th(scope="col") Minimum Value - th(scope="col") Maximum Value - th(scope="col") Steps - - tbody - tr - td=this.model.parameterOne.name - td(data-hook="p1-current-value-viewer") - td=this.model.p1Min - td=this.model.p1Max - td=this.model.p1Steps - tr.collapse(data-hook="p2-variable-viewer") - td=this.model.parameterTwo.name - td(data-hook="p2-current-value-viewer") - td=this.model.p2Min - td=this.model.p2Max - td=this.model.p2Steps \ No newline at end of file diff --git a/client/templates/includes/parametersEditor.pug b/client/templates/includes/parametersEditor.pug index 707ada2a8b..5d2c5af0d6 100644 --- a/client/templates/includes/parametersEditor.pug +++ b/client/templates/includes/parametersEditor.pug @@ -1,43 +1,73 @@ -div#parameters-editor.card.card-body +div#parameters-editor.card - div + div.card-header.pb-0 - h3.inline Parameters - button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-parameters", data-hook="collapse") + + h3.inline.mr-3 Parameters - div.collapse(id="collapse-parameters" data-hook="parameters-list-container") - p + div.inline.mr-3 + + ul.nav.nav-tabs.card-header-tabs(id="parameter-tabs") + + li.nav-item + + a.nav-link.tab.active(data-hook="parameters-edit-tab" data-toggle="tab" href="#edit-parameters") Edit + + li.nav-item + + a.nav-link.tab(data-hook="parameters-view-tab" data-toggle="tab" href="#view-parameters") View + + button.btn.btn-outline-collapse(data-toggle="collapse" data-target="#collapse-parameters" data-hook="collapse") + + + div.card-body + p.mb-0 | Constant values that represents an inherent properties of the system. Used to set the rate of a Reaction. - table.table - thead - tr - th(scope="col") - div - div.inline Name + div.collapse.tab-content(id="collapse-parameters" data-hook="parameters-list-container") + + div.tab-pane.active(id="edit-parameters" data-hook="edit-parameters") + + hr + + div.mx-1.row.head.align-items-baseline + + div.col-sm-3 + + h6.inline Name + + div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.name) + + div.col-sm-5 + + h6.inline Value + + div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.expression) + + div.col-sm-2 + + h6.inline Annotation + + div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.annotation) + + div.col-sm-2 + + h6.inline Remove + + div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.remove) - div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.name) + div.my-3(data-hook="edit-parameter-list") - th(scope="col") - div - div.inline Value + button.btn.btn-outline-primary.box-shadow(data-hook="add-parameter") Add Parameter - div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.expression) + div.tab-pane(id="view-parameters" data-hook="view-parameters") - th(scope="col") - div - div.inline Annotation + hr - div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.annotation) + div.mx-1.row.head.align-items-baseline - th(scope="col") - div - div.inline Remove + div.col-sm-3: h6 Name - div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.remove) - - tbody(data-hook="parameter-list") + div.col-sm-7: h6 Value - button.btn.btn-outline-primary.box-shadow(data-hook="add-parameter") Add Parameter + div.col-sm-2(data-hook="parameters-annotation-header"): h6 Annotation - button.btn.btn-outline-primary.box-shadow.ml-2(data-hook="save-parameters") Save Parameters + div.mt-3(data-hook="view-parameter-list") diff --git a/client/templates/includes/parametersViewer.pug b/client/templates/includes/parametersViewer.pug deleted file mode 100644 index b579141fb2..0000000000 --- a/client/templates/includes/parametersViewer.pug +++ /dev/null @@ -1,21 +0,0 @@ -div#parameters-viewer.card.card-body - - div - - h3.inline Parameters - button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-parameters", data-hook="collapse") - - - div.collapse(class="show", id="collapse-parameters") - - table.table - thead - tr - th.col-md-3-view(scope="col") Name - th.col-md-9-view(scope="col") Value - if this.containsMdlWithAnn - th.col-md-3-view(scope="col") Annotation - - tbody(data-hook="parameter-list") - - if this.collection.parent.for === "edit" - button.btn.btn-outline-primary.box-shadow(data-hook="edit-parameters") Edit Parameters diff --git a/client/templates/includes/plotsView.pug b/client/templates/includes/plotsView.pug deleted file mode 100644 index 0d72e785bc..0000000000 --- a/client/templates/includes/plotsView.pug +++ /dev/null @@ -1,10 +0,0 @@ -div.card.card-body - - div - - h5.inline=this.heading - button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse"+this.model.key+this.model.stamp data-hook="collapse-plot") - - div.collapse(class="show", id="collapse"+this.model.key+this.model.stamp) - - div(data-hook=this.model.key+this.model.stamp) \ No newline at end of file diff --git a/client/templates/includes/projectViewer.pug b/client/templates/includes/projectViewer.pug deleted file mode 100644 index 4ae225f576..0000000000 --- a/client/templates/includes/projectViewer.pug +++ /dev/null @@ -1,12 +0,0 @@ -div#project-viewer.card.card-body - - div - - h3.inline Project Viewer - button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-project", data-hook="collapse-project") + - - div.collapse(id="collapse-project") - - div(id="models-collection-container" data-hook="models-collection-container") - - div(id="workflow-groups-collection-container" data-hook="workflow-groups-collection-container") \ No newline at end of file diff --git a/client/templates/includes/reactionsEditor.pug b/client/templates/includes/reactionsEditor.pug index 0ec990c9c6..b27791913b 100644 --- a/client/templates/includes/reactionsEditor.pug +++ b/client/templates/includes/reactionsEditor.pug @@ -35,6 +35,8 @@ div#reactions-editor.card.card-body tbody(data-hook="reaction-list") div.col-md-5.container-part(data-hook="reaction-details-container") + + div(data-hook="massaction-message"): p.text-info To add a mass action reaction the model must have at least one parameter div(data-hook="process-component-error"): p.text-danger A model must have at least one reaction, event, or rule diff --git a/client/templates/includes/sbmlComponentEditor.pug b/client/templates/includes/sbmlComponentEditor.pug index 1bf36752b4..7d4ec4423d 100644 --- a/client/templates/includes/sbmlComponentEditor.pug +++ b/client/templates/includes/sbmlComponentEditor.pug @@ -28,6 +28,7 @@ div#sbml-components.card.card-body div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.annotation) - th(scope="col") Remove + if(!this.viewMode) + th(scope="col") Remove tbody(data-hook="function-definition-list") \ No newline at end of file diff --git a/client/templates/includes/settings.pug b/client/templates/includes/settings.pug new file mode 100644 index 0000000000..87df9f307a --- /dev/null +++ b/client/templates/includes/settings.pug @@ -0,0 +1,33 @@ +div#workflow-settings.card.card-body + + div + + h3.inline Settings + + button.btn.btn-outline-collapse(data-toggle="collapse" data-target="#collapse-wkfl-settings" data-hook="collapse-settings") - + + div.collapse(class="show" id="collapse-wkfl-settings" data-hook="workflow-editor-container") + + div(data-hook="timespan-settings-container") + + div(data-hook="param-sweep-settings-container") + + div(data-hook="sim-settings-container") + + div.mdl-edit-btn + + button.btn.btn-primary.box-shadow(data-hook="save") Save + + div.mdl-edit-btn.saving-status(data-hook="saving-workflow") + + div.spinner-grow + + span Saving... + + div.mdl-edit-btn.saved-status(data-hook="saved-workflow") + + span Saved + + button.btn.btn-primary.box-shadow(data-hook="start-job") Start Workflow + + button.btn.btn-primary.box-shadow(data-hook="edit-model") Edit Model \ No newline at end of file diff --git a/client/templates/includes/settingsViewer.pug b/client/templates/includes/settingsViewer.pug new file mode 100644 index 0000000000..90ba4f0528 --- /dev/null +++ b/client/templates/includes/settingsViewer.pug @@ -0,0 +1,138 @@ +div#workflow-settings-viewer.card.card-body + + div + + h3.inline Review Settings + + button.btn.btn-outline-collapse(data-toggle="collapse" data-target="#collapse-wkfl-settings-viewer" data-hook="collapse-settings-viewer") + + + div.collapse(id="collapse-wkfl-settings-viewer" data-hook="workflow-settings-viewer-container") + + div.card.card-body(data-hook="timespan-settings-viewer-container") + + div + + h3.inline Timespan + + button.btn.btn-outline-collapse(data-toggle="collapse" data-target="#collapse-timespan-settings" data-hook="collapse-ts-settings") - + + div.collapse(class="show" id="collapse-timespan-settings" data-hook="timespan-settings-container") + + hr + + div.row + + div.col-md-6 + + h5.inline.pr-2 Simulation Time: + + div.inline="0 to " + this.model.timespanSettings.endSim + + div.col-md-6 + + h5.inline.pr-2 Sample Frequency: + + div.inline=this.model.timespanSettings.timeStep + + div.card.card-body(data-hook="param-sweep-settings-viewer-container") + + div + + h3.inline Parameter Settings + + button.btn.btn-outline-collapse(data-toggle="collapse" data-target="#collapse-p-settings-viewer" data-hook="collapse-p-settings") - + + div.collapse(class="show", id="collapse-p-settings-viewer") + + hr + + div + + h5.inline.pr-2 Variable of Interest: + + div.inline=this.model.parameterSweepSettings.speciesOfInterest.name + + hr + + div + + h4 Sweep Parameters + + table.table + thead + tr + th(scope="col") Target + th(scope="col") Current Value + th(scope="col") Minimum Value + th(scope="col") Maximum Value + th(scope="col") Steps + + tbody(data-hook="view-sweep-parameters") + + div.card.card-body(data-hook="sim-settings-viewer-container") + + div + + h3.inline Simulation Settings + + button.btn.btn-outline-collapse(data-toggle="collapse" data-target="#collapse-sim-settings" data-hook="collapse-sim-settings") - + + div.collapse(class="show" id="collapse-sim-settings") + + hr + + div + + h5.inline.pr-2 Simulation Algorithm: + + div.inline=this.algorithm + + div(data-hook="view-deterministic-settings") + + hr + + h4 Deterministic Settings + + hr + + div.row + + div.col-md-6 + + h5.inline.pr-2 Relative Tolerance: + + div.inline=this.model.simulationSettings.relativeTol + + div.col-md-6 + + h5.inline.pr-2 Absolute Tolerance: + + div.inline=this.model.simulationSettings.absoluteTol + + div(data-hook="view-stochastic-settings") + + hr + + h4 Stochastic Settings + + hr + + div.row + + div.col-md-4 + + h5.inline.pr-2 Trajectories: + + div.inline=this.model.simulationSettings.realizations + + div.col-md-4 + + h5.inline.pr-2 Seed: + + div.inline=this.model.simulationSettings.seed + + div.col-md-4(data-hook="view-tau-tolerance") + + h5.inline.pr-2 Tau Tolerance: + + div.inline=this.model.simulationSettings.tauTol diff --git a/client/templates/includes/simulationSettingsViewer.pug b/client/templates/includes/simulationSettingsViewer.pug deleted file mode 100644 index e8725159e6..0000000000 --- a/client/templates/includes/simulationSettingsViewer.pug +++ /dev/null @@ -1,54 +0,0 @@ -div#settings-viewer.card.card-body - - div - - h3.inline Simulation Settings - button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-settings-viewer", data-hook="collapse") - - - div.row.collapse(class="show", id="collapse-settings-viewer") - - div.col-md-12(style="margin-bottom: 0.75rem;")=this.algorithm - - div.col-md-6.collapse(data-hook="deterministic") - - h5.inline Deterministic Settings - - table.table - thead - tr - th(scope="col") Relative Tolerance - th(scope="col") Absolute Tolerance - tbody - tr - td=this.model.relativeTol - td=this.model.absoluteTol - - div.col-md-6.collapse(data-hook="stochastic") - - h5.inline Stochastic Settings - - div.collapse(data-hook="SSA") - - table.table - thead - tr - th(scope="col") Number of Trajectories - th(scope="col") Seed - tbody - tr - td=this.model.realizations - td=this.model.seed - - div.collapse(data-hook="Tau") - - table.table - thead - tr - th(scope="col") Number of Trajectories - th(scope="col") Seed - th(scope="col") Tau Tolerance - tbody - tr - td=this.model.realizations - td=this.model.seed - td=this.model.tauTol \ No newline at end of file diff --git a/client/templates/includes/sweepParameter.pug b/client/templates/includes/sweepParameter.pug new file mode 100644 index 0000000000..7398fa4603 --- /dev/null +++ b/client/templates/includes/sweepParameter.pug @@ -0,0 +1,25 @@ +tr + + td + + div(data-hook=this.model.elementID + "-sweep-target") + + td + + div(data-hook=this.model.elementID + "-target-value")=this.parameter.expression + + td + + div(data-hook=this.model.elementID + "-target-min") + + td + + div(data-hook=this.model.elementID + "-target-max") + + td + + div(data-hook=this.model.elementID + "-target-steps") + + td + + button.btn.btn-outline-secondary.box-shadow(data-hook=this.model.elementID + "-remove") X diff --git a/client/templates/includes/sweepParameterRange.pug b/client/templates/includes/sweepParameterRange.pug new file mode 100644 index 0000000000..eff6534ec5 --- /dev/null +++ b/client/templates/includes/sweepParameterRange.pug @@ -0,0 +1,20 @@ +div + + if(this.model.collection.indexOf(this.model) > 0) + hr + + div + + div.inline.mr-2=this.model.name + ":" + + div.inline(style="max-width: 100%") + + div.horizontal-scroll(data-hook=this.model.elementID + "-current-value")=this.model.range[0] + + input.custom-range( + type="range" + min="0" + max=this.model.range.length - 1 + value=0 + data-hook=this.model.elementID + "-slider" + ) diff --git a/client/templates/includes/modelSettings.pug b/client/templates/includes/timespanSettings.pug similarity index 100% rename from client/templates/includes/modelSettings.pug rename to client/templates/includes/timespanSettings.pug diff --git a/client/templates/includes/viewParameters.pug b/client/templates/includes/viewParameters.pug index a4cae60444..6e338ecbea 100644 --- a/client/templates/includes/viewParameters.pug +++ b/client/templates/includes/viewParameters.pug @@ -1,10 +1,19 @@ -tr - td=this.model.name +div.mx-1 - td=this.model.expression + if(this.model.collection.indexOf(this.model) !== 0) + hr - if this.model.annotation - td: div.tooltip-icon-large(data-hook="annotation-tooltip" data-html="true" data-toggle="tooltip" title=this.model.annotation || "Click 'Add' to add an annotation") + div.row - if this.parent.containsMdlWithAnn && !this.model.annotation - td: div + div.col-sm-3 + + div.pl-2=this.model.name + + div.col-sm-7 + + div=this.model.expression + + div.col-sm-2 + + if this.model.annotation + div.tooltip-icon-large(data-hook="annotation-tooltip" data-html="true" data-toggle="tooltip" title=this.model.annotation || "Click 'Add' to add an annotation") diff --git a/client/templates/includes/viewSweepParameter.pug b/client/templates/includes/viewSweepParameter.pug new file mode 100644 index 0000000000..c0a1ad5acb --- /dev/null +++ b/client/templates/includes/viewSweepParameter.pug @@ -0,0 +1,12 @@ +tr + + td=this.model.name + + td=this.parameter.expression + + td=this.model.min + + td=this.model.max + + td=this.model.steps + \ No newline at end of file diff --git a/client/templates/includes/workflowEditor.pug b/client/templates/includes/workflowEditor.pug deleted file mode 100644 index 631555a4d6..0000000000 --- a/client/templates/includes/workflowEditor.pug +++ /dev/null @@ -1,17 +0,0 @@ -div#workflow-editor.card.card-body - - div - - h3.inline Settings - - button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-wkfl-settings", data-hook="collapse-settings") - - - div.collapse(class="show", id="collapse-wkfl-settings", data-hook="workflow-editor-container") - - div(data-hook="model-name-container") - - div.collapse(class="show" data-hook="param-sweep-settings-container") - - div(data-hook="sim-settings-container") - - div(data-hook="workflow-state-buttons-container") \ No newline at end of file diff --git a/client/templates/includes/workflowGroupListing.pug b/client/templates/includes/workflowGroupListing.pug new file mode 100644 index 0000000000..d318609c52 --- /dev/null +++ b/client/templates/includes/workflowGroupListing.pug @@ -0,0 +1,58 @@ +div + + div.ml-1.row + + div.col-md-6 + + a.btn.btn-outline-secondary.box-shadow.text-break(href=this.model.open role="button" style="width: 100%;")=this.model.name + + div.col-md-5 + + button.btn.btn-outline-secondary.inline.dropdown-toggle.box-shadow( + id=this.model.elementID + "-workflow-btn", + data-hook=this.model.elementID + "-workflow-btn", + data-toggle="dropdown", + aria-haspopup="true", + aria-expanded="false", + type="button" + ) New Workflow Using Model + + ul.dropdown-menu(aria-labelledby=this.model.elementID + "-workflow-btn") + if(!this.model.model.is_spatial) + li.dropdown-item(id=this.model.elementID + "-ensemble-simulation") Ensemble Simulation + li.dropdown-item(id=this.model.elementID + "-parameter-sweep") Parameter Sweep + li.dropdown-item + + a.btn(id=this.model.elementID + "-jupyter-notebook" data-hook=this.model.elementID + "-jupyter-notebook" style="padding: 0;") Jupyter Notebook + + div.col-md-1 + + button.btn.btn-outline-secondary.box-shadow(data-hook=this.model.elementID + "-remove") + + div.ml-4.my-3.pl-2 + + div + + ul.nav.nav-tabs + + li.nav-item + + a.nav-link.tab.active(data-toggle="tab" href="#" + this.model.elementID + "-workflows-tab") Workflows + + li.nav-item + + a.nav-link.tab(data-toggle="tab" href="#" + this.model.elementID + "-notes-tab") Notes + + button.btn.btn-outline-collapse(data-toggle="collapse" data-target="#" + this.model.elementID + "-tab-container" data-hook=this.model.elementID + "-tab-btn") - + + div.card.card-body.tab-content.collapse.show(id=this.model.elementID + "-tab-container") + + div.tab-pane.active(id=this.model.elementID + "-workflows-tab") + + div(id=this.model.elementID + "-workflow-listing" data-hook=this.model.elementID + "-workflow-listing") + + div.tab-pane(id=this.model.elementID + "-notes-tab") + + div + + textarea(id=this.model.elementID + "-annotation" data-hook=this.model.elementID + "-annotation" rows="7" style="width: 100%;")=this.model.model.annotation diff --git a/client/templates/includes/workflowGroupViewer.pug b/client/templates/includes/workflowGroupViewer.pug deleted file mode 100644 index cd0cdc6a0b..0000000000 --- a/client/templates/includes/workflowGroupViewer.pug +++ /dev/null @@ -1,10 +0,0 @@ -div.card.card-body - - div - - h3.inline=this.model.name - button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-workflow-group"+this.model.name data-hook="collapse-workflow-group") + - - div.collapse(id="collapse-workflow-group"+this.model.name) - - div(data-hook="workflows-viewer-container") \ No newline at end of file diff --git a/client/templates/includes/workflowGroupsViewer.pug b/client/templates/includes/workflowGroupsViewer.pug deleted file mode 100644 index cd3f50d613..0000000000 --- a/client/templates/includes/workflowGroupsViewer.pug +++ /dev/null @@ -1,10 +0,0 @@ -div#workflow-groups-viewer.card.card-body - - div - - h3.inline Workflow Groups - button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-workflow-groups", id="collapse-workflow-groups-btn" data-hook="collapse-workflow-groups") + - - div.collapse(id="collapse-workflow-groups") - - div(id="workflow-group-container" data-hook="workflow-group-container") \ No newline at end of file diff --git a/client/templates/includes/workflowInfo.pug b/client/templates/includes/workflowInfo.pug index 735289461b..97132b0ddf 100644 --- a/client/templates/includes/workflowInfo.pug +++ b/client/templates/includes/workflowInfo.pug @@ -3,9 +3,10 @@ div#workflow-info-view.card.card-body div h3.inline Info - button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-info", data-hook="collapse", disabled) + - div.collapse(id="collapse-info", data-hook="workflow-info") + button.btn.btn-outline-collapse(data-toggle="collapse" data-target="#collapse-info" data-hook="collapse-info") + + + div.collapse(id="collapse-info" data-hook="workflow-info") div.collapse(data-hook="workflow-statistics") diff --git a/client/templates/includes/workflowListing.pug b/client/templates/includes/workflowListing.pug new file mode 100644 index 0000000000..f364e78d7b --- /dev/null +++ b/client/templates/includes/workflowListing.pug @@ -0,0 +1,43 @@ +div + + div.ml-1.row + + div.col-md-5 + + a.btn.btn-outline-secondary.box-shadow.text-break(href=this.model.open style="width: 100%" role="button")=this.model.name + + div.col-md-4 + + div(data-hook=this.model.elementID + "-type")="Type: " + this.model.type + + if(this.model.status) + + div(data-hook=this.model.elementID + "-status")="Status: " + this.model.status + + div.col-md-2 + + button.btn.btn-outline-secondary.btn-sm.box-shadow(data-hook=this.model.elementID + "-notes-btn") Edit Notes + + div.col-md-1 + + button.btn.btn-outline-secondary.box-shadow(data-hook=this.model.elementID + "-remove") + + div.mx-5.mt-2.collapse(data-hook=this.model.elementID + "-notes-container") + + div.col-md-2.inline.align-top + + div.inline + + h5 Notes: + + div.inline + + button.btn.btn-outline-collapse(data-toggle="collapse" data-target="#" + this.model.elementID + "-annotation-container" data-hook=this.model.elementID + "-annotation-btn") + + + div.collapse.col-md-10.inline(id=this.model.elementID + "-annotation-container") + + div + + textarea(id=this.model.elementID + "-annotation" data-hook=this.model.elementID + "-annotation" rows="7" style="width: 100%;")=this.model.annotation + + hr(data-hook=this.model.elementID + "-divider") \ No newline at end of file diff --git a/client/templates/includes/workflowStateButtons.pug b/client/templates/includes/workflowStateButtons.pug deleted file mode 100644 index a905c48ec4..0000000000 --- a/client/templates/includes/workflowStateButtons.pug +++ /dev/null @@ -1,21 +0,0 @@ -div.mdl-edit-btn - - button.btn.btn-primary.box-shadow(data-hook="save") Save - - div.mdl-edit-btn.saving-status(data-hook="saving-workflow") - - div.spinner-grow - - span Saving... - - div.mdl-edit-btn.saved-status(data-hook="saved-workflow") - - span Saved - - div.mdl-edit-btn.save-error-status(data-hook="save-error") - - span Error Saving Model - - button.btn.btn-primary.box-shadow(data-hook="start-workflow") Start Workflow - - button.btn.btn-primary.box-shadow(data-hook="edit-model") Edit Model \ No newline at end of file diff --git a/client/templates/includes/workflowStatus.pug b/client/templates/includes/workflowStatus.pug index 4e0de7bf3b..77b44100a6 100644 --- a/client/templates/includes/workflowStatus.pug +++ b/client/templates/includes/workflowStatus.pug @@ -4,30 +4,23 @@ div#workflow-status.card.card-body h3.inline Status - button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-status", data-hook="collapse", disabled) + + button.btn.btn-outline-collapse(data-toggle="collapse" data-target="#collapse-status" data-hook="collapse") - - div.collapse(id="collapse-status", data-hook="workflow-status") + div.collapse.show(id="collapse-status" data-hook="workflow-status") table.table thead tr - th(scope="col") Date th(scope="col") Status tbody tr - - td: div=this.startTime + td + div=this.model.fmtStartTime + td div - div.inline=this.status + div.inline=this.model.status div.inline.spinner-border.status(data-hook="running-spinner") - div(style="display: none;") - - button.btn.btn-outline-primary.box-shadow(data-hook="stop-workflow", type="button", disabled) - | Stop Workflow - - button.btn.btn-outline-primary.box-shadow(data-hook="restart-workflow", type="button", disabled) - | Restart Workflow \ No newline at end of file diff --git a/client/templates/includes/workflowViewer.pug b/client/templates/includes/workflowViewer.pug deleted file mode 100644 index ca65d5d864..0000000000 --- a/client/templates/includes/workflowViewer.pug +++ /dev/null @@ -1,10 +0,0 @@ -div.card.card-body - - div - - h3.inline=this.model.name - button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-workflow"+this.model.name data-hook="collapse-workflow") + - - div.collapse(id="collapse-workflow"+this.model.name) - - div(data-hook="workflow-plots") \ No newline at end of file diff --git a/client/templates/includes/workflowsViewer.pug b/client/templates/includes/workflowsViewer.pug deleted file mode 100644 index 336994a46b..0000000000 --- a/client/templates/includes/workflowsViewer.pug +++ /dev/null @@ -1,10 +0,0 @@ -div.card.card-body - - div - - h3.inline Workflows - button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-workflows"+this.collection.parent.name data-hook="collapse-workflows") + - - div.collapse(id="collapse-workflows"+this.collection.parent.name) - - div(data-hook="workflow-container") \ No newline at end of file diff --git a/client/templates/pages/domainEditor.pug b/client/templates/pages/domainEditor.pug index 69185df463..b300cb47a1 100644 --- a/client/templates/pages/domainEditor.pug +++ b/client/templates/pages/domainEditor.pug @@ -38,6 +38,7 @@ section.page table.table thead tr + th(scope="col") Static Domain th(scope="col") Density th(scope="col") Gravity th(scope="col") @@ -54,6 +55,7 @@ section.page tbody tr + td: input(type="checkbox", id="static-domain", data-hook="static-domain") td: div(data-hook="density") td div(data-target="gravity" data-hook="gravity-x") @@ -179,107 +181,117 @@ section.page div.tab-pane(id="set-particle-types" data-hook="set-particle-types") - div.my-3 + div.card.card-body - div.text-info(data-hook="type-location-message" style="display: none") - | There are multiple type files with that name, please select a location + div.my-3 - div.inline.mr-3 + div.text-info(data-hook="type-location-message" style="display: none") + | There are multiple type files with that name, please select a location - span.inline.mr-2(for="types-file-select") Select type description file: + div.inline.mr-3 - div.inline(id="types-file-select" data-hook="types-file-select") + span.inline.mr-2(for="types-file-select") Select type description file: - div.inline(data-hook="type-location-container" style="display: none") + div.inline(id="types-file-select" data-hook="types-file-select") - span.inlinemr-2(for="types-file-location-select") Location: + div.inline(data-hook="type-location-container" style="display: none") - div.inline(id="types-file-location-select" data-hook="types-file-location-select") + span.inlinemr-2(for="types-file-location-select") Location: - div.inline + div.inline(id="types-file-location-select" data-hook="types-file-location-select") - button.btn.btn-outline-primary.box-shadow(data-hook="set-particle-types-btn" disabled) Set Types + div.inline - div.mdl-edit-btn.saving-status.inline(data-hook="st-in-progress") + button.btn.btn-outline-primary.box-shadow(data-hook="set-particle-types-btn" disabled) Set Types - div.spinner-grow.mr-2 + div.mdl-edit-btn.saving-status.inline(data-hook="st-in-progress") - span(data-hook="st-action-in-progress") + div.spinner-grow.mr-2 - div.mdl-edit-btn.saved-status.inline(data-hook="st-complete") + span(data-hook="st-action-in-progress") - span(data-hook="st-action-complete") + div.mdl-edit-btn.saved-status.inline(data-hook="st-complete") - div.mdl-edit-btn.save-error-status(data-hook="st-error") + span(data-hook="st-action-complete") - span(data-hook="st-action-error") + div.mdl-edit-btn.save-error-status(data-hook="st-error") + + span(data-hook="st-action-error") div.tab-pane(id="import-particles") - div.my-3 + div.card.card-body + + div.my-3 + + span.inline.mr-2(for="meshfile") Please specify a mesh to import: + + input(id="meshfile" type="file" name="meshfile" size="30" accept=".xml" required) - span.inline.mr-2(for="meshfile") Please specify a mesh to import: + div.mb-3 - input(id="meshfile" type="file" name="meshfile" size="30" accept=".xml" required) + span.inline.mr-2(for=typefile) Type descriptions (optional): - div + input(id="typefile" type="file" name="typefile" size="30" accept=".txt") - h4.inline Advanced + div - button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#mesh-advanced", data-hook="collapse-mesh-advanced") + + h4.inline Advanced - div.collapse(id="mesh-advanced" data-hook="mesh-advanced-container") + button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#mesh-advanced", data-hook="collapse-mesh-advanced") + - div(data-hook="mesh-type-select") + div.collapse(id="mesh-advanced" data-hook="mesh-advanced-container") - h5 Type Defaults + div(data-hook="mesh-type-select") - table.table - thead - tr - th(scope="col") Mass - th(scope="col") Volume - th(scope="col") Viscosity - th(scope="col") Fixed + h5 Type Defaults - tbody - tr - td: div(data-hook="mesh-mass") - td: div(data-hook="mesh-volume") - td: div(data-hook="mesh-nu") - td: input(type="checkbox" data-hook="mesh-fixed" disabled) + table.table + thead + tr + th(scope="col") Mass + th(scope="col") Volume + th(scope="col") Viscosity + th(scope="col") Fixed - h5 Particle Transformations + tbody + tr + td: div(data-hook="mesh-mass") + td: div(data-hook="mesh-volume") + td: div(data-hook="mesh-nu") + td: input(type="checkbox" data-hook="mesh-fixed" disabled) - table.table - thead - tr - th(scope="col") X-Axis - th(scope="col") Y-Axis - th(scope="col") Z-Axis - tbody - tr - td: div(data-hook="mesh-x-trans") - td: div(data-hook="mesh-y-trans") - td: div(data-hook="mesh-z-trans") + h5 Particle Transformations - div.inline + table.table + thead + tr + th(scope="col") X-Axis + th(scope="col") Y-Axis + th(scope="col") Z-Axis + tbody + tr + td: div(data-hook="mesh-x-trans") + td: div(data-hook="mesh-y-trans") + td: div(data-hook="mesh-z-trans") - button.btn.btn-outline-primary.box-shadow(data-hook="import-particles-btn" disabled) Import Mesh + div.inline - div.mdl-edit-btn.saving-status.inline(data-hook="im-in-progress") + button.btn.btn-outline-primary.box-shadow(data-hook="import-particles-btn" disabled) Import Mesh - div.spinner-grow.mr-2 + div.mdl-edit-btn.saving-status.inline(data-hook="im-in-progress") - span(data-hook="im-action-in-progress") + div.spinner-grow.mr-2 - div.mdl-edit-btn.saved-status.inline(data-hook="im-complete") + span(data-hook="im-action-in-progress") - span(data-hook="im-action-complete") + div.mdl-edit-btn.saved-status.inline(data-hook="im-complete") - div.mdl-edit-btn.save-error-status(data-hook="im-error") + span(data-hook="im-action-complete") - span(data-hook="im-action-error") + div.mdl-edit-btn.save-error-status(data-hook="im-error") + + span(data-hook="im-action-error") div.card.card-body @@ -287,9 +299,9 @@ section.page h3.inline Domain - button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#domain-plot", data-hook="collapse-domain-plot") - + button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#domain-plot-container", data-hook="collapse-domain-plot") - - div.collapse.show(id="domain-plot" data-hook="domain-plot-container") + div.collapse.show(id="domain-plot-container" data-hook="domain-plot-container") div(id="domain-plot" data-hook="domain-plot" style="height: 800px") @@ -307,6 +319,10 @@ section.page li.dropdown-item(data-hook="save-to-model") to Model li.dropdown-item(data-hook="save-to-file") to File (.domn) + a.btn.btn-primary.box-shadow.text-break(role="button" data-hook="return-to-project") Return to Project + + a.btn.btn-primary.box-shadow.text-break(role="button" data-hook="return-to-model") Return to Model + div.mdl-edit-btn.saving-status.inline(data-hook="sd-in-progress") div.spinner-grow.mr-2 diff --git a/client/templates/pages/fileBrowser.pug b/client/templates/pages/fileBrowser.pug index 6446a44c6e..ea87593238 100644 --- a/client/templates/pages/fileBrowser.pug +++ b/client/templates/pages/fileBrowser.pug @@ -35,4 +35,6 @@ section.page button.btn.btn-primary.box-shadow(id="options-for-node" data-hook="options-for-node" disabled) Actions - button.btn.btn-primary.inline.box-shadow(id="refresh-jstree" data-hook="refresh-jstree") Refresh \ No newline at end of file + button.btn.btn-primary.inline.box-shadow(id="refresh-jstree" data-hook="refresh-jstree") Refresh + + button.btn.btn-primary.inline.box-shadow(id="empty-trash" data-hook="empty-trash") Empty Trash \ No newline at end of file diff --git a/client/templates/pages/home.pug b/client/templates/pages/home.pug index 36f584d211..49b2d48185 100644 --- a/client/templates/pages/home.pug +++ b/client/templates/pages/home.pug @@ -30,13 +30,13 @@ html li Convert Between Stochastic and ODE Models li Import SBML Models li Parameter Sweep Workflows - + li Spatial Simulations + div.col-md-5 h5 Coming soon... ul.home-list li Sciope Integration - li Spatial Simulations li Bring Your Own Cloud div.centered diff --git a/client/templates/pages/loadingPage.pug b/client/templates/pages/loadingPage.pug new file mode 100644 index 0000000000..d7f4133a1b --- /dev/null +++ b/client/templates/pages/loadingPage.pug @@ -0,0 +1,13 @@ +section.page + + div.verticle-space-3 + + h1.centered(data-hook="loading-header") Loading Page Header + + h3.centered(data-hook="loading-target") Loading Page Target + + div.spinner-border(data-hook="loading-spinner") + + div.centered.mt-5 + + p(data-hook="loading-message") Loading Page Message \ No newline at end of file diff --git a/client/templates/pages/multiplePlots.pug b/client/templates/pages/multiplePlots.pug new file mode 100644 index 0000000000..ce59115284 --- /dev/null +++ b/client/templates/pages/multiplePlots.pug @@ -0,0 +1,11 @@ +section.page + + h3="Workflow: "+this.workflow + + h4="Job: "+this.job + + div.card.card-body + + h5 Plot Trajectories: Multiple Graphs + + div(data-hook="figures") \ No newline at end of file diff --git a/client/templates/pages/projectManager.pug b/client/templates/pages/projectManager.pug index 6e65f87e28..6481baa211 100644 --- a/client/templates/pages/projectManager.pug +++ b/client/templates/pages/projectManager.pug @@ -2,81 +2,113 @@ section.page div.verticle-space - h2.inline(id="page-title" data-hook="page-title")= "Project: "+this.projectName + h2.inline(id="page-title" data-hook="page-title")= "Project: " div.no-gutters-padding - if !this.annotation + div(id=this.model.elementID+"-annotation-section") + div.verticle-space-2 - button.btn.btn-outline-secondary.btn-sm.box-shadow(data-hook="edit-annotation-btn") Edit Notes - else - div - button.btn.btn-outline-secondary.btn-sm.box-shadow(data-hook="edit-annotation-btn") Edit Notes + button.btn.btn-outline-secondary.btn-sm.box-shadow(data-hook="edit-annotation-btn") Add Notes + + div.mx-3.mt-2.collapse.verticle-space-2(data-hook="collapse-annotation-container") - div.mx-3.mt-2.collapse.verticle-space-2(data-hook="collapse-annotation-container") + div.col-md-2.inline.align-top - div.col-md-1.inline.align-top + div.row - div.row + div + h5="Notes: " - div: h5="Notes: " + div + button.btn.btn-outline-collapse(data-toggle="collapse" data-target="#annotation-text" data-hook="collapse-annotation-text") + - div: button.btn.btn-outline-collapse(data-toggle="collapse" data-target="#annotation-text" data-hook="collapse-annotation-text") - + div.collapse.col-md-10.inline(id="annotation-text") - div.collapse.show.col-md-11.inline(id="annotation-text") + div + textarea(id="annotation" data-hook="annotation-text-container" rows="7" style="width: 100%;") - div: textarea(id="annotation" data-hook="annotation-text-container" rows="7" style="width: 100%;") - - div(id="edit-models-container" data-hook="edit-models-container") + div.verticle-space-3(id=this.model.elementID + "-models-section") - div.verticle-space-3 - - button.btn.btn-outline-primary.inline.dropdown-toggle.box-shadow( - id="project-manager-add-model-btn", - data-hook="add-element-btn", - data-toggle="dropdown", - aria-haspopup="true", - aria-expanded="false", - type="button" - ) Add Model + div - ul.dropdown-menu(aria-labelledby="project-manager-add-model-btn") - li.dropdown-item(id="new-model" data-hook="new-model" data-type="model") New Model - li.dropdown-item(id="new-model" data-hook="new-model" data-type="spatial") New Spatial Model (beta) - li.dropdown-divider - li.dropdown-item(id="existing-model" data-hook="existing-model") Existing Model - li.dropdown-divider - li.dropdown-item(id="upload-file-btn" data-hook="upload-file-btn", data-type="model") Upload StochSS Model (.mdl or .smdl) + h3.inline Models - div.verticle-space(id="edit-workflow-groups-container" data-hook="edit-workflow-groups-container") + div.mx-1.row.head - div.verticle-space-3(style="display: none;") + div.mt-3(id=this.model.elementID + "-models-list" data-hook="model-listing") - button.btn.btn-outline-primary.inline.box-shadow(id="new-workflow-group-btn" data-hook="new-workflow-group") Add New Workflow Group + div - div(style="display: none;") + button.btn.btn-outline-primary.inline.dropdown-toggle.box-shadow( + id="project-manager-add-model-btn", + data-hook="add-element-btn", + data-toggle="dropdown", + aria-haspopup="true", + aria-expanded="false", + type="button" + ) Add Model + + ul.dropdown-menu(aria-labelledby="project-manager-add-model-btn") + li.dropdown-item(id="new-model" data-hook="new-model" data-type="model") New Model + li.dropdown-item(id="new-model" data-hook="new-model" data-type="spatial") New Spatial Model (beta) + li.dropdown-divider + li.dropdown-item(id="existing-model" data-hook="existing-model") Existing Model + li.dropdown-divider + li.dropdown-item(id="upload-file-btn" data-hook="upload-file-btn", data-type="model") Upload StochSS Model (.mdl or .smdl) + + div.verticle-space-3(id=this.model.elementID + "-workflows-section" style="display: none;") div - h3.inline Most Recent Plot + h3.inline Workflows + + div.mx-1.row.head - button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#project-most-recent-plot-container", data-hook="collapse-most-recent-plot-btn") - + div.mt-3(id=this.model.elementID + "-workflows-list" data-hook="workflow-listing") - div.collapse.show(id="project-most-recent-plot-container") + div - div(id="project-most-recent-plot" data-hook="project-most-recent-plot") + button.btn.btn-outline-primary.inline.dropdown-toggle.box-shadow( + id=this.model.elementID + "-workflow-btn", + data-hook=this.model.elementID + "-workflow-btn", + data-toggle="dropdown", + aria-haspopup="true", + aria-expanded="false", + type="button" + ) Add New Workflow - div(id="project-viewer" data-hook="project-viewer" style="display: none;") + ul.dropdown-menu(aria-labelledby=this.model.elementID + "-workflow-btn") + li.dropdown-item(id="new-ensemble-simulation" data-hook="new-ensemble-simulation" data-type="Ensemble Simulation") Ensemble Simulation + li.dropdown-item(id="new-parameter-sweep" data-hook="new-parameter-sweep" data-type="Parameter Sweep") Parameter Sweep + li.dropdown-item(id="new-jupyter-notebook" data-hook="new-jupyter-notebook" data-type="Jupyter Notebook") Jupyter Notebook - div.card.card-body + div.card.card-body(id=this.model.elementID + "-advanced-section") div h3.inline Advanced - button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#project-manager-advanced", data-hook="project-manager-advanced-btn") + + + button.btn.btn-outline-collapse(data-toggle="collapse" data-target="#project-manager-advanced" data-hook="project-manager-advanced-btn") + div.collapse(id="project-manager-advanced" data-hook="project-manager-advanced") + div.card.card-body(id=this.model.elementID + "-archive-section" style="display: none;") + + div + + h3.inline Archived Workflows + + button.btn.btn-outline-collapse(data-toggle="collapse" data-target="#" + this.model.elementID + "-archive-container" data-hook="archive-btn") + + + div.collapse(id=this.model.elementID + "-archive-container") + + div.mt-1.mb-3.head + + div(id=this.model.elementID + "-archive-list" data-hook="archive-listing") + + div(id="project-meta-data-container" data-hook="project-meta-data-container") + div(id="project-manager-file-browser" data-hook="file-browser") div @@ -96,5 +128,3 @@ section.page button.btn.btn-primary.inline.box-shadow(id="empty-project-trash" data-hook="empty-project-trash") Empty Trash - div.collapse(id="project-meta-data-container" data-hook="project-meta-data-container") - \ No newline at end of file diff --git a/client/templates/pages/workflowManager.pug b/client/templates/pages/workflowManager.pug index 675a191040..b4f85bdb30 100644 --- a/client/templates/pages/workflowManager.pug +++ b/client/templates/pages/workflowManager.pug @@ -2,7 +2,7 @@ section.page div - h2.inline(data-hook="page-title")= "Workflow: "+this.titleType + h2.inline(id="page-title") button.big-tip.btn.information-btn.help(data-hook="edit-workflow-help") @@ -14,32 +14,64 @@ section.page a.active-link(data-hook="project-breadcrumb") li.breadcrumb-item.active(aria-current="page" data-hook="workflow-breadcrumb") - div(data-hook="load-wkfl-error" style="display: none;") + div.card.card-body(data-hook="src-model" style="display: none;") - h4(data-hook="reason") + h3 Model - p(data-hook="message") + div - p(data-hook="traceback") + div.text-warning + | The model used for this workflow could not be found, you will need to select the model to be run by this workflow - div(data-hook="workflow-name") + div.text-info(id="model-location-info" style="display: none;") + | This model was found in multiple locations - div.invalid-feedback.wkfl-name(id="workflowNameSpecialCharError") Names can only include the following characters: (0-9), (a-z), (A-Z) and (., -, _, (, or )) + div.inline(data-hook="model-file") - div(data-hook="model-path") + div.inline(data-hook="model-location") - div.invalid-feedback.mdl-path(id="modelPathSpecialCharError") Names can only include the following characters: (0-9), (a-z), (A-Z) and (., -, _, (, or )) + button.btn.btn-outline-primary.box-shadow(data-hook="save-model") Update Model - div(data-hook="workflow-editor-container") + div(data-hook="settings-container") - div(data-hook="workflow-status-container") + div(data-hook="status-container") + + div.card.card-body(data-hook="jobs-container" style="display: none;") + + div + + h3.inline Jobs + + button.btn.btn-outline-collapse(data-toggle="collapse" data-target="#job-listing-container" data-hook="collapse-jobs") - + + div.collapse.show(id="job-listing-container") + + hr + + div.row + + div.col-md-3: h6 Job + div.col-md-4: h6 Start Time + div.col-md-3: h6 Status + div.col-md-2: h6 Remove + + div.mb-3.head + + div(data-hook="job-listing") + + div.mt-4(data-hook="active-job-header-container" style="display: none") + + h2(data-hook="active-job-header") Job: div(data-hook="workflow-results-container") div(data-hook="workflow-info-container") + div(data-hook="settings-viewer-container") + div(data-hook="model-viewer-container") div(data-hook="computational-resources-container") button.btn.btn-primary.box-shadow(data-hook="return-to-project-btn" style="display: none;") Return to Project + diff --git a/client/templates/pages/workflowSelection.pug b/client/templates/pages/workflowSelection.pug index d87424781e..5316f86ec1 100644 --- a/client/templates/pages/workflowSelection.pug +++ b/client/templates/pages/workflowSelection.pug @@ -1,6 +1,6 @@ section.page - h3="Workflow Selection for " + this.modelFile + h3(data-hook="wkfl-selection-header") div(data-hook="workflow-selection-breadcrumb-links" style="display: none") h5 @@ -18,35 +18,25 @@ section.page table.table thead tr - th(scope="col" colspan="4") StochSS Workflows + th(scope="col" colspan="3") Jupyter Notebook Workflows tbody tr td - button.btn.btn-outline-primary.box-shadow.inline(id="stochss-es" data-hook="stochss-es") Ensemble Simulation - - div.tooltip-icon.horizontal-space(data-html="true" data-toggle="tooltip" title=this.tooltips.ensembleSimulation) - + button.btn.btn-outline-primary.box-shadow(id="ensemble-simulation" data-hook="ensemble-simulation" data-type="gillespy") + | Ensemble Simulation td - button.btn.btn-outline-primary.box-shadow.inline(id="stochss-ps" data-hook="stochss-ps") Parameter Sweep - - div.tooltip-icon.horizontal-space(data-html="true" data-toggle="tooltip" title=this.tooltips.parameterSweep) - - table.table - thead - tr - th(scope="col" colspan="4") Jupyter Notebook Workflows - tbody - tr - td: button.btn.btn-outline-primary.box-shadow(id="ensemble-simulation" data-hook="ensemble-simulation" data-type="gillespy") - | Ensemble Simulation - td: button.btn.btn-outline-primary.box-shadow(id="spatial-simulation" data-hook="spatial-simulation" data-type="spatial") - | Spatial Ensemble Simulation - td: button.btn.btn-outline-primary.box-shadow(id="oned-parameter-sweep" data-hook="oned-parameter-sweep" data-type="1d_parameter_sweep") - | 1D Parameter Sweep + button.btn.btn-outline-primary.box-shadow(id="spatial-simulation" data-hook="spatial-simulation" data-type="spatial") + | Spatial Ensemble Simulation + td + button.btn.btn-outline-primary.box-shadow(id="oned-parameter-sweep" data-hook="oned-parameter-sweep" data-type="1d_parameter_sweep") + | 1D Parameter Sweep tr - td: button.btn.btn-outline-primary.box-shadow(id="twod-parameter-sweep" data-hook="twod-parameter-sweep" data-type="2d_parameter_sweep") - | 2D Parameter Sweep - td: button.btn.btn-outline-primary.box-shadow(id="sciope-model-exploration" data-hook="sciope-model-exploration" data-type="sciope_model_exploration") - | Sciope Model Exploration - td: button.btn.btn-outline-primary.box-shadow(id="model-inference" data-hook="model-inference" data-type="model_inference") - | Sciope Model Inference + td + button.btn.btn-outline-primary.box-shadow(id="twod-parameter-sweep" data-hook="twod-parameter-sweep" data-type="2d_parameter_sweep") + | 2D Parameter Sweep + td + button.btn.btn-outline-primary.box-shadow(id="sciope-model-exploration" data-hook="sciope-model-exploration" data-type="sciope_model_exploration") + | Sciope Model Exploration + td + button.btn.btn-outline-primary.box-shadow(id="model-inference" data-hook="model-inference" data-type="model_inference") + | Sciope Model Inference diff --git a/client/views/archive-listing.js b/client/views/archive-listing.js new file mode 100644 index 0000000000..e5bb93c18b --- /dev/null +++ b/client/views/archive-listing.js @@ -0,0 +1,82 @@ +/* +StochSS is a platform for simulating biochemical systems +Copyright (C) 2019-2020 StochSS developers. + +This program is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with this program. If not, see . +*/ + +let $ = require('jquery'); +let path = require('path'); +//support files +let app = require('../app'); +let modals = require('../modals'); +//views +let View = require('ampersand-view'); +let WorkflowListing = require("./workflow-listing"); +//templates +let template = require('../templates/includes/archiveListing.pug'); + +module.exports = View.extend({ + template: template, + events: function () { + let events = {}; + events['click [data-hook=' + this.model.elementID + '-remove'] = 'handleTrashModelClick'; + events['click [data-hook=' + this.model.elementID + '-tab-btn'] = 'changeCollapseButtonText'; + return events; + }, + initialize: function (attrs, options) { + View.prototype.initialize.apply(this, arguments); + }, + render: function (attrs, options) { + View.prototype.render.apply(this, arguments); + this.renderWorkflowCollection(); + }, + changeCollapseButtonText: function (e) { + app.changeCollapseButtonText(this, e); + }, + handleTrashModelClick: function () { + if(document.querySelector('#moveToTrashConfirmModal')) { + document.querySelector('#moveToTrashConfirmModal').remove(); + } + let self = this; + let modal = $(modals.moveToTrashConfirmHtml("Archive")).modal(); + let yesBtn = document.querySelector('#moveToTrashConfirmModal .yes-modal-btn'); + yesBtn.addEventListener('click', function (e) { + modal.modal('hide'); + let file = self.model.name + ".wkgp"; + let projectPath = self.parent.model.directory; + let trashPath = path.join(projectPath, "trash", file); + let queryString = "?srcPath=" + path.join(projectPath, file) + "&dstPath=" + trashPath; + let endpoint = path.join(app.getApiPath(), 'file/move') + queryString; + app.getXHR(endpoint, { + success: function (err, response, body) { + self.parent.update("WorkflowGroup"); + } + }); + }); + }, + renderWorkflowCollection: function () { + if(this.workflowCollectionView){ + this.workflowCollectionView.remove(); + } + this.workflowCollectionView = this.renderCollection( + this.model.workflows, + WorkflowListing, + this.queryByHook(this.model.elementID + "-workflow-listing") + ); + }, + update: function (target) { + this.parent.update(target); + } +}); diff --git a/client/views/creator-listing.js b/client/views/creator-listing.js index b46fd6bfb4..847f8f1b92 100644 --- a/client/views/creator-listing.js +++ b/client/views/creator-listing.js @@ -17,9 +17,9 @@ along with this program. If not, see . */ //views -var View = require('ampersand-view'); +let View = require('ampersand-view'); //templates -var template = require('../templates/includes/creatorList.pug'); +let template = require('../templates/includes/creatorListing.pug'); module.exports = View.extend({ template: template, @@ -33,6 +33,8 @@ module.exports = View.extend({ View.prototype.render.apply(this, arguments); }, removeCreator: function (e) { - this.model.collection.remove(this.model) + let index = this.parent.metadata.creators.indexOf(this.model.elementID); + this.parent.metadata.creators.splice(index, 1); + this.parent.renderCreatorListingView(); } }); \ No newline at end of file diff --git a/client/views/domain-viewer.js b/client/views/domain-viewer.js index 9e19b3a614..edaff605a7 100644 --- a/client/views/domain-viewer.js +++ b/client/views/domain-viewer.js @@ -16,7 +16,6 @@ You should have received a copy of the GNU General Public License along with this program. If not, see . */ -var xhr = require('xhr'); var $ = require('jquery'); let path = require('path'); var _ = require('underscore'); @@ -113,31 +112,31 @@ module.exports = View.extend({ } this.parent.renderParticleViewer(null); let endpoint = path.join(app.getApiPath(), "spatial-model/domain-plot") + queryStr; - xhr({uri: endpoint, json: true}, function (err, resp, body) { - self.plot = body.fig; - self.displayDomain(); + app.getXHR(endpoint, { + always: function (err, response, body) { + self.plot = body.fig; + self.displayDomain(); + } }); this.toggleDomainError(); }, - registerRenderSubview: function (view, hook) { - this.registerSubview(view); - this.renderSubview(view, this.queryByHook(hook)); - }, renderDomainSelectView: function () { let self = this; let endpoint = path.join(app.getApiPath(), "spatial-model/domain-list"); - xhr({uri: endpoint, json:true}, function (err, resp, body) { - self.externalDomains = body.paths; - var domainSelectView = new SelectView({ - label: '', - name: 'domains', - required: false, - idAttributes: 'cid', - options: body.files, - unselectedText: "-- Select Domain --", - value: self.getDomainSelectValue(body.files) - }); - self.registerRenderSubview(domainSelectView, "select-domain") + app.getXHR(endpoint, { + always: function (err, response, body) { + self.externalDomains = body.paths; + var domainSelectView = new SelectView({ + label: '', + name: 'domains', + required: false, + idAttributes: 'cid', + options: body.files, + unselectedText: "-- Select Domain --", + value: self.getDomainSelectValue(body.files) + }); + app.registerRenderSubview(self, domainSelectView, "select-domain") + } }); }, getDomainSelectValue: function (files) { @@ -162,7 +161,7 @@ module.exports = View.extend({ options: options, unselectedText: "-- Select Location --" }); - this.registerRenderSubview(this.domainLocationSelectView, "select-location") + app.registerRenderSubview(this, this.domainLocationSelectView, "select-location") }, renderTypesViewer: function () { if(this.typesViewer) { @@ -215,12 +214,6 @@ module.exports = View.extend({ } }, changeCollapseButtonText: function (e) { - let source = e.target.dataset.hook - let collapseContainer = $(this.queryByHook(source).dataset.target) - if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) { - let collapseBtn = $(this.queryByHook(source)) - let text = collapseBtn.text(); - text === '+' ? collapseBtn.text('-') : collapseBtn.text('+'); - } + app.changeCollapseButtonText(this, e); } }); \ No newline at end of file diff --git a/client/views/edit-3D-domain.js b/client/views/edit-3D-domain.js index fa60a6dab5..5513d14991 100644 --- a/client/views/edit-3D-domain.js +++ b/client/views/edit-3D-domain.js @@ -16,7 +16,6 @@ You should have received a copy of the GNU General Public License along with this program. If not, see . */ -var xhr = require('xhr'); var $ = require('jquery'); var path = require('path'); //support files @@ -49,34 +48,35 @@ module.exports = View.extend({ } let self = this; let endpoint = path.join(app.getApiPath(), "spatial-model/3d-domain"); - xhr({uri: endpoint, json: true, method: "post", body: this.data}, function (err, resp, body) { - if(resp.statusCode < 400) { + app.postXHR(endpoint, this.data, { + success: function (err, response, body) { self.parent.addParticles(body.particles); if(self.parent.domain.x_lim[0] > body.limits.x_lim[0]) { - self.parent.domain.x_lim[0] = body.limits.x_lim[0] + self.parent.domain.x_lim[0] = body.limits.x_lim[0]; } if(self.parent.domain.y_lim[0] > body.limits.y_lim[0]) { - self.parent.domain.y_lim[0] = body.limits.y_lim[0] + self.parent.domain.y_lim[0] = body.limits.y_lim[0]; } if(self.parent.domain.z_lim[0] > body.limits.z_lim[0]) { - self.parent.domain.z_lim[0] = body.limits.z_lim[0] + self.parent.domain.z_lim[0] = body.limits.z_lim[0]; } if(self.parent.domain.x_lim[1] < body.limits.x_lim[1]) { - self.parent.domain.x_lim[1] = body.limits.x_lim[1] + self.parent.domain.x_lim[1] = body.limits.x_lim[1]; } if(self.parent.domain.y_lim[1] < body.limits.y_lim[1]) { - self.parent.domain.y_lim[1] = body.limits.y_lim[1] + self.parent.domain.y_lim[1] = body.limits.y_lim[1]; } if(self.parent.domain.z_lim[1] < body.limits.z_lim[1]) { - self.parent.domain.z_lim[1] = body.limits.z_lim[1] + self.parent.domain.z_lim[1] = body.limits.z_lim[1]; } self.parent.renderDomainLimitations(); - self.completeAction("Domain successfully created") + self.completeAction("Domain successfully created"); $('html, body').animate({ scrollTop: $("#domain-plot").offset().top }, 20); - }else{ - self.errorAction(body.Message) + }, + error: function (err, response, body) { + self.errorAction(body.Message); } }); }, @@ -99,10 +99,6 @@ module.exports = View.extend({ "yLim":[0, 0], "zLim":[0, 0], "type":0, "volume":1, "transformation": null} }, - registerRenderSubview: function (view, hook) { - this.registerSubview(view); - return this.renderSubview(view, this.queryByHook(hook)); - }, render: function (attrs, options) { View.prototype.render.apply(this, arguments); this.renderNumberOfParticles(); @@ -116,7 +112,6 @@ module.exports = View.extend({ $(this.queryByHook("cd-in-progress")).css("display", "none"); $(this.queryByHook("cd-action-complete")).text(action); $(this.queryByHook("cd-complete")).css("display", "inline-block"); - console.log(action) let self = this setTimeout(function () { $(self.queryByHook("cd-complete")).css("display", "none"); @@ -132,58 +127,58 @@ module.exports = View.extend({ let xtrans = new InputView({parent: this, required: true, name: 'x-transformation', valueType: 'number', value: 0}); - this.registerRenderSubview(xtrans, "domain-x-trans"); + app.registerRenderSubview(this, xtrans, "domain-x-trans"); let ytrans = new InputView({parent: this, required: true, name: 'y-transformation', valueType: 'number', value: 0}); - this.registerRenderSubview(ytrans, "domain-y-trans"); + app.registerRenderSubview(this, ytrans, "domain-y-trans"); let ztrans = new InputView({parent: this, required: true, name: 'z-transformation', valueType: 'number', value: 0}); - this.registerRenderSubview(ztrans, "domain-z-trans"); + app.registerRenderSubview(this, ztrans, "domain-z-trans"); }, renderNumberOfParticles: function () { let nxView = new InputView({parent: this, required: true, name: 'nx', valueType: 'number', tests: tests.valueTests, value: this.data.nx}); - this.registerRenderSubview(nxView, "nx"); + app.registerRenderSubview(this, nxView, "nx"); let nyView = new InputView({parent: this, required: true, name: 'ny', valueType: 'number', tests: tests.valueTests, value: this.data.ny}); - this.registerRenderSubview(nyView, "ny"); + app.registerRenderSubview(this, nyView, "ny"); let nzView = new InputView({parent: this, required: true, name: 'nz', valueType: 'number', tests: tests.valueTests, value: this.data.nz}); - this.registerRenderSubview(nzView, "nz"); + app.registerRenderSubview(this, nzView, "nz"); }, renderParticleLimits: function () { let xLimMinView = new InputView({parent: this, required: true, name: 'x-lim-min', valueType: 'number', value: this.data.xLim[0]}); - this.registerRenderSubview(xLimMinView, "xLim-min"); + app.registerRenderSubview(this, xLimMinView, "xLim-min"); let yLimMinView = new InputView({parent: this, required: true, name: 'y-lim-min', valueType: 'number', value: this.data.yLim[0]}); - this.registerRenderSubview(yLimMinView, "yLim-min"); + app.registerRenderSubview(this, yLimMinView, "yLim-min"); let zLimMinView = new InputView({parent: this, required: true, name: 'z-lim-min', valueType: 'number', value: this.data.zLim[0]}); - this.registerRenderSubview(zLimMinView, "zLim-min"); + app.registerRenderSubview(this, zLimMinView, "zLim-min"); let xLimMaxView = new InputView({parent: this, required: true, name: 'x-lim-max', valueType: 'number', value: this.data.xLim[1]}); - this.registerRenderSubview(xLimMaxView, "xLim-max"); + app.registerRenderSubview(this, xLimMaxView, "xLim-max"); let yLimMaxView = new InputView({parent: this, required: true, name: 'y-lim-max', valueType: 'number', value: this.data.yLim[1]}); - this.registerRenderSubview(yLimMaxView, "yLim-max"); + app.registerRenderSubview(this, yLimMaxView, "yLim-max"); let zLimMaxView = new InputView({parent: this, required: true, name: 'z-lim-max', valueType: 'number', value: this.data.zLim[1]}); - this.registerRenderSubview(zLimMaxView, "zLim-max"); + app.registerRenderSubview(this, zLimMaxView, "zLim-max"); }, renderType: function () { var typeView = new SelectView({ @@ -196,7 +191,7 @@ module.exports = View.extend({ options: this.model.types, value: this.type }); - this.registerRenderSubview(typeView, "type-select") + app.registerRenderSubview(this, typeView, "type-select") }, renderTypeDefaults: function () { $(this.queryByHook("mass")).text(this.type.mass) @@ -208,7 +203,6 @@ module.exports = View.extend({ $(this.queryByHook("cd-complete")).css("display", "none"); $(this.queryByHook("cd-action-in-progress")).text(action); $(this.queryByHook("cd-in-progress")).css("display", "inline-block"); - console.log(action) }, update: function (e) {}, updateTotalParticles: function (e) { diff --git a/client/views/edit-advanced-specie.js b/client/views/edit-advanced-specie.js index 911a8d1664..33c6ac446a 100644 --- a/client/views/edit-advanced-specie.js +++ b/client/views/edit-advanced-specie.js @@ -16,8 +16,10 @@ You should have received a copy of the GNU General Public License along with this program. If not, see . */ -var tests = require('./tests'); var $ = require('jquery'); +//support files +let app = require('../app'); +var tests = require('./tests'); //views var View = require('ampersand-view'); var SelectView = require('ampersand-select-view'); @@ -46,7 +48,7 @@ module.exports = View.extend({ options: ['Concentration','Population','Hybrid Concentration/Population'], value: optionDict[this.model.mode], }); - this.registerRenderSubview(modeSelectView, "specie-mode") + app.registerRenderSubview(this, modeSelectView, "specie-mode") if(this.model.isSwitchTol){ $(this.queryByHook('switching-tol')).prop('checked', true); }else{ @@ -59,10 +61,6 @@ module.exports = View.extend({ }, updateValid: function () { }, - registerRenderSubview: function (view, hook) { - this.registerSubview(view); - this.renderSubview(view, this.queryByHook(hook)); - }, setSpeciesMode: function (e) { var value = e.target.selectedOptions.item(0).text var modeDict = {"Concentration":"continuous","Population":"discrete","Hybrid Concentration/Population":"dynamic"} diff --git a/client/views/edit-domain-type.js b/client/views/edit-domain-type.js index 41636da621..20bba307e3 100644 --- a/client/views/edit-domain-type.js +++ b/client/views/edit-domain-type.js @@ -16,6 +16,8 @@ You should have received a copy of the GNU General Public License along with this program. If not, see . */ +//support files +let app = require('../app'); //views var View = require('ampersand-view'); var InputView = require('./input'); @@ -67,11 +69,7 @@ module.exports = View.extend({ let nameView = new InputView({parent: this, required: true, name: 'name', valueType: 'string', value: this.model.name}); - this.registerRenderSubview(nameView, "type-" + this.model.typeID); - }, - registerRenderSubview: function (view, hook) { - this.registerSubview(view); - return this.renderSubview(view, this.queryByHook(hook)); + app.registerRenderSubview(this, nameView, "type-" + this.model.typeID); }, update: function () {}, updateValid: function () {} diff --git a/client/views/edit-event-assignment.js b/client/views/edit-event-assignment.js index d8122af303..72c4b268d3 100644 --- a/client/views/edit-event-assignment.js +++ b/client/views/edit-event-assignment.js @@ -17,6 +17,8 @@ along with this program. If not, see . */ var $ = require('jquery'); +//support files +let app = require('../app'); //views var View = require('ampersand-view'); var InputView = require('./input'); @@ -44,7 +46,7 @@ module.exports = View.extend({ options: options, value: this.model.variable.name, }); - this.registerRenderSubview(variableSelectView, 'event-assignment-variable'); + app.registerRenderSubview(this, variableSelectView, 'event-assignment-variable'); var inputField = this.queryByHook('event-assignment-Expression').children[0].children[1]; $(inputField).attr("placeholder", "---No Expression Entered---"); }, @@ -64,10 +66,6 @@ module.exports = View.extend({ var parameterNames = parameters.map(function (parameter) { return parameter.name }); return speciesNames.concat(parameterNames); }, - registerRenderSubview: function (view, hook) { - this.registerSubview(view); - this.renderSubview(view, this.queryByHook(hook)); - }, selectAssignmentVariable: function (e) { var species = this.model.collection.parent.collection.parent.species; var parameters = this.model.collection.parent.collection.parent.parameters; diff --git a/client/views/edit-initial-condition.js b/client/views/edit-initial-condition.js index c00bbc4a00..11089e5efc 100644 --- a/client/views/edit-initial-condition.js +++ b/client/views/edit-initial-condition.js @@ -17,6 +17,8 @@ along with this program. If not, see . */ let $ = require('jquery'); +//support files +let app = require('../app'); var tests = require('./tests'); //views var View = require('ampersand-view'); @@ -61,18 +63,14 @@ module.exports = View.extend({ // Else fetch the right Parameter from Parameters based on existing rate value: this.model.specie.name ? this.getSpecieFromSpecies(this.model.specie.name) : this.model.collection.parent.species.at(0), }); - this.registerRenderSubview(typeSelectView, 'initial-condition-type'); - this.registerRenderSubview(speciesSelectView, 'initial-condition-species'); + app.registerRenderSubview(this, typeSelectView, 'initial-condition-type'); + app.registerRenderSubview(this, speciesSelectView, 'initial-condition-species'); this.renderDetailsView(); }, update: function () { }, updateValid: function () { }, - registerRenderSubview: function (view, hook) { - this.registerSubview(view); - this.renderSubview(view, this.queryByHook(hook)); - }, renderDetailsView: function () { if(this.model.icType === "Place") { $(this.queryByHook("scatter-details")).css("display", "none") @@ -95,19 +93,19 @@ module.exports = View.extend({ modelKey: "x", label: 'x: ', tests: tests.valueTests, value: this.model.x}); - this.registerRenderSubview(this.xCoord, "x-container"); + app.registerRenderSubview(this, this.xCoord, "x-container"); this.yCoord = new InputView({parent: this, required: true, name: 'Y', valueType: 'number', modelKey: "y", label: 'y: ', tests: tests.valueTests, value: this.model.y}); - this.registerRenderSubview(this.yCoord, "y-container"); + app.registerRenderSubview(this, this.yCoord, "y-container"); this.zCoord = new InputView({parent: this, required: true, name: 'Z', valueType: 'number', modelKey: "z", label: 'z: ', tests: tests.valueTests, value: this.model.z}); - this.registerRenderSubview(this.zCoord, "z-container"); + app.registerRenderSubview(this, this.zCoord, "z-container"); }, renderTypes: function () { if(this.typesView) { diff --git a/client/views/edit-model-view.js b/client/views/edit-model-view.js deleted file mode 100644 index f79988227f..0000000000 --- a/client/views/edit-model-view.js +++ /dev/null @@ -1,140 +0,0 @@ -/* -StochSS is a platform for simulating biochemical systems -Copyright (C) 2019-2020 StochSS developers. - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . -*/ - -var $ = require('jquery'); -var _ = require('underscore'); -var xhr = require('xhr'); -var path = require('path'); -//support files -var app = require('../app'); -var modals = require('../modals'); -//views -var View = require('ampersand-view'); -//templates -var template = require('../templates/includes/editModelView.pug'); - -module.exports = View.extend({ - template: template, - events: { - 'click [data-hook=project-model-edit]' : 'handleEditModelClick', - 'click [data-hook=new-workflow-btn]' : 'handleNewWorkflowClick', - 'click [data-hook=edit-model-annotation-btn]' : 'handleEditAnnotationClick', - 'click [data-hook=project-model-remove]' : 'handleRemoveModelClick', - 'click [data-hook=collapse-annotation-text]' : 'changeCollapseButtonText', - 'change [data-hook=annotation]' : 'updateAnnotation' - }, - initialize: function (attrs, options) { - View.prototype.initialize.apply(this, arguments); - this.workflowGroupOptions = this.model.collection.parent.workflowGroups.map(function (wg) { - return wg.name - }) - }, - render: function (attrs, options) { - View.prototype.render.apply(this, arguments); - if(!this.model.annotation){ - $(this.queryByHook('edit-model-annotation-btn')).text('Add Notes') - }else{ - $(this.queryByHook('collapse-annotation-container'+this.model.name.replace(/ /g,""))).collapse('show') - } - }, - handleEditModelClick: function (e) { - let queryString = "?path="+this.model.directory - window.location.href = path.join(app.getBasePath(), "stochss/models/edit")+queryString - }, - handleNewWorkflowClick: function (e) { - let wkgpNames = this.model.collection.parent.workflowGroups.map(function (model) { - return model.name - }) - if(this.model.collection.parent.workflowGroups.length <= 0 || !wkgpNames.includes("WorkflowGroup1")) { - this.addNewWorkflowGroup(_.bind(this.openWorkflowManager, this)) - }else{ - let wkgpFile = "WorkflowGroup1.wkgp" - this.openWorkflowManager(wkgpFile) - } - }, - addNewWorkflowGroup: function (cb) { - let self = this - let workflowGroupName = "WorkflowGroup1.wkgp" - let workflowGroupPath = path.join(this.parent.parent.projectPath, workflowGroupName) - let endpoint = path.join(app.getApiPath(), "project/new-workflow-group")+"?path="+workflowGroupPath - xhr({uri: endpoint,json: true}, function (err, response, body) { - if(response.statusCode < 400) { - if(cb) { - cb(workflowGroupName) - }else{ - self.update("workflow-group") - } - }else{ - let errorModel = $(modals.newProjectOrWorkflowGroupErrorHtml(body.Reason, body.Message)).modal() - } - }); - }, - openWorkflowManager: function (wkgpFile) { - let parentPath = path.join(path.dirname(this.model.directory), wkgpFile) - let queryString = "?path="+this.model.directory+"&parentPath="+parentPath - let endpoint = path.join(app.getBasePath(), 'stochss/workflow/selection')+queryString - window.location.href = endpoint - }, - handleRemoveModelClick: function (e) { - let self = this - if(document.querySelector('#moveToTrashConfirmModal')) { - document.querySelector('#moveToTrashConfirmModal').remove(); - } - let modal = $(modals.moveToTrashConfirmHtml("model")).modal(); - let yesBtn = document.querySelector('#moveToTrashConfirmModal .yes-modal-btn'); - yesBtn.addEventListener('click', function (e) { - let trashPath = path.join(path.dirname(self.model.directory), "trash", self.model.directory.split('/').pop()) - let queryString = "?srcPath="+self.model.directory+"&dstPath="+trashPath - let endpoint = path.join(app.getApiPath(), 'file/move')+queryString - xhr({uri: endpoint, json: true}, function (err, response, body) { - if(response.statusCode < 400) { - self.parent.parent.update("model-editor") - } - }); - modal.modal('hide') - }); - }, - handleEditAnnotationClick: function (e) { - let buttonTxt = e.target.innerText; - if(buttonTxt.startsWith("Add")){ - $(this.queryByHook('collapse-annotation-container'+this.model.name.replace(/ /g,""))).collapse('show') - $(this.queryByHook('edit-model-annotation-btn')).text('Edit Notes') - }else if(!$("#annotation-text"+this.model.name.replace(/ /g,"")).attr('class').includes('show')){ - $("#annotation-text"+this.model.name.replace(/ /g,"")).collapse('show') - $(this.queryByHook("collapse-annotation-text")).text('-') - } - document.querySelector("#annotation"+this.model.name.replace(/ /g,"")).focus() - }, - updateAnnotation: function (e) { - this.model.annotation = e.target.value.trim(); - if(this.model.annotation === "") { - $(this.queryByHook('collapse-annotation-container'+this.model.name.replace(/ /g,""))).collapse('hide') - $(this.queryByHook('edit-model-annotation-btn')).text('Add Notes') - } - this.model.saveModel() - }, - changeCollapseButtonText: function (e) { - let source = e.target.dataset.hook - let collapseContainer = $(this.queryByHook(source).dataset.target) - if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) { - let collapseBtn = $(this.queryByHook(source)) - let text = collapseBtn.text(); - text === '+' ? collapseBtn.text('-') : collapseBtn.text('+'); - } - } -}); \ No newline at end of file diff --git a/client/views/edit-models-view.js b/client/views/edit-models-view.js deleted file mode 100644 index 3d4543b771..0000000000 --- a/client/views/edit-models-view.js +++ /dev/null @@ -1,48 +0,0 @@ -/* -StochSS is a platform for simulating biochemical systems -Copyright (C) 2019-2020 StochSS developers. - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . -*/ - -let $ = require('jquery'); -//views -var View = require('ampersand-view'); -var EditModelView = require('./edit-model-view'); -//templates -var template = require('../templates/includes/editModelsView.pug'); - -module.exports = View.extend({ - template: template, - events: {}, - initialize: function (attrs, options) { - View.prototype.initialize.apply(this, arguments) - }, - render: function (attrs, arguments) { - View.prototype.render.apply(this, arguments) - this.renderEditModelview() - }, - renderEditModelview: function () { - if(this.editModelView) { - this.editModelView.remove() - } - this.editModelView = this.renderCollection(this.collection, EditModelView, this.queryByHook("project-models-list")) - $(document).ready(function () { - $('[data-toggle="tooltip"]').tooltip(); - $('[data-toggle="tooltip"]').click(function () { - $('[data-toggle="tooltip"]').tooltip("hide"); - }); - }); - } -}); \ No newline at end of file diff --git a/client/views/edit-parameter.js b/client/views/edit-parameter.js index ff96685435..e8b342f24c 100644 --- a/client/views/edit-parameter.js +++ b/client/views/edit-parameter.js @@ -17,6 +17,7 @@ along with this program. If not, see . */ var $ = require('jquery'); +let _ = require('underscore'); //support files var tests = require('./tests'); var modals = require('../modals') @@ -24,10 +25,10 @@ var modals = require('../modals') var View = require('ampersand-view'); var InputView = require('./input'); //templates -var template = require('../templates/includes/editReactionVar.pug'); +var editTemplate = require('../templates/includes/editParameter.pug'); +let viewTemplate = require('../templates/includes/viewParameters.pug'); module.exports = View.extend({ - template: template, bindings: { 'model.inUse': { hook: 'remove', @@ -43,9 +44,14 @@ module.exports = View.extend({ initialize: function (attrs, options) { View.prototype.initialize.apply(this, arguments); this.previousName = this.model.name + this.viewMode = attrs.viewMode ? attrs.viewMode : false; }, render: function () { + this.template = this.viewMode ? viewTemplate : editTemplate; View.prototype.render.apply(this, arguments); + if(!this.viewMode){ + this.model.on('change', _.bind(this.updateViewer, this)) + } $(document).on('shown.bs.modal', function (e) { $('[autofocus]', e.target).focus(); }); @@ -96,6 +102,9 @@ module.exports = View.extend({ this.model.collection.trigger('remove') } }, + updateViewer: function () { + this.parent.renderViewParameter() + }, subviews: { inputName: { hook: 'input-name-container', diff --git a/client/views/edit-particle.js b/client/views/edit-particle.js index 9b9091d291..099e0a099a 100644 --- a/client/views/edit-particle.js +++ b/client/views/edit-particle.js @@ -19,6 +19,7 @@ along with this program. If not, see . var $ = require('jquery'); var _ = require('underscore'); //support files +let app = require('../app'); var tests = require('../views/tests'); //views var View = require('ampersand-view'); @@ -130,10 +131,6 @@ module.exports = View.extend({ $(this.queryByHook("save-particle")).prop('disabled', true); $(this.queryByHook("remove-particle")).prop('disabled', true); }, - registerRenderSubview: function (view, hook) { - this.registerSubview(view); - return this.renderSubview(view, this.queryByHook(hook)); - }, render: function (attrs, options) { View.prototype.render.apply(this, arguments); this.type = this.parent.domain.types.get(this.model.type, "typeID"); @@ -154,15 +151,15 @@ module.exports = View.extend({ var xCoord = new InputView({parent: this, required: true, name: 'x-coord', valueType: 'number', value: this.model.point[0] || 0}); - this.registerRenderSubview(xCoord, "x-coord-" + this.viewIndex); + app.registerRenderSubview(this, xCoord, "x-coord-" + this.viewIndex); var yCoord = new InputView({parent: this, required: true, name: 'y-coord', valueType: 'number', value: this.model.point[1] || 0}); - this.registerRenderSubview(yCoord, "y-coord-" + this.viewIndex); + app.registerRenderSubview(this, yCoord, "y-coord-" + this.viewIndex); var zCoord = new InputView({parent: this, required: true, name: 'z-coord', valueType: 'number', value: this.model.point[2] || 0}); - this.registerRenderSubview(zCoord, "z-coord-" + this.viewIndex); + app.registerRenderSubview(this, zCoord, "z-coord-" + this.viewIndex); }, renderProperties: function () { if(this.massView) { @@ -177,15 +174,15 @@ module.exports = View.extend({ this.massView = new InputView({parent: this, required: true, name: 'mass', valueType: 'number', value: this.model.mass || this.type.mass}); - this.registerRenderSubview(this.massView, "mass-" + this.viewIndex); + app.registerRenderSubview(this, this.massView, "mass-" + this.viewIndex); this.volView = new InputView({parent: this, required: true, name: 'volume', valueType: 'number', value: this.model.volume || this.type.volume}); - this.registerRenderSubview(this.volView, "volume-" + this.viewIndex); + app.registerRenderSubview(this, this.volView, "volume-" + this.viewIndex); this.nuView = new InputView({parent: this, required: true, name: 'viscosity', valueType: 'number', value: this.model.nu || this.type.nu}); - this.registerRenderSubview(this.nuView, "nu-" + this.viewIndex); + app.registerRenderSubview(this, this.nuView, "nu-" + this.viewIndex); let fixed = this.model.fixed || this.type.fixed; $(this.queryByHook("fixed-" + this.viewIndex)).prop("checked", fixed); }, @@ -200,7 +197,7 @@ module.exports = View.extend({ options: this.parent.domain.types, value: this.parent.domain.types.get(this.model.type, "typeID") }); - this.registerRenderSubview(typeView, "type-" + this.viewIndex) + app.registerRenderSubview(this, typeView, "type-" + this.viewIndex) }, startAction: function (action) { $(this.queryByHook("ep-complete")).css("display", "none"); diff --git a/client/views/edit-project.js b/client/views/edit-project.js index ad12151381..042dddc754 100644 --- a/client/views/edit-project.js +++ b/client/views/edit-project.js @@ -17,7 +17,6 @@ along with this program. If not, see . */ let $ = require('jquery'); -let xhr = require('xhr'); let path = require('path'); //support files let app = require('../app'); @@ -30,46 +29,33 @@ let template = require('../templates/includes/editProject.pug'); module.exports = View.extend({ template: template, events: { - 'click [data-hook=open-project-btn]' : 'handleOpenProjectClick', - 'click [data-hook=remove-project-btn]' : 'handleRemoveProjectClick' + 'click [data-hook=remove-project-btn]' : 'handleMoveToTrash' }, initialize: function (attrs, options) { View.prototype.initialize.apply(this, arguments); - this.projectName = this.model.directory.split('/').pop().split('.')[0] - this.location = this.getLocationString(this.model.directory) }, render: function (attrs, options) { View.prototype.render.apply(this, arguments); }, - getLocationString: function (projectPath) { - let parent = path.dirname(projectPath) - if(parent === '.') { - return '' + handleMoveToTrash: function (e) { + if(document.querySelector('#moveToTrashConfirmModal')) { + document.querySelector('#moveToTrashConfirmModal').remove(); } - return 'Location: '+parent - }, - handleOpenProjectClick: function (e) { - window.location.href = path.join(app.getBasePath(), "stochss/project/manager")+"?path="+this.model.directory - }, - handleRemoveProjectClick: function (e) { - console.log("deleting the project") - let endpoint = path.join(app.getApiPath(), "file/delete")+"?path="+this.model.directory - var self = this - if(document.querySelector('#deleteFileModal')) { - document.querySelector('#deleteFileModal').remove() - } - let modal = $(modals.deleteFileHtml("project")).modal(); - let yesBtn = document.querySelector('#deleteFileModal .yes-modal-btn'); + let self = this; + let modal = $(modals.moveToTrashConfirmHtml("model")).modal(); + let yesBtn = document.querySelector('#moveToTrashConfirmModal .yes-modal-btn'); yesBtn.addEventListener('click', function (e) { - xhr({uri: endpoint}, function(err, response, body) { - if(response.statusCode < 400) { - self.model.collection.remove(self.model) - console.log(body) - }else{ - body = JSON.parse(body) + modal.modal('hide'); + let queryStr = "?srcPath=" + self.model.directory + "&dstPath=" + path.join("trash", self.model.directory.split("/").pop()); + let endpoint = path.join(app.getApiPath(), "file/move") + queryStr + app.getXHR(endpoint, { + success: function (err, response, body) { + self.model.collection.remove(self.model); + }, + error: function (err, response, body) { + body = JSON.parse(body); } - }) - modal.modal('hide') + }); }); } }); \ No newline at end of file diff --git a/client/views/edit-rule.js b/client/views/edit-rule.js index c458c7d12e..9c54a25471 100644 --- a/client/views/edit-rule.js +++ b/client/views/edit-rule.js @@ -18,6 +18,7 @@ along with this program. If not, see . var $ = require('jquery'); //support files +let app = require('../app'); var tests = require('./tests'); var modals = require('../modals'); //views @@ -60,8 +61,8 @@ module.exports = View.extend({ options: varOptions, value: this.model.variable.name, }); - this.registerRenderSubview(typeSelectView, "rule-type"); - this.registerRenderSubview(variableSelectView, 'rule-variable'); + app.registerRenderSubview(this, typeSelectView, "rule-type"); + app.registerRenderSubview(this, variableSelectView, 'rule-variable'); $(document).on('shown.bs.modal', function (e) { $('[autofocus]', e.target).focus(); }); @@ -105,10 +106,6 @@ module.exports = View.extend({ var parameterNames = parameters.map(function (parameter) { return parameter.name }); return speciesNames.concat(parameterNames); }, - registerRenderSubview: function (view, hook) { - this.registerSubview(view); - this.renderSubview(view, this.queryByHook(hook)); - }, selectRuleType: function (e) { var type = e.target.selectedOptions.item(0).text; this.model.type = type; diff --git a/client/views/edit-specie.js b/client/views/edit-specie.js index b920f7c952..1408a6a67e 100644 --- a/client/views/edit-specie.js +++ b/client/views/edit-specie.js @@ -43,6 +43,9 @@ module.exports = View.extend({ initialize: function (attrs, options) { View.prototype.initialize.apply(this, arguments); this.previousName = this.model.name + if(this.model.mode === null && this.model.collection.parent.defaultMode !== "") { + this.model.mode = this.model.collection.parent.defaultMode; + } }, render: function () { View.prototype.render.apply(this, arguments); diff --git a/client/views/edit-workflow-group-view.js b/client/views/edit-workflow-group-view.js deleted file mode 100644 index 4651bfface..0000000000 --- a/client/views/edit-workflow-group-view.js +++ /dev/null @@ -1,91 +0,0 @@ -/* -StochSS is a platform for simulating biochemical systems -Copyright (C) 2019-2020 StochSS developers. - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . -*/ - -var $ = require('jquery'); -var xhr = require('xhr'); -var path = require('path'); -//support files -var app = require('../app'); -var modals = require('../modals'); -//views -var View = require('ampersand-view'); -var EditWorkflowsView = require('./edit-workflows-view'); -//templates -var template = require('../templates/includes/editWorkflowGroupView.pug'); - -module.exports = View.extend({ - template: template, - events: { - 'click [data-hook=project-workflow-group-view]' : 'handleViewWorkflowsClick', - 'click [data-hook=project-workflow-group-remove]' : 'handleRemoveWorkflowGroupClick' - }, - initialize: function (attrs, options) { - View.prototype.initialize.apply(this, arguments); - }, - render: function (attrs, options) { - View.prototype.render.apply(this, arguments); - this.renderEditWorkflowsView(); - if(this.model.collection.length === 1) { - this.handleViewWorkflowsClick(undefined) - $(this.queryByHook("project-workflow-group-remove")).prop('disabled', true) - } - }, - renderEditWorkflowsView: function () { - if(this.editWorkflowsView){ - this.editWorkflowsView.remove() - } - this.editWorkflowsView = new EditWorkflowsView({ - collection: this.model.workflows - }); - this.registerRenderSubview(this.editWorkflowsView, "project-workflows-container") - }, - registerRenderSubview: function (view, hook) { - this.registerSubview(view); - this.renderSubview(view, this.queryByHook(hook)); - }, - handleViewWorkflowsClick: function (e) { - let options = {"+":"show", "-":"hide"} - let newText = {"+":"-", "-":"+"} - let text = $(this.queryByHook("project-workflow-group-view")).text() - $(this.queryByHook("project-workflows-container")).collapse(options[text]) - $(this.queryByHook("project-workflow-group-view")).text(newText[text]) - }, - handleRemoveWorkflowGroupClick: function (e) { - if(this.model.collection.length > 1) { - let self = this - if(document.querySelector('#moveToTrashConfirmModal')) { - document.querySelector('#moveToTrashConfirmModal').remove(); - } - let title = "workflow group and it workflows" - let modal = $(modals.moveToTrashConfirmHtml(title)).modal(); - let yesBtn = document.querySelector('#moveToTrashConfirmModal .yes-modal-btn'); - yesBtn.addEventListener('click', function (e) { - let expPath = path.join(self.parent.parent.projectPath, self.model.name)+".wkgp" - let trashPath = path.join(self.parent.parent.projectPath, "trash", self.model.name + ".wkgp") - let queryString = "?srcPath="+expPath+"&dstPath="+trashPath - let endpoint = path.join(app.getApiPath(), 'file/move')+queryString - xhr({uri: endpoint, json: true}, function (err, response, body) { - if(response.statusCode < 400) { - self.parent.parent.update("workflow-group-editor") - } - }); - modal.modal('hide') - }); - } - }, -}); \ No newline at end of file diff --git a/client/views/edit-workflow-view.js b/client/views/edit-workflow-view.js deleted file mode 100644 index ffe317a78c..0000000000 --- a/client/views/edit-workflow-view.js +++ /dev/null @@ -1,129 +0,0 @@ -/* -StochSS is a platform for simulating biochemical systems -Copyright (C) 2019-2020 StochSS developers. - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . -*/ - -var $ = require('jquery'); -var _ = require('underscore'); -var xhr = require('xhr'); -var path = require('path'); -//support files -var app = require('../app'); -var modals = require('../modals'); -//views -var View = require('ampersand-view'); -//templates -var template = require('../templates/includes/editWorkflowView.pug'); - -module.exports = View.extend({ - template: template, - events: { - 'click [data-hook=project-workflow-open]' : 'handleOpenWorkflowClick', - 'click [data-hook=edit-workflow-annotation-btn]' : 'handleEditAnnotationClick', - 'click [data-hook=project-workflow-remove]' : 'handleDeleteWorkflowClick', - 'click [data-hook=collapse-annotation-text]' : 'changeCollapseButtonText', - 'change [data-hook=annotation]' : 'updateAnnotation' - }, - initialize: function (attrs, options) { - View.prototype.initialize.apply(this, arguments); - }, - render: function (attrs, options) { - View.prototype.render.apply(this, arguments); - if(this.model.status === "running"){ - this.getStatus() - } - if(this.model.path.endsWith('.ipynb')) { - this.queryByHook('annotation-container').style.display = "none" - } - if(!this.model.annotation || !this.model.annotation.trim()){ - $(this.queryByHook('edit-workflow-annotation-btn')).text('Add Notes') - }else{ - $(this.queryByHook('collapse-annotation-container'+this.model.name.replace(/ /g,""))).collapse('show') - } - }, - getStatus: function () { - var self = this; - var endpoint = path.join(app.getApiPath(), "workflow/workflow-status")+"?path="+this.model.path; - xhr({uri: endpoint}, function (err, response, body) { - if(self.model.status !== body ) - self.model.status = body; - if(self.model.status === 'running') - setTimeout(_.bind(self.getStatus, self), 1000); - else{ - $(self.queryByHook("project-workflow-status")).text(self.model.status) - } - }); - }, - handleOpenWorkflowClick: function (e) { - if(this.model.path.endsWith('.ipynb')) { - window.open(path.join(app.getBasePath(), "notebooks", this.model.path)) - }else{ - let endpoint = path.join(app.getBasePath(), "stochss/workflow/edit")+"?path="+this.model.path+"&type=none"; - window.location.href = endpoint - } - }, - handleDeleteWorkflowClick: function (e) { - let self = this - if(document.querySelector('#moveToTrashConfirmModal')) { - document.querySelector('#moveToTrashConfirmModal').remove(); - } - let modal = $(modals.moveToTrashConfirmHtml("workflow")).modal(); - let yesBtn = document.querySelector('#moveToTrashConfirmModal .yes-modal-btn'); - yesBtn.addEventListener('click', function (e) { - let file = self.model.path.split('/').pop() - let trashPath = path.join(path.dirname(path.dirname(self.model.path)), "trash", file) - let queryString = "?srcPath="+self.model.path+"&dstPath="+trashPath - let endpoint = path.join(app.getApiPath(), 'file/move')+queryString - xhr({uri: endpoint, json: true}, function (err, response, body) { - if(response.statusCode < 400) { - self.parent.parent.parent.parent.update("workflows-editor") - } - }); - modal.modal('hide') - }); - }, - handleEditAnnotationClick: function (e) { - let buttonTxt = e.target.innerText; - if(buttonTxt.startsWith("Add")){ - $(this.queryByHook('collapse-annotation-container'+this.model.name.replace(/ /g,""))).collapse('show') - $(this.queryByHook('edit-workflow-annotation-btn')).text('Edit Notes') - }else if(!$("#annotation-text"+this.model.name.replace(/ /g,"")).attr('class').includes('show')){ - $("#annotation-text"+this.model.name.replace(/ /g,"")).collapse('show') - $(this.queryByHook("collapse-annotation-text")).text('-') - } - document.querySelector("#annotation"+this.model.name.replace(/ /g,"")).focus() - }, - updateAnnotation: function (e) { - this.model.annotation = e.target.value.trim(); - if(this.model.annotation === "") { - $(this.queryByHook('collapse-annotation-container'+this.model.name.replace(/ /g,""))).collapse('hide') - $(this.queryByHook('edit-workflow-annotation-btn')).text('Add Notes') - } - let queryString = "?path="+path.join(this.model.path, "info.json") - let endpoint = path.join(app.getApiPath(), "workflow/save-annotation")+queryString - let body = {'annotation':this.model.annotation} - xhr({uri:endpoint, json:true, method:'post', body:body}, function (err, response, body) {console.log("Saved Notes")}) - }, - changeCollapseButtonText: function (e) { - let source = e.target.dataset.hook - let collapseContainer = $(this.queryByHook(source).dataset.target) - if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) { - let collapseBtn = $(this.queryByHook(source)) - let text = collapseBtn.text(); - text === '+' ? collapseBtn.text('-') : collapseBtn.text('+'); - } - } -}); \ No newline at end of file diff --git a/client/views/edit-workflows-view.js b/client/views/edit-workflows-view.js deleted file mode 100644 index 73743f799d..0000000000 --- a/client/views/edit-workflows-view.js +++ /dev/null @@ -1,96 +0,0 @@ -/* -StochSS is a platform for simulating biochemical systems -Copyright (C) 2019-2020 StochSS developers. - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . -*/ - -var $ = require('jquery'); -var xhr = require('xhr'); -var path = require('path'); -//support files -var app = require('../app'); -var modals = require('../modals'); -//views -var View = require('ampersand-view'); -var EditWorkflowView = require('./edit-workflow-view'); -//templates -var template = require('../templates/includes/editWorkflowsView.pug'); - -module.exports = View.extend({ - template: template, - events: { - 'click [data-hook=project-workflow-group-new-workflow]' : 'handleNewWorkflowClick' - }, - initialize: function (attrs, options) { - View.prototype.initialize.apply(this, arguments) - }, - render: function (attrs, options) { - View.prototype.render.apply(this, arguments) - this.renderEditWorkflowView() - }, - renderEditWorkflowView: function () { - if(this.editWorkflowView) { - this.editWorkflowView.remove() - } - this.editWorkflowView = this.renderCollection(this.collection, EditWorkflowView, this.queryByHook("project-workflows-list")) - $(document).ready(function () { - $('[data-toggle="tooltip"]').tooltip(); - $('[data-toggle="tooltip"]').click(function () { - $('[data-toggle="tooltip"]').tooltip("hide"); - }); - }); - }, - validateName(input) { - var error = "" - if(input.endsWith('/')) { - error = 'forward' - } - let invalidChars = "`~!@#$%^&*=+[{]}\"|:;'<,>?\\" - for(var i = 0; i < input.length; i++) { - if(invalidChars.includes(input.charAt(i))) { - error = error === "" || error === "special" ? "special" : "both" - } - } - return error - }, - handleNewWorkflowClick: function (e) { - let models = this.parent.parent.parent.model.models - if(models.length > 0) { - let self = this - if(document.querySelector("#newProjectWorkflowModal")) { - document.querySelector("#newProjectWorkflowModal").remove() - } - let options = models.map(function (model) { return model.name }); - let modal = $(modals.newProjectWorkflowHtml("Name of the model: ", options)).modal() - let okBtn = document.querySelector("#newProjectWorkflowModal .ok-model-btn") - let select = document.querySelector("#newProjectWorkflowModal #select") - okBtn.addEventListener('click', function (e) { - let mdlFile = models.filter(function (model) { - return model.name === select.value; - })[0].directory.split("/").pop(); - let mdlPath = path.join(self.parent.parent.parent.projectPath, mdlFile) - let parentPath = path.join(self.parent.parent.parent.projectPath, self.parent.model.name)+".wkgp" - let queryString = "?path="+mdlPath+"&parentPath="+parentPath - let endpoint = path.join(app.getBasePath(), 'stochss/workflow/selection')+queryString - modal.modal('hide') - window.location.href = endpoint - }); - }else{ - let title = "No Models Found" - let message = "You need to add a model before you can create a new workflow." - let modal = $(modals.noModelsMessageHtml(title, message)).modal() - } - } -}); \ No newline at end of file diff --git a/client/views/event-details.js b/client/views/event-details.js index 0e2307cd98..3d64cdb23d 100644 --- a/client/views/event-details.js +++ b/client/views/event-details.js @@ -17,6 +17,8 @@ along with this program. If not, see . */ var $ = require('jquery'); +//support files +let app = require('../app'); var tests = require('./tests'); //views var View = require('ampersand-view'); @@ -80,11 +82,7 @@ module.exports = View.extend({ this.eventAssignmentsView = new EventAssignment({ collection: this.model.eventAssignments, }); - this.registerRenderSubview(this.eventAssignmentsView, 'event-assignments'); - }, - registerRenderSubview: function (view, hook) { - this.registerSubview(view); - this.renderSubview(view, this.queryByHook(hook)); + app.registerRenderSubview(this, this.eventAssignmentsView, 'event-assignments'); }, openAdvancedSection: function () { if(this.model.advanced_error && !$(this.queryByHook("advanced-event-section")).hasClass('show')) { @@ -103,13 +101,7 @@ module.exports = View.extend({ this.model.useValuesFromTriggerTime = e.target.dataset.name === "trigger"; }, changeCollapseButtonText: function (e) { - let source = e.target.dataset.hook - let collapseContainer = $(this.queryByHook(source).dataset.target) - if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) { - let collapseBtn = $(this.queryByHook(source)) - let text = collapseBtn.text(); - text === '+' ? collapseBtn.text('-') : collapseBtn.text('+'); - } + app.changeCollapseButtonText(this, e); }, subviews: { inputDelay: { diff --git a/client/views/events-editor.js b/client/views/events-editor.js index a62e27c340..73bfbcca24 100644 --- a/client/views/events-editor.js +++ b/client/views/events-editor.js @@ -19,6 +19,7 @@ along with this program. If not, see . var ViewSwitcher = require('ampersand-view-switcher'); var $ = require('jquery'); //support files +let app = require('../app'); var Tooltips = require("../tooltips"); //views var View = require('ampersand-view'); @@ -139,12 +140,6 @@ module.exports = View.extend({ collapseBtn.trigger('click') }, changeCollapseButtonText: function (e) { - let source = e.target.dataset.hook - let collapseContainer = $(this.queryByHook(source).dataset.target) - if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) { - let collapseBtn = $(this.queryByHook(source)) - let text = collapseBtn.text(); - text === '+' ? collapseBtn.text('-') : collapseBtn.text('+'); - } + app.changeCollapseButtonText(this, e); }, }) \ No newline at end of file diff --git a/client/views/events-viewer.js b/client/views/events-viewer.js index c9e3b35611..fd5326b366 100644 --- a/client/views/events-viewer.js +++ b/client/views/events-viewer.js @@ -17,6 +17,8 @@ along with this program. If not, see . */ var $ = require('jquery'); +//support files +let app = require('../app'); //views var View = require('ampersand-view'); var ViewEvent = require('./view-events'); @@ -26,7 +28,7 @@ var template = require('../templates/includes/eventsViewer.pug'); module.exports = View.extend({ template: template, events: { - 'click [data-hook=collapse]' : 'changeSettingsCollapseButtonText', + 'click [data-hook=collapse]' : 'changeCollapseButtonText', 'click [data-hook=edit-events]' : 'switchToEditMode' }, initialize: function (attrs, options) { @@ -46,13 +48,7 @@ module.exports = View.extend({ switchToEditMode: function (e) { this.parent.renderEventsView("edit", true); }, - changeSettingsCollapseButtonText: function (e) { - let source = e.target.dataset.hook - let collapseContainer = $(this.queryByHook(source).dataset.target) - if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) { - let collapseBtn = $(this.queryByHook(source)) - let text = collapseBtn.text(); - text === '+' ? collapseBtn.text('-') : collapseBtn.text('+'); - } + changeCollapseButtonText: function (e) { + app.changeCollapseButtonText(this, e); }, }); \ No newline at end of file diff --git a/client/views/file-browser-view.js b/client/views/file-browser-view.js index 0920897dc2..de8ef0e6d2 100644 --- a/client/views/file-browser-view.js +++ b/client/views/file-browser-view.js @@ -18,7 +18,6 @@ along with this program. If not, see . let jstree = require('jstree'); let path = require('path'); -let xhr = require('xhr'); let $ = require('jquery'); let _ = require('underscore'); //support files @@ -79,72 +78,22 @@ module.exports = View.extend({ }, 5000) return false } - if(op === 'move_node' && node && node.type && node.type === "workflow" && node.original && node.original._status && node.original._status === "running"){ - return false - } - if(op === 'move_node' && more && more.ref && more.ref.original && node && node.type && (node.type === "nonspatial" || node.type === "spatial") && - !(node.original._path.includes("trash") || more.ref.original.text === "trash")) { - return false - } - if(op === 'move_node' && more && more.ref && more.ref.original && node && node.type && node.type === "workflow-group") { - return false - } - if(op === 'move_node' && more && more.ref && more.ref.original && node && node.type && (node.type === "workflow") && - !(node.original._path.includes("trash") || more.ref.original.text === "trash")) { - return false - } - if(op === 'move_node' && more && more.ref && more.ref.type && node.original._path.includes("trash") && - ((node.type === "workflow" && more.ref.type !== 'workflow-group') || - ((node.type === "nonspatial" || node.type === "spatial" || node.type === "workflow-group") && more.ref.type !== 'root'))){ - return false - } - if(op === 'move_node' && more && more.ref && more.ref.type && !(node.type === "workflow" || node.type === "notebook") && !(more.ref.type == 'folder' || more.ref.type == 'root')){ - return false - } - if(op === 'move_node' && more && more.ref && more.ref.type && node.type === "notebook" && !(more.ref.type == 'folder' || more.ref.type == 'root' || more.ref.type == 'workflow-group')) { - return false - } - if(op === 'move_node' && more && more.ref && more.ref.type && node.original._path.includes("trash") && more.ref.original.text == 'trash') { - return false - } - if(op === 'move_node' && more && more.ref && more.ref.type && (more.ref.type === 'folder' || more.ref.type === 'root')){ - if(!more.ref.state.loaded){ - return false - } - var exists = false - var BreakException = {} - var text = node.text - if(!isNaN(text.split(' ').pop().split('.').join(""))){ - text = text.replace(text.split(' ').pop(), '').trim() - } - if(more.ref.text !== "trash"){ - try{ - more.ref.children.forEach(function (child) { - var child_node = $('#models-jstree-view').jstree().get_node(child) - exists = child_node.text === text - if(exists){ - throw BreakException; - } - }) - }catch{ - return false; - } - } - } - if(op === 'move_node' && more && (pos != 0 || more.pos !== "i") && !more.core){ - return false - } if(op === 'move_node' && more && more.core) { var newDir = par.original._path !== "/" ? par.original._path : "" var file = node.original._path.split('/').pop() var oldPath = node.original._path let queryStr = "?srcPath="+oldPath+"&dstPath="+path.join(newDir, file) var endpoint = path.join(app.getApiPath(), "file/move")+queryStr - xhr({uri: endpoint}, function(err, response, body) { - if(response.statusCode < 400) { + app.getXHR(endpoint, { + success: function (err, response, body) { node.original._path = path.join(newDir, file) - self.updateParent(node.type, (oldPath.includes('trash/') || newDir.endsWith('trash'))) - }else{ + if((node.type === "nonspatial" || node.type === "spatial") && (oldPath.includes("trash") || newDir.includes("trash"))) { + self.updateParent("Archive"); + }else if(node.type !== "notebook" || node.original._path.includes(".wkgp") || newDir.includes(".wkgp")) { + self.updateParent(node.type) + } + }, + error: function (err, response, body) { body = JSON.parse(body) if(par.type === 'root'){ $('#models-jstree-view').jstree().refresh() @@ -153,8 +102,61 @@ module.exports = View.extend({ } } }); + }else{ + let isMove = op === 'move_node' + let validSrc = Boolean(node && node.type && node.original && node.original.text !== "trash") + let validDst = Boolean(more && more.ref && more.ref.type && more.ref.original) + let validDsts = ["root", "folder"] + let isModel = Boolean(validSrc && (node.type === "nonspatial" || node.type === "spatial")) + let isWorkflow = Boolean(validSrc && node.type === "workflow") + let isWkgp = Boolean(validSrc && node.type === "workflow-group") + let isNotebook = Boolean(validSrc && node.type === "notebook") + let isOther = Boolean(validSrc && !isModel && !isWorkflow && !isWkgp && !isNotebook) + let trashAction = Boolean((validSrc && node.original._path.includes("trash")) || (validDst && more.ref.original.text === "trash")) + // Check if files are being move directly into the trash and remain static with respect to the trash + if(isMove && validDst && path.dirname(more.ref.original._path).includes("trash")) { return false } + if(isMove && validSrc && validDst && node.original._path.includes("trash") && more.ref.original.text === 'trash') { return false } + // Check if workflow is running + if(isMove && isWorkflow && node.original._status && node.original._status === "running") { return false }; + // Check if model, workflow, or workflow group is moving to or from trash + if(isMove && (isModel || isWorkflow) && !trashAction) { return false }; + if(isMove && isWkgp && !(self.parent.model.newFormat && trashAction)) { return false }; + // Check if model, workflow, or workflow group is moving from trash to the correct location + if(isMove && validSrc && node.original._path.includes("trash")) { + if(isWkgp && (!self.parent.model.newFormat || (validDst && more.ref.type !== "root"))) { return false }; + if(isWorkflow && validDst && more.ref.type !== "workflow-group") { return false }; + if(isModel && validDst) { + if(!self.parent.model.newFormat && more.ref.type !== "root") { return false }; + let length = node.original.text.split(".").length; + let modelName = node.original.text.split(".").slice(0, length - 1).join(".") + if(self.parent.model.newFormat && (more.ref.type !== "workflow-group" || !more.ref.original.text.startsWith(modelName))) { return false }; + } + } + // Check if notebook or other file is moving to a valid location. + if(isOther && validDst && !validDsts.includes(more.ref.type)) { return false }; + validDsts.push("workflow-group") + if(isNotebook && validDst && !validDsts.includes(more.ref.type)) { return false }; + if(isMove && validDst && validDsts.includes(more.ref.type)){ + if(!more.ref.state.loaded) { return false }; + var exists = false + var BreakException = {} + var text = node.text + if(!isNaN(text.split(' ').pop().split('.').join(""))){ + text = text.replace(text.split(' ').pop(), '').trim() + } + if(more.ref.text !== "trash"){ + try{ + more.ref.children.forEach(function (child) { + var child_node = $('#models-jstree-view').jstree().get_node(child) + exists = child_node.text === text + if(exists) { throw BreakException; }; + }) + }catch { return false; }; + } + } + if(isMove && more && (pos != 0 || more.pos !== "i") && !more.core) { return false } + return true } - return true }, 'themes': {'stripes': true, 'variant': 'large'}, 'data': self.ajaxData, @@ -187,12 +189,17 @@ module.exports = View.extend({ } }); }, - updateParent: function (type, trash = false) { - let types = ["nonspatial", "spatial", "workflow", "workflow-group", "notebook"] - if(trash){ - this.parent.update("all") - }else if(types.includes(type)) { - this.parent.update("file-browser") + updateParent: function (type) { + let models = ["nonspatial", "spatial", "sbml", "model"] + let workflows = ["workflow", "notebook"] + if(models.includes(type)) { + this.parent.update("Model") + }else if(workflows.includes(type)) { + this.parent.update("Workflow") + }else if(type === "workflow-group") { + this.parent.update("WorkflowGroup") + }else if(type === "Archive") { + this.parent.update(type); } }, refreshJSTree: function () { @@ -288,7 +295,7 @@ module.exports = View.extend({ }); uploadBtn.addEventListener('click', function (e) { let file = fileInput.files[0] - var fileinfo = {"type":type,"name":"","path":self.parent.projectPath} + var fileinfo = {"type":type,"name":"","path":self.parent.model.directory} if(o && o.original){ fileinfo.path = o.original._path } @@ -322,11 +329,9 @@ module.exports = View.extend({ }, openUploadRequest: function (endpoint, formData, file, type, o) { let self = this - let req = new XMLHttpRequest(); - req.open("POST", endpoint) - req.onload = function (e) { - var resp = JSON.parse(req.response) - if(req.status < 400) { + app.postXHR(endpoint, formData, { + success: function (err, response, body) { + body = JSON.parse(body); if(o){ var node = $('#models-jstree-view').jstree().get_node(o.parent); if(node.type === "root" || node.type === "#"){ @@ -337,17 +342,18 @@ module.exports = View.extend({ }else{ self.refreshJSTree(); } - if(resp.file.endsWith(".mdl") || resp.file.endsWith(".smdl") ||resp.file.endsWith(".sbml")) { - self.parent.update("file-browser") + if(body.file.endsWith(".mdl") || body.file.endsWith(".smdl") ||body.file.endsWith(".sbml")) { + self.updateParent("model") } - if(resp.errors.length > 0){ - let errorModal = $(modals.uploadFileErrorsHtml(file.name, type, resp.message, resp.errors)).modal(); + if(body.errors.length > 0){ + let errorModal = $(modals.uploadFileErrorsHtml(file.name, type, body.message, body.errors)).modal(); } - }else{ - let zipErrorModal = $(modals.projectExportErrorHtml(resp.Reason, resp.Message)).modal() + }, + error: function (err, response, body) { + body = JSON.parse(body); + let zipErrorModal = $(modals.projectExportErrorHtml(body.Reason, body.Message)).modal() } - } - req.send(formData) + }, false); }, deleteFile: function (o) { var fileType = o.type @@ -367,20 +373,20 @@ module.exports = View.extend({ let yesBtn = document.querySelector('#deleteFileModal .yes-modal-btn'); yesBtn.addEventListener('click', function (e) { var endpoint = path.join(app.getApiPath(), "file/delete")+"?path="+o.original._path - xhr({uri: endpoint}, function(err, response, body) { - if(response.statusCode < 400) { + app.getXHR(endpoint, { + success: function (err, response, body) { var node = $('#models-jstree-view').jstree().get_node(o.parent); if(node.type === "root"){ self.refreshJSTree(); }else{ $('#models-jstree-view').jstree().refresh_node(node); } - }else{ - body = JSON.parse(body) } - }) + }); modal.modal('hide') - self.updateParent(o.type) + if(o.type !== "notebook" || o.original._path.includes(".wkgp")) { + self.updateParent(o.type) + } }); }, duplicateFileOrDirectory: function(o, type) { @@ -404,28 +410,25 @@ module.exports = View.extend({ var identifier = "file/duplicate" } var endpoint = path.join(app.getApiPath(), identifier)+queryStr - xhr({uri: endpoint, json: true}, function (err, response, body) { - if(response.statusCode < 400) { - var node = $('#models-jstree-view').jstree().get_node(parentID); - if(node.type === "root" || type === "wkfl_model"){ - self.refreshJSTree() - }else{ - $('#models-jstree-view').jstree().refresh_node(node); - } - if(type === "workflow"){ - var message = "" - if(body.error){ - message = body.error - }else{ - message = "The model for "+body.File+" is located here: "+body.mdlPath+"" - } - let modal = $(modals.duplicateWorkflowHtml(body.File, message)).modal() + app.getXHR(endpoint, { + success: function (err, response, body) { + var node = $('#models-jstree-view').jstree().get_node(parentID); + self.refreshJSTree() + if(type === "workflow"){ + var message = "" + if(body.error){ + message = body.error + }else{ + message = "The model for "+body.File+" is located here: "+body.mdlPath+"" } - self.selectNode(node, body.File) + let modal = $(modals.duplicateWorkflowHtml(body.File, message)).modal() + } + self.selectNode(node, body.File) + if(o.type !== "notebook" || o.original._path.includes(".wkgp")) { self.updateParent(o.type) } } - ); + }); }, getTimeStamp: function () { var date = new Date(); @@ -456,19 +459,14 @@ module.exports = View.extend({ var self = this; var parentID = o.parent; var endpoint = path.join(app.getApiPath(), "model/to-spatial")+"?path="+o.original._path; - xhr({uri: endpoint, json: true}, - function (err, response, body) { - if(response.statusCode < 400) { - var node = $('#models-jstree-view').jstree().get_node(parentID); - if(node.type === "root"){ - self.refreshJSTree() - }else{ - $('#models-jstree-view').jstree().refresh_node(node); - } - self.selectNode(node, body.File) - } + app.getXHR(endpoint, { + success: function (err, response, body) { + var node = $('#models-jstree-view').jstree().get_node(parentID); + self.refreshJSTree() + self.updateParent("spatial") + self.selectNode(node, body.File) } - ); + }); }, toModel: function (o, from) { var self = this; @@ -479,33 +477,27 @@ module.exports = View.extend({ var identifier = "sbml/to-model" } let endpoint = path.join(app.getApiPath(), identifier)+"?path="+o.original._path; - xhr({uri: endpoint, json: true}, function (err, response, body) { - if(response.statusCode < 400) { - var node = $('#models-jstree-view').jstree().get_node(parentID); - if(node.type === "root"){ - self.refreshJSTree() - }else{ - $('#models-jstree-view').jstree().refresh_node(node); - } - self.selectNode(node, body.File) - if(from === "SBML" && body.errors.length > 0){ - var title = "" - var msg = body.message - var errors = body.errors - let modal = $(modals.sbmlToModelHtml(msg, errors)).modal(); - }else{ - console.log(node.type, o.type) - self.updateParent(o.type) - } + app.getXHR(endpoint, { + success: function (err, response, body) { + var node = $('#models-jstree-view').jstree().get_node(parentID); + self.refreshJSTree() + self.selectNode(node, body.File) + if(from === "SBML" && body.errors.length > 0){ + var title = "" + var msg = body.message + var errors = body.errors + let modal = $(modals.sbmlToModelHtml(msg, errors)).modal(); + }else{ + self.updateParent("nonspatial") } } - ); + }); }, toNotebook: function (o, type) { let self = this var endpoint = path.join(app.getApiPath(), "workflow/notebook")+"?type=none&path="+o.original._path - xhr({ uri: endpoint, json: true}, function (err, response, body) { - if(response.statusCode < 400){ + app.getXHR(endpoint, { + success: function (err, response, body) { var node = $('#models-jstree-view').jstree().get_node(o.parent) if(node.type === 'root'){ self.refreshJSTree(); @@ -522,14 +514,10 @@ module.exports = View.extend({ var self = this; var parentID = o.parent; var endpoint = path.join(app.getApiPath(), "model/to-sbml")+"?path="+o.original._path; - xhr({uri: endpoint, json: true}, function (err, response, body) { - if(response.statusCode < 400) { + app.getXHR(endpoint, { + success: function (err, response, body) { var node = $('#models-jstree-view').jstree().get_node(parentID); - if(node.type === "root"){ - self.refreshJSTree() - }else{ - $('#models-jstree-view').jstree().refresh_node(node); - } + self.refreshJSTree() self.selectNode(node, body.File) } }); @@ -543,26 +531,26 @@ module.exports = View.extend({ extensionWarning.collapse('show') $('#models-jstree-view').jstree().edit(o, null, function(node, status) { if(text != node.text){ - var endpoint = path.join(app.getApiPath(), "file/rename")+"?path="+ o.original._path+"&name="+node.text - xhr({uri: endpoint, json: true}, function (err, response, body){ - if(response.statusCode < 400) { - if(body.changed) { - nameWarning.text(body.message) - nameWarning.collapse('show'); - window.scrollTo(0,0) - setTimeout(_.bind(self.hideNameWarning, self), 10000); - } - node.original._path = body._path - } - if(text.split('.').pop() != node.text.split('.').pop()){ + let name = node.type === "root" ? node.text + ".proj" : node.text + var endpoint = path.join(app.getApiPath(), "file/rename")+"?path="+ o.original._path+"&name="+name + app.getXHR(endpoint, { + always: function (err, response, body) { if(parent.type === "root"){ - self.refreshJSTree() + self.refreshJSTree(); }else{ $('#models-jstree-view').jstree().refresh_node(parent); } + }, + success: function (err, response, body) { + if(body.changed) { + nameWarning.text(body.message); + nameWarning.collapse('show'); + window.scrollTo(0,0); + setTimeout(_.bind(self.hideNameWarning, self), 10000); + } + node.original._path = body._path; } - self.updateParent(o.type) - }) + }); } extensionWarning.collapse('hide'); nameWarning.collapse('hide'); @@ -599,10 +587,10 @@ module.exports = View.extend({ } } var endpoint = path.join(app.getApiPath(), identifier)+queryStr - xhr({uri: endpoint, json: isJSON}, function (err, response, body) { - if(response.statusCode < 400) { + app.getXHR(endpoint, { + success: function (err, response, body) { if(dataType === "json") { - let data = nodeType === "domain" ? body.domain : body + let data = nodeType === "domain" ? body.domain : body; self.exportToJsonFile(data, o.original.text); }else if(dataType === "zip") { var node = $('#models-jstree-view').jstree().get_node(o.parent); @@ -611,14 +599,10 @@ module.exports = View.extend({ }else{ $('#models-jstree-view').jstree().refresh_node(node); } - self.exportToZipFile(body.Path) + self.exportToZipFile(body.Path); }else{ self.exportToFile(body, o.original.text); } - }else{ - if(dataType === "plain-text") { - body = JSON.parse(body) - } } }); }, @@ -689,30 +673,31 @@ module.exports = View.extend({ okBtn.addEventListener("click", function (e) { if(Boolean(input.value)) { modal.modal('hide') - var parentPath = self.parent.projectPath + var parentPath = self.parent.model.directory if(o && o.original && o.original._path !== "/") { parentPath = o.original._path } var workflowGroupName = input.value.trim() + ".wkgp" var workflowGroupPath = path.join(parentPath, workflowGroupName) let endpoint = path.join(app.getApiPath(), "project/new-workflow-group")+"?path="+workflowGroupPath - xhr({uri: endpoint,json: true}, function (err, response, body) { - if(response.statusCode < 400) { + app.getXHR(endpoint, { + success: function (err, response, body) { if(o){//directory was created with context menu option var node = $('#models-jstree-view').jstree().get_node(o); if(node.type === "root"){ - self.refreshJSTree() + self.refreshJSTree(); }else{ $('#models-jstree-view').jstree().refresh_node(node); } }else{//directory was created with create directory button - self.refreshJSTree() + self.refreshJSTree(); } - self.updateParent('workflow-group') - }else{ - let errorModel = $(modals.newProjectOrWorkflowGroupErrorHtml(body.Reason, body.Message)).modal() + self.updateParent('workflow-group'); + }, + error: function (err, response, body) { + let errorModel = $(modals.newProjectOrWorkflowGroupErrorHtml(body.Reason, body.Message)).modal(); } - }) + }); } }) }, @@ -724,63 +709,84 @@ module.exports = View.extend({ if(document.querySelector('#newProjectModelModal')){ document.querySelector('#newProjectModelModal').remove() } - let mdlListEP = path.join(app.getApiPath(), 'project/add-existing-model') + "?path="+self.parent.projectPath - xhr({uri:mdlListEP, json:true}, function (err, response, body) { - let modal = $(modals.newProjectModelHtml(body.models)).modal() - let okBtn = document.querySelector('#newProjectModelModal .ok-model-btn') - let select = document.querySelector('#newProjectModelModal #modelPathInput') - okBtn.addEventListener("click", function (e) { - let queryString = "?path="+self.parent.projectPath+"&mdlPath="+select.value - let endpoint = path.join(app.getApiPath(), 'project/add-existing-model') + queryString - xhr({uri:endpoint, json:true, method:"post"}, function (err, response, body) { - if(response.statusCode < 400) { - self.updateParent("nonspatial") - let successModal = $(modals.newProjectModelSuccessHtml(body.message)).modal() - self.refreshJSTree() + let mdlListEP = path.join(app.getApiPath(), 'project/add-existing-model') + "?path="+self.parent.model.directory + app.getXHR(mdlListEP, { + always: function (err, response, body) { + let modal = $(modals.newProjectModelHtml(body.files)).modal(); + let okBtn = document.querySelector('#newProjectModelModal .ok-model-btn'); + let select = document.querySelector('#newProjectModelModal #modelFileInput'); + let location = document.querySelector('#newProjectModelModal #modelPathInput'); + select.addEventListener("change", function (e) { + okBtn.disabled = e.target.value && body.paths[e.target.value].length >= 2; + if(body.paths[e.target.value].length >= 2) { + var locations = body.paths[e.target.value].map(function (path) { + return ``; + }); + locations.unshift(``); + locations = locations.join(" "); + $("#modelPathInput").find('option').remove().end().append(locations); + $("#location-container").css("display", "block"); }else{ - let errorModal = $(modals.newProjectModelErrorHtml(body.Reason, body.Message)).modal() + $("#location-container").css("display", "none"); + $("#modelPathInput").find('option').remove().end(); } }); - modal.modal('hide') - }); + location.addEventListener("change", function (e) { + okBtn.disabled = !Boolean(e.target.value); + }); + okBtn.addEventListener("click", function (e) { + modal.modal('hide'); + let mdlPath = body.paths[select.value].length < 2 ? body.paths[select.value][0] : location.value; + let queryString = "?path="+self.parent.model.directory+"&mdlPath="+mdlPath; + let endpoint = path.join(app.getApiPath(), 'project/add-existing-model') + queryString; + app.postXHR(endpoint, null, { + success: function (err, response, body) { + let successModal = $(modals.newProjectModelSuccessHtml(body.message)).modal(); + self.updateParent("model"); + self.refreshJSTree(); + }, + error: function (err, response, body) { + let errorModal = $(modals.newProjectModelErrorHtml(body.Reason, body.Message)).modal(); + } + }); + }); + } }); }, - addNewWorkflow: function (o) { - if(o.type !== "workflow-group" && this.parent.model.workflowGroups.length <= 0) { - let title = "No Workflow Groups Found" - let message = "You need to create an workflow group before you can create a new workflow." - let modal = $(modals.noWorkflowGroupMessageHtml(title, message)).modal() - }else if(o.type === "workflow-group" && this.parent.model.models.length <= 0) { - let title = "No Models Found" - let message = "You need to add a model before you can create a new workflow." - let modal = $(modals.noWorkflowGroupMessageHtml(title, message)).modal() - }else if(o.type !== "workflow-group" && this.parent.model.workflowGroups.length == 1) { - let expName = this.parent.model.workflowGroups.models[0].name - let parentPath = path.join(path.dirname(o.original._path), expName + ".wkgp") - let modelPath = o.original._path - let endpoint = path.join(app.getBasePath(), "stochss/workflow/selection")+"?path="+modelPath+"&parentPath="+parentPath - window.location.href = endpoint + newWorkflow: function (o, type) { + app.newWorkflow(this, o.original._path, o.type === "spatial", type); + }, + addModel: function (parentPath, modelName, message) { + var endpoint = path.join(app.getBasePath(), "stochss/models/edit") + if(parentPath.endsWith(".proj")) { + let queryString = "?path=" + parentPath + "&mdlFile=" + modelName + let newMdlEP = path.join(app.getApiPath(), "project/new-model") + queryString + app.getXHR(newMdlEP, { + success: function (err, response, body) { + endpoint += "?path="+body.path; + window.location.href = endpoint; + }, + error: function (err, response, body) { + let title = "Model Already Exists"; + let message = "A model already exists with that name"; + let errorModel = $(modals.newProjectOrWorkflowGroupErrorHtml(title, message)).modal(); + } + }); }else{ - let self = this - if(document.querySelector('#newProjectWorkflowModal')){ - document.querySelector('#newProjectWorkflowModal').remove() - } - let options = o.type === "workflow-group" ? - this.parent.model.models.map(function (model) {return model.name}) : - this.parent.model.workflowGroups.map(function (workflowGroup) {return workflowGroup.name}) - let label = o.type === "workflow-group" ? "Model file name: " : "Workflow Group file name: " - let modal = $(modals.newProjectWorkflowHtml(label, options)).modal() - let okBtn = document.querySelector('#newProjectWorkflowModal .ok-model-btn') - let select = document.querySelector('#newProjectWorkflowModal #select') - okBtn.addEventListener("click", function (e) { - modal.modal('hide') - let mdlFile = o.type === "workflow-group" ? self.parent.model.models.filter(function (model) { - return model.name === select.value; - })[0].directory.split("/").pop() : null; - let parentPath = o.type === "workflow-group" ? o.original._path : path.join(path.dirname(o.original._path), select.value + ".wkgp") - let modelPath = o.type === "workflow-group" ? path.join(path.dirname(o.original._path), mdlFile) : o.original._path - let endpoint = path.join(app.getBasePath(), "stochss/workflow/selection")+"?path="+modelPath+"&parentPath="+parentPath - window.location.href = endpoint + let modelPath = path.join(parentPath, modelName) + let queryString = "?path="+modelPath+"&message="+message; + endpoint += queryString + let existEP = path.join(app.getApiPath(), "model/exists")+queryString + app.getXHR(existEP, { + always: function (err, response, body) { + if(body.exists) { + let title = "Model Already Exists"; + let message = "A model already exists with that name"; + let errorModel = $(modals.newProjectOrWorkflowGroupErrorHtml(title, message)).modal(); + }else{ + window.location.href = endpoint; + } + } }); } }, @@ -809,7 +815,7 @@ module.exports = View.extend({ okBtn.addEventListener('click', function (e) { if (Boolean(input.value)) { modal.modal('hide') - var parentPath = self.parent.projectPath + var parentPath = self.parent.model.directory if(o && o.original && o.original._path !== "/"){ parentPath = o.original._path } @@ -818,54 +824,35 @@ module.exports = View.extend({ let modelName = !o || (o && o.type === "root") ? input.value.trim().split("/").pop() + ext : input.value.trim() + ext; let message = modelName !== input.value.trim() + ext? "Warning: Models are saved directly in StochSS Projects and cannot be saved to the "+input.value.trim().split("/")[0]+" directory in the project.

Your model will be saved directly in your project.

" : "" - let modelPath = path.join(parentPath, modelName) - let queryString = "?path="+modelPath+"&message="+message; - let endpoint = path.join(app.getBasePath(), "stochss/models/edit")+queryString - let existEP = path.join(app.getApiPath(), "model/exists")+queryString if(message){ let warningModal = $(modals.newProjectModelWarningHtml(message)).modal() let yesBtn = document.querySelector('#newProjectModelWarningModal .yes-modal-btn'); yesBtn.addEventListener('click', function (e) { - warningModal.modal('hide') - xhr({uri: existEP, json: true}, function (err, response, body) { - if(body.exists) { - let title = "Model Already Exists" - let message = "A model already exists with that name" - let errorModel = $(modals.newProjectOrWorkflowGroupErrorHtml(title, message)).modal() - }else{ - window.location.href = endpoint - } - }) - }) + warningModal.modal('hide'); + self.addModel(parentPath, modelName, message); + }); }else{ - xhr({uri: existEP, json: true}, function (err, response, body) { - if(body.exists) { - let title = "Model Already Exists" - let message = "A model already exists with that name" - let errorModel = $(modals.newProjectOrWorkflowGroupErrorHtml(title, message)).modal() - }else{ - window.location.href = endpoint - } - }) + self.addModel(parentPath, modelName, message); } }else{ let dirName = input.value.trim(); let endpoint = path.join(app.getApiPath(), "directory/create")+"?path="+path.join(parentPath, dirName); - xhr({uri:endpoint}, function (err, response, body) { - if(response.statusCode < 400){ + app.getXHR(endpoint, { + success: function (err, response, body) { if(o){//directory was created with context menu option var node = $('#models-jstree-view').jstree().get_node(o); if(node.type === "root"){ - self.refreshJSTree() + self.refreshJSTree(); }else{ $('#models-jstree-view').jstree().refresh_node(node); } }else{//directory was created with create directory button - self.refreshJSTree() + self.refreshJSTree(); } - }else{//new directory not created no need to refresh - body = JSON.parse(body) - let errorModal = $(modals.newDirectoryErrorHtml(body.Reason, body.Message)).modal() + }, + error: function (err, response, body) { + body = JSON.parse(body); + let errorModal = $(modals.newDirectoryErrorHtml(body.Reason, body.Message)).modal(); } }); } @@ -883,64 +870,83 @@ module.exports = View.extend({ this.newModelOrDirectory(undefined, true, isSpatial); }, handelCreateDomainClick: function (e) { - let queryStr = "?domainPath=" + this.parent.projectPath + "&new" + let queryStr = "?domainPath=" + this.parent.model.directory + "&new" window.location.href = path.join(app.getBasePath(), "stochss/domain/edit") + queryStr }, handleExtractModelClick: function (o) { let self = this - let projectParent = path.dirname(this.parent.projectPath) === '.' ? "" : path.dirname(this.parent.projectPath) + let projectParent = path.dirname(this.parent.model.directory) === '.' ? "" : path.dirname(this.parent.model.directory) let queryString = "?srcPath="+o.original._path+"&dstPath="+path.join(projectParent, o.original._path.split('/').pop()) let endpoint = path.join(app.getApiPath(), "project/extract-model")+queryString - xhr({uri: endpoint}, function (err, response, body) { - if(response.statusCode < 400){ - let successModel = $(modals.projectExportSuccessHtml("Model", body)).modal() - }else{ - body = JSON.parse(body) - let successModel = $(modals.projectExportErrorHtml(body.Reason, body.message)).modal() + app.getXHR(endpoint, { + success: function (err, response, body) { + let successModel = $(modals.projectExportSuccessHtml("Model", body)).modal(); + }, + error: function (err, response, body) { + body = JSON.parse(body); + let successModel = $(modals.projectExportErrorHtml(body.Reason, body.message)).modal(); } }); }, handleExportWorkflowClick: function (o) { let self = this - let projectParent = path.dirname(this.parent.projectPath) === '.' ? "" : path.dirname(this.parent.projectPath) + let projectParent = path.dirname(this.parent.model.directory) === '.' ? "" : path.dirname(this.parent.model.directory) let queryString = "?srcPath="+o.original._path+"&dstPath="+path.join(projectParent, o.original._path.split('/').pop()) let endpoint = path.join(app.getApiPath(), "project/extract-workflow")+queryString - xhr({uri: endpoint}, function (err, response, body) { - if(response.statusCode < 400) { - let successModel = $(modals.projectExportSuccessHtml("Workflow", body)).modal() - } - else { - body = JSON.parse(body) - let successModel = $(modals.projectExportErrorHtml(body.Reason, body.message)).modal() + app.getXHR(endpoint, { + success: function (err, response, body) { + let successModel = $(modals.projectExportSuccessHtml("Workflow", body)).modal(); + }, + error: function (err, response, body) { + body = JSON.parse(body); + let successModel = $(modals.projectExportErrorHtml(body.Reason, body.message)).modal(); } - }) + }); }, handleExportCombineClick: function (o, download) { let target = o.original._path - this.parent.exportAsCombine(target, download) + this.parent.exportAsCombine() }, showContextMenuForNode: function (e) { $('#models-jstree-view').jstree().show_contextmenu(this.nodeForContextMenu) }, editWorkflowModel: function (o) { let endpoint = path.join(app.getApiPath(), "workflow/edit-model")+"?path="+o.original._path - xhr({uri: endpoint, json: true}, function (err, response, body) { - if(response.statusCode < 400) { + app.getXHR(endpoint, { + success: function (err, response, body) { if(body.error){ - let title = o.text + " Not Found" - let message = body.error - let modal = $(modals.duplicateWorkflowHtml(title, message)).modal() + let title = o.text + " Not Found"; + let message = body.error; + let modal = $(modals.duplicateWorkflowHtml(title, message)).modal(); }else{ - window.location.href = path.join(app.routePrefix, "models/edit")+"?path="+body.file + window.location.href = path.join(app.routePrefix, "models/edit")+"?path="+body.file; } } }); }, + extractAll: function (o) { + let self = this; + let queryStr = "?path=" + o.original._path; + let endpoint = path.join(app.getApiPath(), "file/unzip") + queryStr; + app.getXHR(endpoint, { + success: function (err, response, body) { + let node = $('#models-jstree-view').jstree().get_node(o.parent); + if(node.type === "root"){ + self.refreshJSTree(); + }else{ + $('#models-jstree-view').jstree().refresh_node(node); + } + }, + error: function (err, response, body) { + let modal = $(modals.newProjectModelErrorHtml(body.Reason, body.message)).modal(); + } + }); + }, setupJstree: function () { var self = this; $.jstree.defaults.contextmenu.items = (o, cb) => { let nodeType = o.original.type - let zipTypes = ["workflow", "folder", "other", "project", "workflow-group"] + let zipTypes = ["workflow", "folder", "other", "root", "workflow-group"] let asZip = zipTypes.includes(nodeType) // refresh context menu option let refresh = { @@ -1143,13 +1149,31 @@ module.exports = View.extend({ } // menu option for creating new workflows let newWorkflow = { - "NewWorkflow" : { - "label" : "New Workflow", + "ensembleSimulation" : { + "label" : "Ensemble Simulation", "_disabled" : false, "separator_before" : false, - "separator_after" : true, + "separator_after" : false, + "action" : function (data) { + self.newWorkflow(o, "Ensemble Simulation") + } + }, + "parameterSweep" : { + "label" : "Parameter Sweep", + "_disabled" : false, + "separator_before" : false, + "separator_after" : false, + "action" : function (data) { + self.newWorkflow(o, "Parameter Sweep") + } + }, + "jupyterNotebook" : { + "label" : "Jupyter Notebook", + "_disabled" : false, + "separator_before" : false, + "separator_after" : false, "action" : function (data) { - self.addNewWorkflow(o) + window.location.href = path.join(app.getBasePath(), "stochss/workflow/selection")+"?path="+o.original._path; } } } @@ -1174,7 +1198,13 @@ module.exports = View.extend({ self.handleExtractModelClick(o); } }, - "New Workflow" : newWorkflow.NewWorkflow + "New Workflow" : { + "label" : "New Workflow", + "_disabled" : false, + "separator_before" : false, + "separator_after" : false, + "submenu" : o.type === "nonspatial" ? newWorkflow : {"jupyterNotebook":newWorkflow.jupyterNotebook} + } } // convert options for non-spatial models let modelConvert = { @@ -1225,21 +1255,8 @@ module.exports = View.extend({ } } } - // specific to workflow groups - let workflowGroup = { - "Add New Workflow" : newWorkflow.NewWorkflow - } // specific to workflows let workflow = { - "Convert to Notebook" : { - "label" : "To Notebook", - "_disabled" : false, - "separator_before" : false, - "separator_after" : false, - "action" : function (data) { - self.toNotebook(o, "workflow") - } - }, "Start/Restart Workflow" : { "label" : (o.original._status === "ready") ? "Start Workflow" : "Restart Workflow", "_disabled" : true, @@ -1266,7 +1283,7 @@ module.exports = View.extend({ "submenu" : { "Edit" : { "label" : " Edit", - "_disabled" : !(o.original._status === "ready"), + "_disabled" : (!o.original._newFormat && o.original._status !== "ready"), "separator_before" : false, "separator_after" : false, "action" : function (data) { @@ -1275,7 +1292,7 @@ module.exports = View.extend({ }, "Extract" : { "label" : "Extract", - "_disabled" : false, + "_disabled" : (o.original._newFormat && !o.original._hasJobs), "separator_before" : false, "separator_after" : false, "action" : function (data) { @@ -1336,7 +1353,7 @@ module.exports = View.extend({ }, "Delete" : { "label" : "Delete", - "_disabled" : o.type === 'workflow-group' && self.parent.model.workflowGroups.length === 1 ? true : false, + "_disabled" : false, "separator_before" : false, "separator_after" : false, "action" : function (data) { @@ -1344,15 +1361,30 @@ module.exports = View.extend({ } } } + //Specific to zip archives + let extractAll = { + "extractAll" : { + "label" : "Extract All", + "_disabled" : false, + "separator_before" : false, + "separator_after" : false, + "action" : function (data) { + self.extractAll(o); + } + } + } if (o.type === 'root'){ return $.extend(refresh, project, commonFolder, downloadWCombine, {"Rename": common.Rename}) } - if (o.type === 'folder' && o.text !== "trash") { - return $.extend(refresh, commonFolder, download, common) - } if (o.text === "trash"){ return refresh } + if (o.original._path.includes(".proj/trash/")) { + return {"Delete": common.Delete} + } + if (o.type === 'folder') { + return $.extend(refresh, commonFolder, download, common) + } if (o.type === 'spatial') { return $.extend(commonModel, spatialConvert, download, common) } @@ -1360,13 +1392,16 @@ module.exports = View.extend({ return $.extend(commonModel, modelConvert, download, common) } if (o.type === 'workflow-group') { - return $.extend(refresh, workflowGroup, downloadWCombine) + return $.extend(refresh, downloadWCombine) } if (o.type === 'workflow') { return $.extend(open, workflow, downloadWCombine, common) } + if (o.text.endsWith(".zip")) { + return $.extend(open, extractAll, download, common) + } if (o.type === 'notebook' || o.type === "other") { - return $.extend(open, common) + return $.extend(open, download, common) } if (o.type === 'sbml-model') { return $.extend(open, sbml, common) @@ -1406,37 +1441,33 @@ module.exports = View.extend({ var file = e.target.text var node = $('#models-jstree-view').jstree().get_node(e.target) var _path = node.original._path; - if(file.endsWith('.mdl') || file.endsWith('.smdl')){ - window.location.href = path.join(app.getBasePath(), "stochss/models/edit")+"?path="+_path; - }else if(file.endsWith('.ipynb')){ - var notebookPath = path.join(app.getBasePath(), "notebooks", _path) - window.open(notebookPath, '_blank') - }else if(file.endsWith('.sbml')){ - var openPath = path.join(app.getBasePath(), "edit", _path) - window.open(openPath, '_blank') - }else if(file.endsWith('.proj')){ - window.location.href = path.join(app.getBasePath(), "stochss/project/manager")+"?path="+_path; - }else if(file.endsWith('.wkfl')){ - window.location.href = path.join(app.getBasePath(), "stochss/workflow/edit")+"?path="+_path+"&type=none"; - }else if(file.endsWith('.domn')) { - let queryStr = "?domainPath=" + _path - window.location.href = path.join(app.getBasePath(), "stochss/domain/edit") + queryStr - }else if(node.type === "folder" && $('#models-jstree-view').jstree().is_open(node) && $('#models-jstree-view').jstree().is_loaded(node)){ - $('#models-jstree-view').jstree().refresh_node(node) - }else if(node.type === "other"){ - var openPath = path.join(app.getBasePath(), "view", _path); - window.open(openPath, "_blank"); + if(!_path.includes(".proj/trash/")){ + if(file.endsWith('.mdl') || file.endsWith('.smdl')){ + window.location.href = path.join(app.getBasePath(), "stochss/models/edit")+"?path="+_path; + }else if(file.endsWith('.ipynb')){ + var notebookPath = path.join(app.getBasePath(), "notebooks", _path) + window.open(notebookPath, '_blank') + }else if(file.endsWith('.sbml')){ + var openPath = path.join(app.getBasePath(), "edit", _path) + window.open(openPath, '_blank') + }else if(file.endsWith('.proj')){ + window.location.href = path.join(app.getBasePath(), "stochss/project/manager")+"?path="+_path; + }else if(file.endsWith('.wkfl')){ + window.location.href = path.join(app.getBasePath(), "stochss/workflow/edit")+"?path="+_path+"&type=none"; + }else if(file.endsWith('.domn')) { + let queryStr = "?domainPath=" + _path + window.location.href = path.join(app.getBasePath(), "stochss/domain/edit") + queryStr + }else if(node.type === "folder" && $('#models-jstree-view').jstree().is_open(node) && $('#models-jstree-view').jstree().is_loaded(node)){ + $('#models-jstree-view').jstree().refresh_node(node) + }else if(node.type === "other"){ + var openPath = path.join(app.getBasePath(), "view", _path); + window.open(openPath, "_blank"); + } } }); }) }, changeCollapseButtonText: function (e) { - let source = e.target.dataset.hook - let collapseContainer = $(this.queryByHook(source).dataset.target) - if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) { - let collapseBtn = $(this.queryByHook(source)) - let text = collapseBtn.text(); - text === '+' ? collapseBtn.text('-') : collapseBtn.text('+'); - } + app.changeCollapseButtonText(this, e); } }); \ No newline at end of file diff --git a/client/views/hybrid-settings.js b/client/views/hybrid-settings.js deleted file mode 100644 index da2b1434b6..0000000000 --- a/client/views/hybrid-settings.js +++ /dev/null @@ -1,100 +0,0 @@ -/* -StochSS is a platform for simulating biochemical systems -Copyright (C) 2019-2020 StochSS developers. - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . -*/ - -var tests = require('./tests'); -//views -var View = require('ampersand-view'); -var InputView = require('./input'); -var SelectView = require('ampersand-select-view'); -//templates -var template = require('../templates/includes/hybridSettings.pug'); - -module.exports = View.extend({ - template: template, - bindings: { - 'model.seed': { - type: 'value', - hook: 'seed-container' - }, - 'model.tauTol': { - type: 'value', - hook: 'tau-tolerance-container' - }, - 'model.switchTol': { - type: 'value', - hook: 'switching-tolerance-container' - }, - }, - initialize: function (attrs, options) { - View.prototype.initialize.apply(this, arguments); - }, - render: function () { - View.prototype.render.apply(this); - }, - update: function () { - }, - updateValid: function () { - }, - subviews: { - inputSeed: { - hook: 'seed-container', - prepareView: function () { - return new InputView ({ - parent: this, - required: true, - name: 'seed', - label: 'Seed the random number generator (set to -1 for a random seed): ', - tests: '', - modelKey: 'seed', - valueType: 'number', - value: this.model.seed - }); - }, - }, - inputTauTolerance: { - hook: 'tau-tolerance-container', - prepareView: function () { - return new InputView ({ - parent: this, - required: true, - name: 'Tau-Tolerance', - label: 'Set the tau-tolerance (valid value must be between 0.0 and 1.0): ', - tests: tests.valueTests, - modelKey: 'tauTol', - valueType: 'number', - value: this.model.tauTol - }); - }, - }, - inputSwitchingTolerance: { - hook: 'switching-tolerance-container', - prepareView: function () { - return new InputView ({ - parent: this, - required: true, - name: 'Switching Tolerance', - label: 'Set the switching tolerance (valid values must be between 0.0 and 1.0): ', - tests: tests.valueTests, - modelKey: 'switchTol', - valueType: 'number', - value: this.model.switchTol - }); - }, - }, - }, -}); \ No newline at end of file diff --git a/client/views/initial-conditions-editor.js b/client/views/initial-conditions-editor.js index 61cbd0b88b..5e017ecde2 100644 --- a/client/views/initial-conditions-editor.js +++ b/client/views/initial-conditions-editor.js @@ -17,6 +17,8 @@ along with this program. If not, see . */ var $ = require('jquery'); +//support files +let app = require('../app'); //views var View = require('ampersand-view'); var EditInitialCondition = require('./edit-initial-condition'); @@ -74,12 +76,6 @@ module.exports = View.extend({ collapseBtn.trigger('click') }, changeCollapseButtonText: function (e) { - let source = e.target.dataset.hook - let collapseContainer = $(this.queryByHook(source).dataset.target) - if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) { - let collapseBtn = $(this.queryByHook(source)) - let text = collapseBtn.text(); - text === '+' ? collapseBtn.text('-') : collapseBtn.text('+'); - } + app.changeCollapseButtonText(this, e); } }); \ No newline at end of file diff --git a/client/views/initial-conditions-viewer.js b/client/views/initial-conditions-viewer.js index 4132e07e58..777c445851 100644 --- a/client/views/initial-conditions-viewer.js +++ b/client/views/initial-conditions-viewer.js @@ -17,6 +17,8 @@ along with this program. If not, see . */ var $ = require('jquery'); +//support files +let app = require('../app'); //views var View = require('ampersand-view'); var ViewInitialCondition = require('./view-initial-condition'); @@ -47,12 +49,6 @@ module.exports = View.extend({ this.parent.renderInitialConditions("edit", true); }, changeCollapseButtonText: function (e) { - let source = e.target.dataset.hook - let collapseContainer = $(this.queryByHook(source).dataset.target) - if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) { - let collapseBtn = $(this.queryByHook(source)) - let text = collapseBtn.text(); - text === '+' ? collapseBtn.text('-') : collapseBtn.text('+'); - } + app.changeCollapseButtonText(this, e); }, }); \ No newline at end of file diff --git a/client/views/job-listing.js b/client/views/job-listing.js new file mode 100644 index 0000000000..2398dc5861 --- /dev/null +++ b/client/views/job-listing.js @@ -0,0 +1,84 @@ +/* +StochSS is a platform for simulating biochemical systems +Copyright (C) 2019-2020 StochSS developers. + +This program is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with this program. If not, see . +*/ + +let $ = require('jquery'); +let path = require('path'); +let _ = require('underscore'); +//support files +let app = require('../app'); +//views +let View = require('ampersand-view'); +//templates +let template = require('../templates/includes/jobListing.pug'); + +module.exports = View.extend({ + template: template, + events: function () { + let events = {}; + events['click [data-hook=' + this.model.elementID + '-open]'] = 'openActiveJob'; + events['click [data-hook=' + this.model.elementID + '-remove]'] = 'deleteJob'; + return events; + }, + initialize: function (attrs, options) { + View.prototype.initialize.apply(this, arguments); + }, + render: function (attrs, options) { + View.prototype.render.apply(this, arguments); + if(this.model.status === "running") { + $(this.queryByHook(this.model.elementID + "-open")).prop("disabled", true); + this.getJobStatus(); + }else{ + $(this.queryByHook(this.model.elementID + '-running-spinner')).css('display', "none") + } + }, + deleteJob: function (e) { + let self = this; + let endpoint = path.join(app.getApiPath(), "file/delete") + "?path=" + this.model.directory; + app.getXHR(endpoint, { + success: function (err, response, body) { + let job = self.model.collection.remove(self.model); + if(job.name === self.parent.model.activeJob.name){ + self.parent.model.activeJob.status = null; + self.parent.updateWorkflow(); + } + self.remove(); + } + }); + }, + getJobStatus: function () { + let self = this; + let queryString = "?path=" + this.model.directory + let endpoint = path.join(app.getApiPath(), "workflow/workflow-status") + queryString; + app.getXHR(endpoint, { + always: function (err, response, body) { + if(body === 'running') { + setTimeout(_.bind(self.getJobStatus, self), 1000); + }else{ + self.model.status = body; + $(self.queryByHook(self.model.elementID + "-open")).prop("disabled", false); + $(self.queryByHook(self.model.elementID + '-running-spinner')).css('display', "none"); + $(self.queryByHook(self.model.elementID + "-status")).text(body); + self.parent.updateWorkflow(); + } + } + }); + }, + openActiveJob: function (e) { + this.parent.setActiveJob(this.model); + } +}); diff --git a/client/views/main.js b/client/views/main.js index 0c87eac712..d432a10296 100644 --- a/client/views/main.js +++ b/client/views/main.js @@ -19,13 +19,16 @@ along with this program. If not, see . var _ = require('underscore'); var $ = require('jquery'); //var setFavicon = require('favicon-setter'); -var app = require('ampersand-app'); -var View = require('ampersand-view'); -var ViewSwitcher = require('ampersand-view-switcher'); +var App = require('ampersand-app'); var localLinks = require('local-links'); var domify = require('domify'); var path = require('path'); - +// support files +let app = require("../app"); +//views +var View = require('ampersand-view'); +var ViewSwitcher = require('ampersand-view-switcher'); +//templates var headTemplate = require('!pug-loader!../templates/head.pug'); var bodyTemplate = require('!pug-loader!../templates/body.pug'); @@ -94,10 +97,11 @@ module.exports = View.extend({ template: bodyTemplate, autoRender: true, initialize: function () { - this.listenTo(app, 'page', this.handleNewPage); + this.listenTo(App, 'page', this.handleNewPage); }, events: { 'click [data-hook=registration-link-button]' : 'handleRegistrationLinkClick', + 'click [data-hook=user-logs-collapse]' : 'collapseExpandLogs' //'click a[href]': 'handleLinkClick' }, render: function () { @@ -114,16 +118,107 @@ module.exports = View.extend({ document.title = _.result(newView, 'pageTitle') || 'StochSS'; document.scrollTop = 0; - app.currentPage = newView; + App.currentPage = newView; } }); var homePath = window.location.pathname.startsWith("/user") ? "/hub/stochss" : "stochss/home" $(this.queryByHook("home-link")).prop('href', homePath); - + let self = this; + let message = app.getBasePath() === "/" ? "Welcome to StochSS!" : "Welcome to StochSS Live!"; + $("#user-logs").html(message) + this.logBlock = []; + this.logs = []; + this.getUserLogs(); + this.scrolled = false; + this.scrollCount = 0; + $("#user-logs").on("mousewheel", function(e) { + self.scrolled = true; + self.scrollCount = 0; + }); return this; }, - + addNewLogBlock: function () { + if(this.logBlock.length > 0) { + let logBlock = this.logBlock.join("
"); + this.logBlock = []; + $("#user-logs").append("

" + logBlock + "

") + return "" + } + return "
" + }, + addNewLogs: function (newLogs) { + let self = this; + let logList = newLogs.map(function (log) { + if(log.includes("$ ")){ + let head = self.addNewLogBlock(); + var newLog = self.formatLog(log); + $("#user-logs").append(head + newLog); + }else{ + var newLog = log; + if(newLog.trim()) { + self.logBlock.push(newLog); + } + } + self.logs.push(newLog); + }); + this.addNewLogBlock(); + }, + collapseExpandLogs: function (e) { + let logs = $("#user-logs"); + let classes = logs.attr("class").split(/\s+/); + if(classes.includes("show")) { + logs.removeClass("show"); + $(this.queryByHook(e.target.dataset.hook)).html("+"); + $(".user-logs").removeClass("expand-logs"); + $(".side-navbar").css("z-index", 0); + }else{ + logs.addClass("show"); + $(this.queryByHook(e.target.dataset.hook)).html("-"); + if($(".sidebar-sticky").css("position") === "fixed") { + $(".user-logs").addClass("expand-logs"); + $(".side-navbar").css("z-index", 1); + } + } + let element = document.querySelector("#user-logs"); + element.scrollTop = element.scrollHeight; + }, + getUserLogs: function () { + let self = this; + let queryStr = "?logNum=" + this.logs.length; + let endpoint = path.join(app.getApiPath(), "user-logs") + queryStr; + app.getXHR(endpoint, { + success: function (err, response, body) { + if(body) { + let scrolled = self.scrolled; + self.addNewLogs(body.logs); + if(!self.scrolled){ + let element = document.querySelector("#user-logs"); + element.scrollTop = element.scrollHeight; + }else if(self.scrollCount < 60) { + self.scrollCount += 1; + }else{ + self.scrolled = false; + self.scrollCount = 0; + } + } + self.updateUserLogs(); + } + }); + }, + formatLog: function (log) { + var time = log.split('$ ')[0]; + let date = new Date(time); + let months = ['Jan.', 'Feb.', 'Mar.', 'Apr.', 'May', 'Jun.', 'Jul.', 'Aug.', 'Sept.', 'Oct.', 'Nov.', 'Dec.']; + var stamp = months[date.getMonth()] + " "; + stamp += date.getDate() + ", "; + stamp += date.getFullYear() + " "; + let hours = date.getHours(); + stamp += (hours < 10 ? "0" + hours : hours) + ":"; + let minutes = date.getMinutes(); + stamp += (minutes < 10 ? '0' + minutes : minutes) + ":"; + return log.replace(time, stamp); + }, handleNewPage: function (view) { this.pageSwitcher.set(view); //this.updateActiveNav(); @@ -145,5 +240,8 @@ module.exports = View.extend({ navigate: function (page) { window.location = url; + }, + updateUserLogs: function () { + setTimeout(_.bind(this.getUserLogs, this), 1000); } }); diff --git a/client/views/mesh-editor.js b/client/views/mesh-editor.js index 113d190796..c3054cd9db 100644 --- a/client/views/mesh-editor.js +++ b/client/views/mesh-editor.js @@ -16,8 +16,9 @@ You should have received a copy of the GNU General Public License along with this program. If not, see . */ -var app = require('ampersand-app'); var $ = require('jquery'); +//support files +var app = require('../app'); var tests = require('./tests'); //views var View = require('ampersand-view'); @@ -45,13 +46,7 @@ module.exports = View.extend({ this.model.parent.trigger('mesh-update'); }, changeCollapseButtonText: function (e) { - let source = e.target.dataset.hook - let collapseContainer = $(this.queryByHook(source).dataset.target) - if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) { - let collapseBtn = $(this.queryByHook(source)) - let text = collapseBtn.text(); - text === '+' ? collapseBtn.text('-') : collapseBtn.text('+'); - } + app.changeCollapseButtonText(this, e); }, subviews: { inputSubdomains: { diff --git a/client/views/meta-data.js b/client/views/meta-data.js index f82c8987db..37180ea829 100644 --- a/client/views/meta-data.js +++ b/client/views/meta-data.js @@ -16,24 +16,22 @@ You should have received a copy of the GNU General Public License along with this program. If not, see . */ -var $ = require('jquery'); +let $ = require('jquery'); var path = require('path'); -var xhr = require('xhr'); //support files -var app = require('../app'); -var tests = require('./tests'); -var modals = require('../modals'); +let app = require('../app'); +let modals = require('../modals'); //collections -var Collection = require('ampersand-collection'); +let Creators = require('../models/creators'); //models -var Creator = require('../models/creator'); +let Creator = require('../models/creator'); //views -var View = require('ampersand-view'); -var SelectView = require('ampersand-select-view'); -var InputView = require('./input'); -var CreatorListingView = require('./creator-listing'); +let InputView = require('./input'); +let View = require('ampersand-view'); +let SelectView = require('ampersand-select-view'); +let CreatorListingView = require('./creator-listing'); //templates -var template = require('../templates/includes/metaData.pug'); +let template = require('../templates/includes/metaData.pug'); module.exports = View.extend({ template: template, @@ -41,255 +39,186 @@ module.exports = View.extend({ 'change [data-hook=file-select-view]' : 'updateMetaData', 'change [data-hook=description-input-view]' : 'updateFileDescription', 'change [data-hook=creator-select-view]' : 'updateCreator', - 'click [data-hook=add-creator-btn]' : 'handleAddCreatorClick', 'change [data-hook=email-input-view]' : 'toggleAddCreatorBtn', - 'click [data-hook=save-meta-data-button]' : 'saveMetaData', - 'click [data-hook=submit-meta-data-button]' : 'submitMetaData' + 'click [data-hook=metadata-collapse-btn]' : 'changeCollapseButtonText', + 'click [data-hook=add-creator-btn]' : 'handleAddCreatorClick', + 'click [data-hook=save-meta-data-button]' : 'saveMetaData' }, initialize: function(attrs, options) { View.prototype.initialize.apply(this, arguments); - this.projectName = attrs.projectName; - this.files = attrs.files; - this.path = attrs.path; - this.download = attrs.download; - this.selectedFile = attrs.projectName; - this.selectedCreator = "New Creator" - let self = this - let queryString = "?path="+this.parent.projectPath+"&files="+this.files.join(',') - let endpoint = path.join(app.getApiPath(), "project/meta-data")+queryString - xhr({uri:endpoint, json:true}, function(err, response, body) { - if(response.statusCode < 400) { - self.metaData = body.meta_data - self.creators = body.creators - self.renderSubviews() + this.files = this.model.workflowGroups.map(function (wkgp) { + return wkgp.name; + }); + this.files.unshift(this.model.name); + this.metadata = this.model.metadata; + this.selectedCreator = "New Creator"; + this.model.creators.forEach(function (creator) { + if(!creator.elementID) { + creator.elementID = "C" + (creator.collection.indexOf(creator) + 1); } - }) - }, - update: function() {}, - renderSubviews: function () { - this.renderFilesSelectView() - this.renderCreatorListingView() - this.renderCreatorsSelectView() - let fileMetaData = this.metaData[this.selectedFile] - $(this.queryByHook("description-input-view")).val(fileMetaData["description"]) - $(document).ready(function () { - $("html, body").animate({ - scrollTop: $("#project-meta-data-container").offset().top - 50 - }, false); }); }, - renderFilesSelectView: function() { - if(this.filesSelectView) { - this.filesSelectView.remove() + render: function (attrs, options) { + View.prototype.render.apply(this, arguments); + this.renderFilesSelectView(); + this.renderCreatorListingView(); + $(this.queryByHook("description-input-view")).val(this.metadata.description); + this.renderCreatorsSelectView(); + this.renderCreatorsInputViews(); + }, + addCreator: function (status, creator) { + if(status === "new") { + creator = this.model.creators.addCreator(creator); + } + this.metadata.creators.push(creator.elementID); + this.selectedCreator = "New Creator"; + this.renderCreatorListingView(); + this.renderCreatorsSelectView(); + this.renderCreatorsInputViews(); + }, + changeCollapseButtonText: function (e) { + app.changeCollapseButtonText(this, e); + }, + handleAddCreatorClick: function (e) { + let fName = $(this.queryByHook("given-name-input-view")).find("input").val(); + let lName = $(this.queryByHook("family-name-input-view")).find("input").val(); + let email = $(this.queryByHook("email-input-view")).find("input").val(); + let organization = $(this.queryByHook("organization-input-view")).find("input").val(); + if(this.selectedCreator === "New Creator"){ + let creator = {"fname":fName,"lname":lName,"email":email,"organization":organization} + this.addCreator("new", creator); + }else{ + let creator = this.model.creators.get(this.selectedCreator, "elementID"); + creator.fname = fName; + creator.lname = lName; + creator.email = email; + creator.organization = organization; + this.addCreator("existing", creator); } - this.filesSelectView = new SelectView({ - label: 'File: ', - name: 'file', - required: true, - idAttribute: 'cid', - textAttribute: 'name', - eagerValidate: true, - options: this.files, - value: this.projectName - }); - this.registerRenderSubview(this.filesSelectView, "file-select-view"); }, renderCreatorListingView: function () { if(this.creatorListingView) { - this.creatorListingView.remove() + this.creatorListingView.remove(); } - let self = this - let listOfCreators = this.metaData[this.selectedFile].creators.map(function (key) { - return self.creators[key] + let self = this; + let listOfCreators = this.metadata.creators.map(function (key) { + return self.model.creators.get(key, "elementID"); }); - let creators = new Collection(listOfCreators, {model: Creator}) - this.creatorListingView = this.renderCollection(creators, CreatorListingView, this.queryByHook("list-of-creators")) + let creators = new Creators(listOfCreators); + this.creatorListingView = this.renderCollection(creators, CreatorListingView, this.queryByHook("list-of-creators")); + }, + renderCreatorsInputViews: function () { + if(this.emailInputView) { + this.fnameInputView.remove(); + this.lnameInputView.remove(); + this.emailInputView.remove(); + this.orgInputView.remove(); + } + let creator = this.selectedCreator === "New Creator" ? "" : this.model.creators.get(this.selectedCreator, "elementID"); + this.fnameInputView = new InputView({parent: this, required: false, name: 'given-name', label: 'Given Name: ', + modelKey: 'fname', valueType: 'string', + value: this.selectedCreator !== "New Creator" ? creator.fname : ""}); + app.registerRenderSubview(this, this.fnameInputView, "given-name-input-view"); + this.lnameInputView = new InputView({parent: this, required: false, name: 'family-name', label: 'Family Name: ', + modelKey: 'lname', valueType: 'string', + value: creator.lname ? creator.lname : ""}); + app.registerRenderSubview(this, this.lnameInputView, "family-name-input-view"); + this.emailInputView = new InputView({parent: this, required: true, placeholder: 'e-mail required', name: 'email', + label: 'e-Mail: ', modelKey: 'email', valueType: 'string', + value: creator.email ? creator.email : ""}); + app.registerRenderSubview(this, this.emailInputView, "email-input-view"); + this.orgInputView = new InputView({parent: this, required: false, name: 'organization', label: 'Organization: ', + modelKey: 'organization', valueType: 'string', + value: creator.organization ? creator.organization : ""}); + app.registerRenderSubview(this, this.orgInputView, "organization-input-view"); + $(this.queryByHook("add-creator-btn")).prop('disabled', this.selectedCreator === "New Creator"); }, renderCreatorsSelectView: function () { if(this.creatorsSelectView){ - this.creatorsSelectView.remove() + this.creatorsSelectView.remove(); } - var options = Object.keys(this.creators) - options.unshift("New Creator") + let options = this.model.creators.map(function (creator) { + return [creator.elementID, creator.email]; + }); this.creatorsSelectView = new SelectView({ label: 'Creator: ', name: 'creator', required: false, idAttribute: 'cid', - textAttribute: 'name', eagerValidate: true, options: options, - value: this.selectedCreator + unselectedText: "New Creator" }); - this.registerRenderSubview(this.creatorsSelectView, "creator-select-view") - }, - registerRenderSubview: function (view, hook) { - this.registerSubview(view); - this.renderSubview(view, this.queryByHook(hook)); - }, - updateMetaData: function (e) { - this.selectedFile = e.target.selectedOptions.item(0).text - let fileMetaData = this.metaData[this.selectedFile] - $(this.queryByHook("description-input-view")).val(fileMetaData["description"]) - this.renderCreatorListingView() - this.selectedCreator = "New Creator" - this.renderCreatorsSelectView() - this.updateCreator(undefined) + app.registerRenderSubview(this, this.creatorsSelectView, "creator-select-view"); }, - updateFileDescription: function (e) { - let description = e.target.value - this.metaData[this.selectedFile]["description"] = description - }, - updateCreator: function (e) { - if(e){ - this.selectedCreator = e.target.selectedOptions.item(0).text - } - var fName = this.selectedCreator === "New Creator" ? "" : this.creators[this.selectedCreator].fname - var lName = this.selectedCreator === "New Creator" ? "" : this.creators[this.selectedCreator].lname - var email = this.selectedCreator === "New Creator" ? "" : this.creators[this.selectedCreator].email - var organization = this.selectedCreator === "New Creator" ? "" : this.creators[this.selectedCreator].organization - $(this.queryByHook("given-name-input-view")).find("input").val(fName) - $(this.queryByHook("family-name-input-view")).find("input").val(lName) - $(this.queryByHook("email-input-view")).find("input").val(email) - $(this.queryByHook("organization-input-view")).find("input").val(organization) - $(this.queryByHook("add-creator-btn")).prop('disabled', this.selectedCreator === "New Creator") - if(this.metaData[this.selectedFile].creators.includes(this.selectedCreator)) { - $(this.queryByHook("add-creator-btn")).text("Update") - }else{ - $(this.queryByHook("add-creator-btn")).text("Add") - } - }, - handleAddCreatorClick: function (e) { - let fName = $(this.queryByHook("given-name-input-view")).find("input").val() - let lName = $(this.queryByHook("family-name-input-view")).find("input").val() - let email = $(this.queryByHook("email-input-view")).find("input").val() - let organization = $(this.queryByHook("organization-input-view")).find("input").val() - if(email in this.creators && this.selectedCreator === "New Creator"){ - if(document.querySelector("#existingCreatorConfirmationModal")) { - document.querySelector("#existingCreatorConfirmationModal").remove() - } - let self = this - let message = "A creator already exists with this email. Do you wish to update that creators information?" - let modal = $(modals.existingCreatorConfirmationHtml(message)).modal() - let yesBtn = document.querySelector("#existingCreatorConfirmationModal .yes-modal-btn") - yesBtn.addEventListener('click', function (e) { - modal.modal('hide') - let creator = {"fname":fName,"lname":lName,"email":email,"organization":organization} - self.addCreator(email, creator) - }) - console.log("A creator already exists with this name. Do you wish to update that creators data?") - }else if(this.selectedCreator !== "New Creator" && email !== this.selectedCreator){ - let index = this.metaData[this.selectedFile].creators.indexOf(this.selectedCreator) - this.metaData[this.selectedFile].creators.splice(index, 1) - let creator = {"fname":fName,"lname":lName,"email":email,"organization":organization} - this.addCreator(email, creator) - }else{ - let creator = {"fname":fName,"lname":lName,"email":email,"organization":organization} - this.addCreator(email, creator) + renderFilesSelectView: function() { + if(this.filesSelectView) { + this.filesSelectView.remove(); } + this.filesSelectView = new SelectView({ + label: 'File: ', + name: 'file', + required: true, + idAttribute: 'cid', + textAttribute: 'name', + eagerValidate: true, + options: this.files, + value: this.model.name + }); + app.registerRenderSubview(this, this.filesSelectView, "file-select-view"); }, - addCreator: function (key, creator) { - this.creators[key] = creator - if(!this.metaData[this.selectedFile].creators.includes(key)){ - this.metaData[this.selectedFile].creators.push(key) - } - this.selectedCreator = key - this.renderCreatorsSelectView() - $(this.queryByHook("add-creator-btn")).text("Update") - this.renderCreatorListingView() + saved: function () { + $(this.queryByHook('md-in-progress')).css("display", "none"); + $(this.queryByHook('md-complete')).css("display", "inline-block"); + let self = this; + setTimeout(function () { + $(self.queryByHook("md-complete")).css("display", "none"); + }, 5000); }, - toggleAddCreatorBtn: function (e) { - $(this.queryByHook("add-creator-btn")).prop('disabled', !Boolean(e.target.value)) + saving: function () { + $(this.queryByHook('md-in-progress')).css("display", "inline-block"); + $(this.queryByHook('md-complete')).css("display", "none"); }, saveMetaData: function (e) { - let data = {"meta-data":this.metaData,"creators":this.creators} - let endpoint = path.join(app.getApiPath(), "project/meta-data")+"?path="+this.parent.projectPath - xhr({uri:endpoint, json:true, method:"post", body:data}, function (err, response, body) { - if(response.statusCode < 400) { - console.log("Successfully Saved Mete Data") + this.saving(); + let data = {} + data[this.model.directory] = {"metadata":this.model.metadata, "creators":this.model.creators}; + this.model.workflowGroups.forEach(function (wkgp) { + data[wkgp.name + ".wkgp"] = {"metadata": wkgp.metadata}; + }); + let self = this; + let endpoint = path.join(app.getApiPath(), "project/meta-data")+"?path="+this.model.directory; + app.postXHR(endpoint, data, { + success: function (err, response, body) { + self.saved(); } }); }, - submitMetaData: function (e) { - let self = this - $(this.parent.queryByHook("project-meta-data-container")).collapse('hide') - let data = {"meta-data":this.metaData,"creators":this.creators} - let queryString = "?path="+this.path+"&projectPath="+this.parent.projectPath - let endpoint = path.join(app.getApiPath(), "project/export-combine")+queryString - xhr({uri:endpoint, json:true, method:"post", body:data}, function (err, response, body) { - if(response.statusCode < 400) { - if(self.download) { - let downloadEP = path.join(app.getBasePath(), "/files", body.file_path); - window.open(downloadEP) - }else{ - let modal = $(modals.projectExportSuccessHtml(body.file_type, body.message)).modal() - } - }else{ - let modal = $(modals.projectExportErrorHtml(body.Reason, body.Message)).modal() - } - }) + toggleAddCreatorBtn: function (e) { + $(this.queryByHook("add-creator-btn")).prop('disabled', !Boolean(e.target.value)); + }, + update: function () {}, + updateFileDescription: function (e) { + this.metadata.description = e.target.value; + }, + updateCreator: function (e) { + this.selectedCreator = e.target.value ? e.target.value : "New Creator"; + this.renderCreatorsInputViews(); + $(this.queryByHook("add-creator-btn")).prop('disabled', this.selectedCreator === "New Creator"); + let creator = this.model.creators.get(this.selectedCreator, "elementID"); + if(creator && this.metadata.creators.includes(creator.elementID)) { + $(this.queryByHook("add-creator-btn")).text("Update"); + }else{ + $(this.queryByHook("add-creator-btn")).text("Add"); + } + }, + updateMetaData: function (e) { + let selectedFile = e.target.selectedOptions.item(0).text; + this.metadata = selectedFile !== this.model.name ? this.model.workflowGroups.filter(function (wkgp) { + return wkgp.name === selectedFile; + })[0].metadata : this.model.metadata; + $(this.queryByHook("description-input-view")).val(this.metadata.description); + this.renderCreatorListingView(); }, - subviews: { - inputGivenName: { - hook: 'given-name-input-view', - prepareView: function (el) { - return new InputView({ - parent: this, - required: false, - name: 'gvien-name', - label: 'Given Name: ', - tests: null, - modelKey: null, - valueType: 'string', - value: this.selectedCreator === "New Creator" ? "" : this.creators[this.selectedCreator]["fname"], - }); - }, - }, - inputFamilyName: { - hook: 'family-name-input-view', - prepareView: function (el) { - return new InputView({ - parent: this, - required: false, - name: 'family-name', - label: 'Family Name: ', - tests: null, - modelKey: null, - valueType: 'string', - value: this.selectedCreator === "New Creator" ? "" : this.creators[this.selectedCreator]["lname"], - }); - }, - }, - inputEmailName: { - hook: 'email-input-view', - prepareView: function (el) { - return new InputView({ - parent: this, - required: true, - placeholder: 'e-mail required', - name: 'email', - label: 'e-Mail: ', - tests: null, - modelKey: null, - valueType: 'string', - value: this.selectedCreator === "New Creator" ? "" : this.creators[this.selectedCreator]["email"], - }); - }, - }, - inputOrganizationName: { - hook: 'organization-input-view', - prepareView: function (el) { - return new InputView({ - parent: this, - required: false, - name: 'organization', - label: 'Organization: ', - tests: null, - modelKey: null, - valueType: 'string', - value: this.selectedCreator === "New Creator" ? "" : this.creators[this.selectedCreator]["organization"], - }); - }, - }, - } + updateValid: function () {} }); \ No newline at end of file diff --git a/client/views/model-listing.js b/client/views/model-listing.js new file mode 100644 index 0000000000..5d753e17fe --- /dev/null +++ b/client/views/model-listing.js @@ -0,0 +1,106 @@ +/* +StochSS is a platform for simulating biochemical systems +Copyright (C) 2019-2020 StochSS developers. + +This program is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with this program. If not, see . +*/ + +let $ = require('jquery'); +let path = require('path'); +//support files +let app = require('../app'); +let modals = require('../modals'); +//views +let View = require('ampersand-view'); +//templates +let template = require('../templates/includes/modelListing.pug'); + +module.exports = View.extend({ + template: template, + events: function () { + let events = {}; + events['change [data-hook=' + this.model.elementID + '-annotation]'] = 'updateAnnotation'; + events['click #' + this.model.elementID + "-ensemble-simulation"] = 'handleEnsembleSimulationClick'; + events['click #' + this.model.elementID + "-parameter-sweep"] = 'handleParameterSweepClick'; + events['click [data-hook=' + this.model.elementID + '-notes-btn]'] = 'handleEditNotesClick'; + events['click [data-hook=' + this.model.elementID + '-remove]'] = 'handleTrashModelClick'; + events['click [data-hook=' + this.model.elementID + '-annotation-btn'] = 'changeCollapseButtonText'; + return events; + }, + initialize: function (attrs, options) { + View.prototype.initialize.apply(this, arguments); + }, + render: function (attrs, options) { + View.prototype.render.apply(this, arguments); + let parentPath = path.join(path.dirname(this.model.directory), "WorkflowGroup1.wkgp"); + let queryString = "?path=" + this.model.directory + "&parentPath=" + parentPath; + let endpoint = path.join(app.getBasePath(), 'stochss/workflow/selection') + queryString; + $(this.queryByHook(this.model.elementID + "-jupyter-notebook")).prop("href", endpoint); + if(!this.model.annotation){ + $(this.queryByHook(this.model.elementID + '-notes-btn')).text('Add Notes') + }else{ + $(this.queryByHook(this.model.elementID + '-notes-container')).collapse('show') + } + }, + changeCollapseButtonText: function (e) { + app.changeCollapseButtonText(this, e); + }, + handleEditNotesClick: function (e) { + let buttonTxt = e.target.innerText; + if(buttonTxt.startsWith("Add")){ + $(this.queryByHook(this.model.elementID + "-notes-container")).collapse('show'); + $(this.queryByHook(this.model.elementID + "-notes-btn")).text('Edit Notes'); + $("#" + this.model.elementID + "-annotation-container").collapse('show'); + $(this.queryByHook(this.model.elementID + "-annotation-btn")).text('-'); + }else if(!$("#" + this.model.elementID + "-annotation-container").attr('class').includes('show')){ + $("#" + this.model.elementID + "-annotation-container").collapse('show'); + $(this.queryByHook(this.model.elementID + "-annotation-btn")).text('-'); + } + document.querySelector("#" + this.model.elementID + "-annotation").focus(); + }, + handleEnsembleSimulationClick: function (e) { + app.newWorkflow(this, this.model.directory, this.model.is_spatial, "Ensemble Simulation") + }, + handleParameterSweepClick: function (e) { + app.newWorkflow(this, this.model.directory, this.model.is_spatial, "Parameter Sweep") + }, + handleTrashModelClick: function (e) { + if(document.querySelector('#moveToTrashConfirmModal')) { + document.querySelector('#moveToTrashConfirmModal').remove(); + } + let self = this; + let modal = $(modals.moveToTrashConfirmHtml("model")).modal(); + let yesBtn = document.querySelector('#moveToTrashConfirmModal .yes-modal-btn'); + yesBtn.addEventListener('click', function (e) { + modal.modal('hide'); + let projectPath = self.parent.model.directory; + let trashPath = path.join(projectPath, "trash", self.model.directory.split("/").pop()); + let queryString = "?srcPath="+self.model.directory+"&dstPath="+trashPath; + let endpoint = path.join(app.getApiPath(), 'file/move')+queryString; + app.getXHR(endpoint, { + success: function (err, response, body) { + self.parent.update("Model"); + } + }); + }); + }, + updateAnnotation: function (e) { + this.model.annotation = e.target.value.trim(); + if(this.model.annotation === "") { + $(this.queryByHook(this.model.elementID + "-notes-container")).collapse('hide'); + $(this.queryByHook(this.model.elementID + "-notes-btn")).text('Add Notes'); + } + this.model.saveModel(); + } +}); diff --git a/client/views/model-settings-viewer.js b/client/views/model-settings-viewer.js deleted file mode 100644 index 976636e339..0000000000 --- a/client/views/model-settings-viewer.js +++ /dev/null @@ -1,40 +0,0 @@ -/* -StochSS is a platform for simulating biochemical systems -Copyright (C) 2019-2020 StochSS developers. - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . -*/ - -var $ = require('jquery'); -//views -var View = require('ampersand-view'); -//templates -var template = require('../templates/includes/modelSettingsViewer.pug'); - -module.exports = View.extend({ - template: template, - events: { - 'click [data-hook=collapse]' : 'changeSettingsCollapseButtonText', - }, - initialize: function (attrs, options) { - View.prototype.initialize.apply(this, arguments); - }, - render: function () { - View.prototype.render.apply(this, arguments); - }, - changeSettingsCollapseButtonText: function () { - var text = $(this.queryByHook('collapse')).text(); - text === '+' ? $(this.queryByHook('collapse')).text('-') : $(this.queryByHook('collapse')).text('+'); - }, -}); \ No newline at end of file diff --git a/client/views/model-state-buttons.js b/client/views/model-state-buttons.js index 9c70e3d08d..f7d5bebf8a 100644 --- a/client/views/model-state-buttons.js +++ b/client/views/model-state-buttons.js @@ -16,7 +16,6 @@ You should have received a copy of the GNU General Public License along with this program. If not, see . */ -var xhr = require('xhr'); var path = require('path'); var Plotly = require('../lib/plotly'); var $ = require('jquery'); @@ -73,7 +72,11 @@ module.exports = View.extend({ let self = this this.saveModel(function () { self.saved() - var queryString = "?path="+path.dirname(self.model.directory) + var dirname = path.dirname(self.model.directory) + if(dirname.endsWith(".wkgp")) { + dirname = path.dirname(dirname) + } + var queryString = "?path="+dirname window.location.href = path.join(app.getBasePath(), "/stochss/project/manager")+queryString; }) }, @@ -83,7 +86,8 @@ module.exports = View.extend({ self.saved() var queryString = "?path="+self.model.directory if(self.model.directory.includes('.proj')) { - let parentPath = path.join(path.dirname(self.model.directory), "WorkflowGroup1.wkgp") + let wkgp = self.model.directory.includes('.wkgp') ? self.model.name + ".wkgp" : "WorkflowGroup1.wkgp" + let parentPath = path.join(path.dirname(self.model.directory), wkgp) queryString += "&parentPath="+parentPath } let endpoint = path.join(app.getBasePath(), "stochss/workflow/selection")+queryString @@ -125,13 +129,7 @@ module.exports = View.extend({ // this.model is a ModelVersion, the parent of the collection is Model var model = this.model; if (cb) { - model.save(model.attributes, { - success: cb, - error: function (model, response, options) { - console.error("Error saving model:", model); - console.error("Response:", response); - }, - }); + model.saveModel(cb); } else { model.saveModel(); } @@ -151,8 +149,8 @@ module.exports = View.extend({ saved.style.display = "none"; }, 5000); }, - runModel: function (species=undefined) { - if(!species) { + runModel: function (species=null) { + if(typeof species !== "string") { this.saved(); } this.running(); @@ -164,9 +162,11 @@ module.exports = View.extend({ } var endpoint = path.join(app.getApiPath(), 'model/run')+queryStr; var self = this; - xhr({ uri: endpoint, json: true}, function (err, response, body) { - self.outfile = body.Outfile - self.getResults() + app.getXHR(endpoint, { + always: function (err, response, body) { + self.outfile = body.Outfile; + self.getResults(); + } }); }, running: function () { @@ -203,24 +203,30 @@ module.exports = View.extend({ setTimeout(function () { let queryStr = "?cmd=read&outfile="+self.outfile+"&path="+model.directory endpoint = path.join(app.getApiPath(), 'model/run')+queryStr; - xhr({ uri: endpoint, json: true}, function (err, response, body) { - if(typeof body === "string") { - body = body.replace(/NaN/g, null) - body = JSON.parse(body) - } - var data = body.Results; - if(response.statusCode >= 400 || data.errors){ - self.ran(false); - $(self.parent.queryByHook('model-run-error-message')).text(data.errors); - } - else if(!body.Running){ - if(data.timeout){ - $(self.parent.queryByHook('model-timeout-message')).collapse('show'); + let errorCB = function (err, response, body) { + self.ran(false); + $(self.parent.queryByHook('model-run-error-message')).text(body.Results.errors); + } + app.getXHR(endpoint, { + always: function (err, response, body) { + if(typeof body === "string") { + body = body.replace(/NaN/g, null) + body = JSON.parse(body) } - self.plotResults(data.results); - }else{ - self.getResults(); - } + var data = body.Results; + if(response.statusCode >= 400 || data.errors){ + errorCB(err, response, body); + } + else if(!body.Running){ + if(data.timeout){ + $(self.parent.queryByHook('model-timeout-message')).collapse('show'); + } + self.plotResults(data.results); + }else{ + self.getResults(); + } + }, + error: errorCB }); }, 2000); }, @@ -232,25 +238,6 @@ module.exports = View.extend({ Plotly.newPlot(el, data); window.scrollTo(0, document.body.scrollHeight) }, - handleEnsembleSimulationClick: function (e) { - this.launchStochssWorkflow("gillespy") - }, - handleParameterSweepClick: function (e) { - this.launchStochssWorkflow("parameterSweep") - }, - launchStochssWorkflow: function (type) { - let queryString = "?type=" + type + "&path=" + this.model.directory - if(this.model.directory.includes('.proj')) { - var parentPath = path.join(path.dirname(this.model.directory), "WorkflowGroup1.wkgp") - }else{ - var parentPath = path.dirname(this.model.directory) - } - queryString += "&parentPath=" + parentPath - let endpoint = path.join(app.getBasePath(), "stochss/workflow/edit")+queryString - this.saveModel(function () { - window.location.href = endpoint - }); - }, handleSimulateClick: function (e) { var errorMsg = $(this.parent.queryByHook("error-detected-msg")) if(!this.model.valid) { @@ -266,9 +253,9 @@ module.exports = View.extend({ this.clickNewWorkflowHandler(e) }else if(!this.model.is_spatial) { if(simType === "ensemble") { - this.handleEnsembleSimulationClick(e) + app.newWorkflow(this, this.model.directory, this.model.is_spatial, "Ensemble Simulation"); }else if(simType === "psweep") { - this.handleParameterSweepClick(e) + app.newWorkflow(this, this.model.directory, this.model.is_spatial, "Parameter Sweep"); } } } diff --git a/client/views/model-viewer.js b/client/views/model-viewer.js index 8ee7390ed9..4006bc62be 100644 --- a/client/views/model-viewer.js +++ b/client/views/model-viewer.js @@ -16,18 +16,18 @@ You should have received a copy of the GNU General Public License along with this program. If not, see . */ -var path = require('path'); -var $ = require('jquery'); +//support files +let app = require('../app'); //views -var View = require('ampersand-view'); -var SpeciesViewer = require('./species-viewer'); -var ParametersViewer = require('./parameters-viewer'); -var ReactionsViewer = require('./reactions-viewer'); -var EventsViewer = require('./events-viewer'); -var RulesViewer = require('./rules-viewer'); -var ModelSettingsViewer = require('./model-settings-viewer'); +let View = require('ampersand-view'); +let RulesViewer = require('./rules-viewer'); +let EventsViewer = require('./events-viewer'); +let SpeciesViewer = require('./species-viewer'); +let ReactionsViewer = require('./reactions-viewer'); +let ParametersEditor = require('./parameters-editor'); +let SBMLComponentsView = require('./sbml-component-editor'); //templates -var template = require('../templates/includes/modelViewer.pug'); +let template = require('../templates/includes/modelViewer.pug'); module.exports = View.extend({ template: template, @@ -36,50 +36,55 @@ module.exports = View.extend({ }, initialize: function (attrs, options) { View.prototype.initialize.apply(this, arguments); - if(attrs.status) { - this.status = attrs.status; - }else{ - this.status = "complete" - } }, render: function () { View.prototype.render.apply(this, arguments); - var speciesViewer = new SpeciesViewer({ - collection: this.model.species, + this.renderSpeciesView(); + this.renderParametersView(); + this.renderReactionsView(); + this.renderEventsView(); + this.renderRulesView(); + this.renderSBMLComponentsView(); + }, + renderEventsView: function () { + let eventsViewer = new EventsViewer({ + collection: this.model.eventsCollection }); - var parametersViewer = new ParametersViewer({ + app.registerRenderSubview(this, eventsViewer, "events-viewer-container"); + }, + renderParametersView: function () { + let parametersViewer = new ParametersEditor({ collection: this.model.parameters, + readOnly: true }); - var reactionsViewer = new ReactionsViewer({ - collection: this.model.reactions, - }); - var eventsViewer = new EventsViewer({ - collection: this.model.eventsCollection, + app.registerRenderSubview(this, parametersViewer, "parameters-viewer-container"); + }, + renderReactionsView: function () { + let reactionsViewer = new ReactionsViewer({ + collection: this.model.reactions }); - var rulesViewer = new RulesViewer({ - collection: this.model.rules, + app.registerRenderSubview(this, reactionsViewer, "reactions-viewer-container"); + }, + renderRulesView: function () { + let rulesViewer = new RulesViewer({ + collection: this.model.rules }); - var modelSettingsViewer = new ModelSettingsViewer({ - model: this.model.modelSettings, + app.registerRenderSubview(this, rulesViewer, "rules-viewer-container"); + }, + renderSBMLComponentsView: function () { + let sbmlComponentsView = new SBMLComponentsView({ + functionDefinitions: this.model.functionDefinitions, + viewMode: true }); - this.registerRenderSubview(speciesViewer, "species-viewer-container"); - this.registerRenderSubview(parametersViewer, "parameters-viewer-container"); - this.registerRenderSubview(reactionsViewer, "reactions-viewer-container"); - this.registerRenderSubview(eventsViewer, "events-viewer-container"); - this.registerRenderSubview(rulesViewer, "rules-viewer-container"); - this.registerRenderSubview(modelSettingsViewer, "model-settings-viewer-container"); + app.registerRenderSubview(this, sbmlComponentsView, "sbml-components-viewer-container"); }, - registerRenderSubview: function (view, hook) { - this.registerSubview(view); - this.renderSubview(view, this.queryByHook(hook)); + renderSpeciesView: function () { + let speciesViewer = new SpeciesViewer({ + collection: this.model.species + }); + app.registerRenderSubview(this, speciesViewer, "species-viewer-container"); }, changeCollapseButtonText: function (e) { - let source = e.target.dataset.hook - let collapseContainer = $(this.queryByHook(source).dataset.target) - if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) { - let collapseBtn = $(this.queryByHook(source)) - let text = collapseBtn.text(); - text === '+' ? collapseBtn.text('-') : collapseBtn.text('+'); - } - }, -}); \ No newline at end of file + app.changeCollapseButtonText(this, e); + } +}); diff --git a/client/views/models-viewer.js b/client/views/models-viewer.js deleted file mode 100644 index 6efca88b22..0000000000 --- a/client/views/models-viewer.js +++ /dev/null @@ -1,47 +0,0 @@ -/* -StochSS is a platform for simulating biochemical systems -Copyright (C) 2019-2020 StochSS developers. - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . -*/ - -var $ = require('jquery'); -//views -var View = require('ampersand-view'); -var ModelViewer = require('./model-viewer'); -//templates -var template = require('../templates/includes/modelsViewer.pug'); - -module.exports = View.extend({ - template: template, - events: { - 'click [data-hook=collapse-models]' : 'changeCollapseButtonText' - }, - initialize: function (attrs, options) { - View.prototype.initialize.apply(this, arguments); - }, - render: function (attrs, options) { - View.prototype.render.apply(this, arguments); - this.renderCollection(this.collection, ModelViewer, this.queryByHook('model-container')) - }, - changeCollapseButtonText: function (e) { - let source = e.target.dataset.hook - let collapseContainer = $(this.queryByHook(source).dataset.target) - if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) { - let collapseBtn = $(this.queryByHook(source)) - let text = collapseBtn.text(); - text === '+' ? collapseBtn.text('-') : collapseBtn.text('+'); - } - } -}) \ No newline at end of file diff --git a/client/views/parameter-settings.js b/client/views/parameter-settings.js new file mode 100644 index 0000000000..50f47229df --- /dev/null +++ b/client/views/parameter-settings.js @@ -0,0 +1,113 @@ +/* +StochSS is a platform for simulating biochemical systems +Copyright (C) 2019-2020 StochSS developers. + +This program is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with this program. If not, see . +*/ + +let $ = require('jquery'); +//support files +let app = require('../app'); +let Tooltips = require('../tooltips'); +//models +let Model = require('../models/model'); +//views +let View = require('ampersand-view'); +let ParameterView = require('./sweep-parameter'); +let SelectView = require('ampersand-select-view'); +//templates +let template = require('../templates/includes/parameterSettings.pug'); + +module.exports = View.extend({ + template: template, + events: { + 'change [data-hook=variable-of-interest-list]' : 'setVariableOfInterest', + 'click [data-hook=collapse]' : 'changeCollapseButtonText', + 'click [data-hook=add-ps-parameter]' : 'handleAddParameterClick' + }, + initialize: function (attrs, options) { + View.prototype.initialize.apply(this, arguments); + this.tooltips = Tooltips.parameterSweepSettings; + this.stochssModel = new Model({ + directory: attrs.modelDirectory + }); + let self = this; + app.getXHR(this.stochssModel.url(), { + success: function (err, response, body) { + self.stochssModel.set(body) + self.renderSubviews(); + } + }); + }, + changeCollapseButtonText: function (e) { + app.changeCollapseButtonText(this, e); + }, + getParameter: function () { + let parameters = this.model.parameters.map(function (param) { return param.paramID }); + let target = this.stochssModel.parameters.filter(function (param) { + return !parameters.includes(param.compID); + })[0]; + return target; + }, + handleAddParameterClick: function (e) { + let target = this.getParameter(); + this.model.parameters.addSweepParameter(target.compID, target.name); + }, + renderParametersCollection: function () { + let options = {"viewOptions": { + stochssParams: this.stochssModel.parameters + }} + this.renderCollection( + this.model.parameters, + ParameterView, + this.queryByHook("ps-parameter-collection"), + options + ); + }, + renderSpeciesOfInterestView: function () { + let options = this.stochssModel.species.map(function (specie) { + return [specie.compID, specie.name]; + }); + let soi = this.model.speciesOfInterest.compID; + let speciesOfInterestView = new SelectView({ + name: 'species-of-interest', + required: true, + idAttribute: 'cid', + textAttribute: 'name', + eagerValidate: true, + options: options, + value: soi + }); + app.registerRenderSubview(this, speciesOfInterestView, "variable-of-interest-list"); + }, + renderSubviews: function () { + if(!Boolean(this.model.speciesOfInterest.name)) { + this.model.speciesOfInterest = this.stochssModel.species.at(0); + } + this.model.updateVariables(this.stochssModel.parameters); + this.model.parameters.on("add remove", function () { + let disable = this.model.parameters.length >= 6 || this.model.parameters.length >= this.stochssModel.parameters.length + $(this.queryByHook("add-ps-parameter")).prop("disabled", disable) + }, this) + this.renderSpeciesOfInterestView(); + this.renderParametersCollection(); + }, + setVariableOfInterest: function (e) { + let target = e.target.value; + let variable = this.stochssModel.species.filter(function (specie) { + return specie.compID === Number(target); + })[0]; + this.model.speciesOfInterest = variable; + } +}); \ No newline at end of file diff --git a/client/views/parameter-sweep-settings-viewer.js b/client/views/parameter-sweep-settings-viewer.js deleted file mode 100644 index ae33389d35..0000000000 --- a/client/views/parameter-sweep-settings-viewer.js +++ /dev/null @@ -1,52 +0,0 @@ -/* -StochSS is a platform for simulating biochemical systems -Copyright (C) 2019-2020 StochSS developers. - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . -*/ - -var $ = require('jquery'); -//views -var View = require('ampersand-view'); -//templates -var template = require('../templates/includes/parameterSweepSettingsViewer.pug'); - -module.exports = View.extend({ - template: template, - events: { - 'click [data-hook=collapse]' : 'changeSettingsCollapseButtonText', - }, - initialize: function (attrs, options) { - View.prototype.initialize.apply(this, arguments); - }, - render: function () { - View.prototype.render.apply(this, arguments); - var sweepType = "Sweep Type: " - var p1CurrentVal = eval(this.model.parameterOne.expression) - $(this.queryByHook('p1-current-value-viewer')).text(p1CurrentVal) - if(this.model.is1D) { - sweepType += "One Parameter" - }else{ - sweepType += "Two Parameters" - var p2CurrentVal = eval(this.model.parameterTwo.expression) - $(this.queryByHook('p2-current-value-viewer')).text(p2CurrentVal) - $(this.queryByHook('p2-variable-viewer')).collapse('show') - } - $(this.queryByHook('sweep-type-viewer')).text(sweepType) - }, - changeSettingsCollapseButtonText: function () { - var text = $(this.queryByHook('collapse')).text(); - text === '+' ? $(this.queryByHook('collapse')).text('-') : $(this.queryByHook('collapse')).text('+'); - }, -}); \ No newline at end of file diff --git a/client/views/parameter-sweep-settings.js b/client/views/parameter-sweep-settings.js deleted file mode 100644 index 5c1dae9451..0000000000 --- a/client/views/parameter-sweep-settings.js +++ /dev/null @@ -1,247 +0,0 @@ -/* -StochSS is a platform for simulating biochemical systems -Copyright (C) 2019-2020 StochSS developers. - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . -*/ - -var $ = require('jquery'); -//support files -var tests = require('./tests'); -var Tooltips = require('../tooltips'); -//views -var View = require('ampersand-view'); -var InputView = require('./input'); -var SelectView = require('ampersand-select-view'); -//templates -var template = require('../templates/includes/parameterSweepSettings.pug'); - -module.exports = View.extend({ - template: template, - events: { - 'click [data-hook=collapse]' : 'changeCollapseButtonText', - 'change [data-hook=one-parameter]' : 'updateParamSweepType', - 'change [data-hook=two-parameter]' : 'updateParamSweepType', - 'change [data-hook=sweep-variable-one-select]' : 'selectSweepVarOne', - 'change [data-hook=sweep-variable-two-select]' : 'selectSweepVarTwo', - 'change [data-hook=specie-of-interest-list]' : 'selectSpeciesOfInterest' - }, - initialize: function (attrs, options) { - View.prototype.initialize.apply(this, arguments); - this.stochssModel = attrs.stochssModel; - this.tooltips = Tooltips.parameterSweepSettings; - }, - render: function () { - View.prototype.render.apply(this, arguments); - var parameters = this.stochssModel.parameters; - var species = this.stochssModel.species; - var paramNames = parameters.map(function (parameter) { return parameter.name}); - var speciesNames = species.map(function (specie) { return specie.name}); - var speciesOfInterestView = new SelectView({ - label: '', - name: 'species-of-interest', - required: true, - idAttribute: 'cid', - options: speciesNames, - value: this.model.speciesOfInterest.name - }); - var parameterOneView = new SelectView({ - label: '', - name: 'sweep-variable-one', - required: true, - idAttribute: 'cid', - options: paramNames, - value: this.model.parameterOne.name - }); - var parameterTwoView = new SelectView({ - label: '', - name: 'sweep-variable-two', - required: true, - idAttribute: 'cid', - options: paramNames, - value: this.model.parameterTwo.name - }); - if(parameters.length > 1){ - $(this.queryByHook('two-parameter')).prop('disabled', false) - $(this.queryByHook('one-parameter')).prop('checked', this.model.is1D) - $(this.queryByHook('two-parameter')).prop('checked', !this.model.is1D) - $(this.queryByHook('current-value-two-input')).text(eval(this.model.parameterTwo.expression)) - this.toggleParamTwo(); - this.registerRenderSubview(parameterTwoView, 'sweep-variable-two-select'); - } - $(this.queryByHook('current-value-one-input')).text(eval(this.model.parameterOne.expression)) - this.registerRenderSubview(speciesOfInterestView, 'specie-of-interest-list'); - this.registerRenderSubview(parameterOneView, 'sweep-variable-one-select'); - }, - update: function () { - }, - updateValid: function () { - }, - updateParamSweepType: function (e) { - var type = e.target.dataset.name - this.model.is1D = type === '1D' - this.toggleParamTwo() - }, - toggleParamTwo: function () { - if(!this.model.is1D){ - $(this.queryByHook('parameter-two-row')).collapse('show'); - }else{ - $(this.queryByHook('parameter-two-row')).collapse('hide'); - } - }, - registerRenderSubview: function (view, hook) { - this.registerSubview(view); - this.renderSubview(view, this.queryByHook(hook)); - }, - selectSweepVarOne: function (e) { - var val = e.target.selectedOptions.item(0).text; - var parameter = this.getParameter(val); - this.model.parameterOne = parameter - var currentValue = eval(parameter.expression) - this.model.p1Min = currentValue * 0.5; - this.model.p1Max = currentValue * 1.5; - $(this.queryByHook('current-value-one-input')).text(currentValue); - $(this.queryByHook('minimum-value-one-input')).find('input').val(this.model.p1Min) - $(this.queryByHook('maximum-value-one-input')).find('input').val(this.model.p1Max) - }, - selectSweepVarTwo: function (e) { - var val = e.target.selectedOptions.item(0).text; - var parameter = this.getParameter(val); - this.model.parameterTwo = parameter - var currentValue = eval(parameter.expression) - this.model.p2Min = currentValue * 0.5; - this.model.p2Max = currentValue * 1.5; - $(this.queryByHook('current-value-two-input')).text(currentValue); - $(this.queryByHook('minimum-value-two-input')).find('input').val(this.model.p2Min) - $(this.queryByHook('maximum-value-two-input')).find('input').val(this.model.p2Max) - }, - selectSpeciesOfInterest: function (e) { - var val = e.target.selectedOptions.item(0).text; - var species = this.getSpecies(val); - this.model.speciesOfInterest = species - }, - getSpecies: function (name) { - var species = this.stochssModel.species.filter(function (specie) { - if(specie.name === name) return specie - })[0]; - return species; - }, - getParameter: function (val) { - var parameter = this.stochssModel.parameters.filter(function (parameter) { - if(parameter.name === val) return parameter; - })[0]; - return parameter; - }, - changeCollapseButtonText: function (e) { - let source = e.target.dataset.hook - let collapseContainer = $(this.queryByHook(source).dataset.target) - if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) { - let collapseBtn = $(this.queryByHook(source)) - let text = collapseBtn.text(); - text === '+' ? collapseBtn.text('-') : collapseBtn.text('+'); - } - }, - subviews: { - param1MinValueInput: { - hook: 'minimum-value-one-input', - prepareView: function (el) { - return new InputView({ - parent: this, - required: true, - name: 'param-1-min-value', - label: '', - tests: tests.valueTests, - modelKey: 'p1Min', - valueType: 'number', - value: this.model.p1Min - }); - } - }, - param1MaxValueInput: { - hook: 'maximum-value-one-input', - prepareView: function (el) { - return new InputView({ - parent: this, - required: true, - name: 'param-1-max-value', - label: '', - tests: tests.valueTests, - modelKey: 'p1Max', - valueType: 'number', - value: this.model.p1Max - }); - } - }, - param1StepValueInput: { - hook: 'step-one-input', - prepareView: function (el) { - return new InputView({ - parent: this, - required: true, - name: 'param-1-step-value', - label: '', - tests: tests.valueTests, - modelKey: 'p1Steps', - valueType: 'number', - value: this.model.p1Steps - }); - } - }, - param2MinValueInput: { - hook: 'minimum-value-two-input', - prepareView: function (el) { - return new InputView({ - parent: this, - required: true, - name: 'param-2-min-value', - label: '', - tests: tests.valueTests, - modelKey: 'p2Min', - valueType: 'number', - value: this.model.p2Min - }); - } - }, - param2MaxValueInput: { - hook: 'maximum-value-two-input', - prepareView: function (el) { - return new InputView({ - parent: this, - required: true, - name: 'param-2-max-value', - label: '', - tests: tests.valueTests, - modelKey: 'p2Max', - valueType: 'number', - value: this.model.p2Max - }); - } - }, - param2StepValueInput: { - hook: 'step-two-input', - prepareView: function (el) { - return new InputView({ - parent: this, - required: true, - name: 'param-2-step-value', - label: '', - tests: tests.valueTests, - modelKey: 'p2Steps', - valueType: 'number', - value: this.model.p2Steps - }); - } - }, - } -}); \ No newline at end of file diff --git a/client/views/parameters-editor.js b/client/views/parameters-editor.js index 57f71e565b..aa72c100c5 100644 --- a/client/views/parameters-editor.js +++ b/client/views/parameters-editor.js @@ -18,6 +18,7 @@ along with this program. If not, see . var $ = require('jquery'); //support files +let app = require('../app'); var Tooltips = require('../tooltips'); //views var View = require('ampersand-view'); @@ -29,14 +30,13 @@ module.exports = View.extend({ template: template, events: { 'click [data-hook=add-parameter]' : 'addParameter', - 'click [data-hook=save-parameters]' : 'switchToViewMode', 'click [data-hook=collapse]' : 'changeCollapseButtonText', }, initialize: function (attrs, options) { var self = this; View.prototype.initialize.apply(this, arguments); + this.readOnly = attrs.readOnly ? attrs.readOnly : false; this.tooltips = Tooltips.parametersEditor - this.opened = attrs.opened this.collection.on('update-parameters', function (compID, parameter) { self.collection.parent.reactions.map(function (reaction) { if(reaction.rate && reaction.rate.compID === compID){ @@ -62,10 +62,19 @@ module.exports = View.extend({ }, render: function () { View.prototype.render.apply(this, arguments); - this.renderEditParameter(); - if(this.opened) { - this.openParametersContainer(); + if(this.readOnly) { + $(this.queryByHook('parameters-edit-tab')).addClass("disabled"); + $(".nav .disabled>a").on("click", function(e) { + e.preventDefault(); + return false; + }); + $(this.queryByHook('parameters-view-tab')).tab('show'); + $(this.queryByHook('edit-parameters')).removeClass('active'); + $(this.queryByHook('view-parameters')).addClass('active'); + }else{ + this.renderEditParameter(); } + this.renderViewParameter(); }, update: function () { }, @@ -78,15 +87,33 @@ module.exports = View.extend({ this.editParameterView = this.renderCollection( this.collection, EditParameterView, - this.queryByHook('parameter-list') + this.queryByHook('edit-parameter-list') ); - $(document).ready(function () { + $(function () { $('[data-toggle="tooltip"]').tooltip(); $('[data-toggle="tooltip"]').click(function () { $('[data-toggle="tooltip"]').tooltip("hide"); }); }); }, + renderViewParameter: function () { + if(this.viewParameterView) { + this.viewParameterView.remove(); + } + this.containsMdlWithAnn = this.collection.filter(function (model) {return model.annotation}).length > 0; + if(!this.containsMdlWithAnn) { + $(this.queryByHook("parameters-annotation-header")).css("display", "none"); + }else{ + $(this.queryByHook("parameters-annotation-header")).css("display", "block"); + } + let options = {viewOptions: {viewMode: true}}; + this.viewParameterView = this.renderCollection( + this.collection, + EditParameterView, + this.queryByHook('view-parameter-list'), + options + ); + }, addParameter: function () { this.collection.addParameter(); $(document).ready(function () { @@ -97,22 +124,7 @@ module.exports = View.extend({ }); }); }, - switchToViewMode: function (e) { - this.parent.modelStateButtons.clickSaveHandler(e); - this.parent.renderParametersView(mode="view"); - }, - openParametersContainer: function () { - $(this.queryByHook('parameters-list-container')).collapse('show'); - let collapseBtn = $(this.queryByHook('collapse')) - collapseBtn.trigger('click') - }, changeCollapseButtonText: function (e) { - let source = e.target.dataset.hook - let collapseContainer = $(this.queryByHook(source).dataset.target) - if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) { - let collapseBtn = $(this.queryByHook(source)) - let text = collapseBtn.text(); - text === '+' ? collapseBtn.text('-') : collapseBtn.text('+'); - } + app.changeCollapseButtonText(this, e); }, }); \ No newline at end of file diff --git a/client/views/parameters-viewer.js b/client/views/parameters-viewer.js deleted file mode 100644 index 3ec3b45078..0000000000 --- a/client/views/parameters-viewer.js +++ /dev/null @@ -1,58 +0,0 @@ -/* -StochSS is a platform for simulating biochemical systems -Copyright (C) 2019-2020 StochSS developers. - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . -*/ - -var $ = require('jquery'); -//views -var View = require('ampersand-view'); -var ViewParameter = require('./view-parameter'); -//templates -var template = require('../templates/includes/parametersViewer.pug'); - -module.exports = View.extend({ - template: template, - events: { - 'click [data-hook=collapse]' : 'changeCollapseButtonText', - 'click [data-hook=edit-parameters]' : 'switchToEditMode' - }, - initialize: function (attrs, options) { - View.prototype.initialize.apply(this, arguments); - this.containsMdlWithAnn = this.collection.filter(function (model) {return model.annotation}).length > 0 - }, - render: function () { - View.prototype.render.apply(this, arguments); - this.renderCollection(this.collection, ViewParameter, this.queryByHook('parameter-list')) - $(document).ready(function () { - $('[data-toggle="tooltip"]').tooltip(); - $('[data-toggle="tooltip"]').click(function () { - $('[data-toggle="tooltip"]').tooltip("hide"); - }); - }); - }, - switchToEditMode: function (e) { - this.parent.renderParametersView("edit", true); - }, - changeCollapseButtonText: function (e) { - let source = e.target.dataset.hook - let collapseContainer = $(this.queryByHook(source).dataset.target) - if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) { - let collapseBtn = $(this.queryByHook(source)) - let text = collapseBtn.text(); - text === '+' ? collapseBtn.text('-') : collapseBtn.text('+'); - } - }, -}); \ No newline at end of file diff --git a/client/views/plots-view.js b/client/views/plots-view.js deleted file mode 100644 index ec55f6429a..0000000000 --- a/client/views/plots-view.js +++ /dev/null @@ -1,71 +0,0 @@ -/* -StochSS is a platform for simulating biochemical systems -Copyright (C) 2019-2020 StochSS developers. - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . -*/ - -var $ = require('jquery'); -var path = require('path'); -var xhr = require('xhr'); -//support files -var Plotly = require('../lib/plotly'); -var app = require('../app'); -//views -var View = require('ampersand-view'); -//templates -var template = require('../templates/includes/plotsView.pug'); - -module.exports = View.extend({ - template: template, - events: { - 'click [data-hook=collapse-plot]' : 'changeCollapseButtonText', - }, - initialize: function (attrs, options) { - View.prototype.initialize.apply(this, arguments) - this.path = attrs.path ? attrs.path : this.parent.model.path - this.heading = attrs.heading ? attrs.heading + " - " + this.model.key : this.model.key - }, - render: function (attrs, options) { - View.prototype.render.apply(this, arguments) - this.getPlot() - }, - getPlot: function () { - var self = this; - var plotArgs = {"title":this.model.title,"xaxis":this.model.xaxis,"yaxis":this.model.yaxis} - var data = {"plt_key":this.model.key, "plt_data":plotArgs} - var endpoint = path.join(app.getApiPath(), 'workflow/plot-results')+"?path="+this.path+"&data="+JSON.stringify(data); - xhr({uri: endpoint, json: true}, function (err, response, body) { - if(response.statusCode >= 400) { - $(self.queryByHook(self.model.key+self.model.stamp)).html(body.Message) - }else{ - self.plotFigure(body) - } - }); - }, - plotFigure: function (figure) { - var self = this; - var el = this.queryByHook(this.model.key+this.model.stamp); - Plotly.newPlot(el, figure); - }, - changeCollapseButtonText: function (e) { - let source = e.target.dataset.hook - let collapseContainer = $(this.queryByHook(source).dataset.target) - if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) { - let collapseBtn = $(this.queryByHook(source)) - let text = collapseBtn.text(); - text === '+' ? collapseBtn.text('-') : collapseBtn.text('+'); - } - } -}) \ No newline at end of file diff --git a/client/views/project-viewer.js b/client/views/project-viewer.js deleted file mode 100644 index a9cb97d923..0000000000 --- a/client/views/project-viewer.js +++ /dev/null @@ -1,73 +0,0 @@ -/* -StochSS is a platform for simulating biochemical systems -Copyright (C) 2019-2020 StochSS developers. - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . -*/ - -var path = require('path'); -var $ = require('jquery'); -//Views -var View = require('ampersand-view'); -var ModelsCollectionView = require('./models-viewer'); -var WorkflowGroupsCollectionView = require('./workflow-groups-viewer'); -//templates -var template = require('../templates/includes/projectViewer.pug'); - -module.exports = View.extend({ - template: template, - events: { - 'click [data-hook=collapse-project]' : 'changeCollapseButtonText' - }, - initialize: function (attrs, options) { - View.prototype.initialize.apply(this, arguments) - this.name = attrs.name - }, - render: function (attrs, options) { - View.prototype.render.apply(this, arguments) - this.renderModelsCollection() - this.renderWorkflowGroupsCollection() - }, - renderModelsCollection: function () { - if(this.modelsCollectionView) { - this.modelsCollectionView.remove() - } - this.modelsCollectionView = new ModelsCollectionView({ - collection: this.model.models - }); - this.registerRenderSubview(this.modelsCollectionView, "models-collection-container") - }, - renderWorkflowGroupsCollection: function () { - if(this.workflowGroupsCollectionView) { - this.workflowGroupsCollectionView.remove() - } - this.workflowGroupsCollectionView = new WorkflowGroupsCollectionView({ - collection: this.model.workflowGroups - }); - this.registerRenderSubview(this.workflowGroupsCollectionView, "workflow-groups-collection-container") - }, - registerRenderSubview: function (view, hook) { - this.registerSubview(view); - this.renderSubview(view, this.queryByHook(hook)); - }, - changeCollapseButtonText: function (e) { - let source = e.target.dataset.hook - let collapseContainer = $(this.queryByHook(source).dataset.target) - if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) { - let collapseBtn = $(this.queryByHook(source)) - let text = collapseBtn.text(); - text === '+' ? collapseBtn.text('-') : collapseBtn.text('+'); - } - } -}); \ No newline at end of file diff --git a/client/views/reaction-details.js b/client/views/reaction-details.js index 25c362ae72..36e1949844 100644 --- a/client/views/reaction-details.js +++ b/client/views/reaction-details.js @@ -19,6 +19,8 @@ along with this program. If not, see . var _ = require('underscore'); var $ = require('jquery'); var katex = require('katex'); +//support files +let app = require('../app'); //config var ReactionTypes = require('../reaction-types'); //models @@ -100,7 +102,7 @@ module.exports = View.extend({ value: this.model.propensity, placeholder: "--No Expression Entered--" }); - this.registerRenderSubview(propensityView, 'select-rate-parameter') + app.registerRenderSubview(this, propensityView, 'select-rate-parameter') $(this.queryByHook('rate-parameter-label')).text('Propensity:') $(this.queryByHook('rate-parameter-tooltip')).prop('title', this.parent.tooltips.propensity); }else{ @@ -123,7 +125,7 @@ module.exports = View.extend({ // Else fetch the right Parameter from Parameters based on existing rate value: this.model.rate.name ? this.getRateFromParameters(this.model.rate.name) : this.model.collection.parent.parameters.at(0), }); - this.registerRenderSubview(rateParameterView, 'select-rate-parameter'); + app.registerRenderSubview(this, rateParameterView, 'select-rate-parameter'); $(this.queryByHook('rate-parameter-label')).text('Rate Parameter:') $(this.queryByHook('rate-parameter-tooltip')).prop('title', this.parent.tooltips.rate); } @@ -132,10 +134,10 @@ module.exports = View.extend({ model: this.model, parent: this }); - this.registerRenderSubview(typesView, 'domain-types-editor'); + app.registerRenderSubview(this, typesView, 'domain-types-editor'); } - this.registerRenderSubview(reactantsView, 'reactants-editor'); - this.registerRenderSubview(productsView, 'products-editor'); + app.registerRenderSubview(this, reactantsView, 'reactants-editor'); + app.registerRenderSubview(this, productsView, 'products-editor'); this.totalRatio = this.getTotalReactantRatio(); $(document).ready(function () { $('[data-toggle="tooltip"]').tooltip(); @@ -172,7 +174,7 @@ module.exports = View.extend({ value: ReactionTypes[this.model.reactionType].label, }); - this.registerRenderSubview(this.reactionTypesSelectView, 'select-reaction-type'); + app.registerRenderSubview(this, this.reactionTypesSelectView, 'select-reaction-type'); this.renderReactionTypes(); }, selectRateParam: function (e) { @@ -222,10 +224,6 @@ module.exports = View.extend({ getReactionTypeLabels: function () { return _.map(ReactionTypes, function (val, key) { return val.label; }) }, - registerRenderSubview: function (view, hook) { - this.registerSubview(view); - this.renderSubview(view, this.queryByHook(hook)); - }, getTotalReactantRatio: function () { return this.model.reactants.length; }, diff --git a/client/views/reactions-editor.js b/client/views/reactions-editor.js index 4ab2b22b91..c54ef00484 100644 --- a/client/views/reactions-editor.js +++ b/client/views/reactions-editor.js @@ -21,6 +21,7 @@ var katex = require('katex'); var _ = require('underscore'); var $ = require('jquery'); //support files +let app = require('../app'); var ReactionTypes = require('../reaction-types'); var Tooltips = require('../tooltips'); //models @@ -98,6 +99,7 @@ module.exports = View.extend({ this.openReactionsContainer(); } this.toggleProcessError() + $(this.queryByHook('massaction-message')).prop('hidden', this.collection.parent.parameters.length > 0); }, update: function () { }, @@ -132,9 +134,11 @@ module.exports = View.extend({ }, toggleReactionTypes: function (e, prev, curr) { if(curr && curr.add && this.collection.parent.parameters.length === 1){ + $(this.queryByHook('massaction-message')).prop('hidden', true); $(this.queryByHook('add-reaction-full')).prop('hidden', false); $(this.queryByHook('add-reaction-partial')).prop('hidden', true); }else if(curr && !curr.add && this.collection.parent.parameters.length === 0){ + $(this.queryByHook('massaction-message')).prop('hidden', false); $(this.queryByHook('add-reaction-full')).prop('hidden', true); $(this.queryByHook('add-reaction-partial')).prop('hidden', false); } @@ -192,15 +196,7 @@ module.exports = View.extend({ collapseBtn.trigger('click') }, changeCollapseButtonText: function (e) { - if(e.target.dataset && e.target.dataset.toggle === "collapse") { - let source = e.target.dataset.hook - let collapseContainer = $(this.queryByHook(source).dataset.target) - if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) { - let collapseBtn = $(this.queryByHook(source)) - let text = collapseBtn.text(); - text === '+' ? collapseBtn.text('-') : collapseBtn.text('+'); - } - } + app.changeCollapseButtonText(this, e); }, getDefaultSpecie: function () { var value = this.collection.parent.species.models[0]; diff --git a/client/views/reactions-viewer.js b/client/views/reactions-viewer.js index 86acc195a5..ee31d9b390 100644 --- a/client/views/reactions-viewer.js +++ b/client/views/reactions-viewer.js @@ -17,6 +17,8 @@ along with this program. If not, see . */ var $ = require('jquery'); +//support files +let app = require('../app'); //views var View = require('ampersand-view'); var ViewReactions = require('./view-reactions'); @@ -47,12 +49,6 @@ module.exports = View.extend({ this.parent.renderReactionsView("edit", true); }, changeCollapseButtonText: function (e) { - let source = e.target.dataset.hook - let collapseContainer = $(this.queryByHook(source).dataset.target) - if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) { - let collapseBtn = $(this.queryByHook(source)) - let text = collapseBtn.text(); - text === '+' ? collapseBtn.text('-') : collapseBtn.text('+'); - } + app.changeCollapseButtonText(this, e); }, }); \ No newline at end of file diff --git a/client/views/rules-editor.js b/client/views/rules-editor.js index 27ef7d1537..fdba4cb842 100644 --- a/client/views/rules-editor.js +++ b/client/views/rules-editor.js @@ -18,6 +18,7 @@ along with this program. If not, see . var $ = require('jquery'); //support files +let app = require('../app'); var Tooltips = require('../tooltips'); //views var View = require('ampersand-view'); @@ -96,12 +97,6 @@ module.exports = View.extend({ collapseBtn.trigger('click') }, changeCollapseButtonText: function (e) { - let source = e.target.dataset.hook - let collapseContainer = $(this.queryByHook(source).dataset.target) - if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) { - let collapseBtn = $(this.queryByHook(source)) - let text = collapseBtn.text(); - text === '+' ? collapseBtn.text('-') : collapseBtn.text('+'); - } + app.changeCollapseButtonText(this, e); }, }); \ No newline at end of file diff --git a/client/views/rules-viewer.js b/client/views/rules-viewer.js index 88377a2033..a8fce201da 100644 --- a/client/views/rules-viewer.js +++ b/client/views/rules-viewer.js @@ -17,6 +17,8 @@ along with this program. If not, see . */ var $ = require('jquery'); +//support files +let app = require('../app'); //views var View = require('ampersand-view'); var ViewRules = require('./view-rules'); @@ -47,12 +49,6 @@ module.exports = View.extend({ this.parent.renderRulesView("edit", true); }, changeCollapseButtonText: function (e) { - let source = e.target.dataset.hook - let collapseContainer = $(this.queryByHook(source).dataset.target) - if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) { - let collapseBtn = $(this.queryByHook(source)) - let text = collapseBtn.text(); - text === '+' ? collapseBtn.text('-') : collapseBtn.text('+'); - } + app.changeCollapseButtonText(this, e); }, }); \ No newline at end of file diff --git a/client/views/sbml-component-editor.js b/client/views/sbml-component-editor.js index 75e5324e50..565b097bc4 100644 --- a/client/views/sbml-component-editor.js +++ b/client/views/sbml-component-editor.js @@ -18,6 +18,7 @@ along with this program. If not, see . var $ = require('jquery'); //support files +let app = require('../app'); var Tooltips = require('../tooltips'); //views var View = require('ampersand-view'); @@ -35,6 +36,7 @@ module.exports = View.extend({ View.prototype.initialize.apply(this, arguments); this.tooltips = Tooltips.sbmlComponentsEditor this.functionDefinitions = attrs.functionDefinitions; + this.viewMode = attrs.viewMode; }, render: function () { View.prototype.render.apply(this, arguments); @@ -57,12 +59,6 @@ module.exports = View.extend({ }); }, changeCollapseButtonText: function (e) { - let source = e.target.dataset.hook - let collapseContainer = $(this.queryByHook(source).dataset.target) - if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) { - let collapseBtn = $(this.queryByHook(source)) - let text = collapseBtn.text(); - text === '+' ? collapseBtn.text('-') : collapseBtn.text('+'); - } + app.changeCollapseButtonText(this, e); }, }); \ No newline at end of file diff --git a/client/views/settings-viewer.js b/client/views/settings-viewer.js new file mode 100644 index 0000000000..918bfddf2b --- /dev/null +++ b/client/views/settings-viewer.js @@ -0,0 +1,77 @@ +/* +StochSS is a platform for simulating biochemical systems +Copyright (C) 2019-2020 StochSS developers. + +This program is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with this program. If not, see . +*/ + +let $ = require('jquery'); +//support files +let app = require('../app'); +//views +let View = require('ampersand-view'); +let ParameterViewerView = require('./view-sweep-parameter'); +//templates +let template = require('../templates/includes/settingsViewer.pug'); + +module.exports = View.extend({ + template: template, + events: { + 'click [data-hook=collapse-settings-viewer]' : 'changeCollapseButtonText', + 'click [data-hook=collapse-ts-settings]' : 'changeCollapseButtonText', + 'click [data-hook=collapse-sim-settings]' : 'changeCollapseButtonText' + }, + initialize: function (attrs, options) { + View.prototype.initialize.apply(this, arguments); + this.algorithm = this.model.simulationSettings.isAutomatic ? + "The algorithm was chosen based on your model." : + this.model.simulationSettings.algorithm + }, + render: function (attrs, options) { + View.prototype.render.apply(this, arguments); + if(!this.parent.model.newFormat) { + $(this.queryByHook("timespan-settings-viewer-container")).css("display", "none"); + } + let simSettings = this.model.simulationSettings; + let hideDeterministic = simSettings.isAutomatic || simSettings.algorithm === "SSA" || simSettings.algorithm === "Tau-Leaping"; + let hideStochastic = simSettings.isAutomatic || simSettings.algorithm === "ODE" + if(hideDeterministic) { + $(this.queryByHook("view-deterministic-settings")).css("display", "none"); + } + if(hideStochastic) { + $(this.queryByHook("view-stochastic-settings")).css("display", "none"); + }else if(simSettings.algorithm === "SSA") { + $(this.queryByHook("view-tau-tolerance")).css("display", "none"); + } + if(this.parent.model.type === "Parameter Sweep") { + this.renderParametersCollection(); + }else{ + $(this.queryByHook("param-sweep-settings-viewer-container")).css("display", "none"); + } + }, + changeCollapseButtonText: function (e) { + app.changeCollapseButtonText(this, e); + }, + renderParametersCollection: function () { + let options = {"viewOptions": { + parameters: this.model.parent.model.parameters + }} + this.renderCollection( + this.model.parameterSweepSettings.parameters, + ParameterViewerView, + this.queryByHook("view-sweep-parameters"), + options + ); + }, +}); diff --git a/client/views/settings.js b/client/views/settings.js new file mode 100644 index 0000000000..3cec47d4f8 --- /dev/null +++ b/client/views/settings.js @@ -0,0 +1,161 @@ +/* +StochSS is a platform for simulating biochemical systems +Copyright (C) 2019-2020 StochSS developers. + +This program is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with this program. If not, see . +*/ + +let $ = require('jquery'); +let path = require('path'); +let _ = require('underscore'); +//support file +let app = require('../app'); +//views +let View = require('ampersand-view'); +let TimespanSettingsView = require('./timespan-settings'); +let SimulationSettingsView = require('./simulation-settings'); +let ParameterSettingsView = require('./parameter-settings'); +//templates +let template = require('../templates/includes/settings.pug'); + +module.exports = View.extend({ + template: template, + events: { + 'click [data-hook=collapse-settings]' : 'changeCollapseButtonText', + 'click [data-hook=save]' : 'clickSaveHandler', + 'click [data-hook=start-job]' : 'clickStartJobHandler', + 'click [data-hook=edit-model]' : 'clickEditModelHandler' + }, + initialize: function (attrs, options) { + View.prototype.initialize.apply(this, arguments); + }, + render: function() { + View.prototype.render.apply(this, arguments); + if(this.parent.model.newFormat) { + $(this.queryByHook("start-job")).text("Start New Job"); + this.renderTimespanSettingsView(); + } + if(this.parent.model.type === "Parameter Sweep") { + this.renderParameterSettingsView(); + if(this.model.parameterSweepSettings.parameters.length < 1) { + $(this.queryByHook("start-job")).prop("disabled", true); + } + this.model.parameterSweepSettings.parameters.on("add remove", _.bind(function (e) { + let numParams = this.model.parameterSweepSettings.parameters.length; + $(this.queryByHook("start-job")).prop("disabled", numParams < 1); + }, this)) + } + this.renderSimulationSettingsView(); + }, + changeCollapseButtonText: function (e) { + app.changeCollapseButtonText(this, e); + }, + clickEditModelHandler: function (e) { + this.parent.handleSaveWorkflow(e, _.bind(function () { + let queryStr = "?path=" + this.parent.model.model; + let endpoint = path.join(app.getBasePath(), "stochss/models/edit") + queryStr; + window.location.href = endpoint; + }, this)); + }, + clickSaveHandler: function (e) { + this.saving(); + this.parent.handleSaveWorkflow(e, _.bind(this.saved, this)); + }, + clickStartJobHandler: function (e) { + this.saving(); + let self = this; + let type = this.parent.model.type === "Ensemble Simulation" ? "gillespy" : "parameterSweep"; + let data = {"settings": this.parent.model.settings.toJSON(), + "mdl_path": this.parent.model.model, + "type": type, "time_stamp": this.getTimeStamp()}; + let queryStr = "?path=" + this.parent.model.directory + "&data=" + JSON.stringify(data); + let initEndpoint = path.join(app.getApiPath(), "workflow/init-job") + queryStr; + app.getXHR(initEndpoint, { + success: function (err, response, body) { + self.saved(); + let runQuery = "?path=" + body + "&type=" + type; + let runEndpoint = path.join(app.getApiPath(), "workflow/run-job") + runQuery; + app.getXHR(runEndpoint, { + success: function (err, response, body) { + self.parent.updateWorkflow(true); + } + }); + } + }); + }, + getTimeStamp: function () { + if(!this.parent.model.newFormat) { + return null; + } + var date = new Date(); + var year = date.getFullYear(); + var month = date.getMonth() + 1; + if(month < 10){ + month = "0" + month + } + var day = date.getDate(); + if(day < 10){ + day = "0" + day + } + var hours = date.getHours(); + if(hours < 10){ + hours = "0" + hours + } + var minutes = date.getMinutes(); + if(minutes < 10){ + minutes = "0" + minutes + } + var seconds = date.getSeconds(); + if(seconds < 10){ + seconds = "0" + seconds + } + return "_" + month + day + year + "_" + hours + minutes + seconds; + }, + renderParameterSettingsView: function () { + if(this.parameterSettingsView) { + this.parameterSettingsView.remove(); + } + this.parameterSettingsView = new ParameterSettingsView({ + model: this.model.parameterSweepSettings, + modelDirectory: this.parent.model.model + }); + app.registerRenderSubview(this, this.parameterSettingsView, "param-sweep-settings-container"); + }, + renderSimulationSettingsView: function () { + if(this.simulationSettingsView) { + this.simulationSettingsView.remove(); + } + this.simulationSettingsView = new SimulationSettingsView({ + model: this.model.simulationSettings + }); + app.registerRenderSubview(this, this.simulationSettingsView, "sim-settings-container"); + }, + renderTimespanSettingsView: function () { + if(this.timespanSettingsView) { + this.timespanSettingsView.remove(); + } + this.timespanSettingsView = new TimespanSettingsView({ + model: this.model.timespanSettings + }); + app.registerRenderSubview(this, this.timespanSettingsView, "timespan-settings-container"); + }, + saved: function () { + $(this.queryByHook('saving-workflow')).css("display", "none"); + $(this.queryByHook('saved-workflow')).css("display", "inline-block"); + }, + saving: function () { + $(this.queryByHook('saving-workflow')).css("display", "inline-block"); + $(this.queryByHook('saved-workflow')).css("display", "none"); + } +}); \ No newline at end of file diff --git a/client/views/simulation-settings-viewer.js b/client/views/simulation-settings-viewer.js deleted file mode 100644 index e8b8de5145..0000000000 --- a/client/views/simulation-settings-viewer.js +++ /dev/null @@ -1,54 +0,0 @@ -/* -StochSS is a platform for simulating biochemical systems -Copyright (C) 2019-2020 StochSS developers. - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . -*/ - -var $ = require('jquery'); -//views -var View = require('ampersand-view'); -//templates -var template = require('../templates/includes/simulationSettingsViewer.pug'); - -module.exports = View.extend({ - template: template, - events: { - 'click [data-hook=collapse]' : 'changeSettingsCollapseButtonText', - }, - initialize: function (attrs, options) { - View.prototype.initialize.apply(this, arguments); - this.algorithm = this.model.algorithm === "Hybrid-Tau-Leaping" ? - "Algorithm: Hybrid ODE/SSA" : "Algorithm: " + this.model.algorithm - }, - render: function () { - View.prototype.render.apply(this, arguments); - var algorithm = this.model.algorithm - if(!this.model.isAutomatic && (algorithm === "ODE" || algorithm === "Hybrid-Tau-Leaping")){ - $(this.queryByHook('deterministic')).collapse('show') - } - if(!this.model.isAutomatic && (algorithm === "SSA" || algorithm === "Tau-Leaping" || algorithm === "Hybrid-Tau-Leaping")){ - $(this.queryByHook('stochastic')).collapse('show') - if(algorithm === "SSA"){ - $(this.queryByHook('SSA')).collapse('show') - }else{ - $(this.queryByHook('Tau')).collapse('show') - } - } - }, - changeSettingsCollapseButtonText: function () { - var text = $(this.queryByHook('collapse')).text(); - text === '+' ? $(this.queryByHook('collapse')).text('-') : $(this.queryByHook('collapse')).text('+'); - }, -}); \ No newline at end of file diff --git a/client/views/simulation-settings.js b/client/views/simulation-settings.js index 3513730619..024c7d381b 100644 --- a/client/views/simulation-settings.js +++ b/client/views/simulation-settings.js @@ -16,31 +16,30 @@ You should have received a copy of the GNU General Public License along with this program. If not, see . */ -var $ = require('jquery'); +let $ = require('jquery'); //support files -var tests = require('./tests'); -var Tooltips = require('../tooltips'); +let app = require('../app'); +let tests = require('./tests'); +let Tooltips = require('../tooltips'); //views -var View = require('ampersand-view'); -var InputView = require('./input'); +let View = require('ampersand-view'); +let InputView = require('./input'); //templates -var template = require('../templates/includes/simulationSettings.pug'); +let template = require('../templates/includes/simulationSettings.pug'); module.exports = View.extend({ template: template, events: { - 'click [data-hook=collapse]' : 'changeCollapseButtonText', 'change [data-hook=select-ode]' : 'handleSelectSimulationAlgorithmClick', 'change [data-hook=select-ssa]' : 'handleSelectSimulationAlgorithmClick', 'change [data-hook=select-tau-leaping]' : 'handleSelectSimulationAlgorithmClick', 'change [data-hook=select-hybrid-tau]' : 'handleSelectSimulationAlgorithmClick', 'change [data-hook=select-automatic]' : 'handleSelectSimulationAlgorithmClick', + 'click [data-hook=collapse]' : 'changeCollapseButtonText' }, initialize: function (attrs, options) { View.prototype.initialize.apply(this, arguments); - this.model = attrs.model; - this.stochssModel = attrs.stochssModel - this.tooltips = Tooltips.simulationSettings + this.tooltips = Tooltips.simulationSettings; }, render: function () { View.prototype.render.apply(this, arguments); @@ -50,66 +49,51 @@ module.exports = View.extend({ $(this.queryByHook('select-tau-leaping')).prop('checked', Boolean(this.model.algorithm === "Tau-Leaping")); $(this.queryByHook('select-hybrid-tau')).prop('checked', Boolean(this.model.algorithm === "Hybrid-Tau-Leaping")); }else{ - $(this.queryByHook('settings-container')).collapse('hide') + $(this.queryByHook('settings-container')).collapse('hide'); $(this.queryByHook('select-automatic')).prop('checked', this.model.isAutomatic); - this.model.letUsChooseForYou(this.stochssModel); } this.disableInputFieldByAlgorithm(); $(document).ready(function () { $('[data-toggle="tooltip"]').tooltip(); $('[data-toggle="tooltip"]').click(function () { - $('[data-toggle="tooltip"]').tooltip("hide"); - - }); + $('[data-toggle="tooltip"]').tooltip("hide"); + }); }); }, - update: function (e) { - }, - updateValid: function () { - }, changeCollapseButtonText: function (e) { - let source = e.target.dataset.hook - let collapseContainer = $(this.queryByHook(source).dataset.target) - if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) { - let collapseBtn = $(this.queryByHook(source)) - let text = collapseBtn.text(); - text === '+' ? collapseBtn.text('-') : collapseBtn.text('+'); - } - }, - handleSelectSimulationAlgorithmClick: function (e) { - var value = e.target.dataset.name; - if(value === "Automatic"){ - $(this.queryByHook('settings-container')).collapse('hide') - }else{ - $(this.queryByHook('settings-container')).collapse('show') - } - if(value === "ODE"){ - this.model.realizations = 1 - $(this.queryByHook("trajectories")).find("input").val("1") - } - this.setSimulationAlgorithm(value) - }, - setSimulationAlgorithm: function (value) { - this.model.isAutomatic = Boolean(value === 'Automatic') - if(!this.model.isAutomatic){ - this.model.algorithm = value; - }else{ - this.model.letUsChooseForYou(this.stochssModel); - } - this.disableInputFieldByAlgorithm(); + app.changeCollapseButtonText(this, e); }, disableInputFieldByAlgorithm: function () { - var isAutomatic = this.model.isAutomatic - var isODE = this.model.algorithm === "ODE"; - var isSSA = this.model.algorithm === "SSA"; - var isLeaping = this.model.algorithm === "Tau-Leaping"; - var isHybrid = this.model.algorithm === "Hybrid-Tau-Leaping"; + let isAutomatic = this.model.isAutomatic + let isODE = this.model.algorithm === "ODE"; + let isSSA = this.model.algorithm === "SSA"; + let isLeaping = this.model.algorithm === "Tau-Leaping"; + let isHybrid = this.model.algorithm === "Hybrid-Tau-Leaping"; $(this.queryByHook("relative-tolerance")).find('input').prop('disabled', !(isODE || isHybrid || isAutomatic)); $(this.queryByHook("absolute-tolerance")).find('input').prop('disabled', !(isODE || isHybrid || isAutomatic)); $(this.queryByHook("trajectories")).find('input').prop('disabled', !(isSSA || isLeaping || isHybrid || isAutomatic)); $(this.queryByHook("seed")).find('input').prop('disabled', !(isSSA || isLeaping || isHybrid || isAutomatic)); $(this.queryByHook("tau-tolerance")).find('input').prop('disabled', !(isHybrid || isLeaping || isAutomatic)); }, + handleSelectSimulationAlgorithmClick: function (e) { + let value = e.target.dataset.name; + if(value === "Automatic"){ + this.model.isAutomatic = true; + $(this.queryByHook('settings-container')).collapse('hide'); + }else{ + this.model.isAutomatic = false; + this.model.algorithm = value; + $(this.queryByHook('settings-container')).collapse('show'); + if(value === "ODE"){ + $(this.queryByHook("trajectories")).find("input").val("1"); + }else{ + $(this.queryByHook("trajectories")).find("input").val(this.model.realizations); + } + this.disableInputFieldByAlgorithm(); + } + }, + update: function (e) {}, + updateValid: function () {}, subviews: { inputRelativeTolerance: { hook: 'relative-tolerance', @@ -118,13 +102,12 @@ module.exports = View.extend({ parent: this, required: true, name: 'relative-tolerance', - label: '', tests: tests.valueTests, modelKey: 'relativeTol', valueType: 'number', value: this.model.relativeTol }); - }, + } }, inputAbsoluteTolerance: { hook: 'absolute-tolerance', @@ -133,7 +116,6 @@ module.exports = View.extend({ parent: this, required: true, name: 'absolute-tolerance', - label: '', tests: tests.valueTests, modelKey: 'absoluteTol', valueType: 'number', @@ -148,13 +130,12 @@ module.exports = View.extend({ parent: this, required: true, name: 'realizations', - label: '', tests: tests.valueTests, modelKey: 'realizations', valueType: 'number', - value: this.model.parent.isPreview ? 1 : this.model.realizations + value: this.model.algorithm === "ODE" ? 1 : this.model.realizations }); - }, + } }, inputSeed: { hook: 'seed', @@ -163,13 +144,11 @@ module.exports = View.extend({ parent: this, required: true, name: 'seed', - label: '', - tests: '', modelKey: 'seed', valueType: 'number', value: this.model.seed }); - }, + } }, inputTauTolerance: { hook: 'tau-tolerance', @@ -184,7 +163,7 @@ module.exports = View.extend({ valueType: 'number', value: this.model.tauTol }); - }, - }, - }, + } + } + } }); \ No newline at end of file diff --git a/client/views/species-editor.js b/client/views/species-editor.js index 6e47985b90..e144b43d22 100644 --- a/client/views/species-editor.js +++ b/client/views/species-editor.js @@ -18,6 +18,7 @@ along with this program. If not, see . var $ = require('jquery'); //support files +let app = require('../app'); var modals = require('../modals'); var Tooltips = require('../tooltips'); //views @@ -136,16 +137,18 @@ module.exports = View.extend({ }, setAllSpeciesModes: function (defaultMode, cb) { this.collection.parent.defaultMode = defaultMode; + this.collection.forEach(function (specie) { + specie.mode = defaultMode + if(cb) { + cb(specie) + } + }); if(!this.collection.parent.is_spatial) { if(defaultMode === "continuous") { $(this.parent.queryByHook("system-volume-container")).collapse("hide") }else{ $(this.parent.queryByHook("system-volume-container")).collapse("show") } - this.collection.map(function (specie) { - specie.mode = defaultMode - cb(specie) - }); if(defaultMode === "dynamic"){ this.renderSpeciesAdvancedView() $(this.queryByHook('advanced-species')).collapse('show'); @@ -225,12 +228,6 @@ module.exports = View.extend({ this.parent.renderSpeciesView(mode="view"); }, changeCollapseButtonText: function (e) { - let source = e.target.dataset.hook - let collapseContainer = $(this.queryByHook(source).dataset.target) - if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) { - let collapseBtn = $(this.queryByHook(source)) - let text = collapseBtn.text(); - text === '+' ? collapseBtn.text('-') : collapseBtn.text('+'); - } + app.changeCollapseButtonText(this, e); } }); \ No newline at end of file diff --git a/client/views/species-viewer.js b/client/views/species-viewer.js index 9e92ec0048..7087d36bca 100644 --- a/client/views/species-viewer.js +++ b/client/views/species-viewer.js @@ -17,6 +17,8 @@ along with this program. If not, see . */ var $ = require('jquery'); +//support files +let app = require('../app'); //views var View = require('ampersand-view'); var ViewSpecie = require('./view-specie'); @@ -47,12 +49,6 @@ module.exports = View.extend({ this.parent.renderSpeciesView(); }, changeCollapseButtonText: function (e) { - let source = e.target.dataset.hook - let collapseContainer = $(this.queryByHook(source).dataset.target) - if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) { - let collapseBtn = $(this.queryByHook(source)) - let text = collapseBtn.text(); - text === '+' ? collapseBtn.text('-') : collapseBtn.text('+'); - } + app.changeCollapseButtonText(this, e); }, }); \ No newline at end of file diff --git a/client/views/sweep-parameter-range.js b/client/views/sweep-parameter-range.js new file mode 100644 index 0000000000..9b297388dc --- /dev/null +++ b/client/views/sweep-parameter-range.js @@ -0,0 +1,57 @@ +/* +StochSS is a platform for simulating biochemical systems +Copyright (C) 2019-2020 StochSS developers. + +This program is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with this program. If not, see . +*/ + +let $ = require('jquery'); +//views +let View = require('ampersand-view'); +//templates +let template = require('../templates/includes/sweepParameterRange.pug'); + +module.exports = View.extend({ + template: template, + events: function () { + let events = {}; + events['change [data-hook=' + this.model.elementID + '-slider'] = 'setParameterRangeValue'; + events['input [data-hook=' + this.model.elementID + '-slider'] = 'viewParameterRangeValue'; + return events; + }, + initialize: function (attrs, options) { + View.prototype.initialize.apply(this, arguments); + let self = this; + this.parameter = this.parent.model.model.parameters.filter(function (param) { + return param.compID === self.model.paramID + })[0]; + let value = this.model.range[0].toString().includes('.') ? this.model.range[0] : this.model.range[0].toFixed(1) + this.parent.tsPlotData.parameters[this.model.name] = value; + }, + render: function (attrs, options) { + View.prototype.render.apply(this, arguments); + }, + setParameterRangeValue: function (e) { + var value = this.model.range[e.target.value]; + if(!value.toString().includes(".")) { + value = value.toFixed(1) + } + this.parent.tsPlotData.parameters[this.model.name] = value; + this.parent.getPlot("ts-psweep"); + }, + viewParameterRangeValue: function (e) { + let value = this.model.range[e.target.value]; + $(this.queryByHook(this.model.elementID + "-current-value")).html(value); + } +}); diff --git a/client/views/sweep-parameter.js b/client/views/sweep-parameter.js new file mode 100644 index 0000000000..29a092bdf3 --- /dev/null +++ b/client/views/sweep-parameter.js @@ -0,0 +1,156 @@ +/* +StochSS is a platform for simulating biochemical systems +Copyright (C) 2019-2020 StochSS developers. + +This program is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with this program. If not, see . +*/ + +let $ = require('jquery'); +//support files +let app = require('../app'); +let tests = require('./tests'); +//views +let View = require('ampersand-view'); +let InputView = require('./input'); +let SelectView = require('ampersand-select-view'); +//templates +let template = require('../templates/includes/sweepParameter.pug'); + +module.exports = View.extend({ + template: template, + events: function () { + let events = {}; + events['change [data-hook=' + this.model.elementID + '-sweep-target]'] = 'setSelectedTarget'; + events['change [data-hook=' + this.model.elementID + '-target-min]'] = 'setHasChangedRange'; + events['change [data-hook=' + this.model.elementID + '-target-max]'] = 'setHasChangedRange'; + events['click [data-hook=' + this.model.elementID + '-remove'] = 'removeSweepParameter'; + return events; + }, + initialize: function (attrs, options) { + View.prototype.initialize.apply(this, arguments); + let self = this; + this.parameters = attrs.stochssParams; + this.parameter = this.parameters.filter(function (param) { + return param.compID === self.model.paramID; + })[0]; + this.model.updateVariable(this.parameter); + this.model.collection.on('add update-target remove', this.renderTargetSelectView, this); + }, + render: function (attrs, options) { + View.prototype.render.apply(this, arguments); + this.renderTargetSelectView(); + this.renderMinValInputView(); + this.renderMaxValInputView(); + this.renderStepsInputView(); + }, + getAvailableParameters: function () { + let variableTargets = this.model.collection.map(function (variable) { return variable.paramID}); + let availableParameters = this.parameters.filter(function (param) { + return !variableTargets.includes(param.compID); + }).map(function (param) { return param.name }); + if(!availableParameters.includes(this.parameter.name)) { + availableParameters.push(this.parameter.name); + } + return availableParameters; + }, + removeSweepParameter: function () { + this.model.collection.off('add update-target remove', this.renderTargetSelectView, this) + this.model.collection.removeSweepParameter(this.model); + this.remove(); + }, + renderMaxValInputView: function () { + if(this.maxValInputView) { + this.maxValInputView.remove(); + } + this.maxValInputView = new InputView({ + parent: this, + required: true, + name: 'max-value', + tests: tests.valueTests, + modelKey: 'max', + valueType: 'number', + value: this.model.max + }); + app.registerRenderSubview(this, this.maxValInputView, this.model.elementID + "-target-max"); + }, + renderMinValInputView: function () { + if(this.minValInputView) { + this.minValInputView.remove(); + } + this.minValInputView = new InputView({ + parent: this, + required: true, + name: 'min-value', + tests: tests.valueTests, + modelKey: 'min', + valueType: 'number', + value: this.model.min + }); + app.registerRenderSubview(this, this.minValInputView, this.model.elementID + "-target-min"); + }, + renderStepsInputView: function () { + if(this.stepsInputView) { + this.stepsInputView.remove(); + } + this.stepsInputView = new InputView({ + parent: this, + required: true, + name: 'steps', + tests: tests.valueTests, + modelKey: 'steps', + valueType: 'number', + value: this.model.steps + }); + app.registerRenderSubview(this, this.stepsInputView, this.model.elementID + "-target-steps"); + }, + renderTargetSelectView: function (e) { + if(this.model.collection) { + if(this.targetSelectView) { + this.targetSelectView.remove(); + } + let options = this.getAvailableParameters(); + this.targetSelectView = new SelectView({ + name: 'variable-target', + required: true, + idAttribute: 'cid', + options: options, + value: this.parameter.name + }); + app.registerRenderSubview(this, this.targetSelectView, this.model.elementID + "-sweep-target"); + } + }, + setHasChangedRange: function () { + this.model.hasChangedRange = true; + }, + setSelectedTarget: function (e) { + let targetName = e.target.value; + this.parameter = this.parameters.filter(function (param) { + return param.name === targetName + })[0]; + this.model.paramID = this.parameter.compID; + this.model.name = this.parameter.name; + this.model.hasChangedRange = false + this.model.updateVariable(this.parameter) + this.updateModelFields(); + this.model.collection.trigger('update-target'); + }, + update: function () {}, + updateModelFields: function () { + $(this.queryByHook(this.model.elementID + "-target-value")).text(this.parameter.expression) + this.renderMinValInputView(); + this.renderMaxValInputView(); + this.renderStepsInputView(); + }, + updateValid: function () {} +}); diff --git a/client/views/model-settings.js b/client/views/timespan-settings.js similarity index 83% rename from client/views/model-settings.js rename to client/views/timespan-settings.js index 26ff96fcba..22b8cd3fbf 100644 --- a/client/views/model-settings.js +++ b/client/views/timespan-settings.js @@ -18,13 +18,14 @@ along with this program. If not, see . var $ = require('jquery'); //support files +let app = require('../app'); var tests = require('./tests'); var Tooltips = require('../tooltips'); //views var View = require('ampersand-view'); var InputView = require('./input'); //templates -var template = require('../templates/includes/modelSettings.pug'); +var template = require('../templates/includes/timespanSettings.pug'); module.exports = View.extend({ template: template, @@ -46,13 +47,7 @@ module.exports = View.extend({ this.model.parent.updateValid() }, changeCollapseButtonText: function (e) { - let source = e.target.dataset.hook - let collapseContainer = $(this.queryByHook(source).dataset.target) - if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) { - let collapseBtn = $(this.queryByHook(source)) - let text = collapseBtn.text(); - text === '+' ? collapseBtn.text('-') : collapseBtn.text('+'); - } + app.changeCollapseButtonText(this, e); }, subviews: { inputSimEnd: { diff --git a/client/views/view-events.js b/client/views/view-events.js index 437417b836..0b04864060 100644 --- a/client/views/view-events.js +++ b/client/views/view-events.js @@ -17,6 +17,8 @@ along with this program. If not, see . */ var $ = require('jquery'); +//support files +let app = require('../app'); //views var View = require('ampersand-view'); var AssignmentsViewer = require('./event-assignments-viewer'); @@ -46,15 +48,11 @@ module.exports = View.extend({ var assignmentsViewer = new AssignmentsViewer({ collection: this.model.eventAssignments }); - this.registerRenderSubview(assignmentsViewer, 'assignment-viewer'); + app.registerRenderSubview(this, assignmentsViewer, 'assignment-viewer'); if(this.model.useValuesFromTriggerTime) { $(this.queryByHook("trigger-time")).prop('checked', true) }else{ $(this.queryByHook("assignment-time")).prop('checked', true) } - }, - registerRenderSubview: function (view, hook) { - this.registerSubview(view); - this.renderSubview(view, this.queryByHook(hook)); - }, + } }); \ No newline at end of file diff --git a/client/views/edit-workflow-groups-view.js b/client/views/view-sweep-parameter.js similarity index 75% rename from client/views/edit-workflow-groups-view.js rename to client/views/view-sweep-parameter.js index e902f7d876..bc64a1dab2 100644 --- a/client/views/edit-workflow-groups-view.js +++ b/client/views/view-sweep-parameter.js @@ -17,19 +17,20 @@ along with this program. If not, see . */ //views -var View = require('ampersand-view'); -var EditWorkflowGroupView = require('./edit-workflow-group-view'); +let View = require('ampersand-view'); //templates -var template = require('../templates/includes/editWorkflowGroupsView.pug'); +let template = require('../templates/includes/viewSweepParameter.pug'); module.exports = View.extend({ template: template, - events: {}, initialize: function (attrs, options) { View.prototype.initialize.apply(this, arguments); + let self = this; + this.parameter = attrs.parameters.filter(function (param) { + return param.compID === self.model.paramID; + })[0]; }, render: function (attrs, options) { View.prototype.render.apply(this, arguments); - this.renderCollection(this.collection, EditWorkflowGroupView, this.queryByHook("project-workflow-groups-list")) } -}); \ No newline at end of file +}); diff --git a/client/views/workflow-editor.js b/client/views/workflow-editor.js deleted file mode 100644 index 02c3674d81..0000000000 --- a/client/views/workflow-editor.js +++ /dev/null @@ -1,157 +0,0 @@ -/* -StochSS is a platform for simulating biochemical systems -Copyright (C) 2019-2020 StochSS developers. - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . -*/ - -var _ = require('underscore'); -var $ = require('jquery'); -//models -var Model = require('../models/settings'); -//views -var View = require('ampersand-view'); -var InputView = require('./input'); -var SimSettingsView = require('./simulation-settings'); -var SimulationSettingsViewer = require('./simulation-settings-viewer'); -var ParamSweepSettingsView = require('./parameter-sweep-settings'); -var ParameterSweepSettingsViewer = require('./parameter-sweep-settings-viewer'); -var WorkflowStateButtonsView = require('./workflow-state-buttons'); -//templates -var template = require('../templates/includes/workflowEditor.pug'); - -module.exports = View.extend({ - template: template, - events: { - 'click [data-hook=collapse-settings]' : 'changeCollapseButtonText', - }, - initialize: function (attrs, options) { - View.prototype.initialize.apply(this, arguments); - this.settings = new Model(attrs.settings); - this.type = attrs.type; - this.status = attrs.status; - }, - update: function (e) { - }, - updateValid: function (e) { - }, - render: function() { - View.prototype.render.apply(this, arguments); - if(this.status === "new" || this.status === "ready"){ - this.renderSimulationSettingView() - if(this.type === "parameterSweep"){ - this.validatePsweep() - this.renderParameterSweepSettingsView() - } - this.renderWorkflowStateButtons() - }else{ - this.collapseContainer() - this.renderSimulationSettingViewer() - if(this.type === "parameterSweep"){ - this.renderParameterSweepSettingsViewer() - } - } - }, - registerRenderSubview: function (view, hook) { - this.registerSubview(view); - this.renderSubview(view, this.queryByHook(hook)); - }, - renderSimulationSettingView: function () { - let simulationSettingsView = new SimSettingsView({ - parent: this, - model: this.settings.simulationSettings, - stochssModel: this.model - }); - this.registerRenderSubview(simulationSettingsView, 'sim-settings-container'); - }, - renderSimulationSettingViewer: function () { - let simulationSettingsViewer = new SimulationSettingsViewer({ - parent: this, - model: this.settings.simulationSettings, - }) - this.registerRenderSubview(simulationSettingsViewer, 'sim-settings-container'); - }, - renderParameterSweepSettingsViewer: function () { - let parameterSweepSettingsViewer = new ParameterSweepSettingsViewer({ - parent: this, - model: this.settings.parameterSweepSettings, - }); - this.registerRenderSubview(parameterSweepSettingsViewer, 'param-sweep-settings-container'); - }, - renderParameterSweepSettingsView: function () { - let parameterSweepSettingsView = new ParamSweepSettingsView({ - parent: this, - model: this.settings.parameterSweepSettings, - stochssModel: this.model - }); - this.registerRenderSubview(parameterSweepSettingsView, 'param-sweep-settings-container'); - }, - renderWorkflowStateButtons: function () { - if(this.workflowStateButtons) { - this.workflowStateButtons.remove() - } - this.workflowStateButtons = new WorkflowStateButtonsView({ - model: this.model, - type: this.type, - }); - this.registerRenderSubview(this.workflowStateButtons, 'workflow-state-buttons-container'); - }, - validatePsweep: function () { - let species = this.model.species; - var valid = this.validatePsweepChild(species, this.settings.parameterSweepSettings.speciesOfInterest) - if(!valid) // if true update species of interest - this.settings.parameterSweepSettings.speciesOfInterest = species.at(0) - var parameters = this.model.parameters; - var valid = this.validatePsweepChild(parameters, this.settings.parameterSweepSettings.parameterOne) - if(!valid) { // if true update parameter one - let param = parameters.at(0) - this.settings.parameterSweepSettings.parameterOne = param - let val = eval(param.expression) - this.settings.parameterSweepSettings.p1Min = val * 0.5 - this.settings.parameterSweepSettings.p1Max = val * 1.5 - } - if(parameters.at(1)){ // is there more than one parameter - var valid = this.validatePsweepChild(parameters, this.settings.parameterSweepSettings.parameterTwo) - if(!valid){ // if true update parameter 2 - let param = parameters.at(1) - this.settings.parameterSweepSettings.parameterTwo = param - let val = eval(param.expression) - this.settings.parameterSweepSettings.p2Min = val * 0.5 - this.settings.parameterSweepSettings.p2Max = val * 1.5 - } - } - }, - validatePsweepChild: function (collection, child) { - if(!child.compID) // if true child is not set - return false - let exists = Boolean(collection.filter(function (model) { - if(child.compID === model.compID) - return model - }).length) // if true child exits within the model - return exists - }, - changeCollapseButtonText: function (e) { - let source = e.target.dataset.hook - let collapseContainer = $(this.queryByHook(source).dataset.target) - if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) { - let collapseBtn = $(this.queryByHook(source)) - let text = collapseBtn.text(); - text === '+' ? collapseBtn.text('-') : collapseBtn.text('+'); - } - }, - collapseContainer: function () { - $(this.queryByHook("workflow-editor-container")).collapse() - $(this.queryByHook("collapse-settings")).click() - }, -}); \ No newline at end of file diff --git a/client/views/workflow-group-listing.js b/client/views/workflow-group-listing.js new file mode 100644 index 0000000000..1e1d322211 --- /dev/null +++ b/client/views/workflow-group-listing.js @@ -0,0 +1,99 @@ +/* +StochSS is a platform for simulating biochemical systems +Copyright (C) 2019-2020 StochSS developers. + +This program is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with this program. If not, see . +*/ + +let $ = require('jquery'); +let path = require('path'); +//support files +let app = require('../app'); +let modals = require('../modals'); +//views +let View = require('ampersand-view'); +let WorkflowListing = require("./workflow-listing"); +//templates +let template = require('../templates/includes/workflowGroupListing.pug'); + +module.exports = View.extend({ + template: template, + events: function () { + let events = {}; + events['change [data-hook=' + this.model.elementID + '-annotation'] = 'updateAnnotation'; + events['click #' + this.model.elementID + "-ensemble-simulation"] = 'handleEnsembleSimulationClick'; + events['click #' + this.model.elementID + "-parameter-sweep"] = 'handleParameterSweepClick'; + events['click [data-hook=' + this.model.elementID + '-remove'] = 'handleTrashModelClick'; + events['click [data-hook=' + this.model.elementID + '-tab-btn'] = 'changeCollapseButtonText'; + return events; + }, + initialize: function (attrs, options) { + View.prototype.initialize.apply(this, arguments); + }, + render: function (attrs, options) { + View.prototype.render.apply(this, arguments); + let parentPath = path.dirname(this.model.model.directory); + let queryString = "?path=" + this.model.model.directory + "&parentPath=" + parentPath; + let endpoint = path.join(app.getBasePath(), 'stochss/workflow/selection') + queryString; + $(this.queryByHook(this.model.elementID + "-jupyter-notebook")).prop("href", endpoint); + this.renderWorkflowCollection(); + }, + changeCollapseButtonText: function (e) { + app.changeCollapseButtonText(this, e); + }, + handleEnsembleSimulationClick: function (e) { + app.newWorkflow(this, this.model.model.directory, this.model.model.is_spatial, "Ensemble Simulation") + }, + handleParameterSweepClick: function (e) { + app.newWorkflow(this, this.model.model.directory, this.model.model.is_spatial, "Parameter Sweep") + }, + handleTrashModelClick: function () { + if(document.querySelector('#moveToTrashConfirmModal')) { + document.querySelector('#moveToTrashConfirmModal').remove(); + } + let self = this; + let modal = $(modals.moveToTrashConfirmHtml("model", true)).modal(); + let yesBtn = document.querySelector('#moveToTrashConfirmModal .yes-modal-btn'); + yesBtn.addEventListener('click', function (e) { + modal.modal('hide'); + let file = self.model.model.directory.split('/').pop(); + let projectPath = self.parent.model.directory; + let trashPath = path.join(projectPath, "trash", file); + let queryString = "?srcPath=" + self.model.model.directory + "&dstPath=" + trashPath; + let endpoint = path.join(app.getApiPath(), 'file/move') + queryString; + app.getXHR(endpoint, { + success: function (err, response, body) { + self.parent.update("WorkflowGroup"); + } + }); + }); + }, + renderWorkflowCollection: function () { + if(this.workflowCollectionView){ + this.workflowCollectionView.remove(); + } + this.workflowCollectionView = this.renderCollection( + this.model.workflows, + WorkflowListing, + this.queryByHook(this.model.elementID + "-workflow-listing") + ); + }, + update: function (target) { + this.parent.update(target); + }, + updateAnnotation: function (e) { + this.model.model.annotation = e.target.value.trim(); + this.model.model.saveModel(); + } +}); \ No newline at end of file diff --git a/client/views/workflow-group-viewer.js b/client/views/workflow-group-viewer.js deleted file mode 100644 index ea4a93b18e..0000000000 --- a/client/views/workflow-group-viewer.js +++ /dev/null @@ -1,60 +0,0 @@ -/* -StochSS is a platform for simulating biochemical systems -Copyright (C) 2019-2020 StochSS developers. - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . -*/ - -var $ = require('jquery'); -//views -var View = require('ampersand-view'); -var WorkflowCollectionsViewer = require('./workflows-viewer'); -//templates -var template = require('../templates/includes/workflowGroupViewer.pug') - -module.exports = View.extend({ - template: template, - events: { - 'click [data-hook=collapse-workflow-group]' : 'changeCollapseButtonText' - }, - initialize: function (attrs, options) { - View.prototype.initialize.apply(this, arguments) - }, - render: function (attrs, options) { - View.prototype.render.apply(this, arguments) - this.renderWorkflowsCollectionViewer() - }, - renderWorkflowsCollectionViewer: function () { - if(this.workflowsCollectionViewer) { - this.workflowsCollectionViewer.remove() - } - this.workflowsCollectionViewer = new WorkflowCollectionsViewer({ - collection: this.model.workflows - }); - this.registerRenderSubview(this.workflowsCollectionViewer, "workflows-viewer-container") - }, - registerRenderSubview: function (view, hook) { - this.registerSubview(view); - this.renderSubview(view, this.queryByHook(hook)); - }, - changeCollapseButtonText: function (e) { - let source = e.target.dataset.hook - let collapseContainer = $(this.queryByHook(source).dataset.target) - if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) { - let collapseBtn = $(this.queryByHook(source)) - let text = collapseBtn.text(); - text === '+' ? collapseBtn.text('-') : collapseBtn.text('+'); - } - } -}) \ No newline at end of file diff --git a/client/views/workflow-groups-viewer.js b/client/views/workflow-groups-viewer.js deleted file mode 100644 index 2367d81633..0000000000 --- a/client/views/workflow-groups-viewer.js +++ /dev/null @@ -1,47 +0,0 @@ -/* -StochSS is a platform for simulating biochemical systems -Copyright (C) 2019-2020 StochSS developers. - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . -*/ - -var $ = require('jquery'); -//views -var View = require('ampersand-view'); -var WorkflowGroupView = require('./workflow-group-viewer'); -//templates -var template = require('../templates/includes/workflowGroupsViewer.pug'); - -module.exports = View.extend({ - template: template, - events: { - 'click [data-hook=collapse-workflow-groups]' : 'changeCollapseButtonText' - }, - initialize: function (attrs, options) { - View.prototype.initialize.apply(this, arguments) - }, - render: function (attrs, options) { - View.prototype.render.apply(this, arguments) - this.renderCollection(this.collection, WorkflowGroupView, this.queryByHook('workflow-group-container')) - }, - changeCollapseButtonText: function (e) { - let source = e.target.dataset.hook - let collapseContainer = $(this.queryByHook(source).dataset.target) - if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) { - let collapseBtn = $(this.queryByHook(source)) - let text = collapseBtn.text(); - text === '+' ? collapseBtn.text('-') : collapseBtn.text('+'); - } - } -}) \ No newline at end of file diff --git a/client/views/workflow-info.js b/client/views/workflow-info.js index 1ac37fb9ca..cefad55a32 100644 --- a/client/views/workflow-info.js +++ b/client/views/workflow-info.js @@ -16,93 +16,72 @@ You should have received a copy of the GNU General Public License along with this program. If not, see . */ -var $ = require('jquery'); -var path = require('path'); -var xhr = require('xhr'); -var app = require('../app'); +let $ = require('jquery'); +//support files +let app = require('../app'); //views -var View = require('ampersand-view'); +let View = require('ampersand-view'); //tempates -var template = require('../templates/includes/workflowInfo.pug'); +let template = require('../templates/includes/workflowInfo.pug'); module.exports = View.extend({ template: template, events: { - 'click [data-hook=collapse]' : 'changeCollapseButtonText', + 'click [data-hook=collapse-info]' : 'changeCollapseButtonText' }, initialize: function (attrs, options) { View.prototype.initialize.apply(this, arguments); - this.status = attrs.status; - this.logsPath = attrs.logsPath; - var self = this this.listOfWarnings = []; this.listOfErrors = []; this.listOfNotes = []; - if(this.status === 'complete' || this.status === 'error'){ - var endpoint = path.join(app.getApiPath(), "/workflow/workflow-logs")+"?path="+this.logsPath - xhr({uri: endpoint}, function (err, response, body) { - if(response.statusCode < 400){ - var logs = body.split("\n") - logs.forEach(self.parseLogs, self) - self.expandLogContainers(); - }else{ - body = JSON.parse(body) - } - }); + let logs = attrs.logs.split("root - "); + if(logs.length > 1){ + logs.shift() } + logs.forEach(this.parseLogs, this); }, render: function () { View.prototype.render.apply(this, arguments); - if(this.status === 'complete'){ - this.enableCollapseButton() - }else if(this.status === 'error'){ - this.expandInfoContainer() + if(this.parent.model.activeJob.status === "error") { + $(this.queryByHook("workflow-info")).collapse("show"); + $(this.queryByHook("collapse-info")).html("-"); } + this.expandLogContainers() }, - parseLogs: function (log) { - var message = log.split('root - ').pop() - if(message.startsWith("WARNING")){ - this.listOfWarnings.push(message.split("WARNING").pop()) - }else if(message.startsWith("ERROR")){ - this.listOfErrors.push(message.split("ERROR").pop()) - }else if(message.startsWith("CRITICAL")){ - this.listOfErrors.push(message.split("CRITICAL").pop()) - }else{ - this.listOfNotes.push(message) - } - }, - enableCollapseButton: function () { - $(this.queryByHook('collapse')).prop('disabled', false); - }, - expandInfoContainer: function () { - this.enableCollapseButton(); - $(this.queryByHook('workflow-info')).collapse('show'); - $(this.queryByHook("collapse")).click() + changeCollapseButtonText: function (e) { + app.changeCollapseButtonText(this, e); }, expandLogContainers: function () { if(this.listOfWarnings.length) { $(this.queryByHook('workflow-warnings')).collapse('show'); - var listOfWarnings = "

" + this.listOfWarnings.join('
') + "

"; + let listOfWarnings = "

" + this.listOfWarnings.join('
') + "

"; $(this.queryByHook('list-of-warnings')).html(listOfWarnings); } if(this.listOfErrors.length) { $(this.queryByHook('workflow-errors')).collapse('show'); - var listOfErrors = "

" + this.listOfErrors.join('
') + "

"; + let listOfErrors = "

" + this.listOfErrors.join('
') + "

"; $(this.queryByHook('list-of-errors')).html(listOfErrors); } if(this.listOfNotes.length) { $(this.queryByHook('workflow-statistics')).collapse('show'); - var listOfNotes = "

" + this.listOfNotes.join('
') + "

"; + let listOfNotes = "

" + this.listOfNotes.join('
') + "

"; $(this.queryByHook('list-of-notes')).html(listOfNotes); } }, - changeCollapseButtonText: function (e) { - let source = e.target.dataset.hook - let collapseContainer = $(this.queryByHook(source).dataset.target) - if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) { - let collapseBtn = $(this.queryByHook(source)) - let text = collapseBtn.text(); - text === '+' ? collapseBtn.text('-') : collapseBtn.text('+'); + parseLogs: function (log) { + var message = log.split('\n'); + if(message.length > 1) { + message.pop(); } - }, + message = message.join('
'); + if(message.startsWith("WARNING")){ + this.listOfWarnings.push(message.split("WARNING").pop()); + }else if(message.startsWith("ERROR")){ + this.listOfErrors.push(message.split("ERROR").pop()); + }else if(message.startsWith("CRITICAL")){ + this.listOfErrors.push(message.split("CRITICAL").pop()); + }else{ + this.listOfNotes.push(message); + } + } }); diff --git a/client/views/workflow-listing.js b/client/views/workflow-listing.js new file mode 100644 index 0000000000..7ee0006b89 --- /dev/null +++ b/client/views/workflow-listing.js @@ -0,0 +1,127 @@ +/* +StochSS is a platform for simulating biochemical systems +Copyright (C) 2019-2020 StochSS developers. + +This program is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with this program. If not, see . +*/ + +let $ = require('jquery'); +let path = require('path'); +let _ = require('underscore'); +//support files +let app = require('../app'); +let modals = require('../modals'); +//views +let View = require('ampersand-view'); +//templates +let template = require('../templates/includes/workflowListing.pug'); + +module.exports = View.extend({ + template: template, + events: function () { + let events = {}; + events['change [data-hook=' + this.model.elementID + '-annotation]'] = 'updateAnnotation'; + events['click [data-hook=' + this.model.elementID + '-notes-btn]'] = 'handleEditAnnotationClick'; + events['click [data-hook=' + this.model.elementID + '-remove]'] = 'handleTrashWorkflowClick'; + events['click [data-hook=' + this.model.elementID + '-annotation-btn'] = 'changeCollapseButtonText'; + return events; + }, + initialize: function (attrs, options) { + View.prototype.initialize.apply(this, arguments); + }, + render: function (attrs, options) { + View.prototype.render.apply(this, arguments); + if(this.model.collection.parent.collection.parent.newFormat) { + $(this.queryByHook(this.model.elementID + "-status")).css("display", "none"); + if(this.model.collection.indexOf(this.model) === this.model.collection.length - 1) { + $(this.queryByHook(this.model.elementID + "-divider")).css("display", "none"); + } + }else if(this.model.status === "running"){ + this.getStatus(); + } + if(this.model.directory.endsWith('.ipynb')) { + $(this.queryByHook(this.model.elementID + "-notes-btn")).css("display", "none"); + } + if(!this.model.annotation || !this.model.annotation.trim()){ + $(this.queryByHook(this.model.elementID + "-notes-btn")).text('Add Notes'); + }else{ + $(this.queryByHook(this.model.elementID + "-notes-container")).collapse('show') + } + }, + changeCollapseButtonText: function (e) { + app.changeCollapseButtonText(this, e); + }, + getProjectPath: function () { + return this.model.directory.split(".proj")[0] + ".proj"; + }, + getStatus: function () { + var self = this; + var endpoint = path.join(app.getApiPath(), "workflow/workflow-status") + "?path=" + this.model.directory; + app.getXHR(endpoint, { + always: function (err, response, body) { + if(body === 'running') + setTimeout(_.bind(self.getStatus, self), 1000); + else{ + self.model.status = body; + $(self.queryByHook(this.model.elementID + "-status")).text(self.model.status); + } + } + }); + }, + handleEditAnnotationClick: function (e) { + let buttonTxt = e.target.innerText; + if(buttonTxt.startsWith("Add")){ + $(this.queryByHook(this.model.elementID + '-notes-container')).collapse('show'); + $(this.queryByHook(this.model.elementID + '-notes-btn')).text('Edit Notes'); + $("#" + this.model.elementID + "-annotation-container").collapse('show'); + $(this.queryByHook(this.model.elementID + "-annotation-btn")).text('-'); + }else if(!$("#" + this.model.elementID + "-annotation-container").attr('class').includes('show')){ + $("#" + this.model.elementID + "-annotation-container").collapse('show'); + $(this.queryByHook(this.model.elementID + "-annotation-btn")).text('-'); + } + document.querySelector("#" + this.model.elementID + "-annotation").focus(); + }, + handleTrashWorkflowClick: function () { + if(document.querySelector('#moveToTrashConfirmModal')) { + document.querySelector('#moveToTrashConfirmModal').remove(); + } + let self = this; + let modal = $(modals.moveToTrashConfirmHtml("workflow")).modal(); + let yesBtn = document.querySelector('#moveToTrashConfirmModal .yes-modal-btn'); + yesBtn.addEventListener('click', function (e) { + modal.modal('hide'); + let file = self.model.directory.split('/').pop() + let projectPath = self.getProjectPath(); + let trashPath = path.join(projectPath, "trash", file); + let queryString = "?srcPath=" + self.model.directory + "&dstPath=" + trashPath; + let endpoint = path.join(app.getApiPath(), 'file/move') + queryString; + app.getXHR(endpoint, { + success: function (err, response, body) { + self.parent.update("Workflow"); + } + }); + }); + }, + updateAnnotation: function (e) { + this.model.annotation = e.target.value.trim(); + if(this.model.annotation === "") { + $(this.queryByHook(this.model.elementID + "-notes-container")).collapse('hide'); + $(this.queryByHook(this.model.elementID + "-notes-btn")).text('Add Notes'); + } + let queryString = "?path=" + this.model.directory; + let endpoint = path.join(app.getApiPath(), "workflow/save-annotation") + queryString; + let body = {'annotation':this.model.annotation}; + app.postXHR(endpoint, body); + } +}); \ No newline at end of file diff --git a/client/views/workflow-results.js b/client/views/workflow-results.js index 10d1dd312b..adc075079f 100644 --- a/client/views/workflow-results.js +++ b/client/views/workflow-results.js @@ -16,357 +16,368 @@ You should have received a copy of the GNU General Public License along with this program. If not, see . */ -var $ = require('jquery'); -var path = require('path'); -var xhr = require('xhr'); +let $ = require('jquery'); +let path = require('path'); //support files -var Plotly = require('../lib/plotly'); -var app = require('../app'); -var Tooltips = require('../tooltips'); +let app = require('../app'); +let Tooltips = require('../tooltips'); +let Plotly = require('../lib/plotly'); //views -var View = require('ampersand-view'); -var InputView = require('./input'); -var SelectView = require('ampersand-select-view'); +let InputView = require('./input'); +let View = require('ampersand-view'); +let SelectView = require('ampersand-select-view'); +let SweepParametersView = require('./sweep-parameter-range'); //templates -var gillespyResultsTemplate = require('../templates/includes/gillespyResults.pug'); -var gillespyResultsEnsembleTemplate = require('../templates/includes/gillespyResultsEnsemble.pug'); -var parameterSweepResultsTemplate = require('../templates/includes/parameterSweepResults.pug'); +let gillespyResultsTemplate = require('../templates/includes/gillespyResults.pug'); +let gillespyResultsEnsembleTemplate = require('../templates/includes/gillespyResultsEnsemble.pug'); +let parameterSweepResultsTemplate = require('../templates/includes/parameterSweepResults.pug'); +let parameterScanTemplate = require('../templates/includes/parameterScanResults.pug'); module.exports = View.extend({ events: { - 'click [data-hook=collapse-stddevrange]' : 'handleCollapseStddevrangeClick', - 'click [data-hook=collapse-trajectories]' : 'handleCollapseTrajectoriesClick', - 'click [data-hook=collapse-stddev]' : 'handleCollapseStddevClick', - 'click [data-hook=collapse-trajmean]' : 'handleCollapseTrajmeanClick', - 'click [data-hook=collapse-psweep]' : 'handleCollapsePsweepClick', - 'click [data-hook=collapse]' : 'changeCollapseButtonText', 'change [data-hook=title]' : 'setTitle', 'change [data-hook=xaxis]' : 'setXAxis', 'change [data-hook=yaxis]' : 'setYAxis', 'change [data-hook=specie-of-interest-list]' : 'getPlotForSpecies', 'change [data-hook=feature-extraction-list]' : 'getPlotForFeatureExtractor', 'change [data-hook=ensemble-aggragator-list]' : 'getPlotForEnsembleAggragator', - 'click [data-hook=plot]' : function (e) { - $(this.queryByHook("edit-plot-args")).collapse("show"); - $(document).ready(function () { - $("html, body").animate({ - scrollTop: $("#edit-plot-args").offset().top - 50 - }, false); - }); - }, - 'click [data-hook=download-png-custom]' : function (e) { - var type = e.target.id; - this.clickDownloadPNGButton(type) - }, - 'click [data-hook=download-json]' : function (e) { - var type = e.target.id; - this.exportToJsonFile(this.plots[type], type) - }, - 'click [data-hook=save-plot]' : function (e) { - var type = e.target.id; - e.target.disabled = true - $("button[data-hook=save-plot]").filter("#"+type).text('Saved Plot to Project Viewer') - this.savePlot(type) - }, - 'click [data-hook=download-results-csv]' : 'handlerDownloadResultsCsvClick', + 'change [data-hook=plot-type-select]' : 'getTSPlotForType', + 'click [data-hook=collapse-results-btn]' : 'changeCollapseButtonText', + 'click [data-trigger=collapse-plot-container]' : 'handleCollapsePlotContainerClick', + 'click [data-target=edit-plot]' : 'openPlotArgsSection', + 'click [data-hook=multiple-plots]' : 'plotMultiplePlots', + 'click [data-target=download-png-custom]' : 'handleDownloadPNGClick', + 'click [data-target=download-json]' : 'handleDownloadJSONClick', + 'click [data-hook=convert-to-notebook]' : 'handleConvertToNotebookClick', + 'click [data-hook=download-results-csv]' : 'handleDownloadResultsCsvClick' }, initialize: function (attrs, options) { View.prototype.initialize.apply(this, arguments); - this.tooltips = Tooltips.parameterSweepResults - this.trajectories = attrs.trajectories; - this.status = attrs.status; - this.species = attrs.species; - this.type = attrs.type; - this.speciesOfInterest = attrs.speciesOfInterest; - this.featureExtractor = "final"; - this.ensembleAggragator = "avg"; - this.plots = {} - this.plotArgs = {} - this.savedPlots = this.parent.settings.resultsSettings.outputs + this.tooltips = Tooltips.parameterSweepResults; + this.plots = {}; + this.plotArgs = {}; }, - render: function () { - if(this.type === "parameterSweep"){ - this.template = parameterSweepResultsTemplate + render: function (attrs, options) { + let isEnsemble = this.model.settings.simulationSettings.realizations > 1 && + this.model.settings.simulationSettings.algorithm !== "ODE"; + let isParameterScan = this.model.settings.parameterSweepSettings.parameters.length > 2 + if(this.parent.model.type === "Parameter Sweep"){ + this.template = isParameterScan ? parameterScanTemplate : parameterSweepResultsTemplate; }else{ - this.template = this.trajectories > 1 ? gillespyResultsEnsembleTemplate : gillespyResultsTemplate + this.template = isEnsemble ? gillespyResultsEnsembleTemplate : gillespyResultsTemplate; } View.prototype.render.apply(this, arguments); - if(this.status === 'complete'){ - this.expandContainer() - } - var speciesNames = this.species.map(function (specie) { return specie.name}); - var featureExtractors = ["Minimum of population", "Maximum of population", "Average of population", "Variance of population", "Population at last time point"] - var ensembleAggragators = ["Minimum of ensemble", "Maximum of ensemble", "Average of ensemble", "Variance of ensemble"] - var speciesOfInterestView = new SelectView({ - label: '', - name: 'species-of-interest', - required: true, - idAttribute: 'cid', - options: speciesNames, - value: this.speciesOfInterest - }); - var featureExtractorView = new SelectView({ - label: '', - name: 'feature-extractor', - requires: true, - idAttribute: 'cid', - options: featureExtractors, - value: "Population at last time point" - }); - var ensembleAggragatorView = new SelectView({ - label: '', - name: 'ensemble-aggragator', - requires: true, - idAttribute: 'cid', - options: ensembleAggragators, - value: "Average of ensemble" - }); - if(this.type === "parameterSweep"){ - this.registerRenderSubview(speciesOfInterestView, 'specie-of-interest-list'); - this.registerRenderSubview(featureExtractorView, 'feature-extraction-list'); - this.registerRenderSubview(ensembleAggragatorView, 'ensemble-aggragator-list'); - if(this.trajectories <= 1){ - $(this.queryByHook('ensemble-aggragator-container')).collapse() + if(this.parent.model.type === "Ensemble Simulation") { + var type = isEnsemble ? "stddevran" : "trajectories"; + }else{ + this.tsPlotData = {"parameters":{}}; + var type = "ts-psweep"; + if(!isParameterScan) { + this.renderSpeciesOfInterestView(); + this.renderFeatureExtractionView(); + if(isEnsemble) { + this.renderEnsembleAggragatorView(); + }else{ + $(this.queryByHook('ensemble-aggragator-container')).css("display", "none"); + } + this.getPlot("psweep"); + } + if(isEnsemble) { + this.renderPlotTypeSelectView(); + this.tsPlotData["type"] = "stddevran" }else{ - $(this.queryByHook('ensemble-aggragator-container')).addClass("inline") + $(this.queryByHook('plot-type-header')).css("display", "none"); + this.tsPlotData["type"] = "trajectories" } + this.renderSweepParameterView(); } - $(document).ready(function () { - $('[data-toggle="tooltip"]').tooltip(); - $('[data-toggle="tooltip"]').click(function () { - $('[data-toggle="tooltip"]').tooltip("hide"); - }); - }); - }, - update: function () { - }, - updateValid: function () { + this.getPlot(type); }, changeCollapseButtonText: function (e) { - let source = e.target.dataset.hook - let collapseContainer = $(this.queryByHook(source).dataset.target) - if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) { - let collapseBtn = $(this.queryByHook(source)) - let text = collapseBtn.text(); - text === '+' ? collapseBtn.text('-') : collapseBtn.text('+'); - } + app.changeCollapseButtonText(this, e); }, - setTitle: function (e) { - this.plotArgs['title'] = e.target.value - for (var type in this.plots) { - var fig = this.plots[type] - fig.layout.title.text = e.target.value - this.plotFigure(fig, type) + cleanupPlotContainer: function (type) { + let el = this.queryByHook(type + "-plot"); + Plotly.purge(el); + $(this.queryByHook(type + "-plot")).empty(); + if(type === "ts-psweep" || type === "psweep"){ + $(this.queryByHook(type + "-edit-plot")).prop("disabled", true); + $(this.queryByHook(type + "-download-png-custom")).prop("disabled", true); + $(this.queryByHook(type + "-download-json")).prop("disabled", true); + $(this.queryByHook("multiple-plots")).prop("disabled", true); } + $(this.queryByHook(type + "-plot-spinner")).css("display", "block"); }, - setYAxis: function (e) { - this.plotArgs['yaxis'] = e.target.value - for (var type in this.plots) { - var fig = this.plots[type] - fig.layout.yaxis.title.text = e.target.value - this.plotFigure(fig, type) - } - }, - setXAxis: function (e) { - this.plotArgs['xaxis'] = e.target.value - for (var type in this.plots) { - var fig = this.plots[type] - fig.layout.xaxis.title.text = e.target.value - this.plotFigure(fig, type) + getPlot: function (type) { + let self = this; + this.cleanupPlotContainer(type); + let data = this.getPlotData(type); + if(type === "psweep" && Boolean(this.plots[data.plt_key])) { + this.plotFigure(this.plots[data.plt_key], type); + }else if(type === "ts-psweep" && Boolean(this.plots[data.plt_type + data.plt_key])) { + this.plotFigure(this.plots[data.plt_type + data.plt_key], type); + }else{ + let queryStr = "?path=" + this.model.directory + "&data=" + JSON.stringify(data); + let endpoint = path.join(app.getApiPath(), "workflow/plot-results") + queryStr; + app.getXHR(endpoint, { + success: function (err, response, body) { + if(type === "psweep") { + self.plots[data.plt_key] = body; + }else if(type === "ts-psweep"){ + self.plots[data.plt_type + data.plt_key] = body; + }else{ + self.plots[type] = body; + } + self.plotFigure(body, type); + }, + error: function (err, response, body) { + $(self.queryByHook(type + "-plot-spinner")).css("display", "none"); + let message = "

" + body.Message + "

Please re-run this job to get this plot

"; + $(self.queryByHook(type + "-plot")).html(message); + } + }); } }, - getPlot: function (type) { - var self = this; - var el = this.queryByHook(type) - Plotly.purge(el) - this.queryAll("#"+type).filter(function (el) {return el.dataset.hook === "plot-spinner"})[0].style.display = "block" - var data = {} + getPlotData: function (type) { + let data = {}; if(type === 'psweep'){ - let key = this.getPsweepKey() + let key = this.getPsweepKey(); data['plt_key'] = key; + }else if(type === "ts-psweep" || type === "ts-psweep-mp") { + if(type === "ts-psweep-mp"){ + data['plt_type'] = "mltplplt"; + }else{ + data['plt_type'] = this.tsPlotData['type']; + } + let key = this.getTSPsweepKey() + data['plt_key'] = key; + }else if(type === "mltplplt"){ + data['plt_type'] = type; + data['plt_key'] = null; }else{ data['plt_key'] = type; } if(Object.keys(this.plotArgs).length){ - data['plt_data'] = this.plotArgs + data['plt_data'] = this.plotArgs; }else{ - data['plt_data'] = "None" + data['plt_data'] = null; } - var endpoint = path.join(app.getApiPath(), "workflow/plot-results")+"?path="+this.parent.wkflPath+"&data="+JSON.stringify(data); - xhr({url: endpoint, json: true}, function (err, response, body){ - if(response.statusCode >= 400){ - $(self.queryByHook(type)).html(body.Message) - }else{ - self.plots[type] = body - self.plotFigure(body, type); - let plotSaved = Boolean(self.savedPlots.filter(function (plot) { - if(plot.key === data.plt_key) - return true - }).length > 0) - let saveBtn = $("button[data-hook=save-plot]").filter("#"+type) - if(!self.parent.wkflPath.includes('.proj')) { - saveBtn.hide() - }else if(plotSaved) { - saveBtn.prop('disabled', true) - saveBtn.text('Plot Saved to Project Viewer') - } - } + return data + }, + getPlotForEnsembleAggragator: function (e) { + this.model.settings.resultsSettings.reducer = e.target.value; + this.getPlot('psweep') + }, + getPlotForFeatureExtractor: function (e) { + this.model.settings.resultsSettings.mapper = e.target.value; + this.getPlot('psweep') + }, + getPlotForSpecies: function (e) { + let species = this.model.model.species.filter(function (spec) { + return spec.name === e.target.value; + })[0]; + this.model.settings.parameterSweepSettings.speciesOfInterest = species; + this.getPlot('psweep') + }, + getPsweepKey: function () { + let speciesOfInterest = this.model.settings.parameterSweepSettings.speciesOfInterest.name; + let featureExtractor = this.model.settings.resultsSettings.mapper; + let key = speciesOfInterest + "-" + featureExtractor + let realizations = this.model.settings.simulationSettings.realizations; + let algorithm = this.model.settings.simulationSettings.algorithm; + if(algorithm !== "ODE" && realizations > 1){ + let ensembleAggragator = this.model.settings.resultsSettings.reducer; + key += ("-" + ensembleAggragator); + } + return key; + }, + getTSPlotForType: function (e) { + this.tsPlotData['type'] = e.target.value; + let display = this.tsPlotData['type'] === "trajectories" ? "inline-block" : "none"; + $(this.queryByHook("multiple-plots")).css("display", display); + this.getPlot("ts-psweep"); + }, + getTSPsweepKey: function () { + let self = this; + let strs = Object.keys(this.tsPlotData.parameters).map(function (key) { + return key + ":" + self.tsPlotData.parameters[key] }); + let key = strs.join(","); + return key; }, - plotFigure: function (figure, type) { - var self = this; - var hook = type; - var el = this.queryByHook(hook) - Plotly.newPlot(el, figure) - this.queryAll("#" + type).forEach(function (el) { - if(el.dataset.hook === "plot-spinner"){ - el.style.display = "none" - }else if(el.disabled){ - el.disabled = false; + handleCollapsePlotContainerClick: function (e) { + app.changeCollapseButtonText(this, e); + let type = e.target.dataset.type; + if(!this.plots[type]){ + this.getPlot(type); + } + }, + handleConvertToNotebookClick: function (e) { + let self = this; + if(this.parent.model.type === "Ensemble Simulation") { + var type = "gillespy"; + }else if(this.parent.model.type === "Parameter Sweep" && this.model.settings.parameterSweepSettings.parameters.length > 1) { + var type = "2d_parameter_sweep"; + }else{ + var type = "1d_parameter-sweep"; + } + let queryStr = "?path=" + this.model.directory + "&type=" + type; + let endpoint = path.join(app.getApiPath(), "workflow/notebook") + queryStr; + app.getXHR(endpoint, { + success: function (err, response, body) { + window.open(path.join(app.getBasePath(), "notebooks", body.FilePath)); } }); }, - clickDownloadPNGButton: function (type) { - var pngButton = $('div[data-hook='+type+'] a[data-title*="Download plot as a png"]')[0] - pngButton.click() - }, - exportToJsonFile: function (jsonData, plotType) { + handleDownloadJSONClick: function (e) { + let type = e.target.dataset.type; + let jsonData = this.plots[type]; let dataStr = JSON.stringify(jsonData); let dataURI = 'data:application/json;charset=utf-8,' + encodeURIComponent(dataStr); - let exportFileDefaultName = plotType + '-plot.json'; + let exportFileDefaultName = type + '-plot.json'; let linkElement = document.createElement('a'); linkElement.setAttribute('href', dataURI); linkElement.setAttribute('download', exportFileDefaultName); linkElement.click(); }, - handlerDownloadResultsCsvClick: function (e) { - let path = this.parent.wkflPath - this.getExportData(path) + handleDownloadPNGClick: function (e) { + let type = e.target.dataset.type; + let pngButton = $('div[data-hook=' + type + '-plot] a[data-title*="Download plot as a png"]')[0]; + pngButton.click(); }, - getExportData: function (wkflPath) { - var self = this; - var endpoint = path.join(app.getApiPath(), "file/download-zip")+"?path="+wkflPath+"&action=resultscsv" - xhr({uri: endpoint, json: true}, function (err, response, body) { - if(response.statusCode < 400) { - self.exportToZipFile(body.Path) + handleDownloadResultsCsvClick: function (e) { + let self = this; + let queryStr = "?path=" + this.model.directory + "&action=resultscsv"; + let endpoint = path.join(app.getApiPath(), "file/download-zip") + queryStr; + app.getXHR(endpoint, { + success: function (err, response, body) { + window.open(path.join("files", body.Path)); } }); }, - exportToZipFile: function (resultsPath) { - var endpoint = path.join("files", resultsPath); - window.open(endpoint) + openPlotArgsSection: function (e) { + $(this.queryByHook("edit-plot-args")).collapse("show"); + $(document).ready(function () { + $("html, body").animate({ + scrollTop: $("#edit-plot-args").offset().top - 50 + }, false); + }); }, - expandContainer: function () { - $(this.queryByHook('workflow-results')).collapse('show'); - let collapseBtn = $(this.queryByHook('collapse')); - collapseBtn.prop('disabled', false) - collapseBtn.click() - if(this.type === "parameterSweep"){ - this.getPlot("psweep") - }else{ - this.trajectories > 1 ? this.getPlot("stddevran") : this.getPlot("trajectories") + plotFigure: function (figure, type) { + let self = this; + let hook = type + "-plot"; + let el = this.queryByHook(hook); + Plotly.newPlot(el, figure); + $(this.queryByHook(type + "-plot-spinner")).css("display", "none"); + $(this.queryByHook(type + "-edit-plot")).prop("disabled", false); + $(this.queryByHook(type + "-download-png-custom")).prop("disabled", false); + $(this.queryByHook(type + "-download-json")).prop("disabled", false); + if(type === "trajectories" || (this.tsPlotData && this.tsPlotData.type === "trajectories")) { + $(this.queryByHook("multiple-plots")).prop("disabled", false); } }, - registerRenderSubview: function (view, hook) { - this.registerSubview(view); - this.renderSubview(view, this.queryByHook(hook)); - }, - getPlotForSpecies: function (e) { - this.speciesOfInterest = e.target.selectedOptions.item(0).text; - this.getPlot('psweep') - }, - getPlotForFeatureExtractor: function (e) { - var featureExtractors = {"Minimum of population":"min", - "Maximum of population":"max", - "Average of population":"avg", - "Variance of population":"var", - "Population at last time point":"final"} - var value = e.target.selectedOptions.item(0).text; - this.featureExtractor = featureExtractors[value] - this.getPlot('psweep') - }, - getPlotForEnsembleAggragator: function (e) { - var ensembleAggragators = {"Minimum of ensemble":"min", - "Maximum of ensemble":"max", - "Average of ensemble":"avg", - "Variance of ensemble":"var"} - var value = e.target.selectedOptions.item(0).text; - this.ensembleAggragator = ensembleAggragators[value] - this.getPlot('psweep') + plotMultiplePlots: function (e) { + let type = e.target.dataset.type; + let data = this.getPlotData(type); + var queryStr = "?path=" + this.model.directory + "&wkfl=" + this.parent.model.name; + queryStr += "&job=" + this.model.name + "&data=" + JSON.stringify(data); + let endpoint = path.join(app.getBasePath(), "stochss/multiple-plots") + queryStr; + window.open(endpoint); }, - getPsweepKey: function () { - let key = this.speciesOfInterest + "-" + this.featureExtractor - if(this.trajectories > 1){ - key += ("-" + this.ensembleAggragator) - } - return key + renderEnsembleAggragatorView: function () { + let ensembleAggragators = [ + ["min", "Minimum of ensemble"], + ["max", "Maximum of ensemble"], + ["avg", "Average of ensemble"], + ["var", "Variance of ensemble"] + ]; + let ensembleAggragatorView = new SelectView({ + name: 'ensemble-aggragator', + requires: true, + idAttribute: 'cid', + options: ensembleAggragators, + value: this.model.settings.resultsSettings.reducer + }); + app.registerRenderSubview(this, ensembleAggragatorView, 'ensemble-aggragator-list'); }, - savePlot: function (type) { - var species = [] - if(type === "psweep"){ - type = this.getPsweepKey() - species = [this.speciesOfInterest] - }else{ - species = this.species.map(function (specie) { return specie.name; }); - } - let stamp = this.getTimeStamp() - var plotInfo = {"key":type, "stamp":stamp, "species":species}; - plotInfo = Object.assign({}, plotInfo, this.plotArgs) - this.savedPlots.push(plotInfo) - let queryString = "?path="+path.join(this.parent.wkflPath, "settings.json") - let endpoint = path.join(app.getApiPath(), "workflow/save-plot")+queryString - xhr({uri: endpoint, method: "post", json: true, body: plotInfo}, function (err, response, body) { - if(response.statusCode > 400) { - console.log(body.message) - } - }) + renderFeatureExtractionView: function () { + let featureExtractors = [ + ["min", "Minimum of population"], + ["max", "Maximum of population"], + ["avg", "Average of population"], + ["var", "Variance of population"], + ["final", "Population at last time point"] + ]; + let featureExtractionView = new SelectView({ + name: 'feature-extractor', + requires: true, + idAttribute: 'cid', + options: featureExtractors, + value: this.model.settings.resultsSettings.mapper + }); + app.registerRenderSubview(this, featureExtractionView, 'feature-extraction-list'); }, - getTimeStamp: function () { - var date = new Date() - let year = date.getFullYear().toString().slice(-2) - let month = date.getMonth() >= 10 ? date.getMonth().toString() : "0" + date.getMonth() - let day = date.getDate() >= 10 ? date.getDate().toString() : "0" + date.getDate() - let hour = date.getHours() >= 10 ? date.getHours().toString() : "0" + date.getHours() - let minutes = date.getMinutes() >= 10 ? date.getMinutes().toString() : "0" + date.getMinutes() - let seconds = date.getSeconds() >= 10 ? date.getSeconds().toString() : "0" + date.getSeconds() - return parseInt(year+month+day+hour+minutes+seconds) + renderPlotTypeSelectView: function () { + let options = [ + ["stddevran", "Mean and Standard Deviation"], + ["trajectories", "Trajectories"], + ["stddev", "Standard Deviation"], + ["avg", "Trajectory Mean"] + ]; + let plotTypeSelectView = new SelectView({ + name: 'plot-type', + required: true, + idAttribute: 'cid', + options: options, + value: "stddevran" + }); + app.registerRenderSubview(this, plotTypeSelectView, "plot-type-select"); }, - handleCollapseStddevrangeClick: function (e) { - this.changeCollapseButtonText(e) - let type = "stddevran" - if(!this.plots[type]){ - this.getPlot(type); - } + renderSpeciesOfInterestView: function () { + let speciesNames = this.model.model.species.map(function (specie) { return specie.name}); + let speciesOfInterestView = new SelectView({ + name: 'species-of-interest', + required: true, + idAttribute: 'cid', + options: speciesNames, + value: this.model.settings.parameterSweepSettings.speciesOfInterest.name + }); + app.registerRenderSubview(this, speciesOfInterestView, "specie-of-interest-list"); }, - handleCollapseTrajectoriesClick: function (e) { - this.changeCollapseButtonText(e) - let type = "trajectories" - if(!this.plots[type]){ - this.getPlot(type); - } + renderSweepParameterView: function () { + let sweepParameterView = this.renderCollection( + this.model.settings.parameterSweepSettings.parameters, + SweepParametersView, + this.queryByHook("parameter-ranges") + ); }, - handleCollapseStddevClick: function (e) { - this.changeCollapseButtonText(e) - let type = "stddev" - if(!this.plots[type]){ - this.getPlot(type); + setTitle: function (e) { + this.plotArgs['title'] = e.target.value + for (var type in this.plots) { + let fig = this.plots[type] + fig.layout.title.text = e.target.value + this.plotFigure(fig, type) } }, - handleCollapseTrajmeanClick: function (e) { - this.changeCollapseButtonText(e) - let type = "avg" - if(!this.plots[type]){ - this.getPlot(type); + setXAxis: function (e) { + this.plotArgs['xaxis'] = e.target.value + for (var type in this.plots) { + let fig = this.plots[type] + fig.layout.xaxis.title.text = e.target.value + this.plotFigure(fig, type) } }, - handleCollapsePsweepClick: function (e) { - this.changeCollapseButtonText(e) - let type = "psweep" - if(!this.plots[type]){ - this.getPlot(type); + setYAxis: function (e) { + this.plotArgs['yaxis'] = e.target.value + for (var type in this.plots) { + let fig = this.plots[type] + fig.layout.yaxis.title.text = e.target.value + this.plotFigure(fig, type) } }, + update: function () {}, + updateValid: function () {}, subviews: { inputTitle: { hook: 'title', @@ -375,13 +386,10 @@ module.exports = View.extend({ parent: this, required: false, name: 'title', - label: '', - tests: '', - modelKey: null, valueType: 'string', - value: this.plotArgs.title || "", + value: this.plotArgs.title || "" }); - }, + } }, inputXAxis: { hook: 'xaxis', @@ -390,13 +398,10 @@ module.exports = View.extend({ parent: this, required: false, name: 'xaxis', - label: '', - tests: '', - modelKey: null, valueType: 'string', - value: this.plotArgs.xaxis || "", + value: this.plotArgs.xaxis || "" }); - }, + } }, inputYAxis: { hook: 'yaxis', @@ -405,13 +410,10 @@ module.exports = View.extend({ parent: this, required: false, name: 'yaxis', - label: '', - tests: '', - modelKey: null, valueType: 'string', - value: this.plotArgs.yaxis || "", + value: this.plotArgs.yaxis || "" }); - }, - }, - }, + } + } + } }); diff --git a/client/views/workflow-state-buttons.js b/client/views/workflow-state-buttons.js deleted file mode 100644 index 5a30586beb..0000000000 --- a/client/views/workflow-state-buttons.js +++ /dev/null @@ -1,153 +0,0 @@ -/* -StochSS is a platform for simulating biochemical systems -Copyright (C) 2019-2020 StochSS developers. - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . -*/ - -var $ = require('jquery'); -var xhr = require('xhr'); -var path = require('path'); -//support file -let app = require('../app'); -let modals = require('../modals'); -//views -var View = require('ampersand-view'); -//templates -var template = require('../templates/includes/workflowStateButtons.pug'); - -module.exports = View.extend({ - template: template, - events: { - 'click [data-hook=save]' : 'clickSaveHandler', - 'click [data-hook=start-workflow]' : 'clickStartWorkflowHandler', - 'click [data-hook=edit-model]' : 'clickEditModelHandler', - }, - initialize: function (attrs, options) { - View.prototype.initialize.apply(this, arguments); - this.type = attrs.type - }, - render: function () { - View.prototype.render.apply(this, arguments); - $(this.queryByHook("save")).prop('disabled', this.parent.parent.modelLoadError) - $(this.queryByHook("start-workflow")).prop('disabled', this.parent.parent.modelLoadError) - $(this.queryByHook("edit-model")).prop('disabled', this.parent.parent.modelLoadError) - }, - clickSaveHandler: function (e, cb) { - this.saving(); - var self = this; - var model = this.model - var optType = this.parent.parent.urlPathParam.endsWith(".mdl") ? "sn" : "se"; - this.saveModel(function () { - self.saveWorkflow(model, optType, cb) - }); - }, - saveWorkflow: function (model, optType, cb) { - let self = this - let query = JSON.stringify({"type":self.type, - "optType":optType, - "mdlPath":model.directory, - "wkflPath":self.parent.parent.wkflPath, - "settings":self.parent.settings - }) - var endpoint = path.join(app.getApiPath(), 'workflow/save-workflow') + "?data=" + query; - xhr({uri: endpoint}, function (err, response, body) { - self.saved(); - if(cb){ - cb() - }else if(self.parent.parent.urlPathParam.endsWith('.mdl')){ - self.parent.parent.reloadWkfl(); - } - }); - }, - clickStartWorkflowHandler: function (e) { - this.saveModel(this.runWorkflow.bind(this)); - }, - clickEditModelHandler: function (e) { - var self = this - this.saveModel(function () { - window.location.href = path.join(app.getBasePath(), "stochss/models/edit")+"?path="+self.model.directory; - }); - }, - saveModel: function (cb) { - // this.model is a ModelVersion, the parent of the collection is Model - let self = this - if(this.parent.settings.simulationSettings.isAutomatic){ - this.parent.settings.simulationSettings.letUsChooseForYou(this.model); - } - var model = this.model; - if (cb) { - model.save(model.attributes, { - success: cb, - error: function (model, response, options) { - console.error("Error saving model:", model); - console.error("Response:", response); - self.saveError() - let title = response.body.Reason - let error = response.body.Message - var saveErrorModal = $(modals.modelSaveErrorHtml(title, error)).modal() - }, - }); - } else { - model.saveModel(); - } - }, - saving: function () { - var saving = this.queryByHook('saving-workflow'); - var saved = this.queryByHook('saved-workflow'); - var saveError = this.queryByHook('save-error'); - saved.style.display = "none"; - saveError.style.display = "none"; - saving.style.display = "inline-block"; - }, - saved: function () { - var saving = this.queryByHook('saving-workflow'); - var saved = this.queryByHook('saved-workflow'); - saving.style.display = "none"; - saved.style.display = "inline-block"; - }, - saveError: function () { - var saving = this.queryByHook('saving-workflow'); - var saveError = this.queryByHook('save-error'); - saving.style.display = "none"; - saveError.style.display = "inline-block"; - }, - runWorkflow: function () { - var self = this; - var model = this.model; - var optType = this.parent.parent.urlPathParam.endsWith(".mdl") ? "rn" : "re"; - var query = {"type":this.type, - "optType":"s"+optType, - "mdlPath":model.directory, - "wkflPath":self.parent.parent.wkflPath, - "settings":self.parent.settings - } - let initQuery = JSON.stringify(query) - var initEndpoint = path.join(app.getApiPath(), '/workflow/save-workflow') + "?data=" + initQuery; - query.optType = optType - let runQuery = JSON.stringify(query) - var runEndpoint = path.join(app.getApiPath(), '/workflow/run-workflow') + "?data=" + runQuery; - this.saving() - xhr({uri: initEndpoint}, function (err, response, body) { - if(response.statusCode < 400){ - self.saved() - xhr({uri: runEndpoint}, function (err, response, body) { - self.parent.parent.reloadWkfl(); - }) - }else{ - self.saveError() - } - }); - }, -}); diff --git a/client/views/workflow-status.js b/client/views/workflow-status.js index bc963fd4dc..c4d0947c39 100644 --- a/client/views/workflow-status.js +++ b/client/views/workflow-status.js @@ -16,11 +16,15 @@ You should have received a copy of the GNU General Public License along with this program. If not, see . */ -var $ = require('jquery'); +let $ = require('jquery'); +let path = require('path'); +let _ = require('underscore'); +//support files +let app = require('../app'); //views -var View = require('ampersand-view'); +let View = require('ampersand-view'); //templates -var template = require('../templates/includes/workflowStatus.pug'); +let template = require('../templates/includes/workflowStatus.pug'); module.exports = View.extend({ @@ -30,57 +34,30 @@ module.exports = View.extend({ }, initialize: function (attrs, options) { View.prototype.initialize.apply(this, arguments); - var localDate = new Date(attrs.startTime) - console.log(localDate, typeof localDate) - var localStartTime = this.getFormattedDate(localDate) - console.log(localStartTime, typeof localStartTime) - this.startTime = localStartTime; - this.status = attrs.status; }, render: function () { View.prototype.render.apply(this, arguments); - if(this.status !== 'ready' && this.status !== 'new'){ - this.expandContainer() + if(this.model.status !== 'running') { + $(this.queryByHook('running-spinner')).css('display', "none"); + }else{ + this.getJobStatus(); } - if(this.status !== 'running') { - $(this.queryByHook('running-spinner')).css('display', "none") - } - }, - expandContainer: function () { - $(this.queryByHook('workflow-status')).collapse('show'); - let collapseBtn = $(this.queryByHook('collapse')) - collapseBtn.prop('disabled', false); - collapseBtn.trigger('click') }, changeCollapseButtonText: function (e) { - let source = e.target.dataset.hook - let collapseContainer = $(this.queryByHook(source).dataset.target) - if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) { - let collapseBtn = $(this.queryByHook(source)) - let text = collapseBtn.text(); - text === '+' ? collapseBtn.text('-') : collapseBtn.text('+'); - } - }, - getFormattedDate: function (date) { - var months = ['Jan.', 'Feb.', 'Mar.', 'Apr.', 'May', 'Jun.', 'Jul.', 'Aug.', 'Sept.', 'Oct.', 'Nov.', 'Dec.']; - var month = months[date.getMonth()]; // get the abriviated month - var year = date.getFullYear(); - var day = date.getDate(); - var hours = date.getHours(); - var ampm = hours >= 12 ? 'PM' : 'AM'; // get AM or PM based on hours - hours = hours%12; // format hours to 12 hour time format - hours = hours ? hours : 12; // replace 0 with 12 - var minutes = date.getMinutes(); - minutes = minutes < 10 ? '0' + minutes : minutes; // format minutes to always have two chars - var timeZone = date.toString().split('(').pop().split(')').shift() // get the timezone from the date - if(timeZone.includes(" ")){ - tzparts = timeZone.split(" ") - tzparts = tzparts.map(function (element) { - return element.charAt(0) - }) - timeZone = tzparts.join("") - } - // timeZone = timeZone.replace('(', '').replace(')', '') // remove the '()' from the timezone - return month + " " + day + ", " + year + " " + hours + ":" + minutes + " " + ampm + " " + timeZone; + app.changeCollapseButtonText(this, e); }, -}); \ No newline at end of file + getJobStatus: function () { + let self = this; + let queryString = "?path=" + this.model.directory; + let endpoint = path.join(app.getApiPath(), "workflow/workflow-status") + queryString; + app.getXHR(endpoint, { + always: function (err, response, body) { + if(body === 'running') { + setTimeout(_.bind(self.getJobStatus, self), 1000); + }else{ + self.parent.updateWorkflow(); + } + } + }); + } +}); diff --git a/client/views/workflow-viewer.js b/client/views/workflow-viewer.js deleted file mode 100644 index 13feb24f33..0000000000 --- a/client/views/workflow-viewer.js +++ /dev/null @@ -1,58 +0,0 @@ -/* -StochSS is a platform for simulating biochemical systems -Copyright (C) 2019-2020 StochSS developers. - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . -*/ - -var $ = require('jquery'); -//collection -var Collection = require('ampersand-collection'); -//models -var Plot = require('../models/plots'); -//views -var View = require('ampersand-view'); -var PlotsView = require('./plots-view'); -//templates -var template = require('../templates/includes/workflowViewer.pug'); - -module.exports = View.extend({ - template: template, - events: { - 'click [data-hook=collapse-workflow]' : 'renderPlots' - }, - initialize: function (attrs, options) { - View.prototype.initialize.apply(this, arguments) - }, - render: function (attrs, options) { - View.prototype.render.apply(this, arguments) - }, - renderPlots: function (e) { - this.changeCollapseButtonText(e) - if(this.plotsView) { - return - } - var outputs = new Collection(this.model.outputs, {model: Plot}) - this.plotsView = this.renderCollection(outputs, PlotsView, this.queryByHook("workflow-plots")) - }, - changeCollapseButtonText: function (e) { - let source = e.target.dataset.hook - let collapseContainer = $(this.queryByHook(source).dataset.target) - if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) { - let collapseBtn = $(this.queryByHook(source)) - let text = collapseBtn.text(); - text === '+' ? collapseBtn.text('-') : collapseBtn.text('+'); - } - } -}) \ No newline at end of file diff --git a/client/views/workflows-viewer.js b/client/views/workflows-viewer.js deleted file mode 100644 index d540abf6ad..0000000000 --- a/client/views/workflows-viewer.js +++ /dev/null @@ -1,47 +0,0 @@ -/* -StochSS is a platform for simulating biochemical systems -Copyright (C) 2019-2020 StochSS developers. - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . -*/ - -var $ = require('jquery'); -//views -var View = require('ampersand-view'); -var WorkflowViewer = require('./workflow-viewer'); -//templates -var template = require('../templates/includes/workflowsViewer.pug'); - -module.exports = View.extend({ - template: template, - events: { - 'click [data-hook=collapse-workflows]' : 'changeCollapseButtonText' - }, - initialize: function (attrs, options) { - View.prototype.initialize.apply(this, arguments) - }, - render: function (attrs, options) { - View.prototype.render.apply(this, arguments) - this.renderCollection(this.collection, WorkflowViewer, this.queryByHook('workflow-container')) - }, - changeCollapseButtonText: function (e) { - let source = e.target.dataset.hook - let collapseContainer = $(this.queryByHook(source).dataset.target) - if(!collapseContainer.length || !collapseContainer.attr("class").includes("collapsing")) { - let collapseBtn = $(this.queryByHook(source)) - let text = collapseBtn.text(); - text === '+' ? collapseBtn.text('-') : collapseBtn.text('+'); - } - } -}) \ No newline at end of file diff --git a/public_models/3D_Cylinder/3D_cylinder.ipynb b/public_models/3D_Cylinder/3D_cylinder.ipynb new file mode 100644 index 0000000000..b9d21b09ff --- /dev/null +++ b/public_models/3D_Cylinder/3D_cylinder.ipynb @@ -0,0 +1 @@ +{"cells":[{"cell_type":"code","execution_count":1,"metadata":{},"outputs":[],"source":["%load_ext autoreload\n","%autoreload 2\n","\n","import numpy as np\n","import spatialpy\n","from spatialpy import Model, Species, Parameter, Reaction, Mesh,\\\n"," PlaceInitialCondition, \\\n"," UniformInitialCondition, \\\n"," ScatterInitialCondition"]},{"cell_type":"markdown","metadata":{},"source":["# 3D_cylinder"]},{"cell_type":"code","execution_count":2,"metadata":{},"outputs":[],"source":["class M3Dcylinder(Model):\n"," def __init__(self):\n"," Model.__init__(self, name=\"3D_cylinder\")\n","\n"," # Domain\n"," mesh = Mesh.read_stochss_domain('3D_cylinder.smdl')\n"," self.add_mesh(mesh)\n","\n"," self.staticDomain = True\n","\n"," # Variables\n"," A = Species(name=\"A\", diffusion_constant=0.1)\n"," B = Species(name=\"B\", diffusion_constant=0.1)\n"," self.add_species([A, B])\n","\n"," self.restrict(A, [1, 2])\n"," self.restrict(B, [1, 3])\n","\n"," # Parameters\n"," k_react = Parameter(name=\"k_react\", expression=\"1\")\n"," k_creat1 = Parameter(name=\"k_creat1\", expression=\"196.38595510240296\")\n"," k_creat2 = Parameter(name=\"k_creat2\", expression=\"197.70475491603773\")\n"," self.add_parameter([k_react, k_creat1, k_creat2])\n","\n"," # Reactions\n"," r1 = Reaction(name=\"r1\", restrict_to=[2], reactants={}, products={B: 1}, rate=self.listOfParameters[\"k_creat1\"])\n"," r2 = Reaction(name=\"r2\", restrict_to=[3], reactants={}, products={B: 1}, rate=self.listOfParameters[\"k_creat2\"])\n"," r3 = Reaction(name=\"r3\", reactants={B: 2}, products={}, rate=self.listOfParameters[\"k_react\"])\n"," self.add_reaction([r1, r2, r3])\n","\n"," # Timespan\n"," self.timespan(np.arange(0, 500, 1), timestep_size=1)"]},{"cell_type":"code","execution_count":3,"metadata":{},"outputs":[],"source":["model = M3Dcylinder()"]},{"cell_type":"markdown","metadata":{},"source":["# Simulation Parameters"]},{"cell_type":"code","execution_count":4,"metadata":{},"outputs":[],"source":["def configure_simulation():\n"," kwargs = {\n"," # \"number_of_trajectories\":1,\n"," # \"seed\":None,\n"," }\n"," return kwargs"]},{"cell_type":"code","execution_count":5,"metadata":{},"outputs":[],"source":["kwargs = configure_simulation()\n","results = model.run(**kwargs)"]},{"cell_type":"markdown","metadata":{},"source":["# Visualization"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["results.plot_species('A', animated=True, width=None, height=None)"]}],"metadata":{"kernelspec":{"display_name":"Python 3","language":"python","name":"python3"},"language_info":{"codemirror_mode":{"name":"ipython","version":3},"file_extension":".py","mimetype":"text/x-python","name":"python","nbconvert_exporter":"python","pygments_lexer":"ipython3","version":"3.8.5"}},"nbformat":4,"nbformat_minor":4} \ No newline at end of file diff --git a/public_models/Brusselator/Brusselator.ipynb b/public_models/Brusselator/Brusselator.ipynb index d9ae8c91c9..5f0e2539dd 100644 --- a/public_models/Brusselator/Brusselator.ipynb +++ b/public_models/Brusselator/Brusselator.ipynb @@ -1,37128 +1 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Brusselator" - ] - }, - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [], - "source": [ - "import numpy as np\n", - "import gillespy2\n", - "from gillespy2 import Model, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition\n", - "from gillespy2 import EventAssignment, EventTrigger, Event\n", - "from gillespy2 import SSACSolver\n", - "# from gillespy2 import VariableSSACSolver\n", - "# from gillespy2 import BasicTauLeapingSolver\n", - "# from gillespy2 import BasicTauHybridSolver\n", - "# from gillespy2 import BasicODESolver" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [], - "source": [ - "class Brusselator(Model):\n", - " def __init__(self, parameter_values=None):\n", - " Model.__init__(self, name=\"Brusselator\")\n", - " self.volume = 1000\n", - "\n", - " # Parameters\n", - " self.add_parameter(Parameter(name=\"rate1\", expression=5000))\n", - " self.add_parameter(Parameter(name=\"rate2\", expression=50))\n", - " self.add_parameter(Parameter(name=\"rate3\", expression=0.00005))\n", - " self.add_parameter(Parameter(name=\"rate4\", expression=5))\n", - "\n", - " # Species\n", - " self.add_species(Species(name=\"A\", initial_value=100000, mode=\"discrete\"))\n", - " self.add_species(Species(name=\"B\", initial_value=100000, mode=\"discrete\"))\n", - " self.add_species(Species(name=\"C\", initial_value=0, mode=\"discrete\"))\n", - " self.add_species(Species(name=\"D\", initial_value=0, mode=\"discrete\"))\n", - " self.add_species(Species(name=\"X\", initial_value=2000, mode=\"discrete\"))\n", - " self.add_species(Species(name=\"Y\", initial_value=1000, mode=\"discrete\"))\n", - "\n", - " # Reactions\n", - " self.add_reaction(Reaction(name=\"reaction1\", reactants={'A': 1}, products={'X': 1, 'A': 1}, propensity_function=\"rate1\"))\n", - " self.add_reaction(Reaction(name=\"reaction2\", reactants={'B': 1, 'X': 1}, products={'Y': 1, 'C': 1, 'B': 1}, propensity_function=\"rate2*X\"))\n", - " self.add_reaction(Reaction(name=\"reaction3\", reactants={'X': 2, 'Y': 1}, products={'X': 3}, propensity_function=\"rate3*Y*X*(X-1)/2\"))\n", - " self.add_reaction(Reaction(name=\"reaction4\", reactants={'X': 1}, products={'D': 1}, propensity_function=\"rate4*X\"))\n", - "\n", - " # Timespan\n", - " self.timespan(np.linspace(0, 30, 3001))" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [], - "source": [ - "model = Brusselator()" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [], - "source": [ - "solver = SSACSolver(model=model)" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "metadata": {}, - "outputs": [], - "source": [ - "def configure_simulation():\n", - " kwargs = {\n", - " \"solver\":solver,\n", - " \"number_of_trajectories\":1,\n", - " \"seed\":None,\n", - " # \"tau_tol\":0.03,\n", - " # \"integrator_options\":{'rtol': 0.001, 'atol': 1e-06}\n", - " }\n", - " return kwargs" - ] - 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" - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "results.plotplotly()" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.7.6" - } - }, - "nbformat": 4, - "nbformat_minor": 4 -} +{"cells":[{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["import numpy as np\n","import gillespy2\n","from gillespy2 import Model, Species, Parameter, Reaction, Event, \\\n"," EventTrigger, EventAssignment, RateRule, \\\n"," AssignmentRule, FunctionDefinition\n","# from gillespy2 import SSACSolver\n","# from gillespy2 import TauLeapingCSolver\n","# from gillespy2 import ODECSolver\n","# from gillespy2 import TauHybridSolver"]},{"cell_type":"markdown","metadata":{},"source":["# Brusselator"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["class Brusselator(Model):\n"," def __init__(self, parameter_values=None):\n"," Model.__init__(self, name=\"Brusselator\")\n"," self.volume = 1000\n","\n"," # Parameters\n"," self.add_parameter(Parameter(name=\"rate1\", expression=\"5000\"))\n"," self.add_parameter(Parameter(name=\"rate2\", expression=\"50\"))\n"," self.add_parameter(Parameter(name=\"rate3\", expression=\"5e-05\"))\n"," self.add_parameter(Parameter(name=\"rate4\", expression=\"5\"))\n","\n"," # Variables\n"," self.add_species(Species(name=\"A\", initial_value=100000, mode=\"discrete\"))\n"," self.add_species(Species(name=\"B\", initial_value=100000, mode=\"discrete\"))\n"," self.add_species(Species(name=\"C\", initial_value=0, mode=\"discrete\"))\n"," self.add_species(Species(name=\"D\", initial_value=0, mode=\"discrete\"))\n"," self.add_species(Species(name=\"X\", initial_value=2000, mode=\"discrete\"))\n"," self.add_species(Species(name=\"Y\", initial_value=1000, mode=\"discrete\"))\n","\n"," # Reactions\n"," self.add_reaction(Reaction(name=\"reaction1\", reactants={'A': 1}, products={'X': 1, 'A': 1}, propensity_function=\"rate1\"))\n"," self.add_reaction(Reaction(name=\"reaction2\", reactants={'B': 1, 'X': 1}, products={'Y': 1, 'C': 1, 'B': 1}, propensity_function=\"rate2*X\"))\n"," self.add_reaction(Reaction(name=\"reaction3\", reactants={'X': 2, 'Y': 1}, products={'X': 3}, propensity_function=\"rate3*Y*X*(X-1)/2\"))\n"," self.add_reaction(Reaction(name=\"reaction4\", reactants={'X': 1}, products={'D': 1}, propensity_function=\"rate4*X\"))\n","\n"," # Timespan\n"," self.timespan(np.arange(0, 30, 0.01))"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["model = Brusselator()"]},{"cell_type":"markdown","metadata":{},"source":["# Simulation Parameters"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["def configure_simulation():\n"," # solver = SSACSolver(model=model)\n"," kwargs = {\n"," # \"solver\":solver,\n"," \"number_of_trajectories\":100,\n"," # \"seed\":None,\n"," # \"tau_tol\":0.03,\n"," # \"integrator_options\":{'rtol': 0.001, 'atol': 1e-06},\n"," }\n"," return kwargs"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["kwargs = configure_simulation()\n","results = model.run(**kwargs)"]},{"cell_type":"markdown","metadata":{},"source":["# Visualization"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["results.plotplotly()"]}],"metadata":{},"nbformat":4,"nbformat_minor":4} \ No newline at end of file diff --git a/public_models/Degradation/Degradation.ipynb b/public_models/Degradation/Degradation.ipynb index 0c2c174373..153133ff46 100644 --- a/public_models/Degradation/Degradation.ipynb +++ b/public_models/Degradation/Degradation.ipynb @@ -1,1247 +1 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Degradation" - ] - }, - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [], - "source": [ - "import numpy as np\n", - "import gillespy2\n", - "from gillespy2 import Model, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition\n", - "from gillespy2 import EventAssignment, EventTrigger, Event\n", - "from gillespy2 import SSACSolver\n", - "# from gillespy2 import VariableSSACSolver\n", - "# from gillespy2 import BasicTauLeapingSolver\n", - "# from gillespy2 import BasicTauHybridSolver\n", - "# from gillespy2 import BasicODESolver" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [], - "source": [ - "class Degradation(Model):\n", - " def __init__(self, parameter_values=None):\n", - " Model.__init__(self, name=\"Degradation\")\n", - " self.volume = 1\n", - "\n", - " # Parameters\n", - " self.add_parameter(Parameter(name=\"decayrate\", expression=0.05))\n", - 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"cells": [ - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Dimerization" - ] - }, - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [], - "source": [ - "import numpy as np\n", - "import gillespy2\n", - "from gillespy2 import Model, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition\n", - "from gillespy2 import EventAssignment, EventTrigger, Event\n", - "from gillespy2 import SSACSolver\n", - "# from gillespy2 import VariableSSACSolver\n", - "# from gillespy2 import BasicTauLeapingSolver\n", - "# from gillespy2 import BasicTauHybridSolver\n", - "# from gillespy2 import BasicODESolver" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [], - "source": [ - "class Dimerization(Model):\n", - " def __init__(self, parameter_values=None):\n", - " Model.__init__(self, name=\"Dimerization\")\n", - " self.volume = 1\n", - "\n", - " # Parameters\n", - " self.add_parameter(Parameter(name=\"k_c\", expression=0.005))\n", - 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TauHybridSolver"]},{"cell_type":"markdown","metadata":{},"source":["# Dimerization"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["class Dimerization(Model):\n"," def __init__(self, parameter_values=None):\n"," Model.__init__(self, name=\"Dimerization\")\n"," self.volume = 1\n","\n"," # Parameters\n"," self.add_parameter(Parameter(name=\"k_c\", expression=\"0.005\"))\n"," self.add_parameter(Parameter(name=\"k_d\", expression=\"0.08\"))\n","\n"," # Variables\n"," self.add_species(Species(name=\"Monomer\", initial_value=30, mode=\"discrete\"))\n"," self.add_species(Species(name=\"Dimer\", initial_value=0, mode=\"discrete\"))\n","\n"," # Reactions\n"," self.add_reaction(Reaction(name=\"r_creation\", reactants={'Monomer': 2}, products={'Dimer': 1}, rate=self.listOfParameters[\"k_c\"]))\n"," self.add_reaction(Reaction(name=\"r_dissociation\", reactants={'Dimer': 1}, products={'Monomer': 2}, rate=self.listOfParameters[\"k_d\"]))\n","\n"," # Timespan\n"," self.timespan(np.arange(0, 100, 1))"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["model = Dimerization()"]},{"cell_type":"markdown","metadata":{},"source":["# Simulation Parameters"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["def configure_simulation():\n"," # solver = SSACSolver(model=model)\n"," kwargs = {\n"," # \"solver\":solver,\n"," \"number_of_trajectories\":100,\n"," # \"seed\":None,\n"," # \"tau_tol\":0.03,\n"," # \"integrator_options\":{'rtol': 0.001, 'atol': 1e-06},\n"," }\n"," return kwargs"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["kwargs = configure_simulation()\n","results = model.run(**kwargs)"]},{"cell_type":"markdown","metadata":{},"source":["# Visualization"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["results.plotplotly()"]}],"metadata":{},"nbformat":4,"nbformat_minor":4} \ No newline at end of file diff --git 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0000000000..e0ac5277f4 --- /dev/null +++ b/public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/settings.json @@ -0,0 +1,74 @@ +{ + "model": "Examples/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/SIR Epidemic Model.mdl", + "settings": { + "parameterSweepSettings": { + "parameters": [ + { + "max": 0.01245, + "min": 0.00415, + "name": "beta", + "paramID": 4, + "steps": 11 + }, + { + "max": 0.44999999999999996, + "min": 0.15, + "name": "gamma", + "paramID": 5, + "steps": 11 + } + ], + "speciesOfInterest": { + "annotation": "Initial population of a species that are infected\n", + "compID": 2, + "isSwitchTol": true, + "mode": "discrete", + "name": "Infected", + "switchMin": 100, + "switchTol": 0.03, + "value": 1 + } + }, + "resultsSettings": { + "mapper": "final", + "outputs": [ + { + "key": "Recovered-max-var", + "species": [ + "Recovered" + ], + "stamp": 200727163621 + }, + { + "key": "Infected-max-var", + 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--git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/logs.txt b/public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/COMPLETE similarity index 100% rename from public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/logs.txt rename to public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/COMPLETE diff --git a/public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/RUNNING b/public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/RUNNING new file mode 100644 index 0000000000..e69de29bb2 diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 1D Parameter Sweep Workflow Incomplete.wkfl/SIR Epidemic Model.mdl b/public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/SIR Epidemic Model.mdl similarity index 100% rename from public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 1D Parameter Sweep Workflow Incomplete.wkfl/SIR Epidemic Model.mdl rename to public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/SIR Epidemic Model.mdl diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/info.json b/public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/info.json similarity index 100% rename from public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/info.json rename to public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/info.json diff --git a/public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/logs.txt b/public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/logs.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/plots.json b/public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/results/plots.json similarity index 100% rename from public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/plots.json rename to public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/results/plots.json diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv0.csv b/public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/results/results_csv_08272020_162750/results_csv0.csv similarity index 100% rename from public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv0.csv rename to public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/results/results_csv_08272020_162750/results_csv0.csv diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv1.csv b/public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/results/results_csv_08272020_162750/results_csv1.csv similarity index 100% rename from public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv1.csv rename to public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/results/results_csv_08272020_162750/results_csv1.csv diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv10.csv b/public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/results/results_csv_08272020_162750/results_csv10.csv similarity index 100% rename from public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv10.csv rename to public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/results/results_csv_08272020_162750/results_csv10.csv diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv11.csv b/public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/results/results_csv_08272020_162750/results_csv11.csv similarity index 100% rename from public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv11.csv rename to public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/results/results_csv_08272020_162750/results_csv11.csv diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv12.csv b/public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/results/results_csv_08272020_162750/results_csv12.csv similarity index 100% rename from public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv12.csv rename to public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/results/results_csv_08272020_162750/results_csv12.csv diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv13.csv b/public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/results/results_csv_08272020_162750/results_csv13.csv similarity index 100% rename from public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv13.csv rename to public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/results/results_csv_08272020_162750/results_csv13.csv diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv14.csv b/public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/results/results_csv_08272020_162750/results_csv14.csv similarity index 100% rename from public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv14.csv rename to public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/results/results_csv_08272020_162750/results_csv14.csv diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv15.csv b/public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/results/results_csv_08272020_162750/results_csv15.csv similarity index 100% rename from public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv15.csv rename to public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/results/results_csv_08272020_162750/results_csv15.csv diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv16.csv b/public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/results/results_csv_08272020_162750/results_csv16.csv similarity index 100% rename from public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv16.csv rename to public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/results/results_csv_08272020_162750/results_csv16.csv diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv17.csv b/public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/results/results_csv_08272020_162750/results_csv17.csv similarity index 100% rename from public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv17.csv rename to public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/results/results_csv_08272020_162750/results_csv17.csv diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv18.csv b/public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/results/results_csv_08272020_162750/results_csv18.csv similarity index 100% rename from public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv18.csv rename to public_models/Example SIR Epidemic 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Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv4.csv rename to public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/results/results_csv_08272020_162750/results_csv4.csv diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv5.csv b/public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/results/results_csv_08272020_162750/results_csv5.csv similarity index 100% rename from public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv5.csv rename to public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/results/results_csv_08272020_162750/results_csv5.csv diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv6.csv b/public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/results/results_csv_08272020_162750/results_csv6.csv similarity index 100% rename from public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv6.csv rename to public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/results/results_csv_08272020_162750/results_csv6.csv diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv7.csv b/public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/results/results_csv_08272020_162750/results_csv7.csv similarity index 100% rename from public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv7.csv rename to public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/results/results_csv_08272020_162750/results_csv7.csv diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv8.csv b/public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/results/results_csv_08272020_162750/results_csv8.csv similarity index 100% rename from public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv8.csv rename to public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/results/results_csv_08272020_162750/results_csv8.csv diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv9.csv b/public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/results/results_csv_08272020_162750/results_csv9.csv similarity index 100% rename from public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/results/results_csv_08272020_162750/results_csv9.csv rename to public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/results/results_csv_08272020_162750/results_csv9.csv diff --git a/public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/settings.json b/public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/settings.json new file mode 100644 index 0000000000..86d31924e2 --- /dev/null +++ b/public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/job_03222021_190022/settings.json @@ -0,0 +1,44 @@ +{ + "parameterSweepSettings": { + "parameters": [], + "speciesOfInterest": {} + }, + "resultsSettings": { + "mapper": "final", + "outputs": [ + { + "key": "stddev", + "species": [ + "Susceptible", + "Infected", + "Recovered" + ], + "stamp": 200727162833 + }, + { + "key": "stddevran", + "species": [ + "Susceptible", + "Infected", + "Recovered" + ], + "stamp": 200727162836 + } + ], + "reducer": "avg" + }, + "simulationSettings": { + "absoluteTol": 1e-06, + "algorithm": "SSA", + "isAutomatic": false, + "realizations": 20, + "relativeTol": 0.001, + "seed": -1, + "tauTol": 0.03 + }, + "timespanSettings": { + "endSim": 20, + "timeStep": 0.05, + "volume": 1 + } +} \ No newline at end of file diff --git a/public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/settings.json b/public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/settings.json new file mode 100644 index 0000000000..de30e6b17b --- /dev/null +++ b/public_models/Example 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a/public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/SIR Epidemic Model.mdl b/public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/SIR Epidemic Model.mdl new file mode 100644 index 0000000000..320f352f31 --- /dev/null +++ b/public_models/Example SIR Epidemic Project.proj/SIR Epidemic Model.wkgp/SIR Epidemic Model.mdl @@ -0,0 +1 @@ +{"is_spatial":false,"defaultID":8,"defaultMode":"discrete","annotation":"The SIR model is a simple mathematical model of epidemics. An epidemic is when the number of people infected with a disease is increasing in a population. S, I, and R stand for:\n\nS - susceptible: These are people that are not infected with the disease yet. However, they are not immune to it either and so they can become infected with the disease in the future.\nI - infected or infectious: These are people that are infected with the disease and can transmit the disease to susceptible people.\nR - recovered: These are people who have recovered from the disease and are immune, so they can no longer be infected with the disease.\n\nThis model is reasonably predictive for infectious diseases that are transmitted from human to human, and where recovery confers lasting resistance, such as measles, mumps and rubella.\nThese variables (S, I, and R) represent the number of people in each compartment at a particular time. To represent that the number of susceptible, infectious and removed individuals may vary over time (even if the total population size remains constant), we make the precise numbers a function of t (time): S(t), I(t) and R(t). For a specific disease in a specific population, these functions may be worked out in order to predict possible outbreaks and bring them under control.\nAs implied by the variable function of t, the model is dynamic in that the numbers in each compartment may fluctuate over time. The importance of this dynamic aspect is most obvious in an endemic disease with a short infectious period, such as measles in the UK prior to the introduction of a vaccine in 1968. Such diseases tend to occur in cycles of outbreaks due to the variation in number of susceptibles (S(t)) over time. During an epidemic, the number of susceptible individuals falls rapidly as more of them are infected and thus enter the infectious and removed compartments. The disease cannot break out again until the number of susceptibles has built back up, e.g. as a result of offspring being born into the susceptible compartment.\nEach member of the population typically progresses from susceptible to infectious to recovered.","modelSettings":{"endSim":20,"timeStep":0.05,"volume":1},"meshSettings":{"count":2},"species":[{"compID":1,"name":"Susceptible","value":999,"mode":"discrete","switchTol":0.03,"switchMin":100,"isSwitchTol":true,"annotation":"Initial population of a species that are\n susceptible to infection\n","diffusionCoeff":0,"subdomains":["subdomain 1:","subdomain 2:"]},{"compID":2,"name":"Infected","value":1,"mode":"discrete","switchTol":0.03,"switchMin":100,"isSwitchTol":true,"annotation":"Initial population of a species that are infected\n","diffusionCoeff":0,"subdomains":["subdomain 1:","subdomain 2:"]},{"compID":3,"name":"Recovered","value":0,"mode":"discrete","switchTol":0.03,"switchMin":100,"isSwitchTol":true,"annotation":"Initial 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a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/SIR Epidemic Model.mdl +++ /dev/null @@ -1 +0,0 @@ -{"is_spatial":false,"defaultID":8,"defaultMode":"discrete","annotation":"Susceptible, Infected, Recovered epidemiology (SIR) Model.\n","modelSettings":{"endSim":20,"timeStep":0.05,"volume":1},"meshSettings":{"count":2},"species":[{"compID":1,"name":"Susceptible","value":999,"mode":"discrete","switchTol":0.03,"switchMin":100,"isSwitchTol":true,"annotation":"Initial population of a species that are\n susceptible to infection\n","diffusionCoeff":0,"subdomains":["subdomain 1:","subdomain 2:"]},{"compID":2,"name":"Infected","value":1,"mode":"discrete","switchTol":0.03,"switchMin":100,"isSwitchTol":true,"annotation":"Initial population of a species that are infected\n","diffusionCoeff":0,"subdomains":["subdomain 1:","subdomain 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b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/info.json deleted file mode 100644 index 17a1f7280d..0000000000 --- a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/info.json +++ /dev/null @@ -1 +0,0 @@ -{"source_model": "Examples/Example SIR Epidemic Project.proj/SIR Epidemic Model.mdl", "wkfl_model": "Examples/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/SIR Epidemic Model.mdl", "type": "parameterSweep", "start_time": "Aug 27, 2020 08:34 PM UTC"} \ No newline at end of file diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/plots.json b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/plots.json deleted file mode 100644 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905.2 , 895. , 882.7 , 828.7 , 818.75,\n 809.8 , 798.7 , 832.8 , 823.95, 813.65, 804.95, 794.8 ],\n [946.5 , 934.3 , 923.75, 866.25, 900.95, 888.25, 878.7 , 867.2 ,\n 814.95, 807.5 , 798.6 , 830.85, 823.3 , 812.9 , 803.45],\n [949.1 , 891.7 , 927.15, 915.7 , 901.6 , 849.75, 840.5 , 876.3 ,\n 866.5 , 859.2 , 849.4 , 841.85, 833.05, 825.15, 817.1 ],\n [951.85, 943.35, 931.6 , 918.85, 906.15, 898.75, 845.25, 837.1 ,\n 872.1 , 777.85, 814.05, 719.85, 713.65, 705.8 , 699.45],\n [955.35, 942.85, 930.9 , 874.05, 912. , 901.6 , 850.35, 841.55,\n 877.75, 782.3 , 817.75, 725.45, 760.75, 753.45, 747.35],\n [958.6 , 943.75, 935.5 , 878.55, 871.1 , 908.85, 901.4 , 891. ,\n 882.15, 874.4 , 780. , 773.6 , 766.95, 759.2 , 753.15]]), 'var': array([[37480.46 , 125.8475, 186.6275, 31697.66 , 185.09 ,\n 53719.3275, 90726.6275, 69001.26 , 24889.6475, 23759.5475,\n 22688.25 , 40512.8475, 20760.61 , 51738.09 , 61739.1275],\n [ 80.44 , 167.61 , 65633.69 , 172.0875, 274.9475,\n 30065.4275, 184.9 , 27487.74 , 26263.9275, 47471.96 ,\n 81051.6275, 43797.0475, 22349.56 , 21537.29 , 329.91 ],\n [ 90.64 , 162.5475, 68000.9875, 194.1 , 237.64 ,\n 59347.0275, 29987.3875, 152.8875, 27652.7275, 50622.49 ,\n 25723.9275, 153.9475, 23677.74 , 22759.45 , 21814.1875],\n [ 61.1475, 77.31 , 77.8275, 35207.6475, 64387.34 ,\n 61643.94 , 59372.16 , 30167.64 , 143.0275, 54221.1275,\n 52471.21 , 50582.8475, 49073.34 , 47343.1275, 81242.95 ],\n [ 91.46 , 39105.54 , 45.3875, 151.7275, 138.5875,\n 129.4275, 175.11 , 207.4875, 58366.7475, 29967.29 ,\n 55056.3275, 53262.41 , 51507.7475, 49928.5275, 48133.8875],\n [ 34.04 , 66.6475, 38050.4475, 36763.7475, 67784.5475,\n 65193.4275, 33682.4275, 172.5275, 31714.69 , 103.29 ,\n 29918.95 , 54962.9475, 53594.94 , 52216.44 , 50592.6275],\n [41314.55 , 67.84 , 215.15 , 111.71 , 68063.79 ,\n 34950.34 , 63887.2275, 150.61 , 158.8 , 193.6475,\n 194.3475, 29631.3275, 221.4475, 194.74 , 176.8875],\n [ 57.19 , 62.3875, 209.7275, 96.2275, 36748.4475,\n 35716.9875, 253.6275, 221.7875, 33334.4475, 200.4275,\n 158.1475, 30949.7875, 30186.2475, 29411.46 , 28694.79 ],\n [ 58.9475, 107.54 , 106.41 , 120.6 , 202.24 ,\n 196.45 , 192.34 , 201.1275, 206.0275, 211.14 ,\n 158.1475, 188.0275, 205.46 , 30237.44 , 29499.8475],\n [79827.3275, 59.75 , 40011.55 , 56.46 , 70.5 ,\n 112.71 , 36144.81 , 35347.7875, 34569.96 , 33628.31 ,\n 137.86 , 164.6475, 187.3275, 203.6475, 170.56 ],\n [ 35.25 , 54.91 , 73.2875, 39489.8875, 69.4475,\n 69.4875, 78.51 , 75.26 , 34953.7475, 34320.55 ,\n 33586.64 , 127.3275, 168.11 , 144.59 , 144.0475],\n [ 41.99 , 41795.61 , 64.3275, 75.01 , 90.04 ,\n 38001.4875, 37176.25 , 98.21 , 100.85 , 102.76 ,\n 97.44 , 122.6275, 117.1475, 130.7275, 118.39 ],\n [ 47.3275, 104.1275, 101.54 , 82.2275, 100.1275,\n 78.4875, 37596.4875, 36970.39 , 181.59 , 67260.9275,\n 35035.4475, 91392.6275, 89856.0275, 87866.86 , 86269.8475],\n [ 34.8275, 49.0275, 40.69 , 40161.8475, 117.1 ,\n 148.14 , 38097.2275, 37331.8475, 155.3875, 67995.61 ,\n 35302.5875, 92809.8475, 64202.2875, 63003.1475, 62004.9275],\n [ 20.74 , 38.4875, 56.85 , 40640.0475, 39889.19 ,\n 68.1275, 65.34 , 79.4 , 65.3275, 53.94 ,\n 67484.1 , 66391.24 , 65246.7475, 63947.06 , 62945.7275]])}, 'avg': {'min': array([[ 0.0074813 , 332.02244389, 285.98503741, 0.02743142,\n 214.54862843, 0.00249377, 0.00498753, 0.00498753,\n 0.00249377, 0.00249377, 0.01246883, 0.01246883,\n 0.00498753, 0.00249377, 0.00498753],\n [401.78304239, 327.97256858, 0.00249377, 249.49625935,\n 220.01496259, 0.01246883, 174.07730673, 0.01496259,\n 0.00498753, 0.00249377, 0.00249377, 0.00249377,\n 0.00249377, 0.00249377, 95.19950125],\n [397.56608479, 327.26932668, 0.00249377, 249.87281796,\n 218.10473815, 0.00249377, 0.00498753, 152.7680798 ,\n 0.0074813 , 0.00498753, 0.01995012, 110.50623441,\n 0.00997506, 0.00997506, 0.00997506],\n [398.12718204, 330.81795511, 281.44638404, 0.01745636,\n 0.00498753, 0.00249377, 0.00249377, 0.00997506,\n 139.86783042, 0.00997506, 0.00498753, 0.00498753,\n 0.00498753, 0.00498753, 0.00249377],\n [407.25187032, 0.01995012, 283.43640898, 247.15461347,\n 216.90274314, 191.55610973, 173.83790524, 156.86783042,\n 0.00498753, 0.00997506, 0.00498753, 0.00498753,\n 0.00498753, 0.00498753, 0.00498753],\n [416.78553616, 341.7755611 , 0.00498753, 0.0074813 ,\n 0.00249377, 0.00249377, 0.00498753, 154.69326683,\n 0.00498753, 132.09975062, 0.0074813 , 0.00498753,\n 0.00498753, 0.00498753, 0.00498753],\n [ 0.00997506, 340.71321696, 281.52369077, 241.87281796,\n 0.00249377, 0.00498753, 0.00249377, 154.7680798 ,\n 141.10473815, 130.31421446, 120.840399 , 0.0074813 ,\n 104.06982544, 97.56109726, 92.18453865],\n [401.87032419, 337.43142145, 282.17206983, 242.77306733,\n 0.00498753, 0.01496259, 164. , 149.41895262,\n 0.00249377, 126.16708229, 117.1446384 , 0.00249377,\n 0.00249377, 0.00249377, 0.00249377],\n [395.8553616 , 324.12219451, 274.94513716, 237.60349127,\n 207.55361596, 183.82044888, 164.73067332, 148.99750623,\n 136.76309227, 125.82543641, 124.77306733, 115.34413965,\n 107.86783042, 0.00249377, 0.00249377],\n [ 0.00249377, 337.7605985 , 0.01496259, 246.79052369,\n 218.90024938, 196.8478803 , 0.00249377, 0.01496259,\n 0.00498753, 0.00249377, 124.79551122, 116.18703242,\n 107.840399 , 101.17955112, 93.11970075],\n [402.46134663, 335.50124688, 282.55860349, 0.00249377,\n 213.60598504, 188.82044888, 171.28678304, 154.73566085,\n 0.00498753, 0.00249377, 0.00249377, 112.03241895,\n 104.9925187 , 98.5436409 , 92.93516209],\n [402.34164589, 0.01745636, 282.28179551, 248.58354115,\n 216.02244389, 0.0074813 , 0.00498753, 156.60349127,\n 143.07481297, 131.56359102, 122.10723192, 113.96009975,\n 106.2319202 , 99.95261845, 94.25436409],\n [406.07730673, 337.28179551, 285.66334165, 248.12468828,\n 217.5436409 , 192.05735661, 0.00498753, 0.00498753,\n 143.63341646, 0.0074813 , 0.00498753, 0.00249377,\n 0.00249377, 0.00249377, 0.00249377],\n [416.50374065, 333.66084788, 291.159601 , 0.00498753,\n 221.38154613, 192.42144638, 0.00498753, 0.00498753,\n 143.47880299, 0.0074813 , 0.00498753, 0.00249377,\n 0.00249377, 0.00249377, 0.00249377],\n [415.02992519, 335.90274314, 288.63341646, 0.00249377,\n 0.00249377, 196.83042394, 176.6957606 , 159.30174564,\n 145.60099751, 133.91521197, 0.00249377, 0.00249377,\n 0.00249377, 0.00249377, 0.00249377]]), 'max': array([[439.97506234, 369.24688279, 315.33915212, 274.4638404 ,\n 239.96758105, 213.17456359, 190.87032419, 173.88778055,\n 159.17206983, 146.02493766, 135.35411471, 125.99002494,\n 118.9925187 , 111.71820449, 105.04738155],\n [443.55610973, 365.36907731, 311.74563591, 270.21197007,\n 239.29426434, 216.03990025, 194.01246883, 177.20698254,\n 162.41396509, 149.85785536, 138.64837905, 129.80548628,\n 120.87531172, 114.28927681, 108.20199501],\n [438.31421446, 370.18952618, 310.7032419 , 270.05486284,\n 239.66583541, 211.18453865, 190.58104738, 172.67082294,\n 156.82294264, 144.82294264, 134.89526185, 125.3117207 ,\n 117.02992519, 109.87032419, 103.93266833],\n [434.46134663, 370.86284289, 314.3915212 , 270.58354115,\n 238.46882793, 210.83291771, 189.93516209, 172.20947631,\n 157.89276808, 145.41147132, 134.11970075, 124.34164589,\n 116.67581047, 109.90274314, 103.88528678],\n [432.55610973, 360.99002494, 321.15461347, 274.98503741,\n 235.67581047, 210.87531172, 190.9276808 , 172.39900249,\n 157.89526185, 145.27930175, 134.9127182 , 125.69326683,\n 117.08977556, 110.50623441, 104.3042394 ],\n [443.25436409, 378.66583541, 319.11471322, 276.97007481,\n 243.54613466, 216.33167082, 192.55610973, 174.19700748,\n 159.66334165, 146.70074813, 135.58104738, 126.22693267,\n 118.33915212, 111.47381546, 104.44638404],\n [446.28678304, 380.58603491, 322.43391521, 271.13715711,\n 237.85037406, 212.27431421, 190.9276808 , 173.83541147,\n 158.66334165, 146.3042394 , 136.32668329, 126.2967581 ,\n 118.08977556, 111.36159601, 105.21945137],\n [443.91521197, 379.42394015, 321.96259352, 272.00249377,\n 237.51371571, 211.81795511, 190.86284289, 173.75810474,\n 160.18453865, 147.25685786, 137.5361596 , 127.68578554,\n 119.03740648, 111.16458853, 104.54613466],\n [440.14962594, 372.5436409 , 313.54613466, 271.77057357,\n 239.49875312, 212.01745636, 191.83042394, 173.99501247,\n 160.19451372, 147.69326683, 135.63591022, 126.46633416,\n 118.34912718, 111.680798 , 105.24688279],\n [446.94264339, 375.32418953, 313.1521197 , 275.49625935,\n 243.69825436, 215.52119701, 192.93765586, 173.90523691,\n 159.77805486, 145.54862843, 135.04987531, 126.29925187,\n 118.38902743, 111.19451372, 103.65087282],\n [445.41396509, 369.27431421, 319.93266833, 279.16957606,\n 236.94763092, 210.00249377, 189.37905237, 172.03491272,\n 158.20947631, 144.38154613, 133.69825436, 124.159601 ,\n 116.26932668, 109.12718204, 103.01246883],\n [446.61845387, 370.14962594, 319.29426434, 277.67581047,\n 240.64339152, 214.06982544, 190.98503741, 173.59850374,\n 158.92518703, 146.52618454, 135.21695761, 126.2244389 ,\n 117.66583541, 110.93017456, 104.63092269],\n [447.03740648, 371.25935162, 319.43142145, 277.40149626,\n 240.68329177, 213.28927681, 190.87780549, 181.28428928,\n 165.95261845, 153.02992519, 142.73067332, 132.09975062,\n 124.02493766, 116.28927681, 109.50872818],\n [446.39401496, 378.10972569, 327.64837905, 284.69825436,\n 251.29177057, 222.5436409 , 200.02493766, 181.24189526,\n 165.50623441, 152.39900249, 142.13715711, 132.54114713,\n 119.43391521, 112.70573566, 106.06234414],\n [438.8553616 , 367.16957606, 310.5436409 , 273.90773067,\n 237.32418953, 212.53865337, 193.32418953, 174.72069825,\n 159.65336658, 147.78304239, 136.91521197, 127.00498753,\n 119.12967581, 112.25685786, 105.95012469]]), 'avg': array([[397.97531172, 347.80723192, 297.5446384 , 246.55498753,\n 227.78379052, 182.47955112, 146.0286783 , 140.93017456,\n 144.46433915, 132.70561097, 122.91882793, 108.22269327,\n 107.19189526, 89.86683292, 79.6127182 ],\n [421.34189526, 347.67755611, 267.80773067, 258.72269327,\n 227.89139651, 191.55112219, 180.39177057, 156.11932668,\n 142.98990025, 124.86558603, 103.00972569, 107.75985037,\n 106.32680798, 99.90074813, 98.96022444],\n [417.06234414, 347.59526185, 268.98516209, 259.28566085,\n 228.13179551, 181.53566085, 171.78815461, 163.47219451,\n 142.07481297, 124.32306733, 121.50311721, 118.93441397,\n 105.66970075, 99.2584788 , 93.59451372],\n [420.65149626, 353.35149626, 300.14887781, 246.22107232,\n 204.26084788, 181.74077307, 163.08640898, 155.4882793 ,\n 149.64451372, 124.66122195, 115.44912718, 107.49987531,\n 100.67107232, 94.54950125, 79.10124688],\n [421.07356608, 333.67518703, 301.32680798, 260.57369077,\n 227.83129676, 201.81995012, 181.47618454, 164.68354115,\n 135.33453865, 131.95773067, 115.63428928, 107.5553616 ,\n 100.57082294, 95.29862843, 89.72992519],\n [426.40523691, 356.00511222, 285.31246883, 246.63628429,\n 204.59937656, 182.3478803 , 173.29164589, 165.10124688,\n 143.74663342, 139.24301746, 122.68042394, 108.14002494,\n 101.25311721, 95.21583541, 89.84226933],\n [405.39401496, 355.96209476, 299.44339152, 257.74551122,\n 202.64800499, 191.28054863, 162.1372818 , 163.49413965,\n 149.26209476, 137.62418953, 127.48890274, 113.20461347,\n 111.18366584, 104.58690773, 98.59663342],\n [421.74127182, 354.73129676, 299.36770574, 257.65473815,\n 214.50511222, 191.48753117, 182.05399002, 165.53291771,\n 143.56508728, 139.08952618, 128.86957606, 114.10985037,\n 106.63852868, 100.19326683, 94.56620948],\n [423.95760599, 352.62668329, 299.39875312, 260.17705736,\n 228.55860349, 203.06184539, 182.3521197 , 165.40586035,\n 151.33790524, 139.17917706, 129.49139651, 120.64189526,\n 112.97967581, 100.84239401, 95.02381546],\n [382.67244389, 355.02581047, 286.77730673, 261.25810474,\n 230.04451372, 204.42618454, 174.30660848, 157.91733167,\n 144.45087282, 132.78316708, 129.52406484, 120.619202 ,\n 112.88441397, 106.10511222, 98.43229426],\n [425.68004988, 353.13840399, 301.71857855, 246.4744389 ,\n 227.13790524, 201.17256858, 180.65012469, 163.68229426,\n 142.1032419 , 131.00660848, 121.35561097, 118.82493766,\n 111.34900249, 104.40698254, 98.39214464],\n [425.83715711, 336.52319202, 301.66608479, 261.87157107,\n 229.07955112, 192.74376559, 172.65486284, 164.85548628,\n 150.65897756, 138.7925187 , 128.55386534, 119.75361596,\n 112.01932668, 105.25 , 99.36396509],\n [424.95985037, 352.80598504, 304.29800499, 261.89837905,\n 229.05997506, 202.78503741, 172.61895262, 157.21197007,\n 151.29077307, 125.18204489, 122.38466334, 102.00910224,\n 95.46197007, 89.58703242, 84.44276808],\n [430.84900249, 355.34476309, 303.67830424, 249.29763092,\n 230.06321696, 203.24114713, 173.40224439, 157.12793017,\n 151.38852868, 125.19825436, 122.29887781, 102.11209476,\n 101.28927681, 95.11608479, 89.6936409 ],\n [425.88391521, 352.51945137, 300.89413965, 248.32468828,\n 217.48977556, 204.24538653, 183.71583541, 166.2798005 ,\n 151.91683292, 139.87955112, 116.24887781, 108.24850374,\n 101.31770574, 95.16022444, 89.67256858]]), 'var': array([[ 8415.59986748, 87.67101081, 77.02625941, 3250.44950434,\n 37.50036387, 3732.18277691, 5358.63263941, 3527.95638087,\n 1116.04440868, 943.56119643, 808.04301309, 1312.51545084,\n 615.70528882, 1434.6243098 , 1592.27760903],\n [ 104.4909546 , 64.76884976, 8009.00900672, 36.62905057,\n 31.4783605 , 1955.49663746, 20.165905 , 1300.93737245,\n 1092.29816697, 1746.04106996, 2664.97665493, 1301.9487709 ,\n 605.320109 , 535.1538172 , 9.16755025],\n [ 116.18358592, 84.15541763, 8071.31726014, 34.57815528,\n 33.08885658, 3699.30224352, 1586.86523683, 27.81640741,\n 1085.59721208, 1737.04467601, 795.74348037, 16.22220142,\n 601.29664522, 530.9758946 , 472.09081187],\n [ 100.32251284, 131.04013002, 71.65690705, 3247.14207018,\n 4683.83056287, 3706.44795025, 2987.03520455, 1298.29928893,\n 21.98172678, 1738.95368392, 1490.94168127, 1291.28104208,\n 1132.52005827, 999.13330718, 1567.85533635],\n [ 37.38230453, 5880.71536799, 73.87257447, 43.96848805,\n 28.02983892, 25.48434313, 22.80645734, 20.08934951,\n 2049.9381666 , 930.24727861, 1496.25780081, 1294.58753559,\n 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672.78304239, 706.8478803 ,\n 743.28179551, 766.63092269, 784.57107232, 801.17456359,\n 816.10224439, 828.89276808, 839.2967581 , 845.20448878,\n 852.39900249, 858.58354115, 864.17955112],\n [552.48129676, 622.47630923, 675.57605985, 712.64588529,\n 743.6159601 , 767.50623441, 790.56359102, 812.29925187,\n 824.6084788 , 838.11221945, 844.23441397, 852.22693267,\n 859.52369077, 865.2394015 , 870.3117207 ],\n [567.60349127, 636.46633416, 678.99002494, 731.04488778,\n 744.52618454, 778.49376559, 793.16708229, 815.3042394 ,\n 827.59850374, 840.86533666, 839.01995012, 846.66334165,\n 854.16458853, 860.33665835, 866.16957606],\n [551.37157107, 628.02992519, 678.56608479, 710.37157107,\n 748.32917706, 770.58104738, 786.97506234, 802.21197007,\n 820.3915212 , 831.64089776, 841.44638404, 848.94264339,\n 856.52618454, 863.11471322, 876.05236908],\n [562.71321696, 629.02992519, 677.45386534, 724.66832918,\n 753.53865337, 773.32668329, 796.36658354, 813.7605985 ,\n 830.27930175, 841.25935162, 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72850.4487783 ,\n 68248.85570363, 66732.92041716, 65283.38552621]]), 'avg': array([[ 70306.31759691, 88817.57279059, 98112.1436154 ,\n 98493.05019247, 107173.30477982, 95383.80303108,\n 86040.51590475, 93938.10464736, 101361.91229346,\n 105107.05631184, 105649.75773285, 99544.13912165,\n 101904.72211802, 89228.2627409 , 84031.0373729 ],\n [ 72748.74257498, 85865.8146075 , 85993.12574051,\n 99807.78786015, 102391.36303008, 97134.12197996,\n 104547.36499462, 99293.26713826, 99782.40465296,\n 94239.32324986, 81517.07645972, 91421.80864049,\n 96699.00884074, 96101.89023824, 101309.52286118],\n [ 72110.76406925, 84500.44360732, 82346.08275881,\n 95291.94023047, 97677.71421073, 87820.87105553,\n 90729.31097195, 99012.70386814, 93743.99444717,\n 89150.81807825, 92783.79933583, 96887.41552416,\n 91433.29076312, 90947.98787072, 90257.99671084],\n [ 71766.95132928, 82859.78232722, 88427.30499748,\n 88235.40538243, 86719.73437976, 86560.04432933,\n 83900.74427895, 91133.91533448, 94554.07307604,\n 85070.29801991, 82666.46044241, 81780.67958595,\n 82550.16811525, 81876.52137114, 71484.34831624],\n [ 69481.35057431, 77512.48616302, 87649.02566464,\n 91829.77301323, 92430.44970491, 93194.04052214,\n 91722.07869603, 91130.87674082, 81381.96942867,\n 85452.06860156, 78997.09610015, 77889.09498946,\n 78298.56489139, 76867.67910274, 75868.04401776],\n [ 69300.05350215, 79709.28400259, 82373.67856792,\n 84529.64013905, 82763.98177064, 80340.44664399,\n 84803.52095758, 88995.37269296, 83184.31970199,\n 87215.21688671, 80902.77209594, 74631.84630817,\n 73666.46511589, 73233.41454344, 72433.17922463],\n [ 64712.45976518, 77746.58222523, 84815.36442995,\n 86314.34622484, 79140.15579754, 81874.65845237,\n 77648.35217318, 85092.73496558, 84094.10616787,\n 81568.07514195, 80166.87385651, 75733.8723248 ,\n 78038.01087058, 76867.26820418, 76421.14627894],\n [ 68078.85760412, 79107.57088513, 83718.71415103,\n 85630.19177741, 81720.30962929, 80225.2285446 ,\n 84603.50777918, 84394.86048408, 78548.87907351,\n 79542.58712819, 80101.60826176, 74294.11168525,\n 73267.77137767, 72119.61862364, 71013.28870716],\n [ 68208.98262013, 76281.93273736, 81477.05435476,\n 83858.50298568, 85697.47679492, 84158.00977108,\n 83292.42221939, 82671.46303319, 81096.93270378,\n 77699.88951623, 76398.02657819, 75735.64077835,\n 74542.68365806, 69314.12525855, 68164.32445258],\n [ 59725.3311901 , 75333.68002687, 76642.55711967,\n 82743.73257318, 81810.00664859, 83500.05192692,\n 79581.22194638, 77216.53025354, 74649.25274345,\n 73893.34733988, 74687.25977948, 73900.08827806,\n 72646.29901618, 70883.95707863, 69615.29414307],\n [ 66464.56009042, 75063.0144371 , 81765.96960031,\n 77464.40891848, 81395.33081635, 81989.32232013,\n 80550.61913483, 78745.37492055, 73675.12299115,\n 72464.14568628, 70559.43844939, 72621.57356795,\n 70625.70382149, 69149.22808129, 67831.12925977],\n [ 66131.92529648, 70461.95089521, 81040.46064515,\n 81891.93131262, 80905.52697185, 76485.62671812,\n 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a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/max-max.csv +++ /dev/null @@ -1,226 +0,0 @@ -beta,gamma,Infected,Recovered,Susceptible -0.004,0.1,910.0,868.0,999.0 -0.004,0.1285714285714286,883.0,926.0,999.0 -0.004,0.15714285714285714,865.0,949.0,999.0 -0.004,0.18571428571428572,840.0,974.0,999.0 -0.004,0.2142857142857143,817.0,986.0,999.0 -0.004,0.24285714285714288,802.0,989.0,999.0 -0.004,0.27142857142857146,782.0,998.0,999.0 -0.004,0.30000000000000004,766.0,998.0,999.0 -0.004,0.3285714285714286,746.0,1000.0,999.0 -0.004,0.3571428571428572,728.0,1000.0,999.0 -0.004,0.3857142857142858,712.0,1000.0,999.0 -0.004,0.41428571428571437,697.0,1000.0,999.0 -0.004,0.44285714285714284,688.0,1000.0,999.0 -0.004,0.4714285714285714,673.0,1000.0,999.0 -0.004,0.5,652.0,1000.0,999.0 -0.004642857142857143,0.1,915.0,871.0,999.0 -0.004642857142857143,0.1285714285714286,895.0,929.0,999.0 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Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/max-min.csv deleted file mode 100644 index cc5281c13b..0000000000 --- a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example 2D Parameter Sweep Workflow Complete.wkfl/results/results_csv_08272020_163323/max-min.csv +++ /dev/null @@ -1,226 +0,0 @@ -beta,gamma,Infected,Recovered,Susceptible -0.004,0.1,1.0,1.0,999.0 -0.004,0.1285714285714286,840.0,881.0,999.0 -0.004,0.15714285714285714,813.0,926.0,999.0 -0.004,0.18571428571428572,1.0,1.0,999.0 -0.004,0.2142857142857143,766.0,969.0,999.0 -0.004,0.24285714285714288,1.0,1.0,999.0 -0.004,0.27142857142857146,1.0,1.0,999.0 -0.004,0.30000000000000004,1.0,1.0,999.0 -0.004,0.3285714285714286,1.0,1.0,999.0 -0.004,0.3571428571428572,1.0,1.0,999.0 -0.004,0.3857142857142858,1.0,1.0,999.0 -0.004,0.41428571428571437,1.0,1.0,999.0 -0.004,0.44285714285714284,1.0,1.0,999.0 -0.004,0.4714285714285714,1.0,1.0,999.0 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{"isAutomatic": false, "relativeTol": 0.001, "absoluteTol": 1e-06, "realizations": 20, "algorithm": "SSA", "seed": -1, "tauTol": 0.03}, "parameterSweepSettings": {"is1D": false, "p1Min": 0.004, "p1Max": 0.013, "p1Steps": 15, "p2Min": 0.1, "p2Max": 0.5, "p2Steps": 15, "parameterOne": {"compID": 4, "name": "beta", "expression": "0.0083", "annotation": "Rate at which a Susceptible species becomes infected\n"}, "parameterTwo": {"compID": 5, "name": "gamma", "expression": "0.3", "annotation": "Rate at which an Infected species recovers from the infection.\n\n"}, "speciesOfInterest": {"compID": 2, "name": "Infected", "value": 1, "mode": "discrete", "switchTol": 0.03, "switchMin": 100, "isSwitchTol": true, "annotation": "Initial population of a species that are infected\n", "diffusionCoeff": 0, "subdomains": ["subdomain 1:", "subdomain 2:"]}}, "resultsSettings": {"mapper": "final", "reducer": "avg", "outputs": [{"key": "Recovered-max-var", "stamp": 200727163621, "species": ["Recovered"]}, {"key": "Infected-max-var", "stamp": 200727163636, "species": ["Infected"]}, {"key": "Infected-avg-var", "stamp": 200727163726, "species": ["Infected"]}]}} \ No newline at end of file diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/SIR Epidemic Model.mdl b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/SIR Epidemic Model.mdl deleted file mode 100644 index 51a3fd2585..0000000000 --- a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/SIR Epidemic Model.mdl +++ /dev/null @@ -1 +0,0 @@ -{"is_spatial":false,"defaultID":8,"defaultMode":"discrete","annotation":"Susceptible, Infected, Recovered epidemiology (SIR) Model.\n","modelSettings":{"endSim":20,"timeStep":0.05,"volume":1},"meshSettings":{"count":2},"species":[{"compID":1,"name":"Susceptible","value":999,"mode":"discrete","switchTol":0.03,"switchMin":100,"isSwitchTol":true,"annotation":"Initial population of a species that are\n susceptible to infection\n","diffusionCoeff":0,"subdomains":["subdomain 1:","subdomain 2:"]},{"compID":2,"name":"Infected","value":1,"mode":"discrete","switchTol":0.03,"switchMin":100,"isSwitchTol":true,"annotation":"Initial population of a species that are infected\n","diffusionCoeff":0,"subdomains":["subdomain 1:","subdomain 2:"]},{"compID":3,"name":"Recovered","value":0,"mode":"discrete","switchTol":0.03,"switchMin":100,"isSwitchTol":true,"annotation":"Initial population of a species that have recovered from infection\n","diffusionCoeff":0,"subdomains":["subdomain 1:","subdomain 2:"]}],"initialConditions":[],"parameters":[{"compID":4,"name":"beta","expression":"0.0083","annotation":"Rate at which a Susceptible species becomes infected\n"},{"compID":5,"name":"gamma","expression":"0.3","annotation":"Rate at which an Infected species recovers from the infection.\n\n"}],"reactions":[{"compID":6,"name":"r1","reactionType":"custom-massaction","summary":"Susceptible+Infected \\rightarrow 2Infected","massaction":true,"propensity":"","annotation":"","subdomains":["subdomain 1:","subdomain 2:"],"rate":{"compID":4,"name":"beta","expression":"8.3","annotation":""},"reactants":[{"ratio":1,"specie":{"compID":1,"name":"Susceptible","value":999,"mode":"discrete","switchTol":0.03,"switchMin":100,"isSwitchTol":true,"annotation":"Initial population of a species that are\n susceptible to infection\n","diffusionCoeff":0,"subdomains":["subdomain 1:","subdomain 2:"]}},{"ratio":1,"specie":{"compID":2,"name":"Infected","value":1,"mode":"discrete","switchTol":0.03,"switchMin":100,"isSwitchTol":true,"annotation":"Initial population of a species that are infected\n","diffusionCoeff":0,"subdomains":["subdomain 1:","subdomain 2:"]}}],"products":[{"ratio":2,"specie":{"compID":2,"name":"Infected","value":1,"mode":"discrete","switchTol":0.03,"switchMin":100,"isSwitchTol":true,"annotation":"Initial population of a species that are infected\n","diffusionCoeff":0,"subdomains":["subdomain 1:","subdomain 2:"]}}]},{"compID":7,"name":"r2","reactionType":"change","summary":"Infected \\rightarrow Recovered","massaction":false,"propensity":"","annotation":"","subdomains":["subdomain 1:","subdomain 2:"],"rate":{"compID":5,"name":"gamma","expression":"0.3","annotation":""},"reactants":[{"ratio":1,"specie":{"compID":2,"name":"Infected","value":1,"mode":"discrete","switchTol":0.03,"switchMin":100,"isSwitchTol":true,"annotation":"Initial population of a species that are infected\n","diffusionCoeff":0,"subdomains":["subdomain 1:","subdomain 2:"]}}],"products":[{"ratio":1,"specie":{"compID":3,"name":"Recovered","value":0,"mode":"discrete","switchTol":0.03,"switchMin":100,"isSwitchTol":true,"annotation":"Initial population of a species that have recovered from infection\n","diffusionCoeff":0,"subdomains":["subdomain 1:","subdomain 2:"]}}]}],"rules":[],"eventsCollection":[],"functionDefinitions":[]} \ No newline at end of file diff --git a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/settings.json b/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/settings.json deleted file mode 100644 index 962a83f97e..0000000000 --- a/public_models/Example SIR Epidemic Project.proj/WorkflowGroup1.wkgp/Example Ensemble Simulation Workflow Complete.wkfl/settings.json +++ /dev/null @@ -1 +0,0 @@ -{"simulationSettings": {"isAutomatic": false, "relativeTol": 0.001, "absoluteTol": 1e-06, "realizations": 20, "algorithm": "SSA", "seed": -1, "tauTol": 0.03}, "parameterSweepSettings": {"is1D": true, "p1Min": 0, "p1Max": 0, "p1Steps": 11, "p2Min": 0, "p2Max": 0, "p2Steps": 11, "parameterOne": {}, "parameterTwo": {}, "speciesOfInterest": {}}, "resultsSettings": {"mapper": "final", "reducer": "avg", "outputs": [{"key": "stddev", "stamp": 200727162833, "species": ["Susceptible", "Infected", "Recovered"]}, {"key": "stddevran", "stamp": 200727162836, "species": ["Susceptible", "Infected", "Recovered"]}]}} \ No newline at end of file diff --git a/public_models/Gene_Regulatory_Network/.ipynb_checkpoints/GeneRegulatoryNetwork1-checkpoint.ipynb b/public_models/Gene_Regulatory_Network/.ipynb_checkpoints/GeneRegulatoryNetwork1-checkpoint.ipynb new file mode 100644 index 0000000000..27696ed63f --- /dev/null +++ b/public_models/Gene_Regulatory_Network/.ipynb_checkpoints/GeneRegulatoryNetwork1-checkpoint.ipynb @@ -0,0 +1,158 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "%load_ext autoreload\n", + "%autoreload 2\n", + "\n", + "import numpy as np\n", + "import spatialpy\n", + "from spatialpy import Model, Species, Parameter, Reaction, Mesh,\\\n", + " PlaceInitialCondition, \\\n", + " UniformInitialCondition, \\\n", + " ScatterInitialCondition" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# GeneRegulatoryNetwork1" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "class GeneRegulatoryNetwork1(Model):\n", + " def __init__(self):\n", + " Model.__init__(self, name=\"GeneRegulatoryNetwork1\")\n", + "\n", + " # Domain\n", + " mesh = Mesh.read_stochss_domain('GeneRegulatoryNetwork1.smdl')\n", + " self.add_mesh(mesh)\n", + "\n", + " self.staticDomain = True\n", + "\n", + " # Variables\n", + " G_F = Species(name=\"G_F\", diffusion_constant=1e-12)\n", + " G_O = Species(name=\"G_O\", diffusion_constant=1e-12)\n", + " P = Species(name=\"P\", diffusion_constant=1e-12)\n", + " mRNA = Species(name=\"mRNA\", diffusion_constant=1e-12)\n", + " self.add_species([G_F, G_O, P, mRNA])\n", + "\n", + " self.restrict(G_F, [])\n", + " self.restrict(G_O, [])\n", + " self.restrict(P, [1, 2])\n", + " self.restrict(mRNA, [1, 2])\n", + "\n", + " # Initial Conditions\n", + " self.add_initial_condition(PlaceInitialCondition(species=G_F, count=1, location=[0, 0, 0]))\n", + "\n", + " # Parameters\n", + " mu = Parameter(name=\"mu\", expression=\"0.002\")\n", + " kappa = Parameter(name=\"kappa\", expression=\"0.015\")\n", + " ka = Parameter(name=\"ka\", expression=\"10000000\")\n", + " kd = Parameter(name=\"kd\", expression=\"0.01\")\n", + " gamma_m = Parameter(name=\"gamma_m\", expression=\"0.0006\")\n", + " gamma_p = Parameter(name=\"gamma_p\", expression=\"0.0003\")\n", + " self.add_parameter([mu, kappa, ka, kd, gamma_m, gamma_p])\n", + "\n", + " # Reactions\n", + " r1 = Reaction(name=\"r1\", reactants={G_F: 1}, products={G_F: 1, mRNA: 1}, rate=self.listOfParameters[\"mu\"])\n", + " r2 = Reaction(name=\"r2\", reactants={G_O: 1}, products={G_F: 1, P: 1}, rate=self.listOfParameters[\"ka\"])\n", + " r3 = Reaction(name=\"r3\", reactants={G_F: 1, P: 1}, products={G_O: 1}, rate=self.listOfParameters[\"kd\"])\n", + " r4 = Reaction(name=\"r4\", restrict_to=[2], reactants={mRNA: 1}, products={mRNA: 1, P: 1}, rate=self.listOfParameters[\"kappa\"])\n", + " r5 = Reaction(name=\"r5\", reactants={mRNA: 1}, products={}, rate=self.listOfParameters[\"gamma_m\"])\n", + " r6 = Reaction(name=\"r6\", reactants={P: 1}, products={}, rate=self.listOfParameters[\"gamma_p\"])\n", + " self.add_reaction([r1, r2, r3, r4, r5, r6])\n", + "\n", + " # Timespan\n", + " self.timespan(np.arange(0, 1000, 10), timestep_size=10)" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [], + "source": [ + "model = GeneRegulatoryNetwork1()" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Simulation Parameters" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [], + "source": [ + "def configure_simulation():\n", + " kwargs = {\n", + " # \"number_of_trajectories\":1,\n", + " # \"seed\":None,\n", + " }\n", + " return kwargs" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [], + "source": [ + "kwargs = configure_simulation()\n", + "results = model.run(**kwargs)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Visualization" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "results.plot_species('G_F', animated=True, width=None, height=None)" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.8.5" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} diff --git a/public_models/Gene_Regulatory_Network/GeneRegulatoryNetwork1.domn b/public_models/Gene_Regulatory_Network/GeneRegulatoryNetwork1.domn new file mode 100644 index 0000000000..7fa0699edb --- /dev/null +++ b/public_models/Gene_Regulatory_Network/GeneRegulatoryNetwork1.domn @@ -0,0 +1 @@ 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\ No newline at end of file diff --git a/public_models/Gene_Regulatory_Network/GeneRegulatoryNetwork1.ipynb b/public_models/Gene_Regulatory_Network/GeneRegulatoryNetwork1.ipynb new file mode 100644 index 0000000000..27696ed63f --- /dev/null +++ b/public_models/Gene_Regulatory_Network/GeneRegulatoryNetwork1.ipynb @@ -0,0 +1,158 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "%load_ext autoreload\n", + "%autoreload 2\n", + "\n", + "import numpy as np\n", + "import spatialpy\n", + "from spatialpy import Model, Species, Parameter, Reaction, Mesh,\\\n", + " PlaceInitialCondition, \\\n", + " UniformInitialCondition, \\\n", + " ScatterInitialCondition" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# GeneRegulatoryNetwork1" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "class GeneRegulatoryNetwork1(Model):\n", + " def __init__(self):\n", + " Model.__init__(self, name=\"GeneRegulatoryNetwork1\")\n", + "\n", + " # Domain\n", + " mesh = Mesh.read_stochss_domain('GeneRegulatoryNetwork1.smdl')\n", + " self.add_mesh(mesh)\n", + "\n", + " self.staticDomain = True\n", + "\n", + " # Variables\n", + " G_F = Species(name=\"G_F\", diffusion_constant=1e-12)\n", + " G_O = Species(name=\"G_O\", diffusion_constant=1e-12)\n", + " P = Species(name=\"P\", diffusion_constant=1e-12)\n", + " mRNA = Species(name=\"mRNA\", diffusion_constant=1e-12)\n", + " self.add_species([G_F, G_O, P, mRNA])\n", + "\n", + " self.restrict(G_F, [])\n", + " self.restrict(G_O, [])\n", + " self.restrict(P, [1, 2])\n", + " self.restrict(mRNA, [1, 2])\n", + "\n", + " # Initial Conditions\n", + " self.add_initial_condition(PlaceInitialCondition(species=G_F, count=1, location=[0, 0, 0]))\n", + "\n", + " # Parameters\n", + " mu = Parameter(name=\"mu\", expression=\"0.002\")\n", + " kappa = Parameter(name=\"kappa\", expression=\"0.015\")\n", + " ka = Parameter(name=\"ka\", expression=\"10000000\")\n", + " kd = Parameter(name=\"kd\", expression=\"0.01\")\n", + " gamma_m = Parameter(name=\"gamma_m\", expression=\"0.0006\")\n", + " gamma_p = Parameter(name=\"gamma_p\", expression=\"0.0003\")\n", + " self.add_parameter([mu, kappa, ka, kd, gamma_m, gamma_p])\n", + "\n", + " # Reactions\n", + " r1 = Reaction(name=\"r1\", reactants={G_F: 1}, products={G_F: 1, mRNA: 1}, rate=self.listOfParameters[\"mu\"])\n", + " r2 = Reaction(name=\"r2\", reactants={G_O: 1}, products={G_F: 1, P: 1}, rate=self.listOfParameters[\"ka\"])\n", + " r3 = Reaction(name=\"r3\", reactants={G_F: 1, P: 1}, products={G_O: 1}, rate=self.listOfParameters[\"kd\"])\n", + " r4 = Reaction(name=\"r4\", restrict_to=[2], reactants={mRNA: 1}, products={mRNA: 1, P: 1}, rate=self.listOfParameters[\"kappa\"])\n", + " r5 = Reaction(name=\"r5\", reactants={mRNA: 1}, products={}, rate=self.listOfParameters[\"gamma_m\"])\n", + " r6 = Reaction(name=\"r6\", reactants={P: 1}, products={}, rate=self.listOfParameters[\"gamma_p\"])\n", + " self.add_reaction([r1, r2, r3, r4, r5, r6])\n", + "\n", + " # Timespan\n", + " self.timespan(np.arange(0, 1000, 10), timestep_size=10)" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [], + "source": [ + "model = GeneRegulatoryNetwork1()" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Simulation Parameters" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [], + "source": [ + "def configure_simulation():\n", + " kwargs = {\n", + " # \"number_of_trajectories\":1,\n", + " # \"seed\":None,\n", + " }\n", + " return kwargs" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [], + "source": [ + "kwargs = configure_simulation()\n", + "results = model.run(**kwargs)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Visualization" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "results.plot_species('G_F', animated=True, width=None, height=None)" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.8.5" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} diff --git a/public_models/Gene_Regulatory_Network/GeneRegulatoryNetwork1.smdl b/public_models/Gene_Regulatory_Network/GeneRegulatoryNetwork1.smdl new file mode 100644 index 0000000000..a46cd7fabd --- /dev/null +++ b/public_models/Gene_Regulatory_Network/GeneRegulatoryNetwork1.smdl @@ -0,0 +1 @@ +{"is_spatial":true,"defaultID":18,"defaultMode":"discrete","annotation":"This model uses the hes1 mesh 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\ No newline at end of file diff --git a/public_models/Gene_Regulatory_Network/GeneRegulatoryNetwork2.ipynb b/public_models/Gene_Regulatory_Network/GeneRegulatoryNetwork2.ipynb new file mode 100644 index 0000000000..e93d8b2df8 --- /dev/null +++ b/public_models/Gene_Regulatory_Network/GeneRegulatoryNetwork2.ipynb @@ -0,0 +1,156 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "%load_ext autoreload\n", + "%autoreload 2\n", + "\n", + "import numpy as np\n", + "import spatialpy\n", + "from spatialpy import Model, Species, Parameter, Reaction, Mesh,\\\n", + " PlaceInitialCondition, \\\n", + " UniformInitialCondition, \\\n", + " ScatterInitialCondition" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# GeneRegulatoryNetwork2" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "class GeneRegulatoryNetwork2(Model):\n", + " def __init__(self):\n", + " Model.__init__(self, name=\"GeneRegulatoryNetwork2\")\n", + "\n", + " # Domain\n", + " mesh = Mesh.read_stochss_domain('GeneRegulatoryNetwork2.smdl')\n", + " self.add_mesh(mesh)\n", + "\n", + " self.staticDomain = True\n", + "\n", + " # Variables\n", + " G_F = Species(name=\"G_F\", diffusion_constant=1e-12)\n", + " G_O = Species(name=\"G_O\", diffusion_constant=1e-12)\n", + " P = Species(name=\"P\", diffusion_constant=1e-12)\n", + " mRNA = Species(name=\"mRNA\", diffusion_constant=1e-12)\n", + " self.add_species([G_F, G_O, P, mRNA])\n", + "\n", + " self.restrict(G_F, [])\n", + " self.restrict(G_O, [])\n", + "\n", + " # Initial Conditions\n", + " self.add_initial_condition(PlaceInitialCondition(species=G_F, count=1, location=[0, 0, 0]))\n", + "\n", + " # Parameters\n", + " mu = Parameter(name=\"mu\", expression=\"0.002\")\n", + " kappa = Parameter(name=\"kappa\", expression=\"0.015\")\n", + " ka = Parameter(name=\"ka\", expression=\"10000000\")\n", + " kd = Parameter(name=\"kd\", expression=\"0.01\")\n", + " gamma_m = Parameter(name=\"gamma_m\", expression=\"0.0006\")\n", + " gamma_p = Parameter(name=\"gamma_p\", expression=\"0.0003\")\n", + " self.add_parameter([mu, kappa, ka, kd, gamma_m, gamma_p])\n", + "\n", + " # Reactions\n", + " r1 = Reaction(name=\"r1\", reactants={G_F: 1}, products={G_F: 1, mRNA: 1}, rate=self.listOfParameters[\"mu\"])\n", + " r2 = Reaction(name=\"r2\", reactants={G_O: 1}, products={G_F: 1, P: 1}, rate=self.listOfParameters[\"ka\"])\n", + " r3 = Reaction(name=\"r3\", reactants={G_F: 1, P: 1}, products={G_O: 1}, rate=self.listOfParameters[\"kd\"])\n", + " r4 = Reaction(name=\"r4\", restrict_to=[2], reactants={mRNA: 1}, products={mRNA: 1, P: 1}, rate=self.listOfParameters[\"kappa\"])\n", + " r5 = Reaction(name=\"r5\", reactants={mRNA: 1}, products={}, rate=self.listOfParameters[\"gamma_m\"])\n", + " r6 = Reaction(name=\"r6\", reactants={P: 1}, products={}, rate=self.listOfParameters[\"gamma_p\"])\n", + " self.add_reaction([r1, r2, r3, r4, r5, r6])\n", + "\n", + " # Timespan\n", + " self.timespan(np.arange(0, 1000, 10), timestep_size=10)" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [], + "source": [ + "model = GeneRegulatoryNetwork2()" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Simulation Parameters" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [], + "source": [ + "def configure_simulation():\n", + " kwargs = {\n", + " # \"number_of_trajectories\":1,\n", + " # \"seed\":None,\n", + " }\n", + " return kwargs" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [], + "source": [ + "kwargs = configure_simulation()\n", + "results = model.run(**kwargs)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Visualization" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "results.plot_species('G_F', animated=True, width=None, height=None)" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.8.5" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} diff --git a/public_models/Gene_Regulatory_Network/GeneRegulatoryNetwork2.smdl b/public_models/Gene_Regulatory_Network/GeneRegulatoryNetwork2.smdl new file mode 100644 index 0000000000..e7654e1077 --- /dev/null +++ b/public_models/Gene_Regulatory_Network/GeneRegulatoryNetwork2.smdl @@ -0,0 +1 @@ +{"is_spatial":true,"defaultID":17,"defaultMode":"","annotation":"This model uses the cell_coarse mesh (slide 65)\n - This mesh contains 2 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b/public_models/Lotkavolterra_Oscillator/Lotkavolterra_Oscillator.ipynb index 3b16d1335d..d36610645c 100644 --- a/public_models/Lotkavolterra_Oscillator/Lotkavolterra_Oscillator.ipynb +++ b/public_models/Lotkavolterra_Oscillator/Lotkavolterra_Oscillator.ipynb @@ -1,37057 +1 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Lotkavolterra_Oscillator" - ] - }, - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [], - "source": [ - "import numpy as np\n", - "import gillespy2\n", - "from gillespy2 import Model, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition\n", - "from gillespy2 import EventAssignment, EventTrigger, Event\n", - "# To run a simulation using the SSA Solver simply omit the solver argument from model.run().\n", - "# from gillespy2 import VariableSSACSolver\n", - "# from gillespy2 import BasicTauLeapingSolver\n", - "# from gillespy2 import BasicTauHybridSolver\n", - "from gillespy2 import BasicODESolver" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [], - "source": [ - "class Lotkavolterra_Oscillator(Model):\n", - " def __init__(self, parameter_values=None):\n", - " Model.__init__(self, name=\"Lotkavolterra_Oscillator\")\n", - " self.volume = 1\n", - "\n", - " # Parameters\n", - " self.add_parameter(Parameter(name=\"k1\", expression=0.004))\n", - " self.add_parameter(Parameter(name=\"k2\", expression=0.5))\n", - " self.add_parameter(Parameter(name=\"k3\", expression=0.0045))\n", - "\n", - " # Species\n", - " self.add_species(Species(name=\"R\", initial_value=0.0095, mode=\"continuous\"))\n", - " self.add_species(Species(name=\"W\", initial_value=0.008, mode=\"continuous\"))\n", - "\n", - " # Reactions\n", - " self.add_reaction(Reaction(name=\"r1\", reactants={'R': 1}, products={'R': 2}, rate=self.listOfParameters[\"k1\"]))\n", - " self.add_reaction(Reaction(name=\"r2\", reactants={'R': 1, 'W': 1}, products={'W': 2}, rate=self.listOfParameters[\"k2\"]))\n", - " self.add_reaction(Reaction(name=\"r3\", reactants={'W': 1}, products={}, rate=self.listOfParameters[\"k3\"]))\n", - "\n", - " # Timespan\n", - " self.timespan(np.linspace(0, 9000, 9001))" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [], - "source": [ - "model = Lotkavolterra_Oscillator()" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [], - "source": [ - "def configure_simulation():\n", - " kwargs = {\n", - " \"solver\":BasicODESolver,\n", - " # \"number_of_trajectories\":1,\n", - " # \"seed\":None,\n", - " # \"tau_tol\":0.03,\n", - " \"integrator_options\":{'rtol': 0.001, 'atol': 1e-06}\n", - " }\n", - " return kwargs" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "metadata": {}, - "outputs": [], - "source": [ - "kwargs = configure_simulation()\n", - "results = model.run(**kwargs)" - ] - }, - { - "cell_type": "code", - 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"cells": [ - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Michaelis_Menten" - ] - }, - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [], - "source": [ - "import numpy as np\n", - "import gillespy2\n", - "from gillespy2 import Model, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition\n", - "from gillespy2 import EventAssignment, EventTrigger, Event\n", - "from gillespy2 import SSACSolver\n", - "# from gillespy2 import VariableSSACSolver\n", - "# from gillespy2 import BasicTauLeapingSolver\n", - "# from gillespy2 import BasicTauHybridSolver\n", - "# from gillespy2 import BasicODESolver" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [], - "source": [ - "class Michaelis_Menten(Model):\n", - " def __init__(self, parameter_values=None):\n", - " Model.__init__(self, name=\"Michaelis_Menten\")\n", - " self.volume = 1\n", - "\n", - " # Parameters\n", - " self.add_parameter(Parameter(name=\"rate1\", expression=0.0017))\n", - " self.add_parameter(Parameter(name=\"rate2\", expression=0.5))\n", - " self.add_parameter(Parameter(name=\"rate3\", expression=0.1))\n", - "\n", - " # Species\n", - " self.add_species(Species(name=\"A\", initial_value=301, mode=\"discrete\"))\n", - " self.add_species(Species(name=\"B\", initial_value=120, mode=\"discrete\"))\n", - " self.add_species(Species(name=\"C\", initial_value=0, mode=\"discrete\"))\n", - " self.add_species(Species(name=\"D\", initial_value=0, mode=\"discrete\"))\n", - "\n", - " # Reactions\n", - " self.add_reaction(Reaction(name=\"r1\", reactants={'A': 1, 'B': 1}, products={'C': 1}, rate=self.listOfParameters[\"rate1\"]))\n", - " self.add_reaction(Reaction(name=\"r2\", reactants={'C': 1}, products={'A': 1, 'B': 1}, rate=self.listOfParameters[\"rate2\"]))\n", - " self.add_reaction(Reaction(name=\"r3\", reactants={'C': 1}, products={'B': 1, 'D': 1}, rate=self.listOfParameters[\"rate3\"]))\n", - "\n", - " # Timespan\n", - " self.timespan(np.linspace(0, 100, 101))" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [], - "source": [ - "model = Michaelis_Menten()" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [], - "source": [ - "solver = SSACSolver(model=model)" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "metadata": {}, - "outputs": [], - "source": [ - "def configure_simulation():\n", - " kwargs = {\n", - " \"solver\":solver,\n", - " \"number_of_trajectories\":1,\n", - " \"seed\":None,\n", - " # \"tau_tol\":0.03,\n", - " # \"integrator_options\":{'rtol': 0.001, 'atol': 1e-06}\n", - " }\n", - " return kwargs" - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "metadata": {}, - "outputs": [], - "source": [ - "kwargs = configure_simulation()\n", - "results = model.run(**kwargs)" - ] - }, - { - "cell_type": "code", - "execution_count": 7, - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - " \n", - " " - ] - }, - "metadata": {}, - 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"cells": [ - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Opioid" - ] - }, - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [], - "source": [ - "import numpy as np\n", - "import gillespy2\n", - "from gillespy2 import Model, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition\n", - "from gillespy2 import EventAssignment, EventTrigger, Event\n", - "from gillespy2 import SSACSolver\n", - "# from gillespy2 import VariableSSACSolver\n", - "# from gillespy2 import BasicTauLeapingSolver\n", - "# from gillespy2 import BasicTauHybridSolver\n", - "# from gillespy2 import BasicODESolver" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [], - "source": [ - "class Opioid(Model):\n", - " def __init__(self, parameter_values=None):\n", - " Model.__init__(self, name=\"Opioid\")\n", - " self.volume = 1\n", - "\n", - " # Parameters\n", - " self.add_parameter(Parameter(name=\"alpha\", expression=0.15))\n", - " self.add_parameter(Parameter(name=\"epsilon\", expression=0.8))\n", - " self.add_parameter(Parameter(name=\"beta_p\", expression=0.00266))\n", - " self.add_parameter(Parameter(name=\"beta_a\", expression=0.00094))\n", - " self.add_parameter(Parameter(name=\"gamma\", expression=0.00744))\n", - " self.add_parameter(Parameter(name=\"zeta\", expression=0.2))\n", - " self.add_parameter(Parameter(name=\"delta\", expression=0.1))\n", - " self.add_parameter(Parameter(name=\"sigma\", expression=0.9))\n", - " self.add_parameter(Parameter(name=\"mu\", expression=0.00729))\n", - " self.add_parameter(Parameter(name=\"mu_prime\", expression=0.01159))\n", - "\n", - " # Species\n", - " self.add_species(Species(name=\"Susceptible\", initial_value=200, mode=\"discrete\"))\n", - " self.add_species(Species(name=\"Prescribed_User\", initial_value=0, mode=\"discrete\"))\n", - " self.add_species(Species(name=\"Addicted\", initial_value=0, mode=\"discrete\"))\n", - " self.add_species(Species(name=\"Rehab\", initial_value=0, mode=\"discrete\"))\n", - " self.add_species(Species(name=\"Natural_Deaths\", initial_value=0, mode=\"discrete\"))\n", - " self.add_species(Species(name=\"Addicted_Deaths\", initial_value=0, mode=\"discrete\"))\n", - "\n", - " # Reactions\n", - " self.add_reaction(Reaction(name=\"SP\", reactants={'Susceptible': 1}, products={'Prescribed_User': 1}, rate=self.listOfParameters[\"alpha\"]))\n", - " self.add_reaction(Reaction(name=\"SA_a\", reactants={'Susceptible': 1}, products={'Addicted': 1}, rate=self.listOfParameters[\"beta_a\"]))\n", - " self.add_reaction(Reaction(name=\"SA_p\", reactants={'Susceptible': 1}, products={'Addicted': 1}, rate=self.listOfParameters[\"beta_p\"]))\n", - " self.add_reaction(Reaction(name=\"PA\", reactants={'Prescribed_User': 1}, products={'Addicted': 1}, rate=self.listOfParameters[\"gamma\"]))\n", - " self.add_reaction(Reaction(name=\"PS\", reactants={'Prescribed_User': 1}, products={'Susceptible': 1}, rate=self.listOfParameters[\"epsilon\"]))\n", - " self.add_reaction(Reaction(name=\"AR\", reactants={'Addicted': 1}, products={'Rehab': 1}, rate=self.listOfParameters[\"zeta\"]))\n", - " self.add_reaction(Reaction(name=\"RA\", reactants={'Rehab': 1}, products={'Addicted': 1}, rate=self.listOfParameters[\"delta\"]))\n", - " self.add_reaction(Reaction(name=\"RS\", reactants={'Rehab': 1}, products={'Susceptible': 1}, rate=self.listOfParameters[\"sigma\"]))\n", - " self.add_reaction(Reaction(name=\"mu_S\", reactants={'Susceptible': 1}, products={'Susceptible': 1, 'Natural_Deaths': 1}, rate=self.listOfParameters[\"mu\"]))\n", - " self.add_reaction(Reaction(name=\"mu_P\", reactants={'Prescribed_User': 1}, products={'Susceptible': 1, 'Natural_Deaths': 1}, rate=self.listOfParameters[\"mu\"]))\n", - " self.add_reaction(Reaction(name=\"mu_R\", reactants={'Rehab': 1}, products={'Susceptible': 1, 'Natural_Deaths': 1}, rate=self.listOfParameters[\"mu\"]))\n", - " self.add_reaction(Reaction(name=\"mu_prime_A\", reactants={'Addicted': 1}, products={'Susceptible': 1, 'Addicted_Deaths': 1}, rate=self.listOfParameters[\"mu_prime\"]))\n", - "\n", - " # Timespan\n", - " self.timespan(np.linspace(0, 200, 201))" - 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TauHybridSolver"]},{"cell_type":"markdown","metadata":{},"source":["# Opioid"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["class Opioid(Model):\n"," def __init__(self, parameter_values=None):\n"," Model.__init__(self, name=\"Opioid\")\n"," self.volume = 1\n","\n"," # Parameters\n"," self.add_parameter(Parameter(name=\"alpha\", expression=\"0.15\"))\n"," self.add_parameter(Parameter(name=\"epsilon\", expression=\"0.8\"))\n"," self.add_parameter(Parameter(name=\"beta_p\", expression=\"0.00266\"))\n"," self.add_parameter(Parameter(name=\"beta_a\", expression=\"0.00094\"))\n"," self.add_parameter(Parameter(name=\"gamma\", expression=\"0.00744\"))\n"," self.add_parameter(Parameter(name=\"zeta\", expression=\"0.2\"))\n"," self.add_parameter(Parameter(name=\"delta\", expression=\"0.1\"))\n"," self.add_parameter(Parameter(name=\"sigma\", expression=\"0.9\"))\n"," self.add_parameter(Parameter(name=\"mu\", expression=\"0.00729\"))\n"," self.add_parameter(Parameter(name=\"mu_prime\", expression=\"0.01159\"))\n","\n"," # Variables\n"," self.add_species(Species(name=\"Susceptible\", initial_value=200, mode=\"discrete\"))\n"," self.add_species(Species(name=\"Prescribed_User\", initial_value=0, mode=\"discrete\"))\n"," self.add_species(Species(name=\"Addicted\", initial_value=0, mode=\"discrete\"))\n"," self.add_species(Species(name=\"Rehab\", initial_value=0, mode=\"discrete\"))\n"," self.add_species(Species(name=\"Natural_Deaths\", initial_value=0, mode=\"discrete\"))\n"," self.add_species(Species(name=\"Addicted_Deaths\", initial_value=0, mode=\"discrete\"))\n","\n"," # Reactions\n"," self.add_reaction(Reaction(name=\"SP\", reactants={'Susceptible': 1}, products={'Prescribed_User': 1}, rate=self.listOfParameters[\"alpha\"]))\n"," self.add_reaction(Reaction(name=\"SA_a\", reactants={'Susceptible': 1}, products={'Addicted': 1}, rate=self.listOfParameters[\"beta_a\"]))\n"," self.add_reaction(Reaction(name=\"SA_p\", reactants={'Susceptible': 1}, products={'Addicted': 1}, rate=self.listOfParameters[\"beta_p\"]))\n"," self.add_reaction(Reaction(name=\"PA\", reactants={'Prescribed_User': 1}, products={'Addicted': 1}, rate=self.listOfParameters[\"gamma\"]))\n"," self.add_reaction(Reaction(name=\"PS\", reactants={'Prescribed_User': 1}, products={'Susceptible': 1}, rate=self.listOfParameters[\"epsilon\"]))\n"," self.add_reaction(Reaction(name=\"AR\", reactants={'Addicted': 1}, products={'Rehab': 1}, rate=self.listOfParameters[\"zeta\"]))\n"," self.add_reaction(Reaction(name=\"RA\", reactants={'Rehab': 1}, products={'Addicted': 1}, rate=self.listOfParameters[\"delta\"]))\n"," self.add_reaction(Reaction(name=\"RS\", reactants={'Rehab': 1}, products={'Susceptible': 1}, rate=self.listOfParameters[\"sigma\"]))\n"," self.add_reaction(Reaction(name=\"mu_S\", reactants={'Susceptible': 1}, products={'Susceptible': 1, 'Natural_Deaths': 1}, rate=self.listOfParameters[\"mu\"]))\n"," self.add_reaction(Reaction(name=\"mu_P\", reactants={'Prescribed_User': 1}, products={'Susceptible': 1, 'Natural_Deaths': 1}, rate=self.listOfParameters[\"mu\"]))\n"," self.add_reaction(Reaction(name=\"mu_R\", reactants={'Rehab': 1}, products={'Susceptible': 1, 'Natural_Deaths': 1}, rate=self.listOfParameters[\"mu\"]))\n"," self.add_reaction(Reaction(name=\"mu_prime_A\", reactants={'Addicted': 1}, products={'Susceptible': 1, 'Addicted_Deaths': 1}, rate=self.listOfParameters[\"mu_prime\"]))\n","\n"," # Timespan\n"," self.timespan(np.arange(0, 200, 1))"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["model = Opioid()"]},{"cell_type":"markdown","metadata":{},"source":["# Simulation Parameters"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["def configure_simulation():\n"," # solver = SSACSolver(model=model)\n"," kwargs = {\n"," # \"solver\":solver,\n"," \"number_of_trajectories\":100,\n"," # \"seed\":None,\n"," # \"tau_tol\":0.03,\n"," # \"integrator_options\":{'rtol': 0.001, 'atol': 1e-06},\n"," }\n"," return kwargs"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["kwargs = configure_simulation()\n","results = model.run(**kwargs)"]},{"cell_type":"markdown","metadata":{},"source":["# Visualization"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["results.plotplotly()"]}],"metadata":{},"nbformat":4,"nbformat_minor":4} \ No newline at end of file diff --git a/public_models/Oregonator/Oregonator.ipynb b/public_models/Oregonator/Oregonator.ipynb index 6f60bb7a57..02563dae00 100644 --- a/public_models/Oregonator/Oregonator.ipynb +++ b/public_models/Oregonator/Oregonator.ipynb @@ -1,1606 +1 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Oregonator" - ] - }, - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [], - "source": [ - "import numpy as np\n", - "import gillespy2\n", - "from gillespy2 import Model, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition\n", - "from gillespy2 import EventAssignment, EventTrigger, Event\n", - "# To run a simulation using the SSA Solver simply omit the solver argument from model.run().\n", - "# from gillespy2 import VariableSSACSolver\n", - "# from gillespy2 import BasicTauLeapingSolver\n", - "# from gillespy2 import BasicTauHybridSolver\n", - "from gillespy2 import BasicODESolver" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [], - "source": [ - "class Oregonator(Model):\n", - " def __init__(self, parameter_values=None):\n", - " Model.__init__(self, name=\"Oregonator\")\n", - " self.volume = 1\n", - "\n", - " # Parameters\n", - " self.add_parameter(Parameter(name=\"k1\", expression=2))\n", - " self.add_parameter(Parameter(name=\"k2\", expression=0.1))\n", - " self.add_parameter(Parameter(name=\"k3\", expression=104))\n", - " self.add_parameter(Parameter(name=\"k4\", expression=4e-7))\n", - " self.add_parameter(Parameter(name=\"k5\", expression=26))\n", - "\n", - " # Species\n", - " self.add_species(Species(name=\"F\", initial_value=2, mode=\"continuous\"))\n", - " self.add_species(Species(name=\"A\", initial_value=250, mode=\"continuous\"))\n", - " self.add_species(Species(name=\"B\", initial_value=500, mode=\"continuous\"))\n", - " self.add_species(Species(name=\"C\", initial_value=1000, mode=\"continuous\"))\n", - " self.add_species(Species(name=\"P\", initial_value=0, mode=\"continuous\"))\n", - "\n", - " # Reactions\n", - " self.add_reaction(Reaction(name=\"reaction1\", reactants={'B': 1, 'F': 1}, products={'A': 1, 'F': 1}, rate=self.listOfParameters[\"k1\"]))\n", - " self.add_reaction(Reaction(name=\"reaction2\", reactants={'A': 1, 'B': 1}, products={'P': 1}, rate=self.listOfParameters[\"k2\"]))\n", - " self.add_reaction(Reaction(name=\"reaction3\", reactants={'A': 1, 'F': 1}, products={'A': 2, 'C': 1, 'F': 1}, rate=self.listOfParameters[\"k3\"]))\n", - " self.add_reaction(Reaction(name=\"reaction4\", reactants={'A': 2}, products={'P': 1}, rate=self.listOfParameters[\"k4\"]))\n", - " self.add_reaction(Reaction(name=\"reaction5\", reactants={'C': 1, 'F': 1}, products={'B': 1, 'F': 1}, rate=self.listOfParameters[\"k5\"]))\n", - "\n", - " # Timespan\n", - " self.timespan(np.linspace(0, 5, 51))" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [], - "source": [ - "model = Oregonator()" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [], - "source": [ - "def configure_simulation():\n", - " kwargs = {\n", - " \"solver\":BasicODESolver,\n", - " # \"number_of_trajectories\":1,\n", - " # \"seed\":None,\n", - " # \"tau_tol\":0.03,\n", - " \"integrator_options\":{'rtol': 0.001, 'atol': 1e-06}\n", - " }\n", - " return kwargs" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "metadata": {}, - 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TauHybridSolver"]},{"cell_type":"markdown","metadata":{},"source":["# Oregonator"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["class Oregonator(Model):\n"," def __init__(self, parameter_values=None):\n"," Model.__init__(self, name=\"Oregonator\")\n"," self.volume = 1\n","\n"," # Parameters\n"," self.add_parameter(Parameter(name=\"k1\", expression=\"2\"))\n"," self.add_parameter(Parameter(name=\"k2\", expression=\"0.1\"))\n"," self.add_parameter(Parameter(name=\"k3\", expression=\"104\"))\n"," self.add_parameter(Parameter(name=\"k4\", expression=\"4e-07\"))\n"," self.add_parameter(Parameter(name=\"k5\", expression=\"26\"))\n","\n"," # Variables\n"," self.add_species(Species(name=\"F\", initial_value=2, mode=\"continuous\"))\n"," self.add_species(Species(name=\"A\", initial_value=250, mode=\"continuous\"))\n"," self.add_species(Species(name=\"B\", initial_value=500, mode=\"continuous\"))\n"," self.add_species(Species(name=\"C\", initial_value=1000, mode=\"continuous\"))\n"," self.add_species(Species(name=\"P\", initial_value=0, mode=\"continuous\"))\n","\n"," # Reactions\n"," self.add_reaction(Reaction(name=\"reaction1\", reactants={'B': 1, 'F': 1}, products={'A': 1, 'F': 1}, rate=self.listOfParameters[\"k1\"]))\n"," self.add_reaction(Reaction(name=\"reaction2\", reactants={'A': 1, 'B': 1}, products={'P': 1}, rate=self.listOfParameters[\"k2\"]))\n"," self.add_reaction(Reaction(name=\"reaction3\", reactants={'A': 1, 'F': 1}, products={'A': 2, 'C': 1, 'F': 1}, rate=self.listOfParameters[\"k3\"]))\n"," self.add_reaction(Reaction(name=\"reaction4\", reactants={'A': 2}, products={'P': 1}, rate=self.listOfParameters[\"k4\"]))\n"," self.add_reaction(Reaction(name=\"reaction5\", reactants={'C': 1, 'F': 1}, products={'B': 1, 'F': 1}, rate=self.listOfParameters[\"k5\"]))\n","\n"," # Timespan\n"," self.timespan(np.arange(0, 5, 0.1))"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["model = Oregonator()"]},{"cell_type":"markdown","metadata":{},"source":["# Simulation Parameters"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["def configure_simulation():\n"," kwargs = {\n"," # \"solver\":TauHybridSolver,\n"," \"number_of_trajectories\":100,\n"," # \"seed\":None,\n"," # \"tau_tol\":0.03,\n"," # \"integrator_options\":{'rtol': 0.001, 'atol': 1e-06},\n"," }\n"," return kwargs"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["kwargs = configure_simulation()\n","results = model.run(**kwargs)"]},{"cell_type":"markdown","metadata":{},"source":["# Visualization"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["results.plotplotly()"]}],"metadata":{},"nbformat":4,"nbformat_minor":4} \ No newline at end of file diff --git a/public_models/Polarization_In_Yeast/.ipynb_checkpoints/PolarizationInYeast-checkpoint.ipynb b/public_models/Polarization_In_Yeast/.ipynb_checkpoints/PolarizationInYeast-checkpoint.ipynb new file mode 100644 index 0000000000..669f32b3ae --- /dev/null +++ b/public_models/Polarization_In_Yeast/.ipynb_checkpoints/PolarizationInYeast-checkpoint.ipynb @@ -0,0 +1,1263 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "%load_ext autoreload\n", + "%autoreload 2\n", + "\n", + "import numpy as np\n", + "import spatialpy\n", + "from spatialpy import Model, Species, Parameter, Reaction, Mesh,\\\n", + " PlaceInitialCondition, \\\n", + " UniformInitialCondition, \\\n", + " ScatterInitialCondition" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# PolarizationInYeast" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "class PolarizationInYeast(Model):\n", + " def __init__(self):\n", + " Model.__init__(self, name=\"PolarizationInYeast\")\n", + "\n", + " # Domain\n", + " mesh = Mesh.read_stochss_domain('PolarizationInYeast.smdl')\n", + " self.add_mesh(mesh)\n", + "\n", + " self.staticDomain = True\n", + "\n", + " # Variables\n", + " Cdc42c = Species(name=\"Cdc42c\", diffusion_constant=10)\n", + " Cdc42m = Species(name=\"Cdc42m\", diffusion_constant=0.0053)\n", + " self.add_species([Cdc42c, Cdc42m])\n", + "\n", + " self.restrict(Cdc42m, [2])\n", + "\n", + " # Initial Conditions\n", + " self.add_initial_condition(ScatterInitialCondition(species=Cdc42c, count=300, types=[1]))\n", + " self.add_initial_condition(ScatterInitialCondition(species=Cdc42m, count=100, types=[2]))\n", + "\n", + " # Parameters\n", + " kon = Parameter(name=\"kon\", expression=\"1.6666666667e-05\")\n", + " koff = Parameter(name=\"koff\", expression=\"0.15\")\n", + " kfb = Parameter(name=\"kfb\", expression=\"0.166666666666667\")\n", + " self.add_parameter([kon, koff, kfb])\n", + "\n", + " # Reactions\n", + " r1 = Reaction(name=\"r1\", reactants={Cdc42c: 1}, products={Cdc42m: 1}, rate=self.listOfParameters[\"kon\"])\n", + " r2 = Reaction(name=\"r2\", reactants={Cdc42m: 1}, products={Cdc42c: 1}, rate=self.listOfParameters[\"koff\"])\n", + " r3 = Reaction(name=\"r3\", restrict_to=[2], reactants={Cdc42c: 1, Cdc42m: 1}, products={Cdc42m: 2}, rate=self.listOfParameters[\"kfb\"])\n", + " self.add_reaction([r1, r2, r3])\n", + "\n", + " # Timespan\n", + " self.timespan(np.arange(0, 5000, 10), timestep_size=10)" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [], + "source": [ + "model = PolarizationInYeast()" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Simulation Parameters" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "def configure_simulation():\n", + " kwargs = {\n", + " # \"number_of_trajectories\":1,\n", + " # \"seed\":None,\n", + " }\n", + " return kwargs" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "kwargs = configure_simulation()\n", + "results = model.run(**kwargs)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Visualization" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "results.plot_species('Cdc42c', animated=True, width=None, height=None)" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "PolarizationInYeast\n", + "\n", + "**********\n", + "Species\n", + "**********\n", + "\n", + "Cdc42c: 10\n", + "Cdc42m: 0.0053\n", + "\n", + "**********\n", + "Initial Conditions\n", + "**********\n", + "\n", + "Cdc42c: 300, Scatter over: [1]\n", + "Cdc42m: 100, Scatter over: [2]\n", + "\n", + "**********\n", + "Diffusion Restrictions\n", + "**********\n", + "\n", + "Cdc42m is restricted to: [2]\n", + "\n", + "**********\n", + "Parameters\n", + "**********\n", + "\n", + "kon: 1.6666666667e-05\n", + "koff: 0.15\n", + "kfb: 0.166666666666667\n", + "\n", + "**********\n", + "Reactions\n", + "**********\n", + "\n", + "r1, Active in: None\n", + "\tReactants\n", + "\t\tCdc42c: 1\n", + "\tProducts\n", + "\t\tCdc42m: 1\n", + "\tPropensity Function: kon*Cdc42c\n", + "r2, Active in: None\n", + "\tReactants\n", + "\t\tCdc42m: 1\n", + "\tProducts\n", + "\t\tCdc42c: 1\n", + "\tPropensity Function: koff*Cdc42m\n", + "r3, Active in: [2]\n", + "\tReactants\n", + "\t\tCdc42c: 1\n", + "\t\tCdc42m: 1\n", + "\tProducts\n", + "\t\tCdc42m: 2\n", + "\tPropensity Function: kfb*Cdc42c*Cdc42m/vol\n", + "\n", + "**********\n", + "Domain\n", + "**********\n", + "\n", + "Domain Attributes\n", + "\n", + " On Boundary: None\n", + " Mesh Size: None\n", + " RHO_0: 2\n", + " C_0: 10\n", + " P_0: 10\n", + " Gravity: [0, 0, 0]\n", + " X Limit: (-0.9985541604477006, 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Fixed: False\n" + ] + } + ], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.8.5" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} diff --git a/public_models/Polarization_In_Yeast/PolarizationInYeast.ipynb b/public_models/Polarization_In_Yeast/PolarizationInYeast.ipynb new file mode 100644 index 0000000000..76d542b1ee --- /dev/null +++ b/public_models/Polarization_In_Yeast/PolarizationInYeast.ipynb @@ -0,0 +1,130 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "%load_ext autoreload\n", + "%autoreload 2\n", + "\n", + "import numpy as np\n", + "import spatialpy\n", + "from spatialpy import Model, Species, Parameter, Reaction, Mesh,\\\n", + " PlaceInitialCondition, \\\n", + " UniformInitialCondition, \\\n", + " ScatterInitialCondition" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# PolarizationInYeast" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "class PolarizationInYeast(Model):\n", + " def __init__(self):\n", + " Model.__init__(self, name=\"PolarizationInYeast\")\n", + "\n", + " # Domain\n", + " mesh = Mesh.read_stochss_domain('PolarizationInYeast.smdl')\n", + " self.add_mesh(mesh)\n", + "\n", + " self.staticDomain = True\n", + "\n", + " # Variables\n", + " Cdc42c = Species(name=\"Cdc42c\", diffusion_constant=10)\n", + " Cdc42m = Species(name=\"Cdc42m\", diffusion_constant=0.0053)\n", + " self.add_species([Cdc42c, Cdc42m])\n", + "\n", + " self.restrict(Cdc42m, [2])\n", + "\n", + " # Initial Conditions\n", + " self.add_initial_condition(ScatterInitialCondition(species=Cdc42c, count=300, types=[1]))\n", + " self.add_initial_condition(ScatterInitialCondition(species=Cdc42m, count=100, types=[2]))\n", + "\n", + " # Parameters\n", + " kon = Parameter(name=\"kon\", expression=\"1.6666666667e-05\")\n", + " koff = Parameter(name=\"koff\", expression=\"0.15\")\n", + " kfb = Parameter(name=\"kfb\", expression=\"0.166666666666667\")\n", + " self.add_parameter([kon, koff, kfb])\n", + "\n", + " # Reactions\n", + " r1 = Reaction(name=\"r1\", reactants={Cdc42c: 1}, products={Cdc42m: 1}, rate=self.listOfParameters[\"kon\"])\n", + " r2 = Reaction(name=\"r2\", reactants={Cdc42m: 1}, products={Cdc42c: 1}, rate=self.listOfParameters[\"koff\"])\n", + " r3 = Reaction(name=\"r3\", restrict_to=[2], reactants={Cdc42c: 1, Cdc42m: 1}, products={Cdc42m: 2}, rate=self.listOfParameters[\"kfb\"])\n", + " self.add_reaction([r1, r2, r3])\n", + "\n", + " # Timespan\n", + " self.timespan(np.arange(0, 5000, 10), timestep_size=10)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "model = PolarizationInYeast()" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Simulation Parameters" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "def configure_simulation():\n", + " kwargs = {\n", + " # \"number_of_trajectories\":1,\n", + " # \"seed\":None,\n", + " }\n", + " return kwargs" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "kwargs = configure_simulation()\n", + "results = model.run(**kwargs)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Visualization" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "results.plot_species('Cdc42c', animated=True, width=None, height=None)" + ] + } + ], + "metadata": {}, + "nbformat": 4, + "nbformat_minor": 4 +} diff --git a/public_models/Polarization_In_Yeast/PolarizationInYeast.smdl b/public_models/Polarization_In_Yeast/PolarizationInYeast.smdl new file mode 100644 index 0000000000..e0e1ffe698 --- /dev/null +++ b/public_models/Polarization_In_Yeast/PolarizationInYeast.smdl @@ -0,0 +1 @@ +{"is_spatial":true,"defaultID":9,"defaultMode":"","annotation":"Reactions could not be completed from the slides (74 - 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\ No newline at end of file diff --git a/public_models/Schlogl/Schlogl.ipynb b/public_models/Schlogl/Schlogl.ipynb index 9a3a7cfaba..7897e5931e 100644 --- a/public_models/Schlogl/Schlogl.ipynb +++ b/public_models/Schlogl/Schlogl.ipynb @@ -1,1894 +1 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Schlogl" - ] - }, - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [], - "source": [ - "import numpy as np\n", - "import gillespy2\n", - "from gillespy2 import Model, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition\n", - "from gillespy2 import EventAssignment, EventTrigger, Event\n", - "from gillespy2 import SSACSolver\n", - "# from gillespy2 import VariableSSACSolver\n", - "# from gillespy2 import BasicTauLeapingSolver\n", - "# from gillespy2 import BasicTauHybridSolver\n", - "# from gillespy2 import BasicODESolver" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [], - "source": [ - "class Schlogl(Model):\n", - " def __init__(self, parameter_values=None):\n", - " Model.__init__(self, name=\"Schlogl\")\n", - " self.volume = 1\n", - "\n", - " # Parameters\n", - " self.add_parameter(Parameter(name=\"k1\", expression=1))\n", - " self.add_parameter(Parameter(name=\"k2\", expression=1))\n", - "\n", - " # Species\n", - " self.add_species(Species(name=\"s1\", initial_value=300, mode=\"discrete\"))\n", - " self.add_species(Species(name=\"s2\", initial_value=300, mode=\"discrete\"))\n", - " self.add_species(Species(name=\"s3\", initial_value=300, mode=\"discrete\"))\n", - " self.add_species(Species(name=\"s4\", initial_value=300, mode=\"discrete\"))\n", - "\n", - " # Reactions\n", - " self.add_reaction(Reaction(name=\"r1\", reactants={'s1': 1, 's4': 1}, products={'s4': 2}, rate=self.listOfParameters[\"k1\"]))\n", - " self.add_reaction(Reaction(name=\"r2\", reactants={'s2': 1, 's4': 1}, products={'s3': 1}, rate=self.listOfParameters[\"k2\"]))\n", - "\n", - " # Timespan\n", - " self.timespan(np.linspace(0, 100000, 101))" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [], - "source": [ - "model = Schlogl()" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [], - "source": [ - "solver = SSACSolver(model=model)" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "metadata": {}, - "outputs": [], - "source": [ - "def configure_simulation():\n", - " kwargs = {\n", - " \"solver\":solver,\n", - " \"number_of_trajectories\":1,\n", - " \"seed\":None,\n", - " # \"tau_tol\":0.03,\n", - " # \"integrator_options\":{'rtol': 0.001, 'atol': 1e-06}\n", - " }\n", - " return kwargs" - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "metadata": {}, - "outputs": [], - "source": [ - "kwargs = configure_simulation()\n", - "results = model.run(**kwargs)" - ] - }, - { - "cell_type": "code", - 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" - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "results.plotplotly()" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.7.6" - } - }, - "nbformat": 4, - "nbformat_minor": 4 -} +{"cells":[{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["import numpy as np\n","import gillespy2\n","from gillespy2 import Model, Species, Parameter, Reaction, Event, \\\n"," EventTrigger, EventAssignment, RateRule, \\\n"," AssignmentRule, FunctionDefinition\n","# from gillespy2 import SSACSolver\n","# from gillespy2 import TauLeapingCSolver\n","# from gillespy2 import ODECSolver\n","# from gillespy2 import TauHybridSolver"]},{"cell_type":"markdown","metadata":{},"source":["# Schlogl"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["class Schlogl(Model):\n"," def __init__(self, parameter_values=None):\n"," Model.__init__(self, name=\"Schlogl\")\n"," self.volume = 1\n","\n"," # Parameters\n"," self.add_parameter(Parameter(name=\"k1\", expression=\"1\"))\n"," self.add_parameter(Parameter(name=\"k2\", expression=\"1\"))\n","\n"," # Variables\n"," self.add_species(Species(name=\"s1\", initial_value=300, mode=\"discrete\"))\n"," self.add_species(Species(name=\"s2\", initial_value=300, mode=\"discrete\"))\n"," self.add_species(Species(name=\"s3\", initial_value=300, mode=\"discrete\"))\n"," self.add_species(Species(name=\"s4\", initial_value=300, mode=\"discrete\"))\n","\n"," # Reactions\n"," self.add_reaction(Reaction(name=\"r1\", reactants={'s1': 1, 's4': 1}, products={'s4': 2}, rate=self.listOfParameters[\"k1\"]))\n"," self.add_reaction(Reaction(name=\"r2\", reactants={'s2': 1, 's4': 1}, products={'s3': 1}, rate=self.listOfParameters[\"k2\"]))\n","\n"," # Timespan\n"," self.timespan(np.arange(0, 100000, 1000))"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["model = Schlogl()"]},{"cell_type":"markdown","metadata":{},"source":["# Simulation Parameters"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["def configure_simulation():\n"," # solver = SSACSolver(model=model)\n"," kwargs = {\n"," # \"solver\":solver,\n"," \"number_of_trajectories\":100,\n"," # \"seed\":None,\n"," # \"tau_tol\":0.03,\n"," # \"integrator_options\":{'rtol': 0.001, 'atol': 1e-06},\n"," }\n"," return kwargs"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["kwargs = configure_simulation()\n","results = model.run(**kwargs)"]},{"cell_type":"markdown","metadata":{},"source":["# Visualization"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["results.plotplotly()"]}],"metadata":{},"nbformat":4,"nbformat_minor":4} \ No newline at end of file diff --git a/public_models/Toggle_Switch/Toggle_Switch.ipynb b/public_models/Toggle_Switch/Toggle_Switch.ipynb index 2847f5fafb..11eba3b4fc 100644 --- a/public_models/Toggle_Switch/Toggle_Switch.ipynb +++ b/public_models/Toggle_Switch/Toggle_Switch.ipynb @@ -1,2069 +1 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Toggle_Switch" - ] - }, - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [], - "source": [ - "import numpy as np\n", - "import gillespy2\n", - "from gillespy2 import Model, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition\n", - "from gillespy2 import EventAssignment, EventTrigger, Event\n", - "from gillespy2 import SSACSolver\n", - "# from gillespy2 import VariableSSACSolver\n", - "# from gillespy2 import BasicTauLeapingSolver\n", - "# from gillespy2 import BasicTauHybridSolver\n", - "# from gillespy2 import BasicODESolver" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [], - "source": [ - "class Toggle_Switch(Model):\n", - " def __init__(self, parameter_values=None):\n", - " Model.__init__(self, name=\"Toggle_Switch\")\n", - " self.volume = 1\n", - "\n", - " # Parameters\n", - " self.add_parameter(Parameter(name=\"alpha1\", expression=10))\n", - " self.add_parameter(Parameter(name=\"alpha2\", expression=10))\n", - " self.add_parameter(Parameter(name=\"beta\", expression=2))\n", - " self.add_parameter(Parameter(name=\"gamma\", expression=2))\n", - " self.add_parameter(Parameter(name=\"mu\", expression=1))\n", - "\n", - " # Species\n", - " self.add_species(Species(name=\"A\", initial_value=2, mode=\"discrete\"))\n", - " self.add_species(Species(name=\"B\", initial_value=2, mode=\"discrete\"))\n", - "\n", - " # Reactions\n", - " self.add_reaction(Reaction(name=\"cu\", reactants={}, products={'A': 1}, propensity_function=\"alpha1/(1+pow(B, beta))\"))\n", - " self.add_reaction(Reaction(name=\"cv\", reactants={}, products={'B': 1}, propensity_function=\"alpha2/(1+pow(A, gamma))\"))\n", - " self.add_reaction(Reaction(name=\"du\", reactants={'A': 1}, products={}, rate=self.listOfParameters[\"mu\"]))\n", - " self.add_reaction(Reaction(name=\"dv\", reactants={'B': 1}, products={}, rate=self.listOfParameters[\"mu\"]))\n", - "\n", - " # Timespan\n", - " self.timespan(np.linspace(0, 250, 251))" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [], - "source": [ - "model = Toggle_Switch()" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [], - "source": [ - "solver = SSACSolver(model=model)" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "metadata": {}, - "outputs": [], - "source": [ - "def configure_simulation():\n", - " kwargs = {\n", - " \"solver\":solver,\n", - " \"number_of_trajectories\":1,\n", - " \"seed\":None,\n", - " # \"tau_tol\":0.03,\n", - " # \"integrator_options\":{'rtol': 0.001, 'atol': 1e-06}\n", - " }\n", - " return kwargs" - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "metadata": {}, - "outputs": [], - "source": [ - "kwargs = configure_simulation()\n", - "results = model.run(**kwargs)" - ] - }, - { - "cell_type": "code", - "execution_count": 7, - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - 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"cells": [ - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Toggle_Switch" - ] - }, - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [], - "source": [ - "import numpy as np\n", - "import gillespy2\n", - "from gillespy2 import Model, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition\n", - "from gillespy2 import EventAssignment, EventTrigger, Event\n", - "# To run a simulation using the SSA Solver simply omit the solver argument from model.run().\n", - "from gillespy2 import VariableSSACSolver\n", - "# from gillespy2 import BasicTauLeapingSolver\n", - "# from gillespy2 import BasicTauHybridSolver\n", - "# from gillespy2 import BasicODESolver" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [], - "source": [ - "class Toggle_Switch(Model):\n", - " def __init__(self, parameter_values=None):\n", - " Model.__init__(self, name=\"Toggle_Switch\")\n", - " self.volume = 1\n", - "\n", - " # Parameters\n", - " self.add_parameter(Parameter(name=\"alpha1\", expression=10))\n", - " self.add_parameter(Parameter(name=\"alpha2\", expression=10))\n", - " self.add_parameter(Parameter(name=\"beta\", expression=2))\n", - " self.add_parameter(Parameter(name=\"gamma\", expression=2))\n", - " self.add_parameter(Parameter(name=\"mu\", expression=1))\n", - "\n", - " # Species\n", - " self.add_species(Species(name=\"A\", initial_value=2, mode=\"discrete\"))\n", - " self.add_species(Species(name=\"B\", initial_value=2, mode=\"discrete\"))\n", - "\n", - " # Reactions\n", - " self.add_reaction(Reaction(name=\"cu\", reactants={}, products={'A': 1}, propensity_function=\"alpha1/(1+pow(B, beta))\"))\n", - " self.add_reaction(Reaction(name=\"cv\", reactants={}, products={'B': 1}, propensity_function=\"alpha2/(1+pow(A, gamma))\"))\n", - " self.add_reaction(Reaction(name=\"du\", reactants={'A': 1}, products={}, rate=self.listOfParameters[\"mu\"]))\n", - " self.add_reaction(Reaction(name=\"dv\", reactants={'B': 1}, products={}, rate=self.listOfParameters[\"mu\"]))\n", - "\n", - " # Timespan\n", - " self.timespan(np.linspace(0, 250, 251))" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [], - "source": [ - "model = Toggle_Switch()" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [], - "source": [ - "solver = VariableSSACSolver(model=model)" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "metadata": {}, - "outputs": [], - "source": [ - "def configure_simulation():\n", - " kwargs = {\n", - " \"solver\":solver,\n", - " \"number_of_trajectories\":10,\n", - " \"seed\":None,\n", - " # \"tau_tol\":0.03,\n", - " # \"integrator_options\":{'rtol': 0.001, 'atol': 1e-06}\n", - " }\n", - " return kwargs" - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "metadata": {}, - "outputs": [], - "source": [ - "# Feature extraction function. What value(s) do you want to extract\n", - "# from the simulation trajectory\n", - "\n", - "def population_at_last_timepoint(c,res):\n", - " if c.verbose: print('population_at_last_timepoint {0}={1}'.format(c.species_of_interest,res[c.species_of_interest][-1]))\n", - " return res[c.species_of_interest][-1]" - ] - }, - { - "cell_type": "code", - "execution_count": 7, - "metadata": {}, - "outputs": [], - "source": [ - "# Aggregation function, How to we combine the values from multiple \n", - "# trajectores\n", - "\n", - "def mean_std_of_ensemble(c,data):\n", - " a=np.average(data)\n", - " s=np.std(data)\n", - " if c.verbose: print('mean_std_of_ensemble m:{0} s:{1}'.format(a,s))\n", - " return (a,s)" - ] - }, - { - "cell_type": "code", - "execution_count": 8, - "metadata": {}, - "outputs": [], - "source": [ - "class ParameterSweep1D():\n", - " \n", - " def run(c, kwargs, verbose=False):\n", - " c.verbose = verbose\n", - " fn = c.feature_extraction\n", - " ag = c.ensemble_aggragator\n", - " data = np.zeros((len(c.p1_range),2)) # mean and std\n", - " for i,v1 in enumerate(c.p1_range):\n", - " if verbose: print(\"running {0}={1}\".format(c.p1,v1))\n", - " #if verbose: print(\"\t{0}\".format([\"{0}={1},\".format(k,v.value) for k,v in tmp_model.listOfParameters.items()]))\n", - " if(c.number_of_trajectories > 1):\n", - " tmp_results = model.run(**kwargs, variables={c.p1:v1})\n", - " (m,s) = ag([fn(x) for x in tmp_results])\n", - " data[i,0] = m\n", - " data[i,1] = s\n", - " else:\n", - " tmp_result = model.run(**kwargs, variables={c.p1:v1})\n", - " data[i,0] = c.feature_extraction(tmp_result)\n", - " c.data = data\n", - "\n", - " def plot(c):\n", - " from matplotlib import pyplot as plt\n", - " from mpl_toolkits.axes_grid1 import make_axes_locatable\n", - " import numpy\n", - " fig, ax = plt.subplots(figsize=(8,8))\n", - " plt.title(\"Parameter Sweep - Species:{0}\".format(c.species_of_interest))\n", - " plt.errorbar(c.p1_range,c.data[:,0],c.data[:,1])\n", - " plt.xlabel(c.p1, fontsize=16, fontweight='bold')\n", - " plt.ylabel(\"Population\", fontsize=16, fontweight='bold')\n", - "\n", - "\n", - " def plotplotly(c, return_plotly_figure=False, species_of_interest=None):\n", - " from plotly.offline import iplot\n", - " import plotly.graph_objs as go\n", - "\n", - " data = c.data\n", - " visible = c.number_of_trajectories > 1\n", - " error_y = dict(type='data', array=data[:,1], visible=visible)\n", - "\n", - " trace_list = [go.Scatter(x=c.p1_range, y=data[:,0], error_y=error_y)]\n", - "\n", - " title = dict(text=\"Parameter Sweep - Species: {0}\".format(c.species_of_interest), x=0.5)\n", - " yaxis_label = dict(title=\"Population\")\n", - " xaxis_label = dict(title=\"{0}\".format(c.p1))\n", - "\n", - " layout = go.Layout(title=title, xaxis=xaxis_label, yaxis=yaxis_label)\n", - "\n", - " fig = dict(data=trace_list, layout=layout)\n", - "\n", - " if return_plotly_figure:\n", - " return fig\n", - " else:\n", - " iplot(fig)\n", - " " - ] - }, - { - "cell_type": "code", - "execution_count": 9, - "metadata": {}, - "outputs": [], - "source": [ - "# Configuration for the Parameter Sweep\n", - "class ParameterSweepConfig(ParameterSweep1D):\n", - " # What class defines the GillesPy2 model\n", - " ps_class = Toggle_Switch\n", - " model = ps_class()\n", - " p1 = \"alpha1\" # ENTER PARAMETER 1 HERE\n", - " p1_min = 0.5 * float(eval(model.get_parameter(p1).expression)) # ENTER START VALUE FOR P1 RANGE HERE\n", - " p1_max = 1.5 * float(eval(model.get_parameter(p1).expression)) # ENTER END VALUE FOR P1 RANGE HERE\n", - " p1_steps = 11 # ENTER THE NUMBER OF STEPS FOR P1 HERE\n", - " p1_range = np.linspace(p1_min,p1_max,p1_steps)\n", - " species_of_interest = \"A\" # ENTER SPECIES OF INTEREST HERE\n", - " number_of_trajectories = 1\n", - " # What feature of the simulation are we examining\n", - " feature_extraction = population_at_last_timepoint\n", - " # for number_of_trajectories > 1: how do we aggreggate the values\n", - " ensemble_aggragator = mean_std_of_ensemble\n" - ] - }, - { - "cell_type": "code", - "execution_count": 10, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "CPU times: user 56.6 ms, sys: 21.1 ms, total: 77.6 ms\n", - "Wall time: 207 ms\n" - ] - } - ], - "source": [ - "kwargs = configure_simulation()\n", - "ps = ParameterSweepConfig()\n", - "ps.number_of_trajectories = kwargs['number_of_trajectories']\n", - "%time ps.run(kwargs)" - ] - }, - { - "cell_type": "code", - "execution_count": 11, - "metadata": {}, - "outputs": [ - { - "data": { - "image/png": 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" - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "ps.plotplotly()" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.7.6" - } - }, - "nbformat": 4, - "nbformat_minor": 4 -} diff --git a/public_models/Toggle_Switch/Toggle_Switch2dParamSweep.ipynb b/public_models/Toggle_Switch/Toggle_Switch2dParamSweep.ipynb deleted file mode 100644 index 5e615baa7e..0000000000 --- a/public_models/Toggle_Switch/Toggle_Switch2dParamSweep.ipynb +++ /dev/null @@ -1,1432 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Toggle_Switch" - ] - }, - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [], - "source": [ - "import numpy as np\n", - "import gillespy2\n", - "from gillespy2 import Model, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition\n", - "from gillespy2 import EventAssignment, EventTrigger, Event\n", - "# To run a simulation using the SSA Solver simply omit the solver argument from model.run().\n", - "from gillespy2 import VariableSSACSolver\n", - "# from gillespy2 import BasicTauLeapingSolver\n", - "# from gillespy2 import BasicTauHybridSolver\n", - "# from gillespy2 import BasicODESolver" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [], - "source": [ - "class Toggle_Switch(Model):\n", - " def __init__(self, parameter_values=None):\n", - " Model.__init__(self, name=\"Toggle_Switch\")\n", - " self.volume = 1\n", - "\n", - " # Parameters\n", - " self.add_parameter(Parameter(name=\"alpha1\", expression=10))\n", - " self.add_parameter(Parameter(name=\"alpha2\", expression=10))\n", - " self.add_parameter(Parameter(name=\"beta\", expression=2))\n", - " self.add_parameter(Parameter(name=\"gamma\", expression=2))\n", - " self.add_parameter(Parameter(name=\"mu\", expression=1))\n", - "\n", - " # Species\n", - " self.add_species(Species(name=\"A\", initial_value=2, mode=\"discrete\"))\n", - " self.add_species(Species(name=\"B\", initial_value=2, mode=\"discrete\"))\n", - "\n", - " # Reactions\n", - " self.add_reaction(Reaction(name=\"cu\", reactants={}, products={'A': 1}, propensity_function=\"alpha1/(1+pow(B, beta))\"))\n", - " self.add_reaction(Reaction(name=\"cv\", reactants={}, products={'B': 1}, propensity_function=\"alpha2/(1+pow(A, gamma))\"))\n", - " self.add_reaction(Reaction(name=\"du\", reactants={'A': 1}, products={}, rate=self.listOfParameters[\"mu\"]))\n", - " self.add_reaction(Reaction(name=\"dv\", reactants={'B': 1}, products={}, rate=self.listOfParameters[\"mu\"]))\n", - "\n", - " # Timespan\n", - " self.timespan(np.linspace(0, 250, 251))" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [], - "source": [ - "model = Toggle_Switch()" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [], - "source": [ - "solver = VariableSSACSolver(model=model)" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "metadata": {}, - "outputs": [], - "source": [ - "def configure_simulation():\n", - " kwargs = {\n", - " \"solver\":solver,\n", - " \"number_of_trajectories\":10,\n", - " \"seed\":None,\n", - " # \"tau_tol\":0.03,\n", - " # \"integrator_options\":{'rtol': 0.001, 'atol': 1e-06}\n", - " }\n", - " return kwargs" - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "metadata": {}, - "outputs": [], - "source": [ - "# Feature extraction function. What value(s) do you want to extract\n", - "# from the simulation trajectory\n", - "\n", - "def population_at_last_timepoint(c,res):\n", - " if c.verbose: print('population_at_last_timepoint {0}={1}'.format(c.species_of_interest,res[c.species_of_interest][-1]))\n", - " return res[c.species_of_interest][-1]" - ] - }, - { - "cell_type": "code", - "execution_count": 7, - "metadata": {}, - "outputs": [], - "source": [ - "# Aggregation function, How to we combine the values from multiple \n", - "# trajectores\n", - "\n", - "def average_of_ensemble(c,data):\n", - " a=np.average(data)\n", - " if c.verbose: print('average_of_ensemble = {0}'.format(a))\n", - " return a" - ] - }, - { - "cell_type": "code", - "execution_count": 8, - "metadata": {}, - "outputs": [], - "source": [ - "class ParameterSweep2D():\n", - " \n", - " def run(c, kwargs, verbose=False):\n", - " c.verbose = verbose\n", - " fn = c.feature_extraction\n", - " ag = c.ensemble_aggragator\n", - " data = np.zeros((len(c.p1_range),len(c.p2_range)))\n", - " for i,v1 in enumerate(c.p1_range):\n", - " for j,v2 in enumerate(c.p2_range):\n", - " if verbose: print(\"running {0}={1}, {2}={3}\".format(c.p1,v1,c.p2,v2))\n", - " #if verbose: print(\"\t{0}\".format([\"{0}={1}, \".format(k,v.value) for k,v in tmp_model.listOfParameters.items()]))\n", - " if(c.number_of_trajectories > 1):\n", - " tmp_results = model.run(**kwargs, variables={c.p1:v1, c.p2:v2})\n", - " data[i,j] = ag([fn(x) for x in tmp_results])\n", - " else:\n", - " tmp_result = model.run(**kwargs, variables={c.p1:v1, c.p2:v2})\n", - " data[i,j] = c.feature_extraction(tmp_result)\n", - " c.data = data\n", - "\n", - " def plot(c):\n", - " from matplotlib import pyplot as plt\n", - " from mpl_toolkits.axes_grid1 import make_axes_locatable\n", - " import numpy\n", - " fig, ax = plt.subplots(figsize=(8,8))\n", - " plt.imshow(c.data)\n", - " ax.set_xticks(numpy.arange(c.data.shape[1])+0.5, minor=False)\n", - " ax.set_yticks(numpy.arange(c.data.shape[0])+0.5, minor=False)\n", - " plt.title(\"Parameter Sweep - Species: {0}\".format(c.species_of_interest))\n", - " ax.set_xticklabels(c.p1_range, minor=False, rotation=90)\n", - " ax.set_yticklabels(c.p2_range, minor=False)\n", - " ax.set_xlabel(c.p1, fontsize=16, fontweight='bold')\n", - " ax.set_ylabel(c.p2, fontsize=16, fontweight='bold')\n", - " divider = make_axes_locatable(ax)\n", - " cax = divider.append_axes(\"right\", size=\"5%\", pad=0.2)\n", - " _ = plt.colorbar(ax=ax, cax=cax)\n", - "\n", - "\n", - " def plotplotly(c, return_plotly_figure=False):\n", - " from plotly.offline import init_notebook_mode, iplot\n", - " import plotly.graph_objs as go\n", - " \n", - " xaxis_ticks = c.p1_range\n", - " yaxis_ticks = c.p2_range\n", - " data = c.data\n", - "\n", - " trace_list = [go.Heatmap(z=data, x=xaxis_ticks, y=yaxis_ticks)]\n", - "\n", - " title = dict(text=\"Parameter Sweep - Species: {0}\".format(c.species_of_interest), x=0.5)\n", - " xaxis_label = dict(title=\"{0}\".format(c.p1))\n", - " yaxis_label = dict(title=\"{0}\".format(c.p2))\n", - "\n", - " layout = go.Layout(title=title, xaxis=xaxis_label, yaxis=yaxis_label)\n", - "\n", - " fig = dict(data=trace_list, layout=layout)\n", - "\n", - " if return_plotly_figure:\n", - " return fig\n", - " else:\n", - " iplot(fig)\n", - " " - ] - }, - { - "cell_type": "code", - "execution_count": 9, - "metadata": {}, - "outputs": [], - "source": [ - "# Configuration for the Parameter Sweep\n", - "class ParameterSweepConfig(ParameterSweep2D):\n", - " # What class defines the GillesPy2 model\n", - " ps_class = Toggle_Switch\n", - " model = ps_class()\n", - " p1 = \"alpha1\" # ENTER PARAMETER 1 HERE\n", - " p2 = \"alpha2\" # ENTER PARAMETER 2 HERE\n", - " p1_min = 0.5 * float(eval(model.get_parameter(p1).expression)) # ENTER START VALUE FOR P1 RANGE HERE\n", - " p1_max = 1.5 * float(eval(model.get_parameter(p1).expression)) # ENTER END VALUE FOR P1 RANGE HERE\n", - " p1_steps = 11 # ENTER THE NUMBER OF STEPS FOR P1 HERE\n", - " p1_range = np.linspace(p1_min,p1_max,p1_steps)\n", - " p2_min = 0.5 * float(eval(model.get_parameter(p2).expression)) # ENTER START VALUE FOR P2 RANGE HERE\n", - " p2_max = 1.5 * float(eval(model.get_parameter(p2).expression)) # ENTER END VALUE FOR P2 RANGE HERE\n", - " p2_steps = 11 # ENTER THE NUMBER OF STEPS FOR P2 HERE\n", - " p2_range = np.linspace(p2_min,p2_max,p2_steps)\n", - " species_of_interest = \"A\" # ENTER SPECIES OF INTEREST HERE\n", - " number_of_trajectories = 1\n", - " # What feature of the simulation are we examining\n", - " feature_extraction = population_at_last_timepoint\n", - " # for number_of_trajectories > 1: how do we aggreggate the values\n", - " ensemble_aggragator = average_of_ensemble\n" - ] - }, - { - "cell_type": "code", - "execution_count": 10, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "CPU times: user 508 ms, sys: 180 ms, total: 688 ms\n", - "Wall time: 2.05 s\n" - ] - } - ], - "source": [ - "kwargs = configure_simulation()\n", - "ps = ParameterSweepConfig()\n", - "ps.number_of_trajectories = kwargs['number_of_trajectories']\n", - "%time ps.run(kwargs)" - ] - }, - { - "cell_type": "code", - "execution_count": 11, - "metadata": {}, - "outputs": [ - { - "data": { - "image/png": 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\n", 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Parameters\n"," self.add_parameter(Parameter(name=\"alpha1\", expression=\"10\"))\n"," self.add_parameter(Parameter(name=\"alpha2\", expression=\"10\"))\n"," self.add_parameter(Parameter(name=\"beta\", expression=\"2\"))\n"," self.add_parameter(Parameter(name=\"gamma\", expression=\"2\"))\n"," self.add_parameter(Parameter(name=\"mu\", expression=\"1\"))\n","\n"," # Variables\n"," self.add_species(Species(name=\"A\", initial_value=2, mode=\"discrete\"))\n"," self.add_species(Species(name=\"B\", initial_value=2, mode=\"discrete\"))\n","\n"," # Reactions\n"," self.add_reaction(Reaction(name=\"cu\", reactants={}, products={'A': 1}, propensity_function=\"alpha1/(1+pow(B, beta))\"))\n"," self.add_reaction(Reaction(name=\"cv\", reactants={}, products={'B': 1}, propensity_function=\"alpha2/(1+pow(A, gamma))\"))\n"," self.add_reaction(Reaction(name=\"du\", reactants={'A': 1}, products={}, rate=self.listOfParameters[\"mu\"]))\n"," self.add_reaction(Reaction(name=\"dv\", reactants={'B': 1}, products={}, rate=self.listOfParameters[\"mu\"]))\n","\n"," # Timespan\n"," self.timespan(np.arange(0, 250, 1))"]},{"cell_type":"code","execution_count":3,"metadata":{},"outputs":[],"source":["model = ToggleSwitch()"]},{"cell_type":"markdown","metadata":{},"source":["# Simulation Parameters"]},{"cell_type":"code","execution_count":4,"metadata":{},"outputs":[],"source":["def configure_simulation():\n"," solver = VariableSSACSolver(model=model)\n"," kwargs = {\n"," \"solver\":solver,\n"," \"number_of_trajectories\":100,\n"," # \"seed\":None,\n"," # \"tau_tol\":0.03,\n"," # \"integrator_options\":{'rtol': 0.001, 'atol': 1e-06},\n"," }\n"," return kwargs"]},{"cell_type":"markdown","metadata":{},"source":["# Model Exploration"]},{"cell_type":"markdown","metadata":{},"source":["## Define simulator function (using gillespy2 wrapper)"]},{"cell_type":"code","execution_count":5,"metadata":{},"outputs":[],"source":["from sciope.utilities.gillespy2 import wrapper\n","settings = configure_simulation()\n","simulator = wrapper.get_simulator(gillespy_model=model, run_settings=settings, species_of_interest=['A', 'B'])\n","expression_array = wrapper.get_parameter_expression_array(model)"]},{"cell_type":"markdown","metadata":{},"source":["## Start local cluster using dask client"]},{"cell_type":"code","execution_count":6,"metadata":{},"outputs":[],"source":["from dask.distributed import Client\n","\n","c = Client()"]},{"cell_type":"markdown","metadata":{},"source":["## Define parameter sampler/design and summary statistics"]},{"cell_type":"code","execution_count":7,"metadata":{},"outputs":[],"source":["from sciope.designs import latin_hypercube_sampling\n","from sciope.utilities.summarystats.auto_tsfresh import SummariesTSFRESH\n","\n","lhc = latin_hypercube_sampling.LatinHypercube(xmin=expression_array, xmax=expression_array*3)\n","lhc.generate_array(1000) # creates a LHD of size 1000\n","\n","# will use default minimal set of features\n","summary_stats = SummariesTSFRESH()"]},{"cell_type":"markdown","metadata":{},"source":["## Initiate StochMET"]},{"cell_type":"code","execution_count":8,"metadata":{},"outputs":[],"source":["from sciope.stochmet.stochmet import StochMET\n","\n","met = StochMET(simulator, lhc, summary_stats)"]},{"cell_type":"markdown","metadata":{},"source":["## Run parameter sweep"]},{"cell_type":"code","execution_count":9,"metadata":{},"outputs":[],"source":["met.compute(n_points=500, chunk_size=10)"]},{"cell_type":"markdown","metadata":{},"source":["## Explore the result"]},{"cell_type":"code","execution_count":10,"metadata":{},"outputs":[],"source":["# First lets add some appropiate information about the model and features\n","met.data.configurations['listOfParameters'] = list(model.listOfParameters.keys())\n","met.data.configurations['listOfSpecies'] = list(model.listOfSpecies.keys())\n","met.data.configurations['listOfSummaries'] = met.summaries.features\n","met.data.configurations['timepoints'] = model.tspan"]},{"cell_type":"code","execution_count":13,"metadata":{"scrolled":false},"outputs":[{"data":{"application/javascript":["/* Put everything inside the global mpl namespace */\n","/* global mpl */\n","window.mpl = {};\n","\n","mpl.get_websocket_type = function () {\n"," if (typeof WebSocket !== 'undefined') {\n"," return WebSocket;\n"," } else if (typeof MozWebSocket !== 'undefined') {\n"," return MozWebSocket;\n"," } else {\n"," alert(\n"," 'Your browser does not have WebSocket support. ' +\n"," 'Please try Chrome, Safari or Firefox ≥ 6. ' +\n"," 'Firefox 4 and 5 are also supported but you ' +\n"," 'have to enable WebSockets in about:config.'\n"," );\n"," }\n","};\n","\n","mpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n"," this.id = figure_id;\n","\n"," this.ws = websocket;\n","\n"," this.supports_binary = this.ws.binaryType !== undefined;\n","\n"," if (!this.supports_binary) {\n"," var warnings = document.getElementById('mpl-warnings');\n"," if (warnings) {\n"," warnings.style.display = 'block';\n"," warnings.textContent =\n"," 'This browser does not support binary websocket messages. ' +\n"," 'Performance may be slow.';\n"," }\n"," }\n","\n"," this.imageObj = new Image();\n","\n"," this.context = undefined;\n"," this.message = undefined;\n"," this.canvas = undefined;\n"," this.rubberband_canvas = undefined;\n"," this.rubberband_context = undefined;\n"," this.format_dropdown = undefined;\n","\n"," this.image_mode = 'full';\n","\n"," this.root = document.createElement('div');\n"," this.root.setAttribute('style', 'display: inline-block');\n"," this._root_extra_style(this.root);\n","\n"," parent_element.appendChild(this.root);\n","\n"," this._init_header(this);\n"," this._init_canvas(this);\n"," this._init_toolbar(this);\n","\n"," var fig = this;\n","\n"," this.waiting = false;\n","\n"," this.ws.onopen = function () {\n"," fig.send_message('supports_binary', { value: fig.supports_binary });\n"," fig.send_message('send_image_mode', {});\n"," if (fig.ratio !== 1) {\n"," fig.send_message('set_dpi_ratio', { dpi_ratio: fig.ratio });\n"," }\n"," fig.send_message('refresh', {});\n"," };\n","\n"," this.imageObj.onload = function () {\n"," if (fig.image_mode === 'full') {\n"," // Full images could contain transparency (where diff images\n"," // almost always do), so we need to clear the canvas so that\n"," // there is no ghosting.\n"," fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n"," }\n"," fig.context.drawImage(fig.imageObj, 0, 0);\n"," };\n","\n"," this.imageObj.onunload = function () {\n"," fig.ws.close();\n"," };\n","\n"," this.ws.onmessage = this._make_on_message_function(this);\n","\n"," this.ondownload = ondownload;\n","};\n","\n","mpl.figure.prototype._init_header = function () {\n"," var titlebar = document.createElement('div');\n"," titlebar.classList =\n"," 'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n"," var titletext = document.createElement('div');\n"," titletext.classList = 'ui-dialog-title';\n"," titletext.setAttribute(\n"," 'style',\n"," 'width: 100%; text-align: center; padding: 3px;'\n"," );\n"," titlebar.appendChild(titletext);\n"," this.root.appendChild(titlebar);\n"," this.header = titletext;\n","};\n","\n","mpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n","\n","mpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n","\n","mpl.figure.prototype._init_canvas = function () {\n"," var fig = this;\n","\n"," var canvas_div = (this.canvas_div = document.createElement('div'));\n"," canvas_div.setAttribute(\n"," 'style',\n"," 'border: 1px solid #ddd;' +\n"," 'box-sizing: content-box;' +\n"," 'clear: both;' +\n"," 'min-height: 1px;' +\n"," 'min-width: 1px;' +\n"," 'outline: 0;' +\n"," 'overflow: hidden;' +\n"," 'position: relative;' +\n"," 'resize: both;'\n"," );\n","\n"," function on_keyboard_event_closure(name) {\n"," return function (event) {\n"," return fig.key_event(event, name);\n"," };\n"," }\n","\n"," canvas_div.addEventListener(\n"," 'keydown',\n"," on_keyboard_event_closure('key_press')\n"," );\n"," canvas_div.addEventListener(\n"," 'keyup',\n"," on_keyboard_event_closure('key_release')\n"," );\n","\n"," this._canvas_extra_style(canvas_div);\n"," this.root.appendChild(canvas_div);\n","\n"," var canvas = (this.canvas = document.createElement('canvas'));\n"," canvas.classList.add('mpl-canvas');\n"," canvas.setAttribute('style', 'box-sizing: content-box;');\n","\n"," this.context = canvas.getContext('2d');\n","\n"," var backingStore =\n"," this.context.backingStorePixelRatio ||\n"," this.context.webkitBackingStorePixelRatio ||\n"," this.context.mozBackingStorePixelRatio ||\n"," this.context.msBackingStorePixelRatio ||\n"," this.context.oBackingStorePixelRatio ||\n"," this.context.backingStorePixelRatio ||\n"," 1;\n","\n"," this.ratio = (window.devicePixelRatio || 1) / backingStore;\n","\n"," var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n"," 'canvas'\n"," ));\n"," rubberband_canvas.setAttribute(\n"," 'style',\n"," 'box-sizing: content-box; position: absolute; left: 0; top: 0; z-index: 1;'\n"," );\n","\n"," // Apply a ponyfill if ResizeObserver is not implemented by browser.\n"," if (this.ResizeObserver === undefined) {\n"," if (window.ResizeObserver !== undefined) {\n"," this.ResizeObserver = window.ResizeObserver;\n"," } else {\n"," var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n"," this.ResizeObserver = obs.ResizeObserver;\n"," }\n"," }\n","\n"," this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n"," var nentries = entries.length;\n"," for (var i = 0; i < nentries; i++) {\n"," var entry = entries[i];\n"," var width, height;\n"," if (entry.contentBoxSize) {\n"," if (entry.contentBoxSize instanceof Array) {\n"," // Chrome 84 implements new version of spec.\n"," width = entry.contentBoxSize[0].inlineSize;\n"," height = entry.contentBoxSize[0].blockSize;\n"," } else {\n"," // Firefox implements old version of spec.\n"," width = entry.contentBoxSize.inlineSize;\n"," height = entry.contentBoxSize.blockSize;\n"," }\n"," } else {\n"," // Chrome <84 implements even older version of spec.\n"," width = entry.contentRect.width;\n"," height = entry.contentRect.height;\n"," }\n","\n"," // Keep the size of the canvas and rubber band canvas in sync with\n"," // the canvas container.\n"," if (entry.devicePixelContentBoxSize) {\n"," // Chrome 84 implements new version of spec.\n"," canvas.setAttribute(\n"," 'width',\n"," entry.devicePixelContentBoxSize[0].inlineSize\n"," );\n"," canvas.setAttribute(\n"," 'height',\n"," entry.devicePixelContentBoxSize[0].blockSize\n"," );\n"," } else {\n"," canvas.setAttribute('width', width * fig.ratio);\n"," canvas.setAttribute('height', height * fig.ratio);\n"," }\n"," canvas.setAttribute(\n"," 'style',\n"," 'width: ' + width + 'px; height: ' + height + 'px;'\n"," );\n","\n"," rubberband_canvas.setAttribute('width', width);\n"," rubberband_canvas.setAttribute('height', height);\n","\n"," // And update the size in Python. We ignore the initial 0/0 size\n"," // that occurs as the element is placed into the DOM, which should\n"," // otherwise not happen due to the minimum size styling.\n"," if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n"," fig.request_resize(width, height);\n"," }\n"," }\n"," });\n"," this.resizeObserverInstance.observe(canvas_div);\n","\n"," function on_mouse_event_closure(name) {\n"," return function (event) {\n"," return fig.mouse_event(event, name);\n"," };\n"," }\n","\n"," rubberband_canvas.addEventListener(\n"," 'mousedown',\n"," on_mouse_event_closure('button_press')\n"," );\n"," rubberband_canvas.addEventListener(\n"," 'mouseup',\n"," on_mouse_event_closure('button_release')\n"," );\n"," // Throttle sequential mouse events to 1 every 20ms.\n"," rubberband_canvas.addEventListener(\n"," 'mousemove',\n"," on_mouse_event_closure('motion_notify')\n"," );\n","\n"," rubberband_canvas.addEventListener(\n"," 'mouseenter',\n"," on_mouse_event_closure('figure_enter')\n"," );\n"," rubberband_canvas.addEventListener(\n"," 'mouseleave',\n"," on_mouse_event_closure('figure_leave')\n"," );\n","\n"," canvas_div.addEventListener('wheel', function (event) {\n"," if (event.deltaY < 0) {\n"," event.step = 1;\n"," } else {\n"," event.step = -1;\n"," }\n"," on_mouse_event_closure('scroll')(event);\n"," });\n","\n"," canvas_div.appendChild(canvas);\n"," canvas_div.appendChild(rubberband_canvas);\n","\n"," this.rubberband_context = rubberband_canvas.getContext('2d');\n"," this.rubberband_context.strokeStyle = '#000000';\n","\n"," this._resize_canvas = function (width, height, forward) {\n"," if (forward) {\n"," canvas_div.style.width = width + 'px';\n"," canvas_div.style.height = height + 'px';\n"," }\n"," };\n","\n"," // Disable right mouse context menu.\n"," this.rubberband_canvas.addEventListener('contextmenu', function (_e) {\n"," event.preventDefault();\n"," return false;\n"," });\n","\n"," function set_focus() {\n"," canvas.focus();\n"," canvas_div.focus();\n"," }\n","\n"," window.setTimeout(set_focus, 100);\n","};\n","\n","mpl.figure.prototype._init_toolbar = function () {\n"," var fig = this;\n","\n"," var toolbar = document.createElement('div');\n"," toolbar.classList = 'mpl-toolbar';\n"," this.root.appendChild(toolbar);\n","\n"," function on_click_closure(name) {\n"," return function (_event) {\n"," return fig.toolbar_button_onclick(name);\n"," };\n"," }\n","\n"," function on_mouseover_closure(tooltip) {\n"," return function (event) {\n"," if (!event.currentTarget.disabled) {\n"," return fig.toolbar_button_onmouseover(tooltip);\n"," }\n"," };\n"," }\n","\n"," fig.buttons = {};\n"," var buttonGroup = document.createElement('div');\n"," buttonGroup.classList = 'mpl-button-group';\n"," for (var toolbar_ind in mpl.toolbar_items) {\n"," var name = mpl.toolbar_items[toolbar_ind][0];\n"," var tooltip = mpl.toolbar_items[toolbar_ind][1];\n"," var image = mpl.toolbar_items[toolbar_ind][2];\n"," var method_name = mpl.toolbar_items[toolbar_ind][3];\n","\n"," if (!name) {\n"," /* Instead of a spacer, we start a new button group. */\n"," if (buttonGroup.hasChildNodes()) {\n"," toolbar.appendChild(buttonGroup);\n"," }\n"," buttonGroup = document.createElement('div');\n"," buttonGroup.classList = 'mpl-button-group';\n"," continue;\n"," }\n","\n"," var button = (fig.buttons[name] = document.createElement('button'));\n"," button.classList = 'mpl-widget';\n"," button.setAttribute('role', 'button');\n"," button.setAttribute('aria-disabled', 'false');\n"," button.addEventListener('click', on_click_closure(method_name));\n"," button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n","\n"," var icon_img = document.createElement('img');\n"," icon_img.src = '_images/' + image + '.png';\n"," icon_img.srcset = '_images/' + image + '_large.png 2x';\n"," icon_img.alt = tooltip;\n"," button.appendChild(icon_img);\n","\n"," buttonGroup.appendChild(button);\n"," }\n","\n"," if (buttonGroup.hasChildNodes()) {\n"," toolbar.appendChild(buttonGroup);\n"," }\n","\n"," var fmt_picker = document.createElement('select');\n"," fmt_picker.classList = 'mpl-widget';\n"," toolbar.appendChild(fmt_picker);\n"," this.format_dropdown = fmt_picker;\n","\n"," for (var ind in mpl.extensions) {\n"," var fmt = mpl.extensions[ind];\n"," var option = document.createElement('option');\n"," option.selected = fmt === mpl.default_extension;\n"," option.innerHTML = fmt;\n"," fmt_picker.appendChild(option);\n"," }\n","\n"," var status_bar = document.createElement('span');\n"," status_bar.classList = 'mpl-message';\n"," toolbar.appendChild(status_bar);\n"," this.message = status_bar;\n","};\n","\n","mpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n"," // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n"," // which will in turn request a refresh of the image.\n"," this.send_message('resize', { width: x_pixels, height: y_pixels });\n","};\n","\n","mpl.figure.prototype.send_message = function (type, properties) {\n"," properties['type'] = type;\n"," properties['figure_id'] = this.id;\n"," this.ws.send(JSON.stringify(properties));\n","};\n","\n","mpl.figure.prototype.send_draw_message = function () {\n"," if (!this.waiting) {\n"," this.waiting = true;\n"," this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n"," }\n","};\n","\n","mpl.figure.prototype.handle_save = function (fig, _msg) {\n"," var format_dropdown = fig.format_dropdown;\n"," var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n"," fig.ondownload(fig, format);\n","};\n","\n","mpl.figure.prototype.handle_resize = function (fig, msg) {\n"," var size = msg['size'];\n"," if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n"," fig._resize_canvas(size[0], size[1], msg['forward']);\n"," fig.send_message('refresh', {});\n"," }\n","};\n","\n","mpl.figure.prototype.handle_rubberband = function (fig, msg) {\n"," var x0 = msg['x0'] / fig.ratio;\n"," var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n"," var x1 = msg['x1'] / fig.ratio;\n"," var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n"," x0 = Math.floor(x0) + 0.5;\n"," y0 = Math.floor(y0) + 0.5;\n"," x1 = Math.floor(x1) + 0.5;\n"," y1 = Math.floor(y1) + 0.5;\n"," var min_x = Math.min(x0, x1);\n"," var min_y = Math.min(y0, y1);\n"," var width = Math.abs(x1 - x0);\n"," var height = Math.abs(y1 - y0);\n","\n"," fig.rubberband_context.clearRect(\n"," 0,\n"," 0,\n"," fig.canvas.width / fig.ratio,\n"," fig.canvas.height / fig.ratio\n"," );\n","\n"," fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n","};\n","\n","mpl.figure.prototype.handle_figure_label = function (fig, msg) {\n"," // Updates the figure title.\n"," fig.header.textContent = msg['label'];\n","};\n","\n","mpl.figure.prototype.handle_cursor = function (fig, msg) {\n"," var cursor = msg['cursor'];\n"," switch (cursor) {\n"," case 0:\n"," cursor = 'pointer';\n"," break;\n"," case 1:\n"," cursor = 'default';\n"," break;\n"," case 2:\n"," cursor = 'crosshair';\n"," break;\n"," case 3:\n"," cursor = 'move';\n"," break;\n"," }\n"," fig.rubberband_canvas.style.cursor = cursor;\n","};\n","\n","mpl.figure.prototype.handle_message = function (fig, msg) {\n"," fig.message.textContent = msg['message'];\n","};\n","\n","mpl.figure.prototype.handle_draw = function (fig, _msg) {\n"," // Request the server to send over a new figure.\n"," fig.send_draw_message();\n","};\n","\n","mpl.figure.prototype.handle_image_mode = function (fig, msg) {\n"," fig.image_mode = msg['mode'];\n","};\n","\n","mpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n"," for (var key in msg) {\n"," if (!(key in fig.buttons)) {\n"," continue;\n"," }\n"," fig.buttons[key].disabled = !msg[key];\n"," fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n"," }\n","};\n","\n","mpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n"," if (msg['mode'] === 'PAN') {\n"," fig.buttons['Pan'].classList.add('active');\n"," fig.buttons['Zoom'].classList.remove('active');\n"," } else if (msg['mode'] === 'ZOOM') {\n"," fig.buttons['Pan'].classList.remove('active');\n"," fig.buttons['Zoom'].classList.add('active');\n"," } else {\n"," fig.buttons['Pan'].classList.remove('active');\n"," fig.buttons['Zoom'].classList.remove('active');\n"," }\n","};\n","\n","mpl.figure.prototype.updated_canvas_event = function () {\n"," // Called whenever the canvas gets updated.\n"," this.send_message('ack', {});\n","};\n","\n","// A function to construct a web socket function for onmessage handling.\n","// Called in the figure constructor.\n","mpl.figure.prototype._make_on_message_function = function (fig) {\n"," return function socket_on_message(evt) {\n"," if (evt.data instanceof Blob) {\n"," /* FIXME: We get \"Resource interpreted as Image but\n"," * transferred with MIME type text/plain:\" errors on\n"," * Chrome. But how to set the MIME type? It doesn't seem\n"," * to be part of the websocket stream */\n"," evt.data.type = 'image/png';\n","\n"," /* Free the memory for the previous frames */\n"," if (fig.imageObj.src) {\n"," (window.URL || window.webkitURL).revokeObjectURL(\n"," fig.imageObj.src\n"," );\n"," }\n","\n"," fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n"," evt.data\n"," );\n"," fig.updated_canvas_event();\n"," fig.waiting = false;\n"," return;\n"," } else if (\n"," typeof evt.data === 'string' &&\n"," evt.data.slice(0, 21) === 'data:image/png;base64'\n"," ) {\n"," fig.imageObj.src = evt.data;\n"," fig.updated_canvas_event();\n"," fig.waiting = false;\n"," return;\n"," }\n","\n"," var msg = JSON.parse(evt.data);\n"," var msg_type = msg['type'];\n","\n"," // Call the \"handle_{type}\" callback, which takes\n"," // the figure and JSON message as its only arguments.\n"," try {\n"," var callback = fig['handle_' + msg_type];\n"," } catch (e) {\n"," console.log(\n"," \"No handler for the '\" + msg_type + \"' message type: \",\n"," msg\n"," );\n"," return;\n"," }\n","\n"," if (callback) {\n"," try {\n"," // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n"," callback(fig, msg);\n"," } catch (e) {\n"," console.log(\n"," \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n"," e,\n"," e.stack,\n"," msg\n"," );\n"," }\n"," }\n"," };\n","};\n","\n","// from http://stackoverflow.com/questions/1114465/getting-mouse-location-in-canvas\n","mpl.findpos = function (e) {\n"," //this section is from http://www.quirksmode.org/js/events_properties.html\n"," var targ;\n"," if (!e) {\n"," e = window.event;\n"," }\n"," if (e.target) {\n"," targ = e.target;\n"," } else if (e.srcElement) {\n"," targ = e.srcElement;\n"," }\n"," if (targ.nodeType === 3) {\n"," // defeat Safari bug\n"," targ = targ.parentNode;\n"," }\n","\n"," // pageX,Y are the mouse positions relative to the document\n"," var boundingRect = targ.getBoundingClientRect();\n"," var x = e.pageX - (boundingRect.left + document.body.scrollLeft);\n"," var y = e.pageY - (boundingRect.top + document.body.scrollTop);\n","\n"," return { x: x, y: y };\n","};\n","\n","/*\n"," * return a copy of an object with only non-object keys\n"," * we need this to avoid circular references\n"," * http://stackoverflow.com/a/24161582/3208463\n"," */\n","function simpleKeys(original) {\n"," return Object.keys(original).reduce(function (obj, key) {\n"," if (typeof original[key] !== 'object') {\n"," obj[key] = original[key];\n"," }\n"," return obj;\n"," }, {});\n","}\n","\n","mpl.figure.prototype.mouse_event = function (event, name) {\n"," var canvas_pos = mpl.findpos(event);\n","\n"," if (name === 'button_press') {\n"," this.canvas.focus();\n"," this.canvas_div.focus();\n"," }\n","\n"," var x = canvas_pos.x * this.ratio;\n"," var y = canvas_pos.y * this.ratio;\n","\n"," this.send_message(name, {\n"," x: x,\n"," y: y,\n"," button: event.button,\n"," step: event.step,\n"," guiEvent: simpleKeys(event),\n"," });\n","\n"," /* This prevents the web browser from automatically changing to\n"," * the text insertion cursor when the button is pressed. We want\n"," * to control all of the cursor setting manually through the\n"," * 'cursor' event from matplotlib */\n"," event.preventDefault();\n"," return false;\n","};\n","\n","mpl.figure.prototype._key_event_extra = function (_event, _name) {\n"," // Handle any extra behaviour associated with a key event\n","};\n","\n","mpl.figure.prototype.key_event = function (event, name) {\n"," // Prevent repeat events\n"," if (name === 'key_press') {\n"," if (event.which === this._key) {\n"," return;\n"," } else {\n"," this._key = event.which;\n"," }\n"," }\n"," if (name === 'key_release') {\n"," this._key = null;\n"," }\n","\n"," var value = '';\n"," if (event.ctrlKey && event.which !== 17) {\n"," value += 'ctrl+';\n"," }\n"," if (event.altKey && event.which !== 18) {\n"," value += 'alt+';\n"," }\n"," if (event.shiftKey && event.which !== 16) {\n"," value += 'shift+';\n"," }\n","\n"," value += 'k';\n"," value += event.which.toString();\n","\n"," this._key_event_extra(event, name);\n","\n"," this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n"," return false;\n","};\n","\n","mpl.figure.prototype.toolbar_button_onclick = function (name) {\n"," if (name === 'download') {\n"," this.handle_save(this, null);\n"," } else {\n"," this.send_message('toolbar_button', { name: name });\n"," }\n","};\n","\n","mpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n"," this.message.textContent = tooltip;\n","};\n","\n","///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n","// prettier-ignore\n","var _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\n","mpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home icon-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left icon-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right icon-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows icon-move\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-square-o icon-check-empty\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o icon-save\", \"download\"]];\n","\n","mpl.extensions = [\"eps\", \"jpeg\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\"];\n","\n","mpl.default_extension = \"png\";/* global mpl */\n","\n","var comm_websocket_adapter = function (comm) {\n"," // Create a \"websocket\"-like object which calls the given IPython comm\n"," // object with the appropriate methods. Currently this is a non binary\n"," // socket, so there is still some room for performance tuning.\n"," var ws = {};\n","\n"," ws.close = function () {\n"," comm.close();\n"," };\n"," ws.send = function (m) {\n"," //console.log('sending', m);\n"," comm.send(m);\n"," };\n"," // Register the callback with on_msg.\n"," comm.on_msg(function (msg) {\n"," //console.log('receiving', msg['content']['data'], msg);\n"," // Pass the mpl event to the overridden (by mpl) onmessage function.\n"," ws.onmessage(msg['content']['data']);\n"," });\n"," return ws;\n","};\n","\n","mpl.mpl_figure_comm = function (comm, msg) {\n"," // This is the function which gets called when the mpl process\n"," // starts-up an IPython Comm through the \"matplotlib\" channel.\n","\n"," var id = msg.content.data.id;\n"," // Get hold of the div created by the display call when the Comm\n"," // socket was opened in Python.\n"," var element = document.getElementById(id);\n"," var ws_proxy = comm_websocket_adapter(comm);\n","\n"," function ondownload(figure, _format) {\n"," window.open(figure.canvas.toDataURL());\n"," }\n","\n"," var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n","\n"," // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n"," // web socket which is closed, not our websocket->open comm proxy.\n"," ws_proxy.onopen();\n","\n"," fig.parent_element = element;\n"," fig.cell_info = mpl.find_output_cell(\"
\");\n"," if (!fig.cell_info) {\n"," console.error('Failed to find cell for figure', id, fig);\n"," return;\n"," }\n"," fig.cell_info[0].output_area.element.on(\n"," 'cleared',\n"," { fig: fig },\n"," fig._remove_fig_handler\n"," );\n","};\n","\n","mpl.figure.prototype.handle_close = function (fig, msg) {\n"," var width = fig.canvas.width / fig.ratio;\n"," fig.cell_info[0].output_area.element.off(\n"," 'cleared',\n"," fig._remove_fig_handler\n"," );\n"," fig.resizeObserverInstance.unobserve(fig.canvas_div);\n","\n"," // Update the output cell to use the data from the current canvas.\n"," fig.push_to_output();\n"," var dataURL = fig.canvas.toDataURL();\n"," // Re-enable the keyboard manager in IPython - without this line, in FF,\n"," // the notebook keyboard shortcuts fail.\n"," IPython.keyboard_manager.enable();\n"," fig.parent_element.innerHTML =\n"," '';\n"," fig.close_ws(fig, msg);\n","};\n","\n","mpl.figure.prototype.close_ws = function (fig, msg) {\n"," fig.send_message('closing', msg);\n"," // fig.ws.close()\n","};\n","\n","mpl.figure.prototype.push_to_output = function (_remove_interactive) {\n"," // Turn the data on the canvas into data in the output cell.\n"," var width = this.canvas.width / this.ratio;\n"," var dataURL = this.canvas.toDataURL();\n"," this.cell_info[1]['text/html'] =\n"," '';\n","};\n","\n","mpl.figure.prototype.updated_canvas_event = function () {\n"," // Tell IPython that the notebook contents must change.\n"," IPython.notebook.set_dirty(true);\n"," this.send_message('ack', {});\n"," var fig = this;\n"," // Wait a second, then push the new image to the DOM so\n"," // that it is saved nicely (might be nice to debounce this).\n"," setTimeout(function () {\n"," fig.push_to_output();\n"," }, 1000);\n","};\n","\n","mpl.figure.prototype._init_toolbar = function () {\n"," var fig = this;\n","\n"," var toolbar = document.createElement('div');\n"," toolbar.classList = 'btn-toolbar';\n"," this.root.appendChild(toolbar);\n","\n"," function on_click_closure(name) {\n"," return function (_event) {\n"," return fig.toolbar_button_onclick(name);\n"," };\n"," }\n","\n"," function on_mouseover_closure(tooltip) {\n"," return function (event) {\n"," if (!event.currentTarget.disabled) {\n"," return fig.toolbar_button_onmouseover(tooltip);\n"," }\n"," };\n"," }\n","\n"," fig.buttons = {};\n"," var buttonGroup = document.createElement('div');\n"," buttonGroup.classList = 'btn-group';\n"," var button;\n"," for (var toolbar_ind in mpl.toolbar_items) {\n"," var name = mpl.toolbar_items[toolbar_ind][0];\n"," var tooltip = mpl.toolbar_items[toolbar_ind][1];\n"," var image = mpl.toolbar_items[toolbar_ind][2];\n"," var method_name = mpl.toolbar_items[toolbar_ind][3];\n","\n"," if (!name) {\n"," /* Instead of a spacer, we start a new button group. */\n"," if (buttonGroup.hasChildNodes()) {\n"," toolbar.appendChild(buttonGroup);\n"," }\n"," buttonGroup = document.createElement('div');\n"," buttonGroup.classList = 'btn-group';\n"," continue;\n"," }\n","\n"," button = fig.buttons[name] = document.createElement('button');\n"," button.classList = 'btn btn-default';\n"," button.href = '#';\n"," button.title = name;\n"," button.innerHTML = '';\n"," button.addEventListener('click', on_click_closure(method_name));\n"," button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n"," buttonGroup.appendChild(button);\n"," }\n","\n"," if (buttonGroup.hasChildNodes()) {\n"," toolbar.appendChild(buttonGroup);\n"," }\n","\n"," // Add the status bar.\n"," var status_bar = document.createElement('span');\n"," status_bar.classList = 'mpl-message pull-right';\n"," toolbar.appendChild(status_bar);\n"," this.message = status_bar;\n","\n"," // Add the close button to the window.\n"," var buttongrp = document.createElement('div');\n"," buttongrp.classList = 'btn-group inline pull-right';\n"," button = document.createElement('button');\n"," button.classList = 'btn btn-mini btn-primary';\n"," button.href = '#';\n"," button.title = 'Stop Interaction';\n"," button.innerHTML = '';\n"," button.addEventListener('click', function (_evt) {\n"," fig.handle_close(fig, {});\n"," });\n"," button.addEventListener(\n"," 'mouseover',\n"," on_mouseover_closure('Stop Interaction')\n"," );\n"," buttongrp.appendChild(button);\n"," var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n"," titlebar.insertBefore(buttongrp, titlebar.firstChild);\n","};\n","\n","mpl.figure.prototype._remove_fig_handler = function (event) {\n"," var fig = event.data.fig;\n"," if (event.target !== this) {\n"," // Ignore bubbled events from children.\n"," return;\n"," }\n"," fig.close_ws(fig, {});\n","};\n","\n","mpl.figure.prototype._root_extra_style = function (el) {\n"," el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n","};\n","\n","mpl.figure.prototype._canvas_extra_style = function (el) {\n"," // this is important to make the div 'focusable\n"," el.setAttribute('tabindex', 0);\n"," // reach out to IPython and tell the keyboard manager to turn it's self\n"," // off when our div gets focus\n","\n"," // location in version 3\n"," if (IPython.notebook.keyboard_manager) {\n"," IPython.notebook.keyboard_manager.register_events(el);\n"," } else {\n"," // location in version 2\n"," IPython.keyboard_manager.register_events(el);\n"," }\n","};\n","\n","mpl.figure.prototype._key_event_extra = function (event, _name) {\n"," var manager = IPython.notebook.keyboard_manager;\n"," if (!manager) {\n"," manager = IPython.keyboard_manager;\n"," }\n","\n"," // Check for shift+enter\n"," if (event.shiftKey && event.which === 13) {\n"," this.canvas_div.blur();\n"," // select the cell after this one\n"," var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n"," IPython.notebook.select(index + 1);\n"," }\n","};\n","\n","mpl.figure.prototype.handle_save = function (fig, _msg) {\n"," fig.ondownload(fig, null);\n","};\n","\n","mpl.find_output_cell = function (html_output) {\n"," // Return the cell and output element which can be found *uniquely* in the notebook.\n"," // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n"," // IPython event is triggered only after the cells have been serialised, which for\n"," // our purposes (turning an active figure into a static one), is too late.\n"," var cells = IPython.notebook.get_cells();\n"," var ncells = cells.length;\n"," for (var i = 0; i < ncells; i++) {\n"," var cell = cells[i];\n"," if (cell.cell_type === 'code') {\n"," for (var j = 0; j < cell.output_area.outputs.length; j++) {\n"," var data = cell.output_area.outputs[j];\n"," if (data.data) {\n"," // IPython >= 3 moved mimebundle to data attribute of output\n"," data = data.data;\n"," }\n"," if (data['text/html'] === html_output) {\n"," return [cell, data, j];\n"," }\n"," }\n"," }\n"," }\n","};\n","\n","// Register the function which deals with the matplotlib target/channel.\n","// The kernel may be null if the page has been refreshed.\n","if (IPython.notebook.kernel !== null) {\n"," IPython.notebook.kernel.comm_manager.register_target(\n"," 'matplotlib',\n"," mpl.mpl_figure_comm\n"," );\n","}\n"],"text/plain":[""]},"metadata":{},"output_type":"display_data"},{"data":{"text/html":[""],"text/plain":[""]},"metadata":{},"output_type":"display_data"},{"data":{"application/vnd.jupyter.widget-view+json":{"model_id":"6d7bc03497a54ae8a9d9759b01f10d0d","version_major":2,"version_minor":0},"text/plain":["Button(description='Clear all', style=ButtonStyle())"]},"metadata":{},"output_type":"display_data"},{"data":{"application/vnd.jupyter.widget-view+json":{"model_id":"ffbcacb3d05e4a0595e9c2ce041b13c2","version_major":2,"version_minor":0},"text/plain":["Button(description='Submit', style=ButtonStyle())"]},"metadata":{},"output_type":"display_data"},{"data":{"application/vnd.jupyter.widget-view+json":{"model_id":"3f3642ccc85146dcb85af47a540906e2","version_major":2,"version_minor":0},"text/plain":["IntSlider(value=0, max=10, min=-1)"]},"metadata":{},"output_type":"display_data"},{"data":{"application/vnd.jupyter.widget-view+json":{"model_id":"ce21f6cc6f03467eb7b8a2f0d2e489c3","version_major":2,"version_minor":0},"text/plain":["Dropdown(description='Species plot 1', options={'A': 0, 'B': 1}, value=0)"]},"metadata":{},"output_type":"display_data"},{"data":{"application/vnd.jupyter.widget-view+json":{"model_id":"f4fd2c9c572147d683f08cb972e1b3c4","version_major":2,"version_minor":0},"text/plain":["Dropdown(description='Species plot 2', index=1, options={'A': 0, 'B': 1}, value=1)"]},"metadata":{},"output_type":"display_data"},{"data":{"text/html":["
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alpha1alpha2betagammamu
011.44144111.4414412.9009014.8388392.469469
114.56456514.5645653.6056064.2862862.583584
215.72572612.5025035.4674673.4734731.782783
326.57657723.3533532.3923925.0110111.590591
419.62963022.8528534.5905915.9439442.837838
..................
49512.84284312.8428435.5355362.3043042.393393
49626.37637628.7587595.0430432.4164161.520521
49711.52152213.1231234.2662664.9349352.515516
49815.14514515.1451454.0340343.2052051.088088
49927.41741724.1941945.2112112.5845852.845846
\n","

500 rows × 5 columns

\n","
"],"text/plain":[" alpha1 alpha2 beta gamma mu\n","0 11.441441 11.441441 2.900901 4.838839 2.469469\n","1 14.564565 14.564565 3.605606 4.286286 2.583584\n","2 15.725726 12.502503 5.467467 3.473473 1.782783\n","3 26.576577 23.353353 2.392392 5.011011 1.590591\n","4 19.629630 22.852853 4.590591 5.943944 2.837838\n",".. ... ... ... ... ...\n","495 12.842843 12.842843 5.535536 2.304304 2.393393\n","496 26.376376 28.758759 5.043043 2.416416 1.520521\n","497 11.521522 13.123123 4.266266 4.934935 2.515516\n","498 15.145145 15.145145 4.034034 3.205205 1.088088\n","499 27.417417 24.194194 5.211211 2.584585 2.845846\n","\n","[500 rows x 5 columns]"]},"metadata":{},"output_type":"display_data"}],"source":["# Here we use UMAP for dimension reduction\n","met.explore(dr_method='umap')"]},{"cell_type":"code","execution_count":14,"metadata":{},"outputs":[{"name":"stdout","output_type":"stream","text":["basinhopping step 0: f 0.0001\n","basinhopping step 1: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 2: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 3: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 4: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 5: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 6: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 7: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 8: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 9: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 10: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 11: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 12: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 13: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 14: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 15: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 16: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 17: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 18: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 19: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 20: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 21: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 22: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 23: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 24: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 25: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 26: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 27: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 28: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 29: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 30: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 31: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 32: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 33: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 34: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 35: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 36: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 37: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 38: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 39: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 40: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 41: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 42: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 43: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 44: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 45: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 46: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 47: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 48: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","basinhopping step 49: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n","adaptive stepsize: acceptance rate 0.980000 target 0.500000 new stepsize 0.111111 old stepsize 0.1\n","basinhopping step 50: f 0.0001 trial_f 0.0001 accepted 1 lowest_f 0.0001\n"]}],"source":["from sciope.models.label_propagation import LPModel\n","# here lets use the dimension reduction embedding as input data\n","data = met.dr_model.embedding_\n","\n","model_lp = LPModel()\n","# train using basinhopping\n","model_lp.train(data, met.data.user_labels, min_=0.01, max_=10, niter=50)"]},{"cell_type":"code","execution_count":15,"metadata":{},"outputs":[],"source":["# just to vislualize the result we will map the label distribution to the user_labels\n","# (will enable us to see the LP model output when using method 'explore')\n","user_labels = np.copy(met.data.user_labels)\n","# takes the label corresponding to index 0\n","met.data.user_labels = model_lp.model.label_distributions_[:, 0]"]},{"cell_type":"code","execution_count":16,"metadata":{},"outputs":[{"data":{"application/javascript":["/* Put everything inside the global mpl namespace */\n","/* global mpl */\n","window.mpl = {};\n","\n","mpl.get_websocket_type = function () {\n"," if (typeof WebSocket !== 'undefined') {\n"," return WebSocket;\n"," } else if (typeof MozWebSocket !== 'undefined') {\n"," return MozWebSocket;\n"," } else {\n"," alert(\n"," 'Your browser does not have WebSocket support. ' +\n"," 'Please try Chrome, Safari or Firefox ≥ 6. ' +\n"," 'Firefox 4 and 5 are also supported but you ' +\n"," 'have to enable WebSockets in about:config.'\n"," );\n"," }\n","};\n","\n","mpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n"," this.id = figure_id;\n","\n"," this.ws = websocket;\n","\n"," this.supports_binary = this.ws.binaryType !== undefined;\n","\n"," if (!this.supports_binary) {\n"," var warnings = document.getElementById('mpl-warnings');\n"," if (warnings) {\n"," warnings.style.display = 'block';\n"," warnings.textContent =\n"," 'This browser does not support binary websocket messages. ' +\n"," 'Performance may be slow.';\n"," }\n"," }\n","\n"," this.imageObj = new Image();\n","\n"," this.context = undefined;\n"," this.message = undefined;\n"," this.canvas = undefined;\n"," this.rubberband_canvas = undefined;\n"," this.rubberband_context = undefined;\n"," this.format_dropdown = undefined;\n","\n"," this.image_mode = 'full';\n","\n"," this.root = document.createElement('div');\n"," this.root.setAttribute('style', 'display: inline-block');\n"," this._root_extra_style(this.root);\n","\n"," parent_element.appendChild(this.root);\n","\n"," this._init_header(this);\n"," this._init_canvas(this);\n"," this._init_toolbar(this);\n","\n"," var fig = this;\n","\n"," this.waiting = false;\n","\n"," this.ws.onopen = function () {\n"," fig.send_message('supports_binary', { value: fig.supports_binary });\n"," fig.send_message('send_image_mode', {});\n"," if (fig.ratio !== 1) {\n"," fig.send_message('set_dpi_ratio', { dpi_ratio: fig.ratio });\n"," }\n"," fig.send_message('refresh', {});\n"," };\n","\n"," this.imageObj.onload = function () {\n"," if (fig.image_mode === 'full') {\n"," // Full images could contain transparency (where diff images\n"," // almost always do), so we need to clear the canvas so that\n"," // there is no ghosting.\n"," fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n"," }\n"," fig.context.drawImage(fig.imageObj, 0, 0);\n"," };\n","\n"," this.imageObj.onunload = function () {\n"," fig.ws.close();\n"," };\n","\n"," this.ws.onmessage = this._make_on_message_function(this);\n","\n"," this.ondownload = ondownload;\n","};\n","\n","mpl.figure.prototype._init_header = function () {\n"," var titlebar = document.createElement('div');\n"," titlebar.classList =\n"," 'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n"," var titletext = document.createElement('div');\n"," titletext.classList = 'ui-dialog-title';\n"," titletext.setAttribute(\n"," 'style',\n"," 'width: 100%; text-align: center; padding: 3px;'\n"," );\n"," titlebar.appendChild(titletext);\n"," this.root.appendChild(titlebar);\n"," this.header = titletext;\n","};\n","\n","mpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n","\n","mpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n","\n","mpl.figure.prototype._init_canvas = function () {\n"," var fig = this;\n","\n"," var canvas_div = (this.canvas_div = document.createElement('div'));\n"," canvas_div.setAttribute(\n"," 'style',\n"," 'border: 1px solid #ddd;' +\n"," 'box-sizing: content-box;' +\n"," 'clear: both;' +\n"," 'min-height: 1px;' +\n"," 'min-width: 1px;' +\n"," 'outline: 0;' +\n"," 'overflow: hidden;' +\n"," 'position: relative;' +\n"," 'resize: both;'\n"," );\n","\n"," function on_keyboard_event_closure(name) {\n"," return function (event) {\n"," return fig.key_event(event, name);\n"," };\n"," }\n","\n"," canvas_div.addEventListener(\n"," 'keydown',\n"," on_keyboard_event_closure('key_press')\n"," );\n"," canvas_div.addEventListener(\n"," 'keyup',\n"," on_keyboard_event_closure('key_release')\n"," );\n","\n"," this._canvas_extra_style(canvas_div);\n"," this.root.appendChild(canvas_div);\n","\n"," var canvas = (this.canvas = document.createElement('canvas'));\n"," canvas.classList.add('mpl-canvas');\n"," canvas.setAttribute('style', 'box-sizing: content-box;');\n","\n"," this.context = canvas.getContext('2d');\n","\n"," var backingStore =\n"," this.context.backingStorePixelRatio ||\n"," this.context.webkitBackingStorePixelRatio ||\n"," this.context.mozBackingStorePixelRatio ||\n"," this.context.msBackingStorePixelRatio ||\n"," this.context.oBackingStorePixelRatio ||\n"," this.context.backingStorePixelRatio ||\n"," 1;\n","\n"," this.ratio = (window.devicePixelRatio || 1) / backingStore;\n","\n"," var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n"," 'canvas'\n"," ));\n"," rubberband_canvas.setAttribute(\n"," 'style',\n"," 'box-sizing: content-box; position: absolute; left: 0; top: 0; z-index: 1;'\n"," );\n","\n"," // Apply a ponyfill if ResizeObserver is not implemented by browser.\n"," if (this.ResizeObserver === undefined) {\n"," if (window.ResizeObserver !== undefined) {\n"," this.ResizeObserver = window.ResizeObserver;\n"," } else {\n"," var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n"," this.ResizeObserver = obs.ResizeObserver;\n"," }\n"," }\n","\n"," this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n"," var nentries = entries.length;\n"," for (var i = 0; i < nentries; i++) {\n"," var entry = entries[i];\n"," var width, height;\n"," if (entry.contentBoxSize) {\n"," if (entry.contentBoxSize instanceof Array) {\n"," // Chrome 84 implements new version of spec.\n"," width = entry.contentBoxSize[0].inlineSize;\n"," height = entry.contentBoxSize[0].blockSize;\n"," } else {\n"," // Firefox implements old version of spec.\n"," width = entry.contentBoxSize.inlineSize;\n"," height = entry.contentBoxSize.blockSize;\n"," }\n"," } else {\n"," // Chrome <84 implements even older version of spec.\n"," width = entry.contentRect.width;\n"," height = entry.contentRect.height;\n"," }\n","\n"," // Keep the size of the canvas and rubber band canvas in sync with\n"," // the canvas container.\n"," if (entry.devicePixelContentBoxSize) {\n"," // Chrome 84 implements new version of spec.\n"," canvas.setAttribute(\n"," 'width',\n"," entry.devicePixelContentBoxSize[0].inlineSize\n"," );\n"," canvas.setAttribute(\n"," 'height',\n"," entry.devicePixelContentBoxSize[0].blockSize\n"," );\n"," } else {\n"," canvas.setAttribute('width', width * fig.ratio);\n"," canvas.setAttribute('height', height * fig.ratio);\n"," }\n"," canvas.setAttribute(\n"," 'style',\n"," 'width: ' + width + 'px; height: ' + height + 'px;'\n"," );\n","\n"," rubberband_canvas.setAttribute('width', width);\n"," rubberband_canvas.setAttribute('height', height);\n","\n"," // And update the size in Python. We ignore the initial 0/0 size\n"," // that occurs as the element is placed into the DOM, which should\n"," // otherwise not happen due to the minimum size styling.\n"," if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n"," fig.request_resize(width, height);\n"," }\n"," }\n"," });\n"," this.resizeObserverInstance.observe(canvas_div);\n","\n"," function on_mouse_event_closure(name) {\n"," return function (event) {\n"," return fig.mouse_event(event, name);\n"," };\n"," }\n","\n"," rubberband_canvas.addEventListener(\n"," 'mousedown',\n"," on_mouse_event_closure('button_press')\n"," );\n"," rubberband_canvas.addEventListener(\n"," 'mouseup',\n"," on_mouse_event_closure('button_release')\n"," );\n"," // Throttle sequential mouse events to 1 every 20ms.\n"," rubberband_canvas.addEventListener(\n"," 'mousemove',\n"," on_mouse_event_closure('motion_notify')\n"," );\n","\n"," rubberband_canvas.addEventListener(\n"," 'mouseenter',\n"," on_mouse_event_closure('figure_enter')\n"," );\n"," rubberband_canvas.addEventListener(\n"," 'mouseleave',\n"," on_mouse_event_closure('figure_leave')\n"," );\n","\n"," canvas_div.addEventListener('wheel', function (event) {\n"," if (event.deltaY < 0) {\n"," event.step = 1;\n"," } else {\n"," event.step = -1;\n"," }\n"," on_mouse_event_closure('scroll')(event);\n"," });\n","\n"," canvas_div.appendChild(canvas);\n"," canvas_div.appendChild(rubberband_canvas);\n","\n"," this.rubberband_context = rubberband_canvas.getContext('2d');\n"," this.rubberband_context.strokeStyle = '#000000';\n","\n"," this._resize_canvas = function (width, height, forward) {\n"," if (forward) {\n"," canvas_div.style.width = width + 'px';\n"," canvas_div.style.height = height + 'px';\n"," }\n"," };\n","\n"," // Disable right mouse context menu.\n"," this.rubberband_canvas.addEventListener('contextmenu', function (_e) {\n"," event.preventDefault();\n"," return false;\n"," });\n","\n"," function set_focus() {\n"," canvas.focus();\n"," canvas_div.focus();\n"," }\n","\n"," window.setTimeout(set_focus, 100);\n","};\n","\n","mpl.figure.prototype._init_toolbar = function () {\n"," var fig = this;\n","\n"," var toolbar = document.createElement('div');\n"," toolbar.classList = 'mpl-toolbar';\n"," this.root.appendChild(toolbar);\n","\n"," function on_click_closure(name) {\n"," return function (_event) {\n"," return fig.toolbar_button_onclick(name);\n"," };\n"," }\n","\n"," function on_mouseover_closure(tooltip) {\n"," return function (event) {\n"," if (!event.currentTarget.disabled) {\n"," return fig.toolbar_button_onmouseover(tooltip);\n"," }\n"," };\n"," }\n","\n"," fig.buttons = {};\n"," var buttonGroup = document.createElement('div');\n"," buttonGroup.classList = 'mpl-button-group';\n"," for (var toolbar_ind in mpl.toolbar_items) {\n"," var name = mpl.toolbar_items[toolbar_ind][0];\n"," var tooltip = mpl.toolbar_items[toolbar_ind][1];\n"," var image = mpl.toolbar_items[toolbar_ind][2];\n"," var method_name = mpl.toolbar_items[toolbar_ind][3];\n","\n"," if (!name) {\n"," /* Instead of a spacer, we start a new button group. */\n"," if (buttonGroup.hasChildNodes()) {\n"," toolbar.appendChild(buttonGroup);\n"," }\n"," buttonGroup = document.createElement('div');\n"," buttonGroup.classList = 'mpl-button-group';\n"," continue;\n"," }\n","\n"," var button = (fig.buttons[name] = document.createElement('button'));\n"," button.classList = 'mpl-widget';\n"," button.setAttribute('role', 'button');\n"," button.setAttribute('aria-disabled', 'false');\n"," button.addEventListener('click', on_click_closure(method_name));\n"," button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n","\n"," var icon_img = document.createElement('img');\n"," icon_img.src = '_images/' + image + '.png';\n"," icon_img.srcset = '_images/' + image + '_large.png 2x';\n"," icon_img.alt = tooltip;\n"," button.appendChild(icon_img);\n","\n"," buttonGroup.appendChild(button);\n"," }\n","\n"," if (buttonGroup.hasChildNodes()) {\n"," toolbar.appendChild(buttonGroup);\n"," }\n","\n"," var fmt_picker = document.createElement('select');\n"," fmt_picker.classList = 'mpl-widget';\n"," toolbar.appendChild(fmt_picker);\n"," this.format_dropdown = fmt_picker;\n","\n"," for (var ind in mpl.extensions) {\n"," var fmt = mpl.extensions[ind];\n"," var option = document.createElement('option');\n"," option.selected = fmt === mpl.default_extension;\n"," option.innerHTML = fmt;\n"," fmt_picker.appendChild(option);\n"," }\n","\n"," var status_bar = document.createElement('span');\n"," status_bar.classList = 'mpl-message';\n"," toolbar.appendChild(status_bar);\n"," this.message = status_bar;\n","};\n","\n","mpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n"," // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n"," // which will in turn request a refresh of the image.\n"," this.send_message('resize', { width: x_pixels, height: y_pixels });\n","};\n","\n","mpl.figure.prototype.send_message = function (type, properties) {\n"," properties['type'] = type;\n"," properties['figure_id'] = this.id;\n"," this.ws.send(JSON.stringify(properties));\n","};\n","\n","mpl.figure.prototype.send_draw_message = function () {\n"," if (!this.waiting) {\n"," this.waiting = true;\n"," this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n"," }\n","};\n","\n","mpl.figure.prototype.handle_save = function (fig, _msg) {\n"," var format_dropdown = fig.format_dropdown;\n"," var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n"," fig.ondownload(fig, format);\n","};\n","\n","mpl.figure.prototype.handle_resize = function (fig, msg) {\n"," var size = msg['size'];\n"," if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n"," fig._resize_canvas(size[0], size[1], msg['forward']);\n"," fig.send_message('refresh', {});\n"," }\n","};\n","\n","mpl.figure.prototype.handle_rubberband = function (fig, msg) {\n"," var x0 = msg['x0'] / fig.ratio;\n"," var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n"," var x1 = msg['x1'] / fig.ratio;\n"," var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n"," x0 = Math.floor(x0) + 0.5;\n"," y0 = Math.floor(y0) + 0.5;\n"," x1 = Math.floor(x1) + 0.5;\n"," y1 = Math.floor(y1) + 0.5;\n"," var min_x = Math.min(x0, x1);\n"," var min_y = Math.min(y0, y1);\n"," var width = Math.abs(x1 - x0);\n"," var height = Math.abs(y1 - y0);\n","\n"," fig.rubberband_context.clearRect(\n"," 0,\n"," 0,\n"," fig.canvas.width / fig.ratio,\n"," fig.canvas.height / fig.ratio\n"," );\n","\n"," fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n","};\n","\n","mpl.figure.prototype.handle_figure_label = function (fig, msg) {\n"," // Updates the figure title.\n"," fig.header.textContent = msg['label'];\n","};\n","\n","mpl.figure.prototype.handle_cursor = function (fig, msg) {\n"," var cursor = msg['cursor'];\n"," switch (cursor) {\n"," case 0:\n"," cursor = 'pointer';\n"," break;\n"," case 1:\n"," cursor = 'default';\n"," break;\n"," case 2:\n"," cursor = 'crosshair';\n"," break;\n"," case 3:\n"," cursor = 'move';\n"," break;\n"," }\n"," fig.rubberband_canvas.style.cursor = cursor;\n","};\n","\n","mpl.figure.prototype.handle_message = function (fig, msg) {\n"," fig.message.textContent = msg['message'];\n","};\n","\n","mpl.figure.prototype.handle_draw = function (fig, _msg) {\n"," // Request the server to send over a new figure.\n"," fig.send_draw_message();\n","};\n","\n","mpl.figure.prototype.handle_image_mode = function (fig, msg) {\n"," fig.image_mode = msg['mode'];\n","};\n","\n","mpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n"," for (var key in msg) {\n"," if (!(key in fig.buttons)) {\n"," continue;\n"," }\n"," fig.buttons[key].disabled = !msg[key];\n"," fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n"," }\n","};\n","\n","mpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n"," if (msg['mode'] === 'PAN') {\n"," fig.buttons['Pan'].classList.add('active');\n"," fig.buttons['Zoom'].classList.remove('active');\n"," } else if (msg['mode'] === 'ZOOM') {\n"," fig.buttons['Pan'].classList.remove('active');\n"," fig.buttons['Zoom'].classList.add('active');\n"," } else {\n"," fig.buttons['Pan'].classList.remove('active');\n"," fig.buttons['Zoom'].classList.remove('active');\n"," }\n","};\n","\n","mpl.figure.prototype.updated_canvas_event = function () {\n"," // Called whenever the canvas gets updated.\n"," this.send_message('ack', {});\n","};\n","\n","// A function to construct a web socket function for onmessage handling.\n","// Called in the figure constructor.\n","mpl.figure.prototype._make_on_message_function = function (fig) {\n"," return function socket_on_message(evt) {\n"," if (evt.data instanceof Blob) {\n"," /* FIXME: We get \"Resource interpreted as Image but\n"," * transferred with MIME type text/plain:\" errors on\n"," * Chrome. But how to set the MIME type? It doesn't seem\n"," * to be part of the websocket stream */\n"," evt.data.type = 'image/png';\n","\n"," /* Free the memory for the previous frames */\n"," if (fig.imageObj.src) {\n"," (window.URL || window.webkitURL).revokeObjectURL(\n"," fig.imageObj.src\n"," );\n"," }\n","\n"," fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n"," evt.data\n"," );\n"," fig.updated_canvas_event();\n"," fig.waiting = false;\n"," return;\n"," } else if (\n"," typeof evt.data === 'string' &&\n"," evt.data.slice(0, 21) === 'data:image/png;base64'\n"," ) {\n"," fig.imageObj.src = evt.data;\n"," fig.updated_canvas_event();\n"," fig.waiting = false;\n"," return;\n"," }\n","\n"," var msg = JSON.parse(evt.data);\n"," var msg_type = msg['type'];\n","\n"," // Call the \"handle_{type}\" callback, which takes\n"," // the figure and JSON message as its only arguments.\n"," try {\n"," var callback = fig['handle_' + msg_type];\n"," } catch (e) {\n"," console.log(\n"," \"No handler for the '\" + msg_type + \"' message type: \",\n"," msg\n"," );\n"," return;\n"," }\n","\n"," if (callback) {\n"," try {\n"," // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n"," callback(fig, msg);\n"," } catch (e) {\n"," console.log(\n"," \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n"," e,\n"," e.stack,\n"," msg\n"," );\n"," }\n"," }\n"," };\n","};\n","\n","// from http://stackoverflow.com/questions/1114465/getting-mouse-location-in-canvas\n","mpl.findpos = function (e) {\n"," //this section is from http://www.quirksmode.org/js/events_properties.html\n"," var targ;\n"," if (!e) {\n"," e = window.event;\n"," }\n"," if (e.target) {\n"," targ = e.target;\n"," } else if (e.srcElement) {\n"," targ = e.srcElement;\n"," }\n"," if (targ.nodeType === 3) {\n"," // defeat Safari bug\n"," targ = targ.parentNode;\n"," }\n","\n"," // pageX,Y are the mouse positions relative to the document\n"," var boundingRect = targ.getBoundingClientRect();\n"," var x = e.pageX - (boundingRect.left + document.body.scrollLeft);\n"," var y = e.pageY - (boundingRect.top + document.body.scrollTop);\n","\n"," return { x: x, y: y };\n","};\n","\n","/*\n"," * return a copy of an object with only non-object keys\n"," * we need this to avoid circular references\n"," * http://stackoverflow.com/a/24161582/3208463\n"," */\n","function simpleKeys(original) {\n"," return Object.keys(original).reduce(function (obj, key) {\n"," if (typeof original[key] !== 'object') {\n"," obj[key] = original[key];\n"," }\n"," return obj;\n"," }, {});\n","}\n","\n","mpl.figure.prototype.mouse_event = function (event, name) {\n"," var canvas_pos = mpl.findpos(event);\n","\n"," if (name === 'button_press') {\n"," this.canvas.focus();\n"," this.canvas_div.focus();\n"," }\n","\n"," var x = canvas_pos.x * this.ratio;\n"," var y = canvas_pos.y * this.ratio;\n","\n"," this.send_message(name, {\n"," x: x,\n"," y: y,\n"," button: event.button,\n"," step: event.step,\n"," guiEvent: simpleKeys(event),\n"," });\n","\n"," /* This prevents the web browser from automatically changing to\n"," * the text insertion cursor when the button is pressed. We want\n"," * to control all of the cursor setting manually through the\n"," * 'cursor' event from matplotlib */\n"," event.preventDefault();\n"," return false;\n","};\n","\n","mpl.figure.prototype._key_event_extra = function (_event, _name) {\n"," // Handle any extra behaviour associated with a key event\n","};\n","\n","mpl.figure.prototype.key_event = function (event, name) {\n"," // Prevent repeat events\n"," if (name === 'key_press') {\n"," if (event.which === this._key) {\n"," return;\n"," } else {\n"," this._key = event.which;\n"," }\n"," }\n"," if (name === 'key_release') {\n"," this._key = null;\n"," }\n","\n"," var value = '';\n"," if (event.ctrlKey && event.which !== 17) {\n"," value += 'ctrl+';\n"," }\n"," if (event.altKey && event.which !== 18) {\n"," value += 'alt+';\n"," }\n"," if (event.shiftKey && event.which !== 16) {\n"," value += 'shift+';\n"," }\n","\n"," value += 'k';\n"," value += event.which.toString();\n","\n"," this._key_event_extra(event, name);\n","\n"," this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n"," return false;\n","};\n","\n","mpl.figure.prototype.toolbar_button_onclick = function (name) {\n"," if (name === 'download') {\n"," this.handle_save(this, null);\n"," } else {\n"," this.send_message('toolbar_button', { name: name });\n"," }\n","};\n","\n","mpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n"," this.message.textContent = tooltip;\n","};\n","\n","///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n","// prettier-ignore\n","var _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\n","mpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home icon-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left icon-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right icon-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows icon-move\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-square-o icon-check-empty\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o icon-save\", \"download\"]];\n","\n","mpl.extensions = [\"eps\", \"jpeg\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\"];\n","\n","mpl.default_extension = \"png\";/* global mpl */\n","\n","var comm_websocket_adapter = function (comm) {\n"," // Create a \"websocket\"-like object which calls the given IPython comm\n"," // object with the appropriate methods. Currently this is a non binary\n"," // socket, so there is still some room for performance tuning.\n"," var ws = {};\n","\n"," ws.close = function () {\n"," comm.close();\n"," };\n"," ws.send = function (m) {\n"," //console.log('sending', m);\n"," comm.send(m);\n"," };\n"," // Register the callback with on_msg.\n"," comm.on_msg(function (msg) {\n"," //console.log('receiving', msg['content']['data'], msg);\n"," // Pass the mpl event to the overridden (by mpl) onmessage function.\n"," ws.onmessage(msg['content']['data']);\n"," });\n"," return ws;\n","};\n","\n","mpl.mpl_figure_comm = function (comm, msg) {\n"," // This is the function which gets called when the mpl process\n"," // starts-up an IPython Comm through the \"matplotlib\" channel.\n","\n"," var id = msg.content.data.id;\n"," // Get hold of the div created by the display call when the Comm\n"," // socket was opened in Python.\n"," var element = document.getElementById(id);\n"," var ws_proxy = comm_websocket_adapter(comm);\n","\n"," function ondownload(figure, _format) {\n"," window.open(figure.canvas.toDataURL());\n"," }\n","\n"," var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n","\n"," // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n"," // web socket which is closed, not our websocket->open comm proxy.\n"," ws_proxy.onopen();\n","\n"," fig.parent_element = element;\n"," fig.cell_info = mpl.find_output_cell(\"
\");\n"," if (!fig.cell_info) {\n"," console.error('Failed to find cell for figure', id, fig);\n"," return;\n"," }\n"," fig.cell_info[0].output_area.element.on(\n"," 'cleared',\n"," { fig: fig },\n"," fig._remove_fig_handler\n"," );\n","};\n","\n","mpl.figure.prototype.handle_close = function (fig, msg) {\n"," var width = fig.canvas.width / fig.ratio;\n"," fig.cell_info[0].output_area.element.off(\n"," 'cleared',\n"," fig._remove_fig_handler\n"," );\n"," fig.resizeObserverInstance.unobserve(fig.canvas_div);\n","\n"," // Update the output cell to use the data from the current canvas.\n"," fig.push_to_output();\n"," var dataURL = fig.canvas.toDataURL();\n"," // Re-enable the keyboard manager in IPython - without this line, in FF,\n"," // the notebook keyboard shortcuts fail.\n"," IPython.keyboard_manager.enable();\n"," fig.parent_element.innerHTML =\n"," '';\n"," fig.close_ws(fig, msg);\n","};\n","\n","mpl.figure.prototype.close_ws = function (fig, msg) {\n"," fig.send_message('closing', msg);\n"," // fig.ws.close()\n","};\n","\n","mpl.figure.prototype.push_to_output = function (_remove_interactive) {\n"," // Turn the data on the canvas into data in the output cell.\n"," var width = this.canvas.width / this.ratio;\n"," var dataURL = this.canvas.toDataURL();\n"," this.cell_info[1]['text/html'] =\n"," '';\n","};\n","\n","mpl.figure.prototype.updated_canvas_event = function () {\n"," // Tell IPython that the notebook contents must change.\n"," IPython.notebook.set_dirty(true);\n"," this.send_message('ack', {});\n"," var fig = this;\n"," // Wait a second, then push the new image to the DOM so\n"," // that it is saved nicely (might be nice to debounce this).\n"," setTimeout(function () {\n"," fig.push_to_output();\n"," }, 1000);\n","};\n","\n","mpl.figure.prototype._init_toolbar = function () {\n"," var fig = this;\n","\n"," var toolbar = document.createElement('div');\n"," toolbar.classList = 'btn-toolbar';\n"," this.root.appendChild(toolbar);\n","\n"," function on_click_closure(name) {\n"," return function (_event) {\n"," return fig.toolbar_button_onclick(name);\n"," };\n"," }\n","\n"," function on_mouseover_closure(tooltip) {\n"," return function (event) {\n"," if (!event.currentTarget.disabled) {\n"," return fig.toolbar_button_onmouseover(tooltip);\n"," }\n"," };\n"," }\n","\n"," fig.buttons = {};\n"," var buttonGroup = document.createElement('div');\n"," buttonGroup.classList = 'btn-group';\n"," var button;\n"," for (var toolbar_ind in mpl.toolbar_items) {\n"," var name = mpl.toolbar_items[toolbar_ind][0];\n"," var tooltip = mpl.toolbar_items[toolbar_ind][1];\n"," var image = mpl.toolbar_items[toolbar_ind][2];\n"," var method_name = mpl.toolbar_items[toolbar_ind][3];\n","\n"," if (!name) {\n"," /* Instead of a spacer, we start a new button group. */\n"," if (buttonGroup.hasChildNodes()) {\n"," toolbar.appendChild(buttonGroup);\n"," }\n"," buttonGroup = document.createElement('div');\n"," buttonGroup.classList = 'btn-group';\n"," continue;\n"," }\n","\n"," button = fig.buttons[name] = document.createElement('button');\n"," button.classList = 'btn btn-default';\n"," button.href = '#';\n"," button.title = name;\n"," button.innerHTML = '';\n"," button.addEventListener('click', on_click_closure(method_name));\n"," button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n"," buttonGroup.appendChild(button);\n"," }\n","\n"," if (buttonGroup.hasChildNodes()) {\n"," toolbar.appendChild(buttonGroup);\n"," }\n","\n"," // Add the status bar.\n"," var status_bar = document.createElement('span');\n"," status_bar.classList = 'mpl-message pull-right';\n"," toolbar.appendChild(status_bar);\n"," this.message = status_bar;\n","\n"," // Add the close button to the window.\n"," var buttongrp = document.createElement('div');\n"," buttongrp.classList = 'btn-group inline pull-right';\n"," button = document.createElement('button');\n"," button.classList = 'btn btn-mini btn-primary';\n"," button.href = '#';\n"," button.title = 'Stop Interaction';\n"," button.innerHTML = '';\n"," button.addEventListener('click', function (_evt) {\n"," fig.handle_close(fig, {});\n"," });\n"," button.addEventListener(\n"," 'mouseover',\n"," on_mouseover_closure('Stop Interaction')\n"," );\n"," buttongrp.appendChild(button);\n"," var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n"," titlebar.insertBefore(buttongrp, titlebar.firstChild);\n","};\n","\n","mpl.figure.prototype._remove_fig_handler = function (event) {\n"," var fig = event.data.fig;\n"," if (event.target !== this) {\n"," // Ignore bubbled events from children.\n"," return;\n"," }\n"," fig.close_ws(fig, {});\n","};\n","\n","mpl.figure.prototype._root_extra_style = function (el) {\n"," el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n","};\n","\n","mpl.figure.prototype._canvas_extra_style = function (el) {\n"," // this is important to make the div 'focusable\n"," el.setAttribute('tabindex', 0);\n"," // reach out to IPython and tell the keyboard manager to turn it's self\n"," // off when our div gets focus\n","\n"," // location in version 3\n"," if (IPython.notebook.keyboard_manager) {\n"," IPython.notebook.keyboard_manager.register_events(el);\n"," } else {\n"," // location in version 2\n"," IPython.keyboard_manager.register_events(el);\n"," }\n","};\n","\n","mpl.figure.prototype._key_event_extra = function (event, _name) {\n"," var manager = IPython.notebook.keyboard_manager;\n"," if (!manager) {\n"," manager = IPython.keyboard_manager;\n"," }\n","\n"," // Check for shift+enter\n"," if (event.shiftKey && event.which === 13) {\n"," this.canvas_div.blur();\n"," // select the cell after this one\n"," var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n"," IPython.notebook.select(index + 1);\n"," }\n","};\n","\n","mpl.figure.prototype.handle_save = function (fig, _msg) {\n"," fig.ondownload(fig, null);\n","};\n","\n","mpl.find_output_cell = function (html_output) {\n"," // Return the cell and output element which can be found *uniquely* in the notebook.\n"," // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n"," // IPython event is triggered only after the cells have been serialised, which for\n"," // our purposes (turning an active figure into a static one), is too late.\n"," var cells = IPython.notebook.get_cells();\n"," var ncells = cells.length;\n"," for (var i = 0; i < ncells; i++) {\n"," var cell = cells[i];\n"," if (cell.cell_type === 'code') {\n"," for (var j = 0; j < cell.output_area.outputs.length; j++) {\n"," var data = cell.output_area.outputs[j];\n"," if (data.data) {\n"," // IPython >= 3 moved mimebundle to data attribute of output\n"," data = data.data;\n"," }\n"," if (data['text/html'] === html_output) {\n"," return [cell, data, j];\n"," }\n"," }\n"," }\n"," }\n","};\n","\n","// Register the function which deals with the matplotlib target/channel.\n","// The kernel may be null if the page has been refreshed.\n","if (IPython.notebook.kernel !== null) {\n"," IPython.notebook.kernel.comm_manager.register_target(\n"," 'matplotlib',\n"," mpl.mpl_figure_comm\n"," );\n","}\n"],"text/plain":[""]},"metadata":{},"output_type":"display_data"},{"data":{"text/html":[""],"text/plain":[""]},"metadata":{},"output_type":"display_data"},{"data":{"application/vnd.jupyter.widget-view+json":{"model_id":"fc0939117b6041269f471bb3e7f0bb15","version_major":2,"version_minor":0},"text/plain":["Button(description='Clear all', style=ButtonStyle())"]},"metadata":{},"output_type":"display_data"},{"data":{"application/vnd.jupyter.widget-view+json":{"model_id":"45115b5ac15345259cce235abbfdb277","version_major":2,"version_minor":0},"text/plain":["Button(description='Submit', style=ButtonStyle())"]},"metadata":{},"output_type":"display_data"},{"data":{"application/vnd.jupyter.widget-view+json":{"model_id":"924892819d544e27be446f0a269ded99","version_major":2,"version_minor":0},"text/plain":["IntSlider(value=0, max=10, min=-1)"]},"metadata":{},"output_type":"display_data"},{"data":{"application/vnd.jupyter.widget-view+json":{"model_id":"f44afedea0454db2b716a74ca160074e","version_major":2,"version_minor":0},"text/plain":["Dropdown(description='Species plot 1', options={'A': 0, 'B': 1}, value=0)"]},"metadata":{},"output_type":"display_data"},{"data":{"application/vnd.jupyter.widget-view+json":{"model_id":"eca5fc5601424c1686b7a94ab6cab267","version_major":2,"version_minor":0},"text/plain":["Dropdown(description='Species plot 2', index=1, options={'A': 0, 'B': 1}, value=1)"]},"metadata":{},"output_type":"display_data"},{"data":{"text/html":["
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alpha1alpha2betagammamu
011.44144111.4414412.9009014.8388392.469469
114.56456514.5645653.6056064.2862862.583584
215.72572612.5025035.4674673.4734731.782783
326.57657723.3533532.3923925.0110111.590591
419.62963022.8528534.5905915.9439442.837838
..................
49512.84284312.8428435.5355362.3043042.393393
49626.37637628.7587595.0430432.4164161.520521
49711.52152213.1231234.2662664.9349352.515516
49815.14514515.1451454.0340343.2052051.088088
49927.41741724.1941945.2112112.5845852.845846
\n","

500 rows × 5 columns

\n","
"],"text/plain":[" alpha1 alpha2 beta gamma mu\n","0 11.441441 11.441441 2.900901 4.838839 2.469469\n","1 14.564565 14.564565 3.605606 4.286286 2.583584\n","2 15.725726 12.502503 5.467467 3.473473 1.782783\n","3 26.576577 23.353353 2.392392 5.011011 1.590591\n","4 19.629630 22.852853 4.590591 5.943944 2.837838\n",".. ... ... ... ... ...\n","495 12.842843 12.842843 5.535536 2.304304 2.393393\n","496 26.376376 28.758759 5.043043 2.416416 1.520521\n","497 11.521522 13.123123 4.266266 4.934935 2.515516\n","498 15.145145 15.145145 4.034034 3.205205 1.088088\n","499 27.417417 24.194194 5.211211 2.584585 2.845846\n","\n","[500 rows x 5 columns]"]},"metadata":{},"output_type":"display_data"}],"source":["met.explore(dr_method='umap')"]},{"cell_type":"code","execution_count":17,"metadata":{},"outputs":[],"source":["met.data.user_labels = user_labels"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":[]}],"metadata":{"kernelspec":{"display_name":"Python 3","language":"python","name":"python3"},"language_info":{"codemirror_mode":{"name":"ipython","version":3},"file_extension":".py","mimetype":"text/x-python","name":"python","nbconvert_exporter":"python","pygments_lexer":"ipython3","version":"3.8.5"}},"nbformat":4,"nbformat_minor":4} \ No newline at end of file diff --git a/public_models/Toggle_Switch/Toggle_SwitchSciopeModelInference.ipynb b/public_models/Toggle_Switch/Toggle_SwitchSciopeModelInference.ipynb deleted file mode 100644 index 2ec6bf001f..0000000000 --- a/public_models/Toggle_Switch/Toggle_SwitchSciopeModelInference.ipynb +++ /dev/null @@ -1 +0,0 @@ -{"cells":[{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["import numpy as np\n","import gillespy2\n","from gillespy2 import Model, Species, Parameter, Reaction, Event, \\\n"," EventTrigger, EventAssignment, RateRule, \\\n"," AssignmentRule, FunctionDefinition\n","# from gillespy2 import SSACSolver\n","from gillespy2 import VariableSSACSolver\n","# from gillespy2 import TauLeapingSolver\n","# from gillespy2 import TauHybridSolver\n","# from gillespy2 import ODESolver"]},{"cell_type":"markdown","metadata":{},"source":["# Toggle_Switch"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["class ToggleSwitch(Model):\n"," def __init__(self, parameter_values=None):\n"," Model.__init__(self, name=\"Toggle_Switch\")\n"," self.volume = 1\n","\n"," # Parameters\n"," self.add_parameter(Parameter(name=\"alpha1\", expression=\"10\"))\n"," self.add_parameter(Parameter(name=\"alpha2\", expression=\"10\"))\n"," self.add_parameter(Parameter(name=\"beta\", expression=\"2\"))\n"," self.add_parameter(Parameter(name=\"gamma\", expression=\"2\"))\n"," self.add_parameter(Parameter(name=\"mu\", expression=\"1\"))\n","\n"," # Variables\n"," self.add_species(Species(name=\"A\", initial_value=2, mode=\"discrete\"))\n"," self.add_species(Species(name=\"B\", initial_value=2, mode=\"discrete\"))\n","\n"," # Reactions\n"," self.add_reaction(Reaction(name=\"cu\", reactants={}, products={'A': 1}, propensity_function=\"alpha1/(1+pow(B, beta))\"))\n"," self.add_reaction(Reaction(name=\"cv\", reactants={}, products={'B': 1}, propensity_function=\"alpha2/(1+pow(A, gamma))\"))\n"," self.add_reaction(Reaction(name=\"du\", reactants={'A': 1}, products={}, rate=self.listOfParameters[\"mu\"]))\n"," self.add_reaction(Reaction(name=\"dv\", reactants={'B': 1}, products={}, rate=self.listOfParameters[\"mu\"]))\n","\n"," # Timespan\n"," self.timespan(np.arange(0, 250, 1))"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["model = ToggleSwitch()"]},{"cell_type":"markdown","metadata":{},"source":["# Simulation Parameters"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["def configure_simulation():\n"," solver = VariableSSACSolver(model=model)\n"," kwargs = {\n"," \"solver\":solver,\n"," \"number_of_trajectories\":100,\n"," # \"seed\":None,\n"," # \"tau_tol\":0.03,\n"," # \"integrator_options\":{'rtol': 0.001, 'atol': 1e-06},\n"," }\n"," return kwargs"]},{"cell_type":"markdown","metadata":{},"source":["# Model Inference"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["%load_ext autoreload\n","%autoreload 2\n","\n","from tsfresh.feature_extraction.settings import MinimalFCParameters\n","from sciope.utilities.priors import uniform_prior\n","from sciope.utilities.summarystats import auto_tsfresh\n","from sciope.utilities.distancefunctions import naive_squared\n","from sciope.inference.abc_inference import ABC\n","from sklearn.metrics import mean_absolute_error\n","from dask.distributed import Client"]},{"cell_type":"markdown","metadata":{},"source":["## Generate some fixed(observed) data based on default parameters of the model"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["kwargs = configure_simulation()\n","fixed_data = model.run(**kwargs)"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["# Reshape the data and remove timepoints array\n","fixed_data = fixed_data.to_array()\n","fixed_data = np.asarray([x.T for x in fixed_data])\n","fixed_data = fixed_data[:, 1:, :]"]},{"cell_type":"markdown","metadata":{},"source":["## Define prior distribution"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["# take default from mode 1 as reference\n","default_param = np.array(list(model.listOfParameters.items()))[:, 1]\n","\n","bound = []\n","for exp in default_param:\n"," bound.append(float(exp.expression))\n","\n","# Set the bounds\n","bound = np.array(bound)\n","dmin = bound * 0.1\n","dmax = bound * 2.0\n","\n","# Here we use uniform prior\n","uni_prior = uniform_prior.UniformPrior(dmin, dmax)"]},{"cell_type":"markdown","metadata":{},"source":["## Define simulator"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["def get_variables(params, model):\n"," # params - array, need to have the same order as model.listOfParameters\n"," variables = {}\n"," for e, pname in enumerate(model.listOfParameters.keys()):\n"," variables[pname] = params[e]\n"," return variables\n","\n","# Here we use the GillesPy2 Solver\n","def simulator(params, model):\n"," variables = get_variables(params, model)\n","\n"," res = model.run(**kwargs, variables=variables)\n"," res = res.to_array()\n"," tot_res = np.asarray([x.T for x in res]) # reshape to (N, S, T)\n"," # should not contain timepoints\n"," tot_res = tot_res[:, 1:, :]\n","\n"," return tot_res\n","\n","# Wrapper, simulator function to abc should should only take one argument (the parameter point)\n","def simulator2(x):\n"," return simulator(x, model=model)"]},{"cell_type":"markdown","metadata":{},"source":["## Define summary statistics and distance function"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["# Function to generate summary statistics\n","summ_func = auto_tsfresh.SummariesTSFRESH()\n","\n","# Distance\n","ns = naive_squared.NaiveSquaredDistance()"]},{"cell_type":"markdown","metadata":{},"source":["## Start local cluster using dask client"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["c = Client()"]},{"cell_type":"markdown","metadata":{},"source":["## Start abc instance"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["abc = ABC(fixed_data, sim=simulator2, prior_function=uni_prior, summaries_function=summ_func.compute, distance_function=ns)"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["# First compute the fixed(observed) mean\n","abc.compute_fixed_mean(chunk_size=2)"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["res = abc.infer(num_samples=100, batch_size=10, chunk_size=2)"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["mae_inference = mean_absolute_error(bound, abc.results['inferred_parameters'])"]}],"metadata":{"kernelspec":{"display_name":"Python 3","language":"python","name":"python3"},"language_info":{"codemirror_mode":{"name":"ipython","version":3},"file_extension":".py","mimetype":"text/x-python","name":"python","nbconvert_exporter":"python","pygments_lexer":"ipython3","version":"3.8.5"}},"nbformat":4,"nbformat_minor":4} \ No newline at end of file diff --git a/public_models/Toggle_Switch/Toggle_Switch_1D_Parameter_Sweep.ipynb b/public_models/Toggle_Switch/Toggle_Switch_1D_Parameter_Sweep.ipynb new file mode 100644 index 0000000000..9ce97948ff --- /dev/null +++ b/public_models/Toggle_Switch/Toggle_Switch_1D_Parameter_Sweep.ipynb @@ -0,0 +1 @@ +{"cells":[{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["import numpy as np\n","import gillespy2\n","from gillespy2 import Model, Species, Parameter, Reaction, Event, \\\n"," EventTrigger, EventAssignment, RateRule, \\\n"," AssignmentRule, FunctionDefinition\n","from gillespy2 import SSACSolver\n","# from gillespy2 import TauLeapingCSolver\n","# from gillespy2 import ODECSolver\n","# from gillespy2 import TauHybridSolver"]},{"cell_type":"markdown","metadata":{},"source":["# Toggle_Switch"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["class ToggleSwitch(Model):\n"," def __init__(self, parameter_values=None):\n"," Model.__init__(self, name=\"Toggle_Switch\")\n"," self.volume = 1\n","\n"," # Parameters\n"," self.add_parameter(Parameter(name=\"alpha1\", expression=\"10\"))\n"," self.add_parameter(Parameter(name=\"alpha2\", expression=\"10\"))\n"," self.add_parameter(Parameter(name=\"beta\", expression=\"2\"))\n"," self.add_parameter(Parameter(name=\"gamma\", expression=\"2\"))\n"," self.add_parameter(Parameter(name=\"mu\", expression=\"1\"))\n","\n"," # Variables\n"," self.add_species(Species(name=\"A\", initial_value=2, mode=\"discrete\"))\n"," self.add_species(Species(name=\"B\", initial_value=2, mode=\"discrete\"))\n","\n"," # Reactions\n"," self.add_reaction(Reaction(name=\"cu\", reactants={}, products={'A': 1}, propensity_function=\"alpha1/(1+pow(B, beta))\"))\n"," self.add_reaction(Reaction(name=\"cv\", reactants={}, products={'B': 1}, propensity_function=\"alpha2/(1+pow(A, gamma))\"))\n"," self.add_reaction(Reaction(name=\"du\", reactants={'A': 1}, products={}, rate=self.listOfParameters[\"mu\"]))\n"," self.add_reaction(Reaction(name=\"dv\", reactants={'B': 1}, products={}, rate=self.listOfParameters[\"mu\"]))\n","\n"," # Timespan\n"," self.timespan(np.arange(0, 250, 1))"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["model = ToggleSwitch()"]},{"cell_type":"markdown","metadata":{},"source":["# Simulation Parameters"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["def configure_simulation():\n"," solver = SSACSolver(model=model)\n"," kwargs = {\n"," \"solver\":solver,\n"," \"number_of_trajectories\":20,\n"," # \"seed\":None,\n"," # \"tau_tol\":0.03,\n"," # \"integrator_options\":{'rtol': 0.001, 'atol': 1e-06},\n"," }\n"," return kwargs"]},{"cell_type":"markdown","metadata":{},"source":["# Post Processing"]},{"cell_type":"markdown","metadata":{},"source":["## Feature extraction function"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["# What value(s) do you want to extract from the simulation trajectory\n","def population_at_last_timepoint(c, res):\n"," if c.verbose:\n"," print(f'population_at_last_timepoint {c.variable_of_interest}={res[c.variable_of_interest][-1]}')\n"," return res[c.variable_of_interest][-1]"]},{"cell_type":"markdown","metadata":{},"source":["## Aggregation function"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["# How do we combine the values from multiple trajectores\n","def mean_std_of_ensemble(c, data):\n"," a = np.average(data)\n"," s = np.std(data)\n"," if c.verbose:\n"," print(f'mean_std_of_ensemble m:{a} s:{s}')\n"," return (a, s)"]},{"cell_type":"markdown","metadata":{},"source":["# Parameter Sweep"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["class ParameterSweep1D():\n","\n"," def run(c, kwargs, verbose=False):\n"," c.verbose = verbose\n"," fn = c.feature_extraction\n"," ag = c.ensemble_aggragator\n"," data = np.zeros((len(c.p1_range), 2)) # mean and std\n"," for i, v1 in enumerate(c.p1_range):\n"," if c.verbose:\n"," print(f'running {c.p1}={v1}')\n"," if(c.number_of_trajectories > 1):\n"," tmp_results = model.run(**kwargs, variables={c.p1:v1})\n"," (m, s) = ag([fn(x) for x in tmp_results])\n"," data[i, 0] = m\n"," data[i, 1] = s\n"," else:\n"," tmp_result = model.run(**kwargs, variables={c.p1:v1})\n"," data[i, 0] = c.feature_extraction(tmp_result)\n"," c.data = data\n","\n","\n"," def plot(c):\n"," from matplotlib import pyplot as plt\n"," from mpl_toolkits.axes_grid1 import make_axes_locatable\n"," fig, ax = plt.subplots(figsize=(8, 8))\n"," plt.title(f'Parameter Sweep - Variable:{c.variable_of_interest}')\n"," plt.errorbar(c.p1_range, c.data[:, 0], c.data[:, 1])\n"," plt.xlabel(c.p1, fontsize=16, fontweight='bold')\n"," plt.ylabel('Population', fontsize=16, fontweight='bold')\n","\n","\n"," def plotplotly(c, return_plotly_figure=False):\n"," from plotly.offline import iplot\n"," import plotly.graph_objs as go\n","\n"," visible = c.number_of_trajectories > 1\n"," error_y = dict(type='data', array=c.data[:, 1], visible=visible)\n","\n"," trace_list = [go.Scatter(x=c.p1_range, y=c.data[:, 0], error_y=error_y)]\n","\n"," title = dict(text=f'Parameter Sweep - Variable: {c.variable_of_interest}', x=0.5)\n"," yaxis_label = dict(title='Population')\n"," xaxis_label = dict(title=f'{c.p1}')\n","\n"," layout = go.Layout(title=title, xaxis=xaxis_label, yaxis=yaxis_label)\n","\n"," fig = dict(data=trace_list, layout=layout)\n","\n"," if return_plotly_figure:\n"," return fig\n"," iplot(fig)"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["class ParameterSweepConfig(ParameterSweep1D):\n"," # What class defines the GillesPy2 model\n"," model = ToggleSwitch()\n"," # ENTER PARAMETER HERE\n"," p1 = 'alpha1'\n"," # ENTER START VALUE FOR P1 RANGE HERE\n"," p1_min = 0.5 * float(eval(model.get_parameter(p1).expression))\n"," # ENTER END VALUE FOR P1 RANGE HERE\n"," p1_max = 1.5 * float(eval(model.get_parameter(p1).expression))\n"," # ENTER THE NUMBER OF STEPS FOR P1 HERE\n"," p1_steps = 11\n"," p1_range = np.linspace(p1_min, p1_max, p1_steps)\n"," # ENTER VARIABLE OF INTEREST HERE\n"," variable_of_interest = 'A'\n"," number_of_trajectories = 20\n"," # What feature of the simulation are we examining\n"," feature_extraction = population_at_last_timepoint\n"," # for ensemble resutls: how do we aggreggate the values\n"," ensemble_aggragator = mean_std_of_ensemble"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["kwargs = configure_simulation()\n","ps = ParameterSweepConfig()\n","%time ps.run(kwargs)"]},{"cell_type":"markdown","metadata":{},"source":["# Visualization"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["ps.plot()"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["ps.plotplotly()"]}],"metadata":{"kernelspec":{"display_name":"Python 3","language":"python","name":"python3"},"language_info":{"codemirror_mode":{"name":"ipython","version":3},"file_extension":".py","mimetype":"text/x-python","name":"python","nbconvert_exporter":"python","pygments_lexer":"ipython3","version":"3.8.5"}},"nbformat":4,"nbformat_minor":4} \ No newline at end of file diff --git a/public_models/Toggle_Switch/Toggle_Switch_2D_Parameter_Sweep.ipynb b/public_models/Toggle_Switch/Toggle_Switch_2D_Parameter_Sweep.ipynb new file mode 100644 index 0000000000..c5992dd1cf --- /dev/null +++ b/public_models/Toggle_Switch/Toggle_Switch_2D_Parameter_Sweep.ipynb @@ -0,0 +1 @@ +{"cells":[{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["import numpy as np\n","import gillespy2\n","from gillespy2 import Model, Species, Parameter, Reaction, Event, \\\n"," EventTrigger, EventAssignment, RateRule, \\\n"," AssignmentRule, FunctionDefinition\n","from gillespy2 import SSACSolver\n","# from gillespy2 import TauLeapingCSolver\n","# from gillespy2 import ODECSolver\n","# from gillespy2 import TauHybridSolver"]},{"cell_type":"markdown","metadata":{},"source":["# Toggle_Switch"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["class ToggleSwitch(Model):\n"," def __init__(self, parameter_values=None):\n"," Model.__init__(self, name=\"Toggle_Switch\")\n"," self.volume = 1\n","\n"," # Parameters\n"," self.add_parameter(Parameter(name=\"alpha1\", expression=\"10\"))\n"," self.add_parameter(Parameter(name=\"alpha2\", expression=\"10\"))\n"," self.add_parameter(Parameter(name=\"beta\", expression=\"2\"))\n"," self.add_parameter(Parameter(name=\"gamma\", expression=\"2\"))\n"," self.add_parameter(Parameter(name=\"mu\", expression=\"1\"))\n","\n"," # Variables\n"," self.add_species(Species(name=\"A\", initial_value=2, mode=\"discrete\"))\n"," self.add_species(Species(name=\"B\", initial_value=2, mode=\"discrete\"))\n","\n"," # Reactions\n"," self.add_reaction(Reaction(name=\"cu\", reactants={}, products={'A': 1}, propensity_function=\"alpha1/(1+pow(B, beta))\"))\n"," self.add_reaction(Reaction(name=\"cv\", reactants={}, products={'B': 1}, propensity_function=\"alpha2/(1+pow(A, gamma))\"))\n"," self.add_reaction(Reaction(name=\"du\", reactants={'A': 1}, products={}, rate=self.listOfParameters[\"mu\"]))\n"," self.add_reaction(Reaction(name=\"dv\", reactants={'B': 1}, products={}, rate=self.listOfParameters[\"mu\"]))\n","\n"," # Timespan\n"," self.timespan(np.arange(0, 250, 1))"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["model = ToggleSwitch()"]},{"cell_type":"markdown","metadata":{},"source":["# Simulation Parameters"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["def configure_simulation():\n"," solver = SSACSolver(model=model)\n"," kwargs = {\n"," \"solver\":solver,\n"," \"number_of_trajectories\":20,\n"," # \"seed\":None,\n"," # \"tau_tol\":0.03,\n"," # \"integrator_options\":{'rtol': 0.001, 'atol': 1e-06},\n"," }\n"," return kwargs"]},{"cell_type":"markdown","metadata":{},"source":["# Post Processing"]},{"cell_type":"markdown","metadata":{},"source":["## Feature extraction function"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["# What value(s) do you want to extract from the simulation trajectory\n","def population_at_last_timepoint(c, res):\n"," if c.verbose:\n"," print(f'population_at_last_timepoint {c.variable_of_interest}={res[c.variable_of_interest][-1]}')\n"," return res[c.variable_of_interest][-1]"]},{"cell_type":"markdown","metadata":{},"source":["## Aggregation function"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["# How do we combine the values from multiple trajectores\n","def average_of_ensemble(c, data):\n"," a = np.average(data)\n"," if c.verbose:\n"," print(f'average_of_ensemble = {a}')\n"," return a"]},{"cell_type":"markdown","metadata":{},"source":["# Parameter Sweep"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["class ParameterSweep2D():\n","\n"," def run(c, kwargs, verbose=False):\n"," c.verbose = verbose\n"," fn = c.feature_extraction\n"," ag = c.ensemble_aggragator\n"," data = np.zeros((len(c.p1_range), len(c.p2_range)))\n"," for i, v1 in enumerate(c.p1_range):\n"," for j, v2 in enumerate(c.p2_range):\n"," if c.verbose:\n"," print(f'running {c.p1}={v1}, {c.p2}={v2}')\n"," if(c.number_of_trajectories > 1):\n"," tmp_results = model.run(**kwargs, variables={c.p1:v1, c.p2:v2})\n"," data[i, j] = ag([fn(x) for x in tmp_results])\n"," else:\n"," tmp_result = model.run(**kwargs, variables={c.p1:v1, c.p2:v2})\n"," data[i, j] = c.feature_extraction(tmp_result)\n"," c.data = data\n","\n","\n"," def plot(c):\n"," from matplotlib import pyplot as plt\n"," from mpl_toolkits.axes_grid1 import make_axes_locatable\n"," fig, ax = plt.subplots(figsize=(8, 8))\n"," plt.imshow(c.data)\n"," ax.set_xticks(np.arange(c.data.shape[1]) + 0.5, minor=False)\n"," ax.set_yticks(np.arange(c.data.shape[0]) + 0.5, minor=False)\n"," plt.title(f'Parameter Sweep - Variable: {c.variable_of_interest}')\n"," ax.set_xticklabels(c.p1_range, minor=False, rotation=90)\n"," ax.set_yticklabels(c.p2_range, minor=False)\n"," ax.set_xlabel(c.p1, fontsize=16, fontweight='bold')\n"," ax.set_ylabel(c.p2, fontsize=16, fontweight='bold')\n"," divider = make_axes_locatable(ax)\n"," cax = divider.append_axes('right', size='5%', pad=0.2)\n"," _ = plt.colorbar(ax=ax, cax=cax)\n","\n","\n"," def plotplotly(c, return_plotly_figure=False):\n"," from plotly.offline import init_notebook_mode, iplot\n"," import plotly.graph_objs as go\n","\n"," xaxis_ticks = c.p1_range\n"," yaxis_ticks = c.p2_range\n","\n"," trace_list = [go.Heatmap(z=c.data, x=xaxis_ticks, y=yaxis_ticks)]\n"," title = dict(text=f'Parameter Sweep - Variable: {c.variable_of_interest}', x=0.5)\n"," xaxis_label = dict(title=f'{c.p1}')\n"," yaxis_label = dict(title=f'{c.p2}')\n","\n"," layout = go.Layout(title=title, xaxis=xaxis_label, yaxis=yaxis_label)\n","\n"," fig = dict(data=trace_list, layout=layout)\n","\n"," if return_plotly_figure:\n"," return fig\n"," iplot(fig)"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["class ParameterSweepConfig(ParameterSweep2D):\n"," # What class defines the GillesPy2 model\n"," model = ToggleSwitch()\n"," # ENTER PARAMETER 1 HERE\n"," p1 = 'alpha1'\n"," # ENTER PARAMETER 2 HERE\n"," p2 = 'alpha2'\n"," # ENTER START VALUE FOR P1 RANGE HERE\n"," p1_min = 0.5 * float(eval(model.get_parameter(p1).expression))\n"," # ENTER END VALUE FOR P1 RANGE HERE\n"," p1_max = 1.5 * float(eval(model.get_parameter(p1).expression))\n"," # ENTER THE NUMBER OF STEPS FOR P1 HERE\n"," p1_steps = 11\n"," p1_range = np.linspace(p1_min, p1_max, p1_steps)\n"," # ENTER START VALUE FOR P2 RANGE HERE\n"," p2_min = 0.5 * float(eval(model.get_parameter(p2).expression))\n"," # ENTER END VALUE FOR P2 RANGE HERE\n"," p2_max = 1.5 * float(eval(model.get_parameter(p2).expression))\n"," # ENTER THE NUMBER OF STEPS FOR P2 HERE\n"," p2_steps = 11\n"," p2_range = np.linspace(p2_min, p2_max, p2_steps)\n"," # ENTER VARIABLE OF INTEREST HERE\n"," variable_of_interest = 'A'\n"," number_of_trajectories = 20\n"," # What feature of the simulation are we examining\n"," feature_extraction = population_at_last_timepoint\n"," # for ensemble resutls: how do we aggreggate the values\n"," ensemble_aggragator = average_of_ensemble"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["kwargs = configure_simulation()\n","ps = ParameterSweepConfig()\n","%time ps.run(kwargs)"]},{"cell_type":"markdown","metadata":{},"source":["# Visualization"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["ps.plot()"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["ps.plotplotly()"]}],"metadata":{"kernelspec":{"display_name":"Python 3","language":"python","name":"python3"},"language_info":{"codemirror_mode":{"name":"ipython","version":3},"file_extension":".py","mimetype":"text/x-python","name":"python","nbconvert_exporter":"python","pygments_lexer":"ipython3","version":"3.8.5"}},"nbformat":4,"nbformat_minor":4} \ No newline at end of file diff --git a/public_models/Toggle_Switch/Toggle_Switch_SCIOPE_Model_Exploration.ipynb b/public_models/Toggle_Switch/Toggle_Switch_SCIOPE_Model_Exploration.ipynb new file mode 100644 index 0000000000..62f442c900 --- /dev/null +++ b/public_models/Toggle_Switch/Toggle_Switch_SCIOPE_Model_Exploration.ipynb @@ -0,0 +1 @@ +{"cells":[{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["import numpy as np\n","%matplotlib notebook\n","import gillespy2\n","from gillespy2 import Model, Species, Parameter, Reaction, Event, \\\n"," EventTrigger, EventAssignment, RateRule, \\\n"," AssignmentRule, FunctionDefinition\n","from gillespy2 import SSACSolver\n","# from gillespy2 import TauLeapingCSolver\n","# from gillespy2 import ODECSolver\n","# from gillespy2 import TauHybridSolver"]},{"cell_type":"markdown","metadata":{},"source":["# Toggle_Switch"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["class ToggleSwitch(Model):\n"," def __init__(self, parameter_values=None):\n"," Model.__init__(self, name=\"Toggle_Switch\")\n"," self.volume = 1\n","\n"," # Parameters\n"," self.add_parameter(Parameter(name=\"alpha1\", expression=\"10\"))\n"," self.add_parameter(Parameter(name=\"alpha2\", expression=\"10\"))\n"," self.add_parameter(Parameter(name=\"beta\", expression=\"2\"))\n"," self.add_parameter(Parameter(name=\"gamma\", expression=\"2\"))\n"," self.add_parameter(Parameter(name=\"mu\", expression=\"1\"))\n","\n"," # Variables\n"," self.add_species(Species(name=\"A\", initial_value=2, mode=\"discrete\"))\n"," self.add_species(Species(name=\"B\", initial_value=2, mode=\"discrete\"))\n","\n"," # Reactions\n"," self.add_reaction(Reaction(name=\"cu\", reactants={}, products={'A': 1}, propensity_function=\"alpha1/(1+pow(B, beta))\"))\n"," self.add_reaction(Reaction(name=\"cv\", reactants={}, products={'B': 1}, propensity_function=\"alpha2/(1+pow(A, gamma))\"))\n"," self.add_reaction(Reaction(name=\"du\", reactants={'A': 1}, products={}, rate=self.listOfParameters[\"mu\"]))\n"," self.add_reaction(Reaction(name=\"dv\", reactants={'B': 1}, products={}, rate=self.listOfParameters[\"mu\"]))\n","\n"," # Timespan\n"," self.timespan(np.arange(0, 250, 1))"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["model = ToggleSwitch()"]},{"cell_type":"markdown","metadata":{},"source":["# Simulation Parameters"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["def configure_simulation():\n"," solver = SSACSolver(model=model)\n"," kwargs = {\n"," \"solver\":solver,\n"," \"number_of_trajectories\":100,\n"," # \"seed\":None,\n"," # \"tau_tol\":0.03,\n"," # \"integrator_options\":{'rtol': 0.001, 'atol': 1e-06},\n"," }\n"," return kwargs"]},{"cell_type":"markdown","metadata":{},"source":["# Model Exploration"]},{"cell_type":"markdown","metadata":{},"source":["## Define simulator function (using gillespy2 wrapper)"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["from sciope.utilities.gillespy2 import wrapper\n","settings = configure_simulation()\n","simulator = wrapper.get_simulator(gillespy_model=model, run_settings=settings, species_of_interest=['A', 'B'])\n","expression_array = wrapper.get_parameter_expression_array(model)"]},{"cell_type":"markdown","metadata":{},"source":["## Start local cluster using dask client"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["from dask.distributed import Client\n","\n","c = Client()"]},{"cell_type":"markdown","metadata":{},"source":["## Define parameter sampler/design and summary statistics"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["from sciope.designs import latin_hypercube_sampling\n","from sciope.utilities.summarystats.auto_tsfresh import SummariesTSFRESH\n","\n","lhc = latin_hypercube_sampling.LatinHypercube(xmin=expression_array, xmax=expression_array*3)\n","lhc.generate_array(1000) # creates a LHD of size 1000\n","\n","# will use default minimal set of features\n","summary_stats = SummariesTSFRESH()"]},{"cell_type":"markdown","metadata":{},"source":["## Initiate StochMET"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["from sciope.stochmet.stochmet import StochMET\n","\n","met = StochMET(simulator, lhc, summary_stats)"]},{"cell_type":"markdown","metadata":{},"source":["## Run parameter sweep"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["met.compute(n_points=500, chunk_size=10)"]},{"cell_type":"markdown","metadata":{},"source":["## Explore the result"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["# First lets add some appropiate information about the model and features\n","met.data.configurations['listOfParameters'] = list(model.listOfParameters.keys())\n","met.data.configurations['listOfSpecies'] = list(model.listOfSpecies.keys())\n","met.data.configurations['listOfSummaries'] = met.summaries.features\n","met.data.configurations['timepoints'] = model.tspan"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["# Here we use UMAP for dimension reduction\n","met.explore(dr_method='umap')"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["from sciope.models.label_propagation import LPModel\n","# here lets use the dimension reduction embedding as input data\n","data = met.dr_model.embedding_\n","\n","model_lp = LPModel()\n","# train using basinhopping\n","model_lp.train(data, met.data.user_labels, min_=0.01, max_=10, niter=50)"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["# just to vislualize the result we will map the label distribution to the user_labels\n","# (will enable us to see the LP model output when using method 'explore')\n","user_labels = np.copy(met.data.user_labels)\n","# takes the label corresponding to index 0\n","met.data.user_labels = model_lp.model.label_distributions_[:, 0]"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["met.explore(dr_method='umap')"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["met.data.user_labels = user_labels"]}],"metadata":{"kernelspec":{"display_name":"Python 3","language":"python","name":"python3"},"language_info":{"codemirror_mode":{"name":"ipython","version":3},"file_extension":".py","mimetype":"text/x-python","name":"python","nbconvert_exporter":"python","pygments_lexer":"ipython3","version":"3.8.5"}},"nbformat":4,"nbformat_minor":4} \ No newline at end of file diff --git a/public_models/Toggle_Switch/Toggle_Switch_SCIOPE_Model_Inference.ipynb b/public_models/Toggle_Switch/Toggle_Switch_SCIOPE_Model_Inference.ipynb new file mode 100644 index 0000000000..90f880c7cf --- /dev/null +++ b/public_models/Toggle_Switch/Toggle_Switch_SCIOPE_Model_Inference.ipynb @@ -0,0 +1 @@ +{"cells":[{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["import numpy as np\n","import gillespy2\n","from gillespy2 import Model, Species, Parameter, Reaction, Event, \\\n"," EventTrigger, EventAssignment, RateRule, \\\n"," AssignmentRule, FunctionDefinition\n","from gillespy2 import SSACSolver\n","# from gillespy2 import TauLeapingCSolver\n","# from gillespy2 import ODECSolver\n","# from gillespy2 import TauHybridSolver"]},{"cell_type":"markdown","metadata":{},"source":["# Toggle_Switch"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["class ToggleSwitch(Model):\n"," def __init__(self, parameter_values=None):\n"," Model.__init__(self, name=\"Toggle_Switch\")\n"," self.volume = 1\n","\n"," # Parameters\n"," self.add_parameter(Parameter(name=\"alpha1\", expression=\"10\"))\n"," self.add_parameter(Parameter(name=\"alpha2\", expression=\"10\"))\n"," self.add_parameter(Parameter(name=\"beta\", expression=\"2\"))\n"," self.add_parameter(Parameter(name=\"gamma\", expression=\"2\"))\n"," self.add_parameter(Parameter(name=\"mu\", expression=\"1\"))\n","\n"," # Variables\n"," self.add_species(Species(name=\"A\", initial_value=2, mode=\"discrete\"))\n"," self.add_species(Species(name=\"B\", initial_value=2, mode=\"discrete\"))\n","\n"," # Reactions\n"," self.add_reaction(Reaction(name=\"cu\", reactants={}, products={'A': 1}, propensity_function=\"alpha1/(1+pow(B, beta))\"))\n"," self.add_reaction(Reaction(name=\"cv\", reactants={}, products={'B': 1}, propensity_function=\"alpha2/(1+pow(A, gamma))\"))\n"," self.add_reaction(Reaction(name=\"du\", reactants={'A': 1}, products={}, rate=self.listOfParameters[\"mu\"]))\n"," self.add_reaction(Reaction(name=\"dv\", reactants={'B': 1}, products={}, rate=self.listOfParameters[\"mu\"]))\n","\n"," # Timespan\n"," self.timespan(np.arange(0, 250, 1))"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["model = ToggleSwitch()"]},{"cell_type":"markdown","metadata":{},"source":["# Simulation Parameters"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["def configure_simulation():\n"," solver = SSACSolver(model=model)\n"," kwargs = {\n"," \"solver\":solver,\n"," \"number_of_trajectories\":100,\n"," # \"seed\":None,\n"," # \"tau_tol\":0.03,\n"," # \"integrator_options\":{'rtol': 0.001, 'atol': 1e-06},\n"," }\n"," return kwargs"]},{"cell_type":"markdown","metadata":{},"source":["# Model Inference"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["%load_ext autoreload\n","%autoreload 2\n","\n","from tsfresh.feature_extraction.settings import MinimalFCParameters\n","from sciope.utilities.priors import uniform_prior\n","from sciope.utilities.summarystats import auto_tsfresh\n","from sciope.utilities.distancefunctions import naive_squared\n","from sciope.inference.abc_inference import ABC\n","from sklearn.metrics import mean_absolute_error\n","from dask.distributed import Client"]},{"cell_type":"markdown","metadata":{},"source":["## Generate some fixed(observed) data based on default parameters of the model"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["kwargs = configure_simulation()\n","fixed_data = model.run(**kwargs)"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["# Reshape the data and remove timepoints array\n","fixed_data = fixed_data.to_array()\n","fixed_data = np.asarray([x.T for x in fixed_data])\n","fixed_data = fixed_data[:, 1:, :]"]},{"cell_type":"markdown","metadata":{},"source":["## Define prior distribution"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["# take default from mode 1 as reference\n","default_param = np.array(list(model.listOfParameters.items()))[:, 1]\n","\n","bound = []\n","for exp in default_param:\n"," bound.append(float(exp.expression))\n","\n","# Set the bounds\n","bound = np.array(bound)\n","dmin = bound * 0.1\n","dmax = bound * 2.0\n","\n","# Here we use uniform prior\n","uni_prior = uniform_prior.UniformPrior(dmin, dmax)"]},{"cell_type":"markdown","metadata":{},"source":["## Define simulator"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["def get_variables(params, model):\n"," # params - array, need to have the same order as model.listOfParameters\n"," variables = {}\n"," for e, pname in enumerate(model.listOfParameters.keys()):\n"," variables[pname] = params[e]\n"," return variables\n","\n","# Here we use the GillesPy2 Solver\n","def simulator(params, model):\n"," variables = get_variables(params, model)\n","\n"," res = model.run(**kwargs, variables=variables)\n"," res = res.to_array()\n"," tot_res = np.asarray([x.T for x in res]) # reshape to (N, S, T)\n"," # should not contain timepoints\n"," tot_res = tot_res[:, 1:, :]\n","\n"," return tot_res\n","\n","# Wrapper, simulator function to abc should should only take one argument (the parameter point)\n","def simulator2(x):\n"," return simulator(x, model=model)"]},{"cell_type":"markdown","metadata":{},"source":["## Define summary statistics and distance function"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["# Function to generate summary statistics\n","summ_func = auto_tsfresh.SummariesTSFRESH()\n","\n","# Distance\n","ns = naive_squared.NaiveSquaredDistance()"]},{"cell_type":"markdown","metadata":{},"source":["## Start local cluster using dask client"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["c = Client()"]},{"cell_type":"markdown","metadata":{},"source":["## Start abc instance"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["abc = ABC(fixed_data, sim=simulator2, prior_function=uni_prior, summaries_function=summ_func.compute, distance_function=ns)"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["# First compute the fixed(observed) mean\n","abc.compute_fixed_mean(chunk_size=2)"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["res = abc.infer(num_samples=100, batch_size=10, chunk_size=2)"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["mae_inference = mean_absolute_error(bound, abc.results['inferred_parameters'])"]}],"metadata":{"kernelspec":{"display_name":"Python 3","language":"python","name":"python3"},"language_info":{"codemirror_mode":{"name":"ipython","version":3},"file_extension":".py","mimetype":"text/x-python","name":"python","nbconvert_exporter":"python","pygments_lexer":"ipython3","version":"3.8.5"}},"nbformat":4,"nbformat_minor":4} \ No newline at end of file diff --git a/public_models/Tyson_Oscillator/Tyson_Oscillator.ipynb b/public_models/Tyson_Oscillator/Tyson_Oscillator.ipynb index 53ef2f6e1a..67a0db11f3 100644 --- a/public_models/Tyson_Oscillator/Tyson_Oscillator.ipynb +++ b/public_models/Tyson_Oscillator/Tyson_Oscillator.ipynb @@ -1,1472 +1 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Tyson_Oscillator" - ] - }, - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [], - "source": [ - "import numpy as np\n", - "import gillespy2\n", - "from gillespy2 import Model, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition\n", - "from gillespy2 import EventAssignment, EventTrigger, Event\n", - "from gillespy2 import SSACSolver\n", - "# from gillespy2 import VariableSSACSolver\n", - "# from gillespy2 import BasicTauLeapingSolver\n", - "# from gillespy2 import BasicTauHybridSolver\n", - "# from gillespy2 import BasicODESolver" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [], - "source": [ - "class Tyson_Oscillator(Model):\n", - " def __init__(self, parameter_values=None):\n", - " Model.__init__(self, name=\"Tyson_Oscillator\")\n", - " self.volume = 300\n", - "\n", - " # Parameters\n", - " self.add_parameter(Parameter(name=\"P\", expression=2))\n", - " self.add_parameter(Parameter(name=\"kt\", expression=20))\n", - " self.add_parameter(Parameter(name=\"kd\", expression=1))\n", - " self.add_parameter(Parameter(name=\"a0\", expression=0.005))\n", - " self.add_parameter(Parameter(name=\"a1\", expression=0.05))\n", - " self.add_parameter(Parameter(name=\"a2\", expression=0.1))\n", - " self.add_parameter(Parameter(name=\"kdx\", expression=1))\n", - "\n", - " # Species\n", - " self.add_species(Species(name=\"X\", initial_value=197, mode=\"discrete\"))\n", - " self.add_species(Species(name=\"Y\", initial_value=255, mode=\"discrete\"))\n", - "\n", - " # Reactions\n", - " self.add_reaction(Reaction(name=\"rxn1\", reactants={}, products={'X': 1}, propensity_function=\"vol*1/(1+(Y*Y/((vol*vol))))\"))\n", - " self.add_reaction(Reaction(name=\"rxn2\", reactants={'X': 1}, products={}, rate=self.listOfParameters[\"kdx\"]))\n", - " self.add_reaction(Reaction(name=\"rxn3\", reactants={'X': 1}, products={'X': 1, 'Y': 1}, rate=self.listOfParameters[\"kt\"]))\n", - " self.add_reaction(Reaction(name=\"rxn4\", reactants={'Y': 1}, products={}, rate=self.listOfParameters[\"kd\"]))\n", - " self.add_reaction(Reaction(name=\"rxn5\", reactants={'Y': 1}, products={}, propensity_function=\"Y/(a0 + a1*(Y/vol)+a2*Y*Y/(vol*vol))\"))\n", - "\n", - " # Timespan\n", - " self.timespan(np.linspace(0, 100, 101))" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [], - "source": [ - "model = Tyson_Oscillator()" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [], - "source": [ - "solver = SSACSolver(model=model)" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "metadata": {}, - "outputs": [], - "source": [ - "def configure_simulation():\n", - " kwargs = {\n", - " \"solver\":solver,\n", - " \"number_of_trajectories\":1,\n", - " \"seed\":None,\n", - " # \"tau_tol\":0.03,\n", - " # \"integrator_options\":{'rtol': 0.001, 'atol': 1e-06}\n", - " }\n", - " return kwargs" - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "metadata": {}, - "outputs": [], - "source": [ - "kwargs = configure_simulation()\n", - "results = model.run(**kwargs)" - ] - }, - { - "cell_type": "code", - "execution_count": 7, - "metadata": {}, - "outputs": [ - { - "data": { - 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" - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "results.plotplotly()" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.7.6" - } - }, - "nbformat": 4, - "nbformat_minor": 4 -} +{"cells":[{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["import numpy as np\n","import gillespy2\n","from gillespy2 import Model, Species, Parameter, Reaction, Event, \\\n"," EventTrigger, EventAssignment, RateRule, \\\n"," AssignmentRule, FunctionDefinition\n","# from gillespy2 import SSACSolver\n","# from gillespy2 import TauLeapingCSolver\n","# from gillespy2 import ODECSolver\n","# from gillespy2 import TauHybridSolver"]},{"cell_type":"markdown","metadata":{},"source":["# Tyson_Oscillator"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["class TysonOscillator(Model):\n"," def __init__(self, parameter_values=None):\n"," Model.__init__(self, name=\"Tyson_Oscillator\")\n"," self.volume = 300\n","\n"," # Parameters\n"," self.add_parameter(Parameter(name=\"P\", expression=\"2\"))\n"," self.add_parameter(Parameter(name=\"kt\", expression=\"20\"))\n"," self.add_parameter(Parameter(name=\"kd\", expression=\"1\"))\n"," self.add_parameter(Parameter(name=\"a0\", expression=\"0.005\"))\n"," self.add_parameter(Parameter(name=\"a1\", expression=\"0.05\"))\n"," self.add_parameter(Parameter(name=\"a2\", expression=\"0.1\"))\n"," self.add_parameter(Parameter(name=\"kdx\", expression=\"1\"))\n","\n"," # Variables\n"," self.add_species(Species(name=\"X\", initial_value=197, mode=\"discrete\"))\n"," self.add_species(Species(name=\"Y\", initial_value=255, mode=\"discrete\"))\n","\n"," # Reactions\n"," self.add_reaction(Reaction(name=\"rxn1\", reactants={}, products={'X': 1}, propensity_function=\"vol*1/(1+(Y*Y/((vol*vol))))\"))\n"," self.add_reaction(Reaction(name=\"rxn2\", reactants={'X': 1}, products={}, rate=self.listOfParameters[\"kdx\"]))\n"," self.add_reaction(Reaction(name=\"rxn3\", reactants={'X': 1}, products={'X': 1, 'Y': 1}, rate=self.listOfParameters[\"kt\"]))\n"," self.add_reaction(Reaction(name=\"rxn4\", reactants={'Y': 1}, products={}, rate=self.listOfParameters[\"kd\"]))\n"," self.add_reaction(Reaction(name=\"rxn5\", reactants={'Y': 1}, products={}, propensity_function=\"Y/(a0 + a1*(Y/vol)+a2*Y*Y/(vol*vol))\"))\n","\n"," # Timespan\n"," self.timespan(np.arange(0, 100, 1))"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["model = TysonOscillator()"]},{"cell_type":"markdown","metadata":{},"source":["# Simulation Parameters"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["def configure_simulation():\n"," # solver = SSACSolver(model=model)\n"," kwargs = {\n"," # \"solver\":solver,\n"," \"number_of_trajectories\":100,\n"," # \"seed\":None,\n"," # \"tau_tol\":0.03,\n"," # \"integrator_options\":{'rtol': 0.001, 'atol': 1e-06},\n"," }\n"," return kwargs"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["kwargs = configure_simulation()\n","results = model.run(**kwargs)"]},{"cell_type":"markdown","metadata":{},"source":["# Visualization"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["results.plotplotly()"]}],"metadata":{},"nbformat":4,"nbformat_minor":4} \ No newline at end of file diff --git a/public_models/Vilar_Oscillator/Vilar_Oscillator.ipynb b/public_models/Vilar_Oscillator/Vilar_Oscillator.ipynb index 7b9774793c..a893cc22ff 100644 --- a/public_models/Vilar_Oscillator/Vilar_Oscillator.ipynb +++ b/public_models/Vilar_Oscillator/Vilar_Oscillator.ipynb @@ -1,4798 +1 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Vilar_Oscillator" - ] - }, - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [], - "source": [ - "import numpy as np\n", - "import gillespy2\n", - "from gillespy2 import Model, Species, Reaction, Parameter, RateRule, AssignmentRule, FunctionDefinition\n", - "from gillespy2 import EventAssignment, EventTrigger, Event\n", - "from gillespy2 import SSACSolver\n", - "# from gillespy2 import VariableSSACSolver\n", - "# from gillespy2 import BasicTauLeapingSolver\n", - "# from gillespy2 import BasicTauHybridSolver\n", - "# from gillespy2 import BasicODESolver" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [], - "source": [ - "class Vilar_Oscillator(Model):\n", - " def __init__(self, parameter_values=None):\n", - " Model.__init__(self, name=\"Vilar_Oscillator\")\n", - " self.volume = 1\n", - "\n", - " # Parameters\n", - " self.add_parameter(Parameter(name=\"alpha_a\", expression=50))\n", - " self.add_parameter(Parameter(name=\"alpha_a_prime\", expression=500))\n", - " self.add_parameter(Parameter(name=\"alpha_r\", expression=0.01))\n", - " self.add_parameter(Parameter(name=\"alpha_r_prime\", expression=50))\n", - " self.add_parameter(Parameter(name=\"beta_a\", expression=50))\n", - " self.add_parameter(Parameter(name=\"beta_r\", expression=5))\n", - " self.add_parameter(Parameter(name=\"delta_ma\", expression=10))\n", - " self.add_parameter(Parameter(name=\"delta_mr\", expression=0.5))\n", - " self.add_parameter(Parameter(name=\"delta_a\", expression=1))\n", - " self.add_parameter(Parameter(name=\"delta_r\", expression=0.2))\n", - " self.add_parameter(Parameter(name=\"gamma_a\", expression=1))\n", - " self.add_parameter(Parameter(name=\"gamma_r\", expression=1))\n", - " self.add_parameter(Parameter(name=\"gamma_c\", expression=2))\n", - " self.add_parameter(Parameter(name=\"theta_a\", expression=50))\n", - " self.add_parameter(Parameter(name=\"theta_r\", expression=100))\n", - "\n", - " # Species\n", - " self.add_species(Species(name=\"Da\", initial_value=1, mode=\"discrete\"))\n", - " self.add_species(Species(name=\"Da_prime\", initial_value=0, mode=\"discrete\"))\n", - " self.add_species(Species(name=\"Ma\", initial_value=0, mode=\"discrete\"))\n", - " self.add_species(Species(name=\"Dr\", initial_value=1, mode=\"discrete\"))\n", - " self.add_species(Species(name=\"Dr_prime\", initial_value=0, mode=\"discrete\"))\n", - " self.add_species(Species(name=\"Mr\", initial_value=0, mode=\"discrete\"))\n", - " self.add_species(Species(name=\"C\", initial_value=10, mode=\"discrete\"))\n", - " self.add_species(Species(name=\"A\", initial_value=10, mode=\"discrete\"))\n", - " self.add_species(Species(name=\"R\", initial_value=10, mode=\"discrete\"))\n", - "\n", - " # Reactions\n", - " self.add_reaction(Reaction(name=\"r1\", reactants={'Da_prime': 1}, products={'Da': 1}, rate=self.listOfParameters[\"theta_a\"]))\n", - " self.add_reaction(Reaction(name=\"r2\", reactants={'Da': 1, 'A': 1}, products={'Da_prime': 1}, rate=self.listOfParameters[\"gamma_a\"]))\n", - " self.add_reaction(Reaction(name=\"r3\", reactants={'Dr_prime': 1}, products={'Dr': 1}, rate=self.listOfParameters[\"theta_r\"]))\n", - " self.add_reaction(Reaction(name=\"r4\", reactants={'Dr': 1, 'A': 1}, products={'Dr_prime': 1}, rate=self.listOfParameters[\"gamma_r\"]))\n", - " self.add_reaction(Reaction(name=\"r5\", reactants={'Da_prime': 1}, products={'Da_prime': 1, 'Ma': 1}, rate=self.listOfParameters[\"alpha_a_prime\"]))\n", - " self.add_reaction(Reaction(name=\"r6\", reactants={'Da': 1}, products={'Da': 1, 'Ma': 1}, rate=self.listOfParameters[\"alpha_a\"]))\n", - " self.add_reaction(Reaction(name=\"r7\", reactants={'Ma': 1}, products={}, rate=self.listOfParameters[\"delta_ma\"]))\n", - " self.add_reaction(Reaction(name=\"r8\", reactants={'Ma': 1}, products={'A': 1, 'Ma': 1}, rate=self.listOfParameters[\"beta_a\"]))\n", - " self.add_reaction(Reaction(name=\"r9\", reactants={'Da_prime': 1}, products={'Da_prime': 1, 'A': 1}, rate=self.listOfParameters[\"theta_a\"]))\n", - " self.add_reaction(Reaction(name=\"r10\", reactants={'Dr_prime': 1}, products={'Dr_prime': 1, 'A': 1}, rate=self.listOfParameters[\"theta_a\"]))\n", - " self.add_reaction(Reaction(name=\"r11\", reactants={'A': 1}, products={}, rate=self.listOfParameters[\"gamma_c\"]))\n", - " self.add_reaction(Reaction(name=\"r12\", reactants={'A': 1, 'R': 1}, products={'C': 1}, rate=self.listOfParameters[\"gamma_c\"]))\n", - " self.add_reaction(Reaction(name=\"r13\", reactants={'Dr_prime': 1}, products={'Dr_prime': 1, 'Mr': 1}, rate=self.listOfParameters[\"alpha_r_prime\"]))\n", - " self.add_reaction(Reaction(name=\"r14\", reactants={'Dr': 1}, products={'Dr': 1, 'Mr': 1}, rate=self.listOfParameters[\"alpha_r\"]))\n", - " self.add_reaction(Reaction(name=\"r15\", reactants={'Mr': 1}, products={}, rate=self.listOfParameters[\"delta_mr\"]))\n", - " self.add_reaction(Reaction(name=\"r16\", reactants={'Mr': 1}, products={'Mr': 1, 'R': 1}, rate=self.listOfParameters[\"beta_r\"]))\n", - " self.add_reaction(Reaction(name=\"r17\", reactants={'R': 1}, products={}, rate=self.listOfParameters[\"delta_r\"]))\n", - " self.add_reaction(Reaction(name=\"r18\", reactants={'C': 1}, products={'R': 1}, rate=self.listOfParameters[\"delta_a\"]))\n", - "\n", - " # Timespan\n", - " self.timespan(np.linspace(0, 200, 201))" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [], - "source": [ - "model = Vilar_Oscillator()" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [], - "source": [ - "solver = SSACSolver(model=model)" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "metadata": {}, - "outputs": [], - "source": [ - "def configure_simulation():\n", - " kwargs = {\n", - " \"solver\":solver,\n", - " \"number_of_trajectories\":1,\n", - " \"seed\":None,\n", - " # \"tau_tol\":0.03,\n", - " # \"integrator_options\":{'rtol': 0.001, 'atol': 1e-06}\n", - " }\n", - " return kwargs" - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "metadata": {}, - "outputs": [], - "source": [ - "kwargs = configure_simulation()\n", - "results = model.run(**kwargs)" - ] - }, - { - "cell_type": "code", - "execution_count": 7, - "metadata": {}, - "outputs": [ - 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Parameters\n"," self.add_parameter(Parameter(name=\"alpha_a\", expression=\"50\"))\n"," self.add_parameter(Parameter(name=\"alpha_a_prime\", expression=\"500\"))\n"," self.add_parameter(Parameter(name=\"alpha_r\", expression=\"0.01\"))\n"," self.add_parameter(Parameter(name=\"alpha_r_prime\", expression=\"50\"))\n"," self.add_parameter(Parameter(name=\"beta_a\", expression=\"50\"))\n"," self.add_parameter(Parameter(name=\"beta_r\", expression=\"5\"))\n"," self.add_parameter(Parameter(name=\"delta_ma\", expression=\"10\"))\n"," self.add_parameter(Parameter(name=\"delta_mr\", expression=\"0.5\"))\n"," self.add_parameter(Parameter(name=\"delta_a\", expression=\"1\"))\n"," self.add_parameter(Parameter(name=\"delta_r\", expression=\"0.2\"))\n"," self.add_parameter(Parameter(name=\"gamma_a\", expression=\"1\"))\n"," self.add_parameter(Parameter(name=\"gamma_r\", expression=\"1\"))\n"," self.add_parameter(Parameter(name=\"gamma_c\", expression=\"2\"))\n"," self.add_parameter(Parameter(name=\"theta_a\", expression=\"50\"))\n"," self.add_parameter(Parameter(name=\"theta_r\", expression=\"100\"))\n","\n"," # Variables\n"," self.add_species(Species(name=\"Da\", initial_value=1, mode=\"discrete\"))\n"," self.add_species(Species(name=\"Da_prime\", initial_value=0, mode=\"discrete\"))\n"," self.add_species(Species(name=\"Ma\", initial_value=0, mode=\"discrete\"))\n"," self.add_species(Species(name=\"Dr\", initial_value=1, mode=\"discrete\"))\n"," self.add_species(Species(name=\"Dr_prime\", initial_value=0, mode=\"discrete\"))\n"," self.add_species(Species(name=\"Mr\", initial_value=0, mode=\"discrete\"))\n"," self.add_species(Species(name=\"C\", initial_value=10, mode=\"discrete\"))\n"," self.add_species(Species(name=\"A\", initial_value=10, mode=\"discrete\"))\n"," self.add_species(Species(name=\"R\", initial_value=10, mode=\"discrete\"))\n","\n"," # Reactions\n"," self.add_reaction(Reaction(name=\"r1\", reactants={'Da_prime': 1}, products={'Da': 1}, rate=self.listOfParameters[\"theta_a\"]))\n"," self.add_reaction(Reaction(name=\"r2\", reactants={'Da': 1, 'A': 1}, products={'Da_prime': 1}, rate=self.listOfParameters[\"gamma_a\"]))\n"," self.add_reaction(Reaction(name=\"r3\", reactants={'Dr_prime': 1}, products={'Dr': 1}, rate=self.listOfParameters[\"theta_r\"]))\n"," self.add_reaction(Reaction(name=\"r4\", reactants={'Dr': 1, 'A': 1}, products={'Dr_prime': 1}, rate=self.listOfParameters[\"gamma_r\"]))\n"," self.add_reaction(Reaction(name=\"r5\", reactants={'Da_prime': 1}, products={'Da_prime': 1, 'Ma': 1}, rate=self.listOfParameters[\"alpha_a_prime\"]))\n"," self.add_reaction(Reaction(name=\"r6\", reactants={'Da': 1}, products={'Da': 1, 'Ma': 1}, rate=self.listOfParameters[\"alpha_a\"]))\n"," self.add_reaction(Reaction(name=\"r7\", reactants={'Ma': 1}, products={}, rate=self.listOfParameters[\"delta_ma\"]))\n"," self.add_reaction(Reaction(name=\"r8\", reactants={'Ma': 1}, products={'A': 1, 'Ma': 1}, rate=self.listOfParameters[\"beta_a\"]))\n"," self.add_reaction(Reaction(name=\"r9\", reactants={'Da_prime': 1}, products={'Da_prime': 1, 'A': 1}, rate=self.listOfParameters[\"theta_a\"]))\n"," self.add_reaction(Reaction(name=\"r10\", reactants={'Dr_prime': 1}, products={'Dr_prime': 1, 'A': 1}, rate=self.listOfParameters[\"theta_a\"]))\n"," self.add_reaction(Reaction(name=\"r11\", reactants={'A': 1}, products={}, rate=self.listOfParameters[\"gamma_c\"]))\n"," self.add_reaction(Reaction(name=\"r12\", reactants={'A': 1, 'R': 1}, products={'C': 1}, rate=self.listOfParameters[\"gamma_c\"]))\n"," self.add_reaction(Reaction(name=\"r13\", reactants={'Dr_prime': 1}, products={'Dr_prime': 1, 'Mr': 1}, rate=self.listOfParameters[\"alpha_r_prime\"]))\n"," self.add_reaction(Reaction(name=\"r14\", reactants={'Dr': 1}, products={'Dr': 1, 'Mr': 1}, rate=self.listOfParameters[\"alpha_r\"]))\n"," self.add_reaction(Reaction(name=\"r15\", reactants={'Mr': 1}, products={}, rate=self.listOfParameters[\"delta_mr\"]))\n"," self.add_reaction(Reaction(name=\"r16\", reactants={'Mr': 1}, products={'Mr': 1, 'R': 1}, rate=self.listOfParameters[\"beta_r\"]))\n"," self.add_reaction(Reaction(name=\"r17\", reactants={'R': 1}, products={}, rate=self.listOfParameters[\"delta_r\"]))\n"," self.add_reaction(Reaction(name=\"r18\", reactants={'C': 1}, products={'R': 1}, rate=self.listOfParameters[\"delta_a\"]))\n","\n"," # Timespan\n"," self.timespan(np.arange(0, 200, 1))"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["model = VilarOscillator()"]},{"cell_type":"markdown","metadata":{},"source":["# Simulation Parameters"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["def configure_simulation():\n"," # solver = SSACSolver(model=model)\n"," kwargs = {\n"," # \"solver\":solver,\n"," \"number_of_trajectories\":100,\n"," # \"seed\":None,\n"," # \"tau_tol\":0.03,\n"," # \"integrator_options\":{'rtol': 0.001, 'atol': 1e-06},\n"," }\n"," return kwargs"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["kwargs = configure_simulation()\n","results = model.run(**kwargs)"]},{"cell_type":"markdown","metadata":{},"source":["# Visualization"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["results.plotplotly()"]}],"metadata":{},"nbformat":4,"nbformat_minor":4} \ No newline at end of file diff --git a/public_models/Vilar_Oscillator/Vilar_OscillatorSciopeModelExploration.ipynb b/public_models/Vilar_Oscillator/Vilar_OscillatorSciopeModelExploration.ipynb deleted file mode 100644 index 7aa8e36021..0000000000 --- a/public_models/Vilar_Oscillator/Vilar_OscillatorSciopeModelExploration.ipynb +++ /dev/null @@ -1 +0,0 @@ -{"cells":[{"cell_type":"code","execution_count":1,"metadata":{},"outputs":[],"source":["import numpy as np\n","%matplotlib notebook\n","import gillespy2\n","from gillespy2 import Model, Species, Parameter, Reaction, Event, \\\n"," EventTrigger, EventAssignment, RateRule, \\\n"," AssignmentRule, FunctionDefinition\n","# from gillespy2 import SSACSolver\n","from gillespy2 import VariableSSACSolver\n","# from gillespy2 import TauLeapingSolver\n","# from gillespy2 import TauHybridSolver\n","# from gillespy2 import ODESolver"]},{"cell_type":"markdown","metadata":{},"source":["# Vilar_Oscillator"]},{"cell_type":"code","execution_count":2,"metadata":{},"outputs":[],"source":["class VilarOscillator(Model):\n"," def __init__(self, parameter_values=None):\n"," Model.__init__(self, name=\"Vilar_Oscillator\")\n"," self.volume = 1\n","\n"," # Parameters\n"," self.add_parameter(Parameter(name=\"alpha_a\", expression=\"50\"))\n"," self.add_parameter(Parameter(name=\"alpha_a_prime\", expression=\"500\"))\n"," self.add_parameter(Parameter(name=\"alpha_r\", expression=\"0.01\"))\n"," self.add_parameter(Parameter(name=\"alpha_r_prime\", expression=\"50\"))\n"," self.add_parameter(Parameter(name=\"beta_a\", expression=\"50\"))\n"," self.add_parameter(Parameter(name=\"beta_r\", expression=\"5\"))\n"," self.add_parameter(Parameter(name=\"delta_ma\", expression=\"10\"))\n"," self.add_parameter(Parameter(name=\"delta_mr\", expression=\"0.5\"))\n"," self.add_parameter(Parameter(name=\"delta_a\", expression=\"1\"))\n"," self.add_parameter(Parameter(name=\"delta_r\", expression=\"0.2\"))\n"," self.add_parameter(Parameter(name=\"gamma_a\", expression=\"1\"))\n"," self.add_parameter(Parameter(name=\"gamma_r\", expression=\"1\"))\n"," self.add_parameter(Parameter(name=\"gamma_c\", expression=\"2\"))\n"," self.add_parameter(Parameter(name=\"theta_a\", expression=\"50\"))\n"," self.add_parameter(Parameter(name=\"theta_r\", expression=\"100\"))\n","\n"," # Variables\n"," self.add_species(Species(name=\"Da\", initial_value=1, mode=\"discrete\"))\n"," self.add_species(Species(name=\"Da_prime\", initial_value=0, mode=\"discrete\"))\n"," self.add_species(Species(name=\"Ma\", initial_value=0, mode=\"discrete\"))\n"," self.add_species(Species(name=\"Dr\", initial_value=1, mode=\"discrete\"))\n"," self.add_species(Species(name=\"Dr_prime\", initial_value=0, mode=\"discrete\"))\n"," self.add_species(Species(name=\"Mr\", initial_value=0, mode=\"discrete\"))\n"," self.add_species(Species(name=\"C\", initial_value=10, mode=\"discrete\"))\n"," self.add_species(Species(name=\"A\", initial_value=10, mode=\"discrete\"))\n"," self.add_species(Species(name=\"R\", initial_value=10, mode=\"discrete\"))\n","\n"," # Reactions\n"," self.add_reaction(Reaction(name=\"r1\", reactants={'Da_prime': 1}, products={'Da': 1}, rate=self.listOfParameters[\"theta_a\"]))\n"," self.add_reaction(Reaction(name=\"r2\", reactants={'Da': 1, 'A': 1}, products={'Da_prime': 1}, rate=self.listOfParameters[\"gamma_a\"]))\n"," self.add_reaction(Reaction(name=\"r3\", reactants={'Dr_prime': 1}, products={'Dr': 1}, rate=self.listOfParameters[\"theta_r\"]))\n"," self.add_reaction(Reaction(name=\"r4\", reactants={'Dr': 1, 'A': 1}, products={'Dr_prime': 1}, rate=self.listOfParameters[\"gamma_r\"]))\n"," self.add_reaction(Reaction(name=\"r5\", reactants={'Da_prime': 1}, products={'Da_prime': 1, 'Ma': 1}, rate=self.listOfParameters[\"alpha_a_prime\"]))\n"," self.add_reaction(Reaction(name=\"r6\", reactants={'Da': 1}, products={'Da': 1, 'Ma': 1}, rate=self.listOfParameters[\"alpha_a\"]))\n"," self.add_reaction(Reaction(name=\"r7\", reactants={'Ma': 1}, products={}, rate=self.listOfParameters[\"delta_ma\"]))\n"," self.add_reaction(Reaction(name=\"r8\", reactants={'Ma': 1}, products={'A': 1, 'Ma': 1}, rate=self.listOfParameters[\"beta_a\"]))\n"," self.add_reaction(Reaction(name=\"r9\", reactants={'Da_prime': 1}, products={'Da_prime': 1, 'A': 1}, rate=self.listOfParameters[\"theta_a\"]))\n"," self.add_reaction(Reaction(name=\"r10\", reactants={'Dr_prime': 1}, products={'Dr_prime': 1, 'A': 1}, rate=self.listOfParameters[\"theta_a\"]))\n"," self.add_reaction(Reaction(name=\"r11\", reactants={'A': 1}, products={}, rate=self.listOfParameters[\"gamma_c\"]))\n"," self.add_reaction(Reaction(name=\"r12\", reactants={'A': 1, 'R': 1}, products={'C': 1}, rate=self.listOfParameters[\"gamma_c\"]))\n"," self.add_reaction(Reaction(name=\"r13\", reactants={'Dr_prime': 1}, products={'Dr_prime': 1, 'Mr': 1}, rate=self.listOfParameters[\"alpha_r_prime\"]))\n"," self.add_reaction(Reaction(name=\"r14\", reactants={'Dr': 1}, products={'Dr': 1, 'Mr': 1}, rate=self.listOfParameters[\"alpha_r\"]))\n"," self.add_reaction(Reaction(name=\"r15\", reactants={'Mr': 1}, products={}, rate=self.listOfParameters[\"delta_mr\"]))\n"," self.add_reaction(Reaction(name=\"r16\", reactants={'Mr': 1}, products={'Mr': 1, 'R': 1}, rate=self.listOfParameters[\"beta_r\"]))\n"," self.add_reaction(Reaction(name=\"r17\", reactants={'R': 1}, products={}, rate=self.listOfParameters[\"delta_r\"]))\n"," self.add_reaction(Reaction(name=\"r18\", reactants={'C': 1}, products={'R': 1}, rate=self.listOfParameters[\"delta_a\"]))\n","\n"," # Timespan\n"," self.timespan(np.arange(0, 200, 1))"]},{"cell_type":"code","execution_count":3,"metadata":{},"outputs":[],"source":["model = VilarOscillator()"]},{"cell_type":"markdown","metadata":{},"source":["# Simulation Parameters"]},{"cell_type":"code","execution_count":4,"metadata":{},"outputs":[],"source":["def configure_simulation():\n"," solver = VariableSSACSolver(model=model)\n"," kwargs = {\n"," \"solver\":solver,\n"," \"number_of_trajectories\":100,\n"," # \"seed\":None,\n"," # \"tau_tol\":0.03,\n"," # \"integrator_options\":{'rtol': 0.001, 'atol': 1e-06},\n"," }\n"," return kwargs"]},{"cell_type":"markdown","metadata":{},"source":["# Model Exploration"]},{"cell_type":"markdown","metadata":{},"source":["## Define simulator function (using gillespy2 wrapper)"]},{"cell_type":"code","execution_count":5,"metadata":{},"outputs":[],"source":["from sciope.utilities.gillespy2 import wrapper\n","settings = configure_simulation()\n","simulator = wrapper.get_simulator(gillespy_model=model, run_settings=settings, species_of_interest=['Da', 'Da_prime', 'Ma', 'Dr', 'Dr_prime', 'Mr', 'C', 'A', 'R'])\n","expression_array = wrapper.get_parameter_expression_array(model)"]},{"cell_type":"markdown","metadata":{},"source":["## Start local cluster using dask client"]},{"cell_type":"code","execution_count":6,"metadata":{},"outputs":[],"source":["from dask.distributed import Client\n","\n","c = Client()"]},{"cell_type":"markdown","metadata":{},"source":["## Define parameter sampler/design and summary statistics"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[{"name":"stderr","output_type":"stream","text":["distributed.nanny - WARNING - Worker exceeded 95% memory budget. Restarting\n","distributed.nanny - WARNING - Restarting worker\n","distributed.nanny - WARNING - Worker exceeded 95% memory budget. Restarting\n","distributed.nanny - WARNING - Restarting worker\n"]}],"source":["from sciope.designs import latin_hypercube_sampling\n","from sciope.utilities.summarystats.auto_tsfresh import SummariesTSFRESH\n","\n","lhc = latin_hypercube_sampling.LatinHypercube(xmin=expression_array, xmax=expression_array*3)\n","lhc.generate_array(1000) # creates a LHD of size 1000\n","\n","# will use default minimal set of features\n","summary_stats = SummariesTSFRESH()"]},{"cell_type":"markdown","metadata":{},"source":["## Initiate StochMET"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["from sciope.stochmet.stochmet import StochMET\n","\n","met = StochMET(simulator, lhc, summary_stats)"]},{"cell_type":"markdown","metadata":{},"source":["## Run parameter sweep"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["met.compute(n_points=500, chunk_size=10)"]},{"cell_type":"markdown","metadata":{},"source":["## Explore the result"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["# First lets add some appropiate information about the model and features\n","met.data.configurations['listOfParameters'] = list(model.listOfParameters.keys())\n","met.data.configurations['listOfSpecies'] = list(model.listOfSpecies.keys())\n","met.data.configurations['listOfSummaries'] = met.summaries.features\n","met.data.configurations['timepoints'] = model.tspan"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["# Here we use UMAP for dimension reduction\n","met.explore(dr_method='umap')"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["from sciope.models.label_propagation import LPModel\n","# here lets use the dimension reduction embedding as input data\n","data = met.dr_model.embedding_\n","\n","model_lp = LPModel()\n","# train using basinhopping\n","model_lp.train(data, met.data.user_labels, min_=0.01, max_=10, niter=50)"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["# just to vislualize the result we will map the label distribution to the user_labels\n","# (will enable us to see the LP model output when using method 'explore')\n","user_labels = np.copy(met.data.user_labels)\n","# takes the label corresponding to index 0\n","met.data.user_labels = model_lp.model.label_distributions_[:, 0]"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["met.explore(dr_method='umap')"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["met.data.user_labels = user_labels"]}],"metadata":{"kernelspec":{"display_name":"Python 3","language":"python","name":"python3"},"language_info":{"codemirror_mode":{"name":"ipython","version":3},"file_extension":".py","mimetype":"text/x-python","name":"python","nbconvert_exporter":"python","pygments_lexer":"ipython3","version":"3.8.5"}},"nbformat":4,"nbformat_minor":4} \ No newline at end of file diff --git a/public_models/Vilar_Oscillator/Vilar_OscillatorSciopeModelInference.ipynb b/public_models/Vilar_Oscillator/Vilar_OscillatorSciopeModelInference.ipynb deleted file mode 100644 index c580ee7b7a..0000000000 --- a/public_models/Vilar_Oscillator/Vilar_OscillatorSciopeModelInference.ipynb +++ /dev/null @@ -1 +0,0 @@ -{"cells":[{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["import numpy as np\n","import gillespy2\n","from gillespy2 import Model, Species, Parameter, Reaction, Event, \\\n"," EventTrigger, EventAssignment, RateRule, \\\n"," AssignmentRule, FunctionDefinition\n","# from gillespy2 import SSACSolver\n","from gillespy2 import VariableSSACSolver\n","# from gillespy2 import TauLeapingSolver\n","# from gillespy2 import TauHybridSolver\n","# from gillespy2 import ODESolver"]},{"cell_type":"markdown","metadata":{},"source":["# Vilar_Oscillator"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["class VilarOscillator(Model):\n"," def __init__(self, parameter_values=None):\n"," Model.__init__(self, name=\"Vilar_Oscillator\")\n"," self.volume = 1\n","\n"," # Parameters\n"," self.add_parameter(Parameter(name=\"alpha_a\", expression=\"50\"))\n"," self.add_parameter(Parameter(name=\"alpha_a_prime\", expression=\"500\"))\n"," self.add_parameter(Parameter(name=\"alpha_r\", expression=\"0.01\"))\n"," self.add_parameter(Parameter(name=\"alpha_r_prime\", expression=\"50\"))\n"," self.add_parameter(Parameter(name=\"beta_a\", expression=\"50\"))\n"," self.add_parameter(Parameter(name=\"beta_r\", expression=\"5\"))\n"," self.add_parameter(Parameter(name=\"delta_ma\", expression=\"10\"))\n"," self.add_parameter(Parameter(name=\"delta_mr\", expression=\"0.5\"))\n"," self.add_parameter(Parameter(name=\"delta_a\", expression=\"1\"))\n"," self.add_parameter(Parameter(name=\"delta_r\", expression=\"0.2\"))\n"," self.add_parameter(Parameter(name=\"gamma_a\", expression=\"1\"))\n"," self.add_parameter(Parameter(name=\"gamma_r\", expression=\"1\"))\n"," self.add_parameter(Parameter(name=\"gamma_c\", expression=\"2\"))\n"," self.add_parameter(Parameter(name=\"theta_a\", expression=\"50\"))\n"," self.add_parameter(Parameter(name=\"theta_r\", expression=\"100\"))\n","\n"," # Variables\n"," self.add_species(Species(name=\"Da\", initial_value=1, mode=\"discrete\"))\n"," self.add_species(Species(name=\"Da_prime\", initial_value=0, mode=\"discrete\"))\n"," self.add_species(Species(name=\"Ma\", initial_value=0, mode=\"discrete\"))\n"," self.add_species(Species(name=\"Dr\", initial_value=1, mode=\"discrete\"))\n"," self.add_species(Species(name=\"Dr_prime\", initial_value=0, mode=\"discrete\"))\n"," self.add_species(Species(name=\"Mr\", initial_value=0, mode=\"discrete\"))\n"," self.add_species(Species(name=\"C\", initial_value=10, mode=\"discrete\"))\n"," self.add_species(Species(name=\"A\", initial_value=10, mode=\"discrete\"))\n"," self.add_species(Species(name=\"R\", initial_value=10, mode=\"discrete\"))\n","\n"," # Reactions\n"," self.add_reaction(Reaction(name=\"r1\", reactants={'Da_prime': 1}, products={'Da': 1}, rate=self.listOfParameters[\"theta_a\"]))\n"," self.add_reaction(Reaction(name=\"r2\", reactants={'Da': 1, 'A': 1}, products={'Da_prime': 1}, rate=self.listOfParameters[\"gamma_a\"]))\n"," self.add_reaction(Reaction(name=\"r3\", reactants={'Dr_prime': 1}, products={'Dr': 1}, rate=self.listOfParameters[\"theta_r\"]))\n"," self.add_reaction(Reaction(name=\"r4\", reactants={'Dr': 1, 'A': 1}, products={'Dr_prime': 1}, rate=self.listOfParameters[\"gamma_r\"]))\n"," self.add_reaction(Reaction(name=\"r5\", reactants={'Da_prime': 1}, products={'Da_prime': 1, 'Ma': 1}, rate=self.listOfParameters[\"alpha_a_prime\"]))\n"," self.add_reaction(Reaction(name=\"r6\", reactants={'Da': 1}, products={'Da': 1, 'Ma': 1}, rate=self.listOfParameters[\"alpha_a\"]))\n"," self.add_reaction(Reaction(name=\"r7\", reactants={'Ma': 1}, products={}, rate=self.listOfParameters[\"delta_ma\"]))\n"," self.add_reaction(Reaction(name=\"r8\", reactants={'Ma': 1}, products={'A': 1, 'Ma': 1}, rate=self.listOfParameters[\"beta_a\"]))\n"," self.add_reaction(Reaction(name=\"r9\", reactants={'Da_prime': 1}, products={'Da_prime': 1, 'A': 1}, rate=self.listOfParameters[\"theta_a\"]))\n"," self.add_reaction(Reaction(name=\"r10\", reactants={'Dr_prime': 1}, products={'Dr_prime': 1, 'A': 1}, rate=self.listOfParameters[\"theta_a\"]))\n"," self.add_reaction(Reaction(name=\"r11\", reactants={'A': 1}, products={}, rate=self.listOfParameters[\"gamma_c\"]))\n"," self.add_reaction(Reaction(name=\"r12\", reactants={'A': 1, 'R': 1}, products={'C': 1}, rate=self.listOfParameters[\"gamma_c\"]))\n"," self.add_reaction(Reaction(name=\"r13\", reactants={'Dr_prime': 1}, products={'Dr_prime': 1, 'Mr': 1}, rate=self.listOfParameters[\"alpha_r_prime\"]))\n"," self.add_reaction(Reaction(name=\"r14\", reactants={'Dr': 1}, products={'Dr': 1, 'Mr': 1}, rate=self.listOfParameters[\"alpha_r\"]))\n"," self.add_reaction(Reaction(name=\"r15\", reactants={'Mr': 1}, products={}, rate=self.listOfParameters[\"delta_mr\"]))\n"," self.add_reaction(Reaction(name=\"r16\", reactants={'Mr': 1}, products={'Mr': 1, 'R': 1}, rate=self.listOfParameters[\"beta_r\"]))\n"," self.add_reaction(Reaction(name=\"r17\", reactants={'R': 1}, products={}, rate=self.listOfParameters[\"delta_r\"]))\n"," self.add_reaction(Reaction(name=\"r18\", reactants={'C': 1}, products={'R': 1}, rate=self.listOfParameters[\"delta_a\"]))\n","\n"," # Timespan\n"," self.timespan(np.arange(0, 200, 1))"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["model = VilarOscillator()"]},{"cell_type":"markdown","metadata":{},"source":["# Simulation Parameters"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["def configure_simulation():\n"," solver = VariableSSACSolver(model=model)\n"," kwargs = {\n"," \"solver\":solver,\n"," \"number_of_trajectories\":100,\n"," # \"seed\":None,\n"," # \"tau_tol\":0.03,\n"," # \"integrator_options\":{'rtol': 0.001, 'atol': 1e-06},\n"," }\n"," return kwargs"]},{"cell_type":"markdown","metadata":{},"source":["# Model Inference"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["%load_ext autoreload\n","%autoreload 2\n","\n","from tsfresh.feature_extraction.settings import MinimalFCParameters\n","from sciope.utilities.priors import uniform_prior\n","from sciope.utilities.summarystats import auto_tsfresh\n","from sciope.utilities.distancefunctions import naive_squared\n","from sciope.inference.abc_inference import ABC\n","from sklearn.metrics import mean_absolute_error\n","from dask.distributed import Client"]},{"cell_type":"markdown","metadata":{},"source":["## Generate some fixed(observed) data based on default parameters of the model"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["kwargs = configure_simulation()\n","fixed_data = model.run(**kwargs)"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["# Reshape the data and remove timepoints array\n","fixed_data = fixed_data.to_array()\n","fixed_data = np.asarray([x.T for x in fixed_data])\n","fixed_data = fixed_data[:, 1:, :]"]},{"cell_type":"markdown","metadata":{},"source":["## Define prior distribution"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["# take default from mode 1 as reference\n","default_param = np.array(list(model.listOfParameters.items()))[:, 1]\n","\n","bound = []\n","for exp in default_param:\n"," bound.append(float(exp.expression))\n","\n","# Set the bounds\n","bound = np.array(bound)\n","dmin = bound * 0.1\n","dmax = bound * 2.0\n","\n","# Here we use uniform prior\n","uni_prior = uniform_prior.UniformPrior(dmin, dmax)"]},{"cell_type":"markdown","metadata":{},"source":["## Define simulator"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["def get_variables(params, model):\n"," # params - array, need to have the same order as model.listOfParameters\n"," variables = {}\n"," for e, pname in enumerate(model.listOfParameters.keys()):\n"," variables[pname] = params[e]\n"," return variables\n","\n","# Here we use the GillesPy2 Solver\n","def simulator(params, model):\n"," variables = get_variables(params, model)\n","\n"," res = model.run(**kwargs, variables=variables)\n"," res = res.to_array()\n"," tot_res = np.asarray([x.T for x in res]) # reshape to (N, S, T)\n"," # should not contain timepoints\n"," tot_res = tot_res[:, 1:, :]\n","\n"," return tot_res\n","\n","# Wrapper, simulator function to abc should should only take one argument (the parameter point)\n","def simulator2(x):\n"," return simulator(x, model=model)"]},{"cell_type":"markdown","metadata":{},"source":["## Define summary statistics and distance function"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["# Function to generate summary statistics\n","summ_func = auto_tsfresh.SummariesTSFRESH()\n","\n","# Distance\n","ns = naive_squared.NaiveSquaredDistance()"]},{"cell_type":"markdown","metadata":{},"source":["## Start local cluster using dask client"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["c = Client()"]},{"cell_type":"markdown","metadata":{},"source":["## Start abc instance"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["abc = ABC(fixed_data, sim=simulator2, prior_function=uni_prior, summaries_function=summ_func.compute, distance_function=ns)"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["# First compute the fixed(observed) mean\n","abc.compute_fixed_mean(chunk_size=2)"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["res = abc.infer(num_samples=100, batch_size=10, chunk_size=2)"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["mae_inference = mean_absolute_error(bound, abc.results['inferred_parameters'])"]}],"metadata":{"kernelspec":{"display_name":"Python 3","language":"python","name":"python3"},"language_info":{"codemirror_mode":{"name":"ipython","version":3},"file_extension":".py","mimetype":"text/x-python","name":"python","nbconvert_exporter":"python","pygments_lexer":"ipython3","version":"3.8.5"}},"nbformat":4,"nbformat_minor":4} \ No newline at end of file diff --git a/public_models/Vilar_Oscillator/Vilar_Oscillator_SCIOPE_Model_Exploration.ipynb b/public_models/Vilar_Oscillator/Vilar_Oscillator_SCIOPE_Model_Exploration.ipynb new file mode 100644 index 0000000000..ffdbb77f69 --- /dev/null +++ b/public_models/Vilar_Oscillator/Vilar_Oscillator_SCIOPE_Model_Exploration.ipynb @@ -0,0 +1 @@ +{"cells":[{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["import numpy as np\n","%matplotlib notebook\n","import gillespy2\n","from gillespy2 import Model, Species, Parameter, Reaction, Event, \\\n"," EventTrigger, EventAssignment, RateRule, \\\n"," AssignmentRule, FunctionDefinition\n","from gillespy2 import SSACSolver\n","# from gillespy2 import TauLeapingCSolver\n","# from gillespy2 import ODECSolver\n","# from gillespy2 import TauHybridSolver"]},{"cell_type":"markdown","metadata":{},"source":["# Vilar_Oscillator"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["class VilarOscillator(Model):\n"," def __init__(self, parameter_values=None):\n"," Model.__init__(self, name=\"Vilar_Oscillator\")\n"," self.volume = 1\n","\n"," # Parameters\n"," self.add_parameter(Parameter(name=\"alpha_a\", expression=\"50\"))\n"," self.add_parameter(Parameter(name=\"alpha_a_prime\", expression=\"500\"))\n"," self.add_parameter(Parameter(name=\"alpha_r\", expression=\"0.01\"))\n"," self.add_parameter(Parameter(name=\"alpha_r_prime\", expression=\"50\"))\n"," self.add_parameter(Parameter(name=\"beta_a\", expression=\"50\"))\n"," self.add_parameter(Parameter(name=\"beta_r\", expression=\"5\"))\n"," self.add_parameter(Parameter(name=\"delta_ma\", expression=\"10\"))\n"," self.add_parameter(Parameter(name=\"delta_mr\", expression=\"0.5\"))\n"," self.add_parameter(Parameter(name=\"delta_a\", expression=\"1\"))\n"," self.add_parameter(Parameter(name=\"delta_r\", expression=\"0.2\"))\n"," self.add_parameter(Parameter(name=\"gamma_a\", expression=\"1\"))\n"," self.add_parameter(Parameter(name=\"gamma_r\", expression=\"1\"))\n"," self.add_parameter(Parameter(name=\"gamma_c\", expression=\"2\"))\n"," self.add_parameter(Parameter(name=\"theta_a\", expression=\"50\"))\n"," self.add_parameter(Parameter(name=\"theta_r\", expression=\"100\"))\n","\n"," # Variables\n"," self.add_species(Species(name=\"Da\", initial_value=1, mode=\"discrete\"))\n"," self.add_species(Species(name=\"Da_prime\", initial_value=0, mode=\"discrete\"))\n"," self.add_species(Species(name=\"Ma\", initial_value=0, mode=\"discrete\"))\n"," self.add_species(Species(name=\"Dr\", initial_value=1, mode=\"discrete\"))\n"," self.add_species(Species(name=\"Dr_prime\", initial_value=0, mode=\"discrete\"))\n"," self.add_species(Species(name=\"Mr\", initial_value=0, mode=\"discrete\"))\n"," self.add_species(Species(name=\"C\", initial_value=10, mode=\"discrete\"))\n"," self.add_species(Species(name=\"A\", initial_value=10, mode=\"discrete\"))\n"," self.add_species(Species(name=\"R\", initial_value=10, mode=\"discrete\"))\n","\n"," # Reactions\n"," self.add_reaction(Reaction(name=\"r1\", reactants={'Da_prime': 1}, products={'Da': 1}, rate=self.listOfParameters[\"theta_a\"]))\n"," self.add_reaction(Reaction(name=\"r2\", reactants={'Da': 1, 'A': 1}, products={'Da_prime': 1}, rate=self.listOfParameters[\"gamma_a\"]))\n"," self.add_reaction(Reaction(name=\"r3\", reactants={'Dr_prime': 1}, products={'Dr': 1}, rate=self.listOfParameters[\"theta_r\"]))\n"," self.add_reaction(Reaction(name=\"r4\", reactants={'Dr': 1, 'A': 1}, products={'Dr_prime': 1}, rate=self.listOfParameters[\"gamma_r\"]))\n"," self.add_reaction(Reaction(name=\"r5\", reactants={'Da_prime': 1}, products={'Da_prime': 1, 'Ma': 1}, rate=self.listOfParameters[\"alpha_a_prime\"]))\n"," self.add_reaction(Reaction(name=\"r6\", reactants={'Da': 1}, products={'Da': 1, 'Ma': 1}, rate=self.listOfParameters[\"alpha_a\"]))\n"," self.add_reaction(Reaction(name=\"r7\", reactants={'Ma': 1}, products={}, rate=self.listOfParameters[\"delta_ma\"]))\n"," self.add_reaction(Reaction(name=\"r8\", reactants={'Ma': 1}, products={'A': 1, 'Ma': 1}, rate=self.listOfParameters[\"beta_a\"]))\n"," self.add_reaction(Reaction(name=\"r9\", reactants={'Da_prime': 1}, products={'Da_prime': 1, 'A': 1}, rate=self.listOfParameters[\"theta_a\"]))\n"," self.add_reaction(Reaction(name=\"r10\", reactants={'Dr_prime': 1}, products={'Dr_prime': 1, 'A': 1}, rate=self.listOfParameters[\"theta_a\"]))\n"," self.add_reaction(Reaction(name=\"r11\", reactants={'A': 1}, products={}, rate=self.listOfParameters[\"gamma_c\"]))\n"," self.add_reaction(Reaction(name=\"r12\", reactants={'A': 1, 'R': 1}, products={'C': 1}, rate=self.listOfParameters[\"gamma_c\"]))\n"," self.add_reaction(Reaction(name=\"r13\", reactants={'Dr_prime': 1}, products={'Dr_prime': 1, 'Mr': 1}, rate=self.listOfParameters[\"alpha_r_prime\"]))\n"," self.add_reaction(Reaction(name=\"r14\", reactants={'Dr': 1}, products={'Dr': 1, 'Mr': 1}, rate=self.listOfParameters[\"alpha_r\"]))\n"," self.add_reaction(Reaction(name=\"r15\", reactants={'Mr': 1}, products={}, rate=self.listOfParameters[\"delta_mr\"]))\n"," self.add_reaction(Reaction(name=\"r16\", reactants={'Mr': 1}, products={'Mr': 1, 'R': 1}, rate=self.listOfParameters[\"beta_r\"]))\n"," self.add_reaction(Reaction(name=\"r17\", reactants={'R': 1}, products={}, rate=self.listOfParameters[\"delta_r\"]))\n"," self.add_reaction(Reaction(name=\"r18\", reactants={'C': 1}, products={'R': 1}, rate=self.listOfParameters[\"delta_a\"]))\n","\n"," # Timespan\n"," self.timespan(np.arange(0, 200, 1))"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["model = VilarOscillator()"]},{"cell_type":"markdown","metadata":{},"source":["# Simulation Parameters"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["def configure_simulation():\n"," solver = SSACSolver(model=model)\n"," kwargs = {\n"," \"solver\":solver,\n"," \"number_of_trajectories\":100,\n"," # \"seed\":None,\n"," # \"tau_tol\":0.03,\n"," # \"integrator_options\":{'rtol': 0.001, 'atol': 1e-06},\n"," }\n"," return kwargs"]},{"cell_type":"markdown","metadata":{},"source":["# Model Exploration"]},{"cell_type":"markdown","metadata":{},"source":["## Define simulator function (using gillespy2 wrapper)"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["from sciope.utilities.gillespy2 import wrapper\n","settings = configure_simulation()\n","simulator = wrapper.get_simulator(gillespy_model=model, run_settings=settings, species_of_interest=['Da', 'Da_prime', 'Ma', 'Dr', 'Dr_prime', 'Mr', 'C', 'A', 'R'])\n","expression_array = wrapper.get_parameter_expression_array(model)"]},{"cell_type":"markdown","metadata":{},"source":["## Start local cluster using dask client"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["from dask.distributed import Client\n","\n","c = Client()"]},{"cell_type":"markdown","metadata":{},"source":["## Define parameter sampler/design and summary statistics"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["from sciope.designs import latin_hypercube_sampling\n","from sciope.utilities.summarystats.auto_tsfresh import SummariesTSFRESH\n","\n","lhc = latin_hypercube_sampling.LatinHypercube(xmin=expression_array, xmax=expression_array*3)\n","lhc.generate_array(1000) # creates a LHD of size 1000\n","\n","# will use default minimal set of features\n","summary_stats = SummariesTSFRESH()"]},{"cell_type":"markdown","metadata":{},"source":["## Initiate StochMET"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["from sciope.stochmet.stochmet import StochMET\n","\n","met = StochMET(simulator, lhc, summary_stats)"]},{"cell_type":"markdown","metadata":{},"source":["## Run parameter sweep"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["met.compute(n_points=500, chunk_size=10)"]},{"cell_type":"markdown","metadata":{},"source":["## Explore the result"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["# First lets add some appropiate information about the model and features\n","met.data.configurations['listOfParameters'] = list(model.listOfParameters.keys())\n","met.data.configurations['listOfSpecies'] = list(model.listOfSpecies.keys())\n","met.data.configurations['listOfSummaries'] = met.summaries.features\n","met.data.configurations['timepoints'] = model.tspan"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["# Here we use UMAP for dimension reduction\n","met.explore(dr_method='umap')"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["from sciope.models.label_propagation import LPModel\n","# here lets use the dimension reduction embedding as input data\n","data = met.dr_model.embedding_\n","\n","model_lp = LPModel()\n","# train using basinhopping\n","model_lp.train(data, met.data.user_labels, min_=0.01, max_=10, niter=50)"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["# just to vislualize the result we will map the label distribution to the user_labels\n","# (will enable us to see the LP model output when using method 'explore')\n","user_labels = np.copy(met.data.user_labels)\n","# takes the label corresponding to index 0\n","met.data.user_labels = model_lp.model.label_distributions_[:, 0]"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["met.explore(dr_method='umap')"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["met.data.user_labels = user_labels"]}],"metadata":{},"nbformat":4,"nbformat_minor":4} \ No newline at end of file diff --git a/public_models/Vilar_Oscillator/Vilar_Oscillator_SCIOPE_Model_Inference.ipynb b/public_models/Vilar_Oscillator/Vilar_Oscillator_SCIOPE_Model_Inference.ipynb new file mode 100644 index 0000000000..2d512ebf14 --- /dev/null +++ b/public_models/Vilar_Oscillator/Vilar_Oscillator_SCIOPE_Model_Inference.ipynb @@ -0,0 +1 @@ +{"cells":[{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["import numpy as np\n","import gillespy2\n","from gillespy2 import Model, Species, Parameter, Reaction, Event, \\\n"," EventTrigger, EventAssignment, RateRule, \\\n"," AssignmentRule, FunctionDefinition\n","from gillespy2 import SSACSolver\n","# from gillespy2 import TauLeapingCSolver\n","# from gillespy2 import ODECSolver\n","# from gillespy2 import TauHybridSolver"]},{"cell_type":"markdown","metadata":{},"source":["# Vilar_Oscillator"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["class VilarOscillator(Model):\n"," def __init__(self, parameter_values=None):\n"," Model.__init__(self, name=\"Vilar_Oscillator\")\n"," self.volume = 1\n","\n"," # Parameters\n"," self.add_parameter(Parameter(name=\"alpha_a\", expression=\"50\"))\n"," self.add_parameter(Parameter(name=\"alpha_a_prime\", expression=\"500\"))\n"," self.add_parameter(Parameter(name=\"alpha_r\", expression=\"0.01\"))\n"," self.add_parameter(Parameter(name=\"alpha_r_prime\", expression=\"50\"))\n"," self.add_parameter(Parameter(name=\"beta_a\", expression=\"50\"))\n"," self.add_parameter(Parameter(name=\"beta_r\", expression=\"5\"))\n"," self.add_parameter(Parameter(name=\"delta_ma\", expression=\"10\"))\n"," self.add_parameter(Parameter(name=\"delta_mr\", expression=\"0.5\"))\n"," self.add_parameter(Parameter(name=\"delta_a\", expression=\"1\"))\n"," self.add_parameter(Parameter(name=\"delta_r\", expression=\"0.2\"))\n"," self.add_parameter(Parameter(name=\"gamma_a\", expression=\"1\"))\n"," self.add_parameter(Parameter(name=\"gamma_r\", expression=\"1\"))\n"," self.add_parameter(Parameter(name=\"gamma_c\", expression=\"2\"))\n"," self.add_parameter(Parameter(name=\"theta_a\", expression=\"50\"))\n"," self.add_parameter(Parameter(name=\"theta_r\", expression=\"100\"))\n","\n"," # Variables\n"," self.add_species(Species(name=\"Da\", initial_value=1, mode=\"discrete\"))\n"," self.add_species(Species(name=\"Da_prime\", initial_value=0, mode=\"discrete\"))\n"," self.add_species(Species(name=\"Ma\", initial_value=0, mode=\"discrete\"))\n"," self.add_species(Species(name=\"Dr\", initial_value=1, mode=\"discrete\"))\n"," self.add_species(Species(name=\"Dr_prime\", initial_value=0, mode=\"discrete\"))\n"," self.add_species(Species(name=\"Mr\", initial_value=0, mode=\"discrete\"))\n"," self.add_species(Species(name=\"C\", initial_value=10, mode=\"discrete\"))\n"," self.add_species(Species(name=\"A\", initial_value=10, mode=\"discrete\"))\n"," self.add_species(Species(name=\"R\", initial_value=10, mode=\"discrete\"))\n","\n"," # Reactions\n"," self.add_reaction(Reaction(name=\"r1\", reactants={'Da_prime': 1}, products={'Da': 1}, rate=self.listOfParameters[\"theta_a\"]))\n"," self.add_reaction(Reaction(name=\"r2\", reactants={'Da': 1, 'A': 1}, products={'Da_prime': 1}, rate=self.listOfParameters[\"gamma_a\"]))\n"," self.add_reaction(Reaction(name=\"r3\", reactants={'Dr_prime': 1}, products={'Dr': 1}, rate=self.listOfParameters[\"theta_r\"]))\n"," self.add_reaction(Reaction(name=\"r4\", reactants={'Dr': 1, 'A': 1}, products={'Dr_prime': 1}, rate=self.listOfParameters[\"gamma_r\"]))\n"," self.add_reaction(Reaction(name=\"r5\", reactants={'Da_prime': 1}, products={'Da_prime': 1, 'Ma': 1}, rate=self.listOfParameters[\"alpha_a_prime\"]))\n"," self.add_reaction(Reaction(name=\"r6\", reactants={'Da': 1}, products={'Da': 1, 'Ma': 1}, rate=self.listOfParameters[\"alpha_a\"]))\n"," self.add_reaction(Reaction(name=\"r7\", reactants={'Ma': 1}, products={}, rate=self.listOfParameters[\"delta_ma\"]))\n"," self.add_reaction(Reaction(name=\"r8\", reactants={'Ma': 1}, products={'A': 1, 'Ma': 1}, rate=self.listOfParameters[\"beta_a\"]))\n"," self.add_reaction(Reaction(name=\"r9\", reactants={'Da_prime': 1}, products={'Da_prime': 1, 'A': 1}, rate=self.listOfParameters[\"theta_a\"]))\n"," self.add_reaction(Reaction(name=\"r10\", reactants={'Dr_prime': 1}, products={'Dr_prime': 1, 'A': 1}, rate=self.listOfParameters[\"theta_a\"]))\n"," self.add_reaction(Reaction(name=\"r11\", reactants={'A': 1}, products={}, rate=self.listOfParameters[\"gamma_c\"]))\n"," self.add_reaction(Reaction(name=\"r12\", reactants={'A': 1, 'R': 1}, products={'C': 1}, rate=self.listOfParameters[\"gamma_c\"]))\n"," self.add_reaction(Reaction(name=\"r13\", reactants={'Dr_prime': 1}, products={'Dr_prime': 1, 'Mr': 1}, rate=self.listOfParameters[\"alpha_r_prime\"]))\n"," self.add_reaction(Reaction(name=\"r14\", reactants={'Dr': 1}, products={'Dr': 1, 'Mr': 1}, rate=self.listOfParameters[\"alpha_r\"]))\n"," self.add_reaction(Reaction(name=\"r15\", reactants={'Mr': 1}, products={}, rate=self.listOfParameters[\"delta_mr\"]))\n"," self.add_reaction(Reaction(name=\"r16\", reactants={'Mr': 1}, products={'Mr': 1, 'R': 1}, rate=self.listOfParameters[\"beta_r\"]))\n"," self.add_reaction(Reaction(name=\"r17\", reactants={'R': 1}, products={}, rate=self.listOfParameters[\"delta_r\"]))\n"," self.add_reaction(Reaction(name=\"r18\", reactants={'C': 1}, products={'R': 1}, rate=self.listOfParameters[\"delta_a\"]))\n","\n"," # Timespan\n"," self.timespan(np.arange(0, 200, 1))"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["model = VilarOscillator()"]},{"cell_type":"markdown","metadata":{},"source":["# Simulation Parameters"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["def configure_simulation():\n"," solver = SSACSolver(model=model)\n"," kwargs = {\n"," \"solver\":solver,\n"," \"number_of_trajectories\":100,\n"," # \"seed\":None,\n"," # \"tau_tol\":0.03,\n"," # \"integrator_options\":{'rtol': 0.001, 'atol': 1e-06},\n"," }\n"," return kwargs"]},{"cell_type":"markdown","metadata":{},"source":["# Model Inference"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["%load_ext autoreload\n","%autoreload 2\n","\n","from tsfresh.feature_extraction.settings import MinimalFCParameters\n","from sciope.utilities.priors import uniform_prior\n","from sciope.utilities.summarystats import auto_tsfresh\n","from sciope.utilities.distancefunctions import naive_squared\n","from sciope.inference.abc_inference import ABC\n","from sklearn.metrics import mean_absolute_error\n","from dask.distributed import Client"]},{"cell_type":"markdown","metadata":{},"source":["## Generate some fixed(observed) data based on default parameters of the model"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["kwargs = configure_simulation()\n","fixed_data = model.run(**kwargs)"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["# Reshape the data and remove timepoints array\n","fixed_data = fixed_data.to_array()\n","fixed_data = np.asarray([x.T for x in fixed_data])\n","fixed_data = fixed_data[:, 1:, :]"]},{"cell_type":"markdown","metadata":{},"source":["## Define prior distribution"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["# take default from mode 1 as reference\n","default_param = np.array(list(model.listOfParameters.items()))[:, 1]\n","\n","bound = []\n","for exp in default_param:\n"," bound.append(float(exp.expression))\n","\n","# Set the bounds\n","bound = np.array(bound)\n","dmin = bound * 0.1\n","dmax = bound * 2.0\n","\n","# Here we use uniform prior\n","uni_prior = uniform_prior.UniformPrior(dmin, dmax)"]},{"cell_type":"markdown","metadata":{},"source":["## Define simulator"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["def get_variables(params, model):\n"," # params - array, need to have the same order as model.listOfParameters\n"," variables = {}\n"," for e, pname in enumerate(model.listOfParameters.keys()):\n"," variables[pname] = params[e]\n"," return variables\n","\n","# Here we use the GillesPy2 Solver\n","def simulator(params, model):\n"," variables = get_variables(params, model)\n","\n"," res = model.run(**kwargs, variables=variables)\n"," res = res.to_array()\n"," tot_res = np.asarray([x.T for x in res]) # reshape to (N, S, T)\n"," # should not contain timepoints\n"," tot_res = tot_res[:, 1:, :]\n","\n"," return tot_res\n","\n","# Wrapper, simulator function to abc should should only take one argument (the parameter point)\n","def simulator2(x):\n"," return simulator(x, model=model)"]},{"cell_type":"markdown","metadata":{},"source":["## Define summary statistics and distance function"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["# Function to generate summary statistics\n","summ_func = auto_tsfresh.SummariesTSFRESH()\n","\n","# Distance\n","ns = naive_squared.NaiveSquaredDistance()"]},{"cell_type":"markdown","metadata":{},"source":["## Start local cluster using dask client"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["c = Client()"]},{"cell_type":"markdown","metadata":{},"source":["## Start abc instance"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["abc = ABC(fixed_data, sim=simulator2, prior_function=uni_prior, summaries_function=summ_func.compute, distance_function=ns)"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["# First compute the fixed(observed) mean\n","abc.compute_fixed_mean(chunk_size=2)"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["res = abc.infer(num_samples=100, batch_size=10, chunk_size=2)"]},{"cell_type":"code","execution_count":null,"metadata":{},"outputs":[],"source":["mae_inference = mean_absolute_error(bound, abc.results['inferred_parameters'])"]}],"metadata":{},"nbformat":4,"nbformat_minor":4} \ No newline at end of file diff --git a/requirements.txt b/requirements.txt index 17dedc446f..eb3d418969 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,7 +1,7 @@ python-libsbml==5.18.0 python-libsedml==2.0.9 python-libcombine==0.2.7 -gillespy2==1.5.7 +gillespy2==1.5.11 sciope==0.4 pygmsh==5.0.2 meshio==2.3.10 diff --git a/stochss/dist/stochss-loading-page.html b/stochss/dist/stochss-loading-page.html new file mode 100644 index 0000000000..0fc52098f5 --- /dev/null +++ b/stochss/dist/stochss-loading-page.html @@ -0,0 +1,4 @@ + \ No newline at end of file diff --git a/stochss/handlers/__init__.py b/stochss/handlers/__init__.py index 1320db3450..426635b43e 100644 --- a/stochss/handlers/__init__.py +++ b/stochss/handlers/__init__.py @@ -48,19 +48,24 @@ def get_page_handlers(route_start): (r'/stochss/quickstart\/?', QuickstartHandler), (r'/stochss/project/browser\/?', ProjectBrowserHandler), (r'/stochss/project/manager\/?', ProjectManagerHandler), + (r'/stochss/loading-page\/?', LoadingPageHandler), + (r'/stochss/multiple-plots\/?', MultiplePlotsHandler), # ## API Handlers # + (r'/stochss/api/user-logs\/?', UserLogsAPIHandler), (r"/stochss/api/file/browser-list\/?", ModelBrowserFileList), (r"/stochss/api/file/upload\/?", UploadFileAPIHandler), (r"/stochss/api/file/upload-from-link\/?", UploadFileFromLinkAPIHandler), (r"/stochss/api/file/move\/?", MoveFileAPIHandler), + (r"/stochss/api/file/empty-trash\/?", EmptyTrashAPIHandler), (r"/stochss/api/file/delete\/?", DeleteFileAPIHandler), (r"/stochss/api/file/rename\/?", RenameAPIHandler), (r"/stochss/api/file/download\/?", DownloadAPIHandler), (r"/stochss/api/file/download-zip\/?", DownloadZipFileAPIHandler), (r"/stochss/api/file/json-data\/?", JsonFileAPIHandler), (r"/stochss/api/file/duplicate\/?", DuplicateModelHandler), + (r"/stochss/api/file/unzip\/?", UnzipFileAPIHandler), (r"/stochss/api/directory/duplicate\/?", DuplicateDirectoryHandler), (r"/stochss/api/directory/create\/?", CreateDirectoryHandler), (r"/stochss/api/spatial/to-model\/?", ConvertToModelAPIHandler), @@ -80,25 +85,26 @@ def get_page_handlers(route_start): (r"/stochss/api/project/new-project\/?", NewProjectAPIHandler), (r"/stochss/api/project/load-project\/?", LoadProjectAPIHandler), (r"/stochss/api/project/load-browser\/?", LoadProjectBrowserAPIHandler), - (r"/stochss/api/project/new-workflow-group\/?", NewWorkflowGroupAPIHandler), + (r"/stochss/api/project/new-model\/?", NewModelAPIHandler), (r"/stochss/api/project/add-existing-model\/?", AddExistingModelAPIHandler), (r"/stochss/api/project/extract-model\/?", ExtractModelAPIHandler), (r"/stochss/api/project/extract-workflow\/?", ExtractWorkflowAPIHandler), - (r"/stochss/api/project/empty-trash\/?", EmptyTrashAPIHandler), (r"/stochss/api/project/export-combine\/?", ExportAsCombineAPIHandler), (r"/stochss/api/project/meta-data\/?", ProjectMetaDataAPIHandler), (r"/stochss/api/project/save-annotation\/?", UpdateAnnotationAPIHandler), + (r"/stochss/api/project/update-format\/?", UpadteProjectAPIHandler), (r"/stochss/api/workflow/notebook\/?", WorkflowNotebookHandler), + (r"/stochss/api/workflow/new\/?", NewWorkflowAPIHandler), (r"/stochss/api/workflow/load-workflow\/?", LoadWorkflowAPIHandler), - (r"/stochss/api/workflow/save-workflow\/?", SaveWorkflowAPIHandler), - (r"/stochss/api/workflow/run-workflow\/?", RunWorkflowAPIHandler), + (r"/stochss/api/workflow/init-job\/?", InitializeJobAPIHandler), + (r"/stochss/api/workflow/run-job\/?", RunWorkflowAPIHandler), (r"/stochss/api/workflow/workflow-status\/?", WorkflowStatusAPIHandler), - (r"/stochss/api/workflow/workflow-logs\/?", WorkflowLogsAPIHandler), (r"/stochss/api/workflow/plot-results\/?", PlotWorkflowResultsAPIHandler), (r"/stochss/api/workflow/duplicate\/?", DuplicateWorkflowAsNewHandler), (r"/stochss/api/workflow/edit-model\/?", GetWorkflowModelPathAPIHandler), (r"/stochss/api/workflow/save-plot\/?", SavePlotAPIHandler), - (r"/stochss/api/workflow/save-annotation\/?", SaveAnnotationAPIHandler) + (r"/stochss/api/workflow/save-annotation\/?", SaveAnnotationAPIHandler), + (r"/stochss/api/workflow/update-format\/?", UpadteWorkflowAPIHandler) ] full_handlers = list(map(lambda h: (url_path_join(route_start, h[0]), h[1]), handlers)) return full_handlers diff --git a/stochss/handlers/file_browser.py b/stochss/handlers/file_browser.py index a40a7fd346..50fbbb523f 100644 --- a/stochss/handlers/file_browser.py +++ b/stochss/handlers/file_browser.py @@ -29,13 +29,15 @@ # Use finish() for json, write() for text from .util import StochSSBase, StochSSFolder, StochSSFile, StochSSModel, StochSSSpatialModel, \ - StochSSSBMLModel, StochSSNotebook, StochSSWorkflow, StochSSAPIError, report_error + StochSSSBMLModel, StochSSNotebook, StochSSWorkflow, StochSSJob, StochSSProject, \ + StochSSAPIError, report_error log = logging.getLogger('stochss') # pylint: disable=abstract-method +# pylint: disable=too-few-public-methods class ModelBrowserFileList(APIHandler): ''' ################################################################################################ @@ -52,7 +54,7 @@ async def get(self): ''' path = self.get_query_argument(name="path") is_root = self.get_query_argument(name="isRoot", default=False) - log.info("Path to the directory: %s", path) + log.debug("Path to the directory: %s", path) try: folder = StochSSFolder(path=path) node = folder.get_jstree_node(is_root=is_root) @@ -84,11 +86,14 @@ async def get(self): self.set_header('Content-Type', 'application/json') try: is_spatial = path.endswith(".smdl") + log.info("Getting data from %s", path.split('/').pop()) model = StochSSSpatialModel(path=path) if is_spatial else StochSSModel(path=path) data = model.get_notebook_data() log.debug("Notebook data: %s", data) + log.info("Converting %s to notebook", path.split('/').pop()) notebook = StochSSNotebook(**data) resp = notebook.create_ses_notebook() if is_spatial else notebook.create_es_notebook() + log.info("Successfully created the notebook for %s", path.split('/').pop()) log.debug("Notebook file path: %s", resp) self.write(resp) except StochSSAPIError as err: @@ -96,6 +101,35 @@ async def get(self): self.finish() +class EmptyTrashAPIHandler(APIHandler): + ''' + ############################################################################## + Handler for a projects trash directory + ############################################################################## + ''' + @web.authenticated + def get(self): + ''' + Empty the trash directory. + + Attributes + ---------- + ''' + self.set_header('Content-Type', 'application/json') + path = self.get_query_argument(name="path") + log.debug("Path to the trash directory: %s", path) + try: + log.info("Emptying the trash") + folder = StochSSFolder(path=path) + resp = folder.empty() + log.debug("Response message: %s", resp) + log.info("Successfully emptied the trash") + self.write(resp) + except StochSSAPIError as err: + report_error(self, log, err) + self.finish() + + class DeleteFileAPIHandler(APIHandler): ''' ################################################################################################ @@ -113,9 +147,11 @@ async def get(self): path = self.get_query_argument(name="path") log.debug("Deleting path: %s", path) try: + log.info("Deleting %s", path.split('/').pop()) is_dir = os.path.isdir(path) file_obj = StochSSFolder(path=path) if is_dir else StochSSFile(path=path) resp = file_obj.delete() + log.info("Successfully deleted %s", path.split('/').pop()) self.write(resp) except StochSSAPIError as err: report_error(self, log, err) @@ -141,10 +177,15 @@ async def get(self): dst_path = self.get_query_argument(name="dstPath") log.debug("Destination path: %s", dst_path) try: + dst = os.path.dirname(dst_path).split('/').pop() + if not dst: + dst = "/" + log.info("Moving %s to %s", src_path.split('/').pop(), dst) is_dir = os.path.isdir(src_path) file_obj = StochSSFolder(path=src_path) if is_dir else StochSSFile(path=src_path) resp = file_obj.move(location=dst_path) file_obj.print_logs(log) + log.info("Successfully moved %s to %s", src_path.split('/').pop(), dst) self.write(resp) except StochSSAPIError as err: report_error(self, log, err) @@ -166,13 +207,15 @@ async def get(self): Attributes ---------- ''' - path = self.get_query_argument(name="path") self.set_header('Content-Type', 'application/json') - log.debug("Copying file: %s", path) + path = self.get_query_argument(name="path") + log.debug("Path to the file: %s", path) try: + log.info("Coping %s", path.split('/').pop()) file = StochSSFile(path=path) resp = file.duplicate() file.print_logs(log) + log.info("Successfully copied %s", path.split('/').pop()) log.debug("Response message: %s", resp) self.write(resp) except StochSSAPIError as err: @@ -195,13 +238,15 @@ async def get(self): Attributes ---------- ''' - path = self.get_query_argument(name="path") self.set_header('Content-Type', 'application/json') - log.debug("Copying directory: %s", path) + path = self.get_query_argument(name="path") + log.debug("Path to the directory: %s", path) try: + log.info("Coping %s", path.split('/').pop()) folder = StochSSFolder(path=path) resp = folder.duplicate() folder.print_logs(log) + log.info("Successfully copied %s", path.split('/').pop()) log.debug("Response message: %s", resp) self.write(resp) except StochSSAPIError as err: @@ -225,14 +270,25 @@ async def get(self): Attributes ---------- ''' + self.set_header('Content-Type', 'application/json') path = self.get_query_argument(name="path") log.debug("Path to the file or directory: %s", path) new_name = self.get_query_argument(name="name") log.debug("New filename: %s", new_name) - self.set_header('Content-Type', 'application/json') try: - file_obj = StochSSBase(path=path) - resp = file_obj.rename(name=new_name) + log.info("Renaming %s to %s", path.split('/').pop(), new_name) + is_model = path.endswith(".mdl") or path.endswith(".smdl") + if ".proj" in path and ".wkgp" in path and is_model: + wkgp = StochSSBase(path=os.path.dirname(path)) + new_path, _ = wkgp.get_unique_path(name=f"{wkgp.get_name(path=new_name)}.wkgp") + wkgp.rename(name=wkgp.get_file(path=new_path)) + file_obj = StochSSBase(path=os.path.join(wkgp.path, wkgp.get_file(path=path))) + file_name = f"{wkgp.get_name(path=new_path)}.{path.split('.').pop()}" + resp = file_obj.rename(name=file_name) + else: + file_obj = StochSSBase(path=path) + resp = file_obj.rename(name=new_name) + log.info("Successfully renamed %s to %s", path.split('/').pop(), file_obj.get_file()) log.debug("Response message: %s", resp) self.write(resp) except StochSSAPIError as err: @@ -255,13 +311,16 @@ async def get(self): Attributes ---------- ''' + self.set_header('Content-Type', 'application/json') path = self.get_query_argument(name="path") log.debug("Converting non-spatial model to spatial model: %s", path) - self.set_header('Content-Type', 'application/json') try: + log.info("Convert %s to a spatial model", path.split('/').pop()) model = StochSSModel(path=path) + log.info("Getting spatial model data") resp, data = model.convert_to_spatial() _ = StochSSModel(path=data['path'], new=True, model=data['spatial']) + log.info("Successfully converted %s to a spatial model", path.split('/').pop()) log.debug("Response: %s", resp) self.write(resp) except StochSSAPIError as err: @@ -284,13 +343,16 @@ async def get(self): Attributes ---------- ''' + self.set_header('Content-Type', 'application/json') path = self.get_query_argument(name="path") log.debug("Converting spatial model to non-spatial model: %s", path) - self.set_header('Content-Type', 'application/json') try: + log.info("Convert %s to a model", path.split('/').pop()) model = StochSSSpatialModel(path=path) + log.info("Getting model data") resp, data = model.convert_to_model() _ = StochSSModel(path=data['path'], new=True, model=data['model']) + log.info("Successfully converted %s to a model", path.split('/').pop()) log.debug("Response: %s", resp) self.write(resp) except StochSSAPIError as err: @@ -313,15 +375,18 @@ async def get(self): Attributes ---------- ''' + self.set_header('Content-Type', 'application/json') path = self.get_query_argument(name="path") log.debug("Converting to SBML: %s", path) - self.set_header('Content-Type', 'application/json') try: + log.info("Convert %s to sbml", path.split('/').pop()) model = StochSSModel(path=path) + log.info("Getting sbml data") resp, data = model.convert_to_sbml() model.print_logs(log) sbml = StochSSSBMLModel(path=data['path'], new=True, document=data['document']) resp["File"] = sbml.get_file() + log.info("Successfully converted %s to sbml", path.split('/').pop()) log.debug("Response: %s", resp) self.write(resp) except StochSSAPIError as err: @@ -345,18 +410,26 @@ async def get(self): Attributes ---------- ''' + self.set_header('Content-Type', 'application/json') path = self.get_query_argument(name="path") log.debug("Converting SBML: %s", path) - self.set_header('Content-Type', 'application/json') try: + log.info("Convert %s to a model", path.split('/').pop()) sbml = StochSSSBMLModel(path=path) - convert_resp = sbml.convert_to_model(name=sbml.get_name()) + log.info("Getting model data") + if ".proj" in path: + proj = StochSSProject(path=sbml.get_dir_name()) + wkgp = proj.check_project_format(path=proj.path) + else: + wkgp = False + convert_resp = sbml.convert_to_model(name=sbml.get_name(), wkgp=wkgp) sbml.print_logs(log) resp = {"message":convert_resp['message'], "errors":convert_resp['errors'], "File":""} if convert_resp['model'] is not None: model = StochSSModel(path=convert_resp['path'], new=True, model=convert_resp['model']) resp['File'] = model.get_file() + log.info("Successfully converted %s to a model", path.split('/').pop()) log.debug("Response: %s", resp) self.write(resp) except StochSSAPIError as err: @@ -381,6 +454,7 @@ async def get(self): path = self.get_query_argument(name="path") log.debug("Path to the model: %s", path) try: + log.info("Getting the file contents for download") file = StochSSFile(path=path) data = file.read() file.print_logs(log) @@ -406,17 +480,19 @@ async def get(self): Attributes ---------- ''' + self.set_header('Content-Type', 'application/json') path = self.get_query_argument(name="path") log.debug("Path to the model: %s", path) action = self.get_query_argument(name="action") log.debug("Action: %s", action) - self.set_header('Content-Type', 'application/json') try: if action == "generate": + log.info("Zipping the directory for download") folder = StochSSFolder(path=path) resp = folder.generate_zip_file() else: - wkfl = StochSSWorkflow(path=path) + log.info("Zipping the csv files for download") + wkfl = StochSSJob(path=path) resp = wkfl.generate_csv_zip() log.debug("Response: %s", resp) self.write(resp) @@ -443,9 +519,11 @@ async def get(self): directories = self.get_query_argument(name="path") log.debug("Path of directories: %s", directories) try: + log.info("Creating %s directory", directories.split('/').pop()) folder = StochSSFolder(path=directories, new=True) folder.print_logs(log) - self.write("{0} was successfully created!".format(directories)) + log.info("Successfully created %s directory", directories.split('/').pop()) + self.write(f"{directories} was successfully created!") except StochSSAPIError as err: report_error(self, log, err) self.finish() @@ -475,14 +553,23 @@ async def post(self): log.debug("Type of file to be uploaded: %s", file_info['type']) log.debug("Path to the directory where the file will be uploaded: %s", file_info['path']) name = file_info['name'] if file_info['name'] else None + if file_info['path'].split('/').pop(): + dst = file_info['path'].split('/').pop() + else: + dst = "/" if name is not None: + if os.path.dirname(name): + dst = os.path.dirname(name).split('/').pop() + log.info("Uploading %s as %s to %s", file_data['filename'], name, dst) log.debug("Name with 'save as' path for the file: %s", name) else: + log.info("Uploading %s to %s", file_data['filename'], dst) log.debug("No name given: %s", name) try: folder = StochSSFolder(path=file_info['path']) resp = folder.upload(file_type=file_info['type'], file=file_data['filename'], body=file_data['body'], new_name=name) + log.info("Successfully uploaded %s to %s", resp['file'], dst) log.debug("Response: %s", resp) self.write(json.dumps(resp)) except StochSSAPIError as err: @@ -513,20 +600,34 @@ async def get(self): try: wkfl = StochSSWorkflow(path=path) if target == "wkfl_model": + log.info("Extracting the model from %s", wkfl.get_file()) resp, kwargs = wkfl.extract_model() model = StochSSModel(**kwargs) resp['mdlPath'] = model.path resp['File'] = model.get_file() + log.info("Successfully extracted the model from %s", wkfl.get_file()) else: - time_stamp = self.get_query_argument(name="stamp") - if time_stamp == "None": - time_stamp = None - log.debug("The time stamp for the new workflow: %s", time_stamp) - resp, kwargs = wkfl.duplicate_as_new(stamp=time_stamp) - new_wkfl = StochSSWorkflow(**kwargs) - new_wkfl.update_info(new_info={"source_model":resp['mdlPath']}) + log.info("Duplicating %s as new", wkfl.get_file()) + if wkfl.check_workflow_format(path=path): + log.info("Getting the workflow data") + resp, kwargs = wkfl.duplicate_as_new() + new_wkfl = StochSSWorkflow(**kwargs) + else: + time_stamp = self.get_query_argument(name="stamp") + if time_stamp == "None": + time_stamp = None + log.debug("The time stamp for the new workflow: %s", time_stamp) + job = StochSSJob(path=path) + log.info("Getting the workflow data") + resp, kwargs = job.duplicate_as_new(stamp=time_stamp) + new_wkfl = StochSSJob(**kwargs) + new_wkfl.update_info(new_info={"source_model":resp['mdlPath']}) + c_resp = wkfl.check_for_external_model(path=resp['mdlPath']) + if "error" in c_resp.keys(): + resp['error'] = c_resp['error'] resp['wkflPath'] = new_wkfl.path resp['File'] = new_wkfl.get_file() + log.info("Successfully duplicated %s as new", wkfl.get_file()) log.debug("Response: %s", resp) self.write(resp) except StochSSAPIError as err: @@ -602,3 +703,30 @@ async def get(self): log.debug("Response: %s", resp) self.write(resp) self.finish() + + +class UnzipFileAPIHandler(APIHandler): + ''' + ################################################################################################ + Handler for unzipping zip archives. + ################################################################################################ + ''' + + async def get(self): + ''' + Unzip a zip archive. + + Attributes + ---------- + ''' + self.set_header('Content-Type', 'application/json') + path = self.get_query_argument(name="path") + log.debug("The path to the zip archive: %s", path) + try: + file = StochSSFile(path=path) + resp = file.unzip(from_upload=False) + log.debug("Response Message: %s", resp) + self.write(resp) + except StochSSAPIError as err: + report_error(self, log, err) + self.finish() diff --git a/stochss/handlers/log.py b/stochss/handlers/log.py index b18c7ff46e..550e2473be 100644 --- a/stochss/handlers/log.py +++ b/stochss/handlers/log.py @@ -25,6 +25,19 @@ def init_log(): ''' Initialize the StochSS logger + Attributes + ---------- + ''' + setup_stream_handler() + setup_file_handler() + log.setLevel(logging.DEBUG) + log.propagate = False + + +def setup_stream_handler(): + ''' + Initialize the StochSS stream handler + Attributes ---------- ''' @@ -33,6 +46,20 @@ def init_log(): fmt += '%(filename)s:%(lineno)d]%(end_color)s %(message)s' formatter = LogFormatter(fmt=fmt, datefmt='%H:%M:%S') handler.setFormatter(formatter) - log.setLevel(logging.WARNING) + handler.setLevel(logging.WARNING) + log.addHandler(handler) + + +def setup_file_handler(): + ''' + Initialize the StochSS file handler + + Attributes + ---------- + ''' + handler = logging.FileHandler(".user-logs.txt") + fmt = '%(color)s%(asctime)s%(end_color)s$ %(message)s' + formatter = LogFormatter(fmt=fmt, datefmt="%b %d, %Y %I:%M %p UTC") + handler.setFormatter(formatter) + handler.setLevel(logging.INFO) log.addHandler(handler) - log.propagate = False diff --git a/stochss/handlers/models.py b/stochss/handlers/models.py index f89edc6d12..b4a4a62755 100644 --- a/stochss/handlers/models.py +++ b/stochss/handlers/models.py @@ -34,6 +34,7 @@ log = logging.getLogger('stochss') # pylint: disable=abstract-method +# pylint: disable=too-few-public-methods class JsonFileAPIHandler(APIHandler): ''' ################################################################################################ @@ -58,6 +59,12 @@ async def get(self): self.set_header('Content-Type', 'application/json') file_objs = {"ipynb":StochSSNotebook, "mdl":StochSSModel, "smdl":StochSSSpatialModel} ext = path.split(".").pop() + if ext == "ipynb": + log.info("Getting notebook data for download") + elif purpose == "None": + log.info("Getting model data for download") + else: + log.info("Loading model data") try: file = file_objs[ext](path=path) data = file.load() @@ -94,11 +101,14 @@ async def post(self): try: if path.endswith(".domn"): model = StochSSSpatialModel(path=path) + log.info("Saving %s", model.get_file(path=path)) model.save_domain(domain=data) else: model = StochSSModel(path=path) + log.info("Saving %s", model.get_file(path=path)) model.save(model=data) model.print_logs(log) + log.info("Successfully saved %s", model.get_file(path=path)) except StochSSAPIError as err: report_error(self, log, err) self.finish() @@ -126,6 +136,7 @@ async def get(self): log.debug("Path to the domain file: %s", d_path) new = self.get_query_argument(name="new", default=False) log.debug("The domain is new: %s", new) + log.info("Loading the domain data") try: model = StochSSSpatialModel(path=path) domain = model.get_domain(path=d_path, new=new) @@ -160,9 +171,11 @@ async def get(self): log.debug("Path to the domain file: %s", d_path) new = self.get_query_argument(name="new", default=False) log.debug("The domain is new: %s", new) + log.info("Generating the domain plot") try: model = StochSSSpatialModel(path=path) fig = json.loads(model.get_domain_plot(path=d_path, new=new)) + log.info("Loading the domain plot") resp = {"fig":fig} log.debug("Response: %s", resp) self.write(resp) @@ -202,7 +215,8 @@ async def get(self): exec_cmd = ['/stochss/stochss/handlers/util/scripts/run_preview.py', f'{path}', f'{outfile}'] if species is not None: - exec_cmd.append(f"{species}") + exec_cmd.insert(1, "--species") + exec_cmd.insert(2, f"{species}") log.debug("Script commands for running a preview: %s", exec_cmd) subprocess.Popen(exec_cmd) resp['Running'] = True @@ -210,12 +224,15 @@ async def get(self): self.write(resp) else: model = StochSSModel(path=path) + log.info("Check for preview results ...") results = model.get_preview_results(outfile=outfile) log.debug("Results for the model preview: %s", results) if results is None: resp['Running'] = True + log.info("The preview is still running") else: resp['Results'] = results + log.info("Loading the preview results") log.debug("Response to the read command: %s", resp) self.write(resp) self.finish() @@ -260,11 +277,22 @@ async def post(self): ---------- ''' self.set_header('Content-Type', 'application/json') + log.info("Loading the mesh from %s", self.request.files['datafile'][0]['filename']) data = self.request.files['datafile'][0]['body'].decode() + if "typefile" in self.request.files.keys(): + log.info("Loading the particle types from %s", + self.request.files['typefile'][0]['filename']) + types = self.request.files['typefile'][0]['body'].decode().strip().split("\n") + else: + types = None + log.info("Loading particle data") particle_data = json.loads(self.request.body_arguments['particleData'][0].decode()) try: - resp = StochSSSpatialModel.get_particles_from_remote(mesh=data, data=particle_data) + log.info("Generating new particles") + resp = StochSSSpatialModel.get_particles_from_remote(mesh=data, data=particle_data, + types=types) log.debug("Number of Particles: %s", len(resp['particles'])) + log.info("Successfully created new particles") self.write(resp) except StochSSAPIError as err: report_error(self, log, err) @@ -288,7 +316,8 @@ async def get(self): self.set_header('Content-Type', 'application/json') try: folder = StochSSFolder(path="") - resp = folder.get_file_list(ext=".domn") + test = lambda ext, root, file: bool("trash" in root.split("/")) + resp = folder.get_file_list(ext=".domn", test=test) log.debug("Response: %s", resp) self.write(resp) except StochSSAPIError as err: @@ -313,7 +342,8 @@ async def get(self): self.set_header('Content-Type', 'application/json') try: folder = StochSSFolder(path="") - resp = folder.get_file_list(ext=".txt") + test = lambda ext, root, file: bool("trash" in root.split("/")) + resp = folder.get_file_list(ext=".txt", test=test) log.debug("Response: %s", resp) self.write(resp) except StochSSAPIError as err: @@ -336,11 +366,14 @@ async def post(self): ---------- ''' self.set_header('Content-Type', 'application/json') + log.info("Loading particle data") data = json.loads(self.request.body.decode()) log.debug("Data used to create the domain: %s", data) try: + log.info("Generating new particles") resp = StochSSSpatialModel.get_particles_from_3d_domain(data=data) log.debug("Number of Particles: %s", len(resp['particles'])) + log.info("Successfully created new particles") self.write(resp) except StochSSAPIError as err: report_error(self, log, err) @@ -365,6 +398,7 @@ async def get(self): path = self.get_query_argument(name="path") log.debug("Path to the file: %s", path) try: + log.info("Loading particle types from %s", path.split('/').pop()) model = StochSSSpatialModel(path="") resp = model.get_types_from_file(path=path) log.debug("Number of Particles: %s", len(resp['types'])) diff --git a/stochss/handlers/pages.py b/stochss/handlers/pages.py index 470b473610..23cece06b1 100644 --- a/stochss/handlers/pages.py +++ b/stochss/handlers/pages.py @@ -19,11 +19,16 @@ import os import logging from tornado import web -from notebook.base.handlers import IPythonHandler +from notebook.base.handlers import IPythonHandler, APIHandler +# APIHandler documentation: +# https://github.com/jupyter/notebook/blob/master/notebook/base/handlers.py#L583 +# Note APIHandler.finish() sets Content-Type handler to 'application/json' +# Use finish() for json, write() for text log = logging.getLogger('stochss') # pylint: disable=abstract-method +# pylint: disable=too-few-public-methods class PageHandler(IPythonHandler): ''' ################################################################################################ @@ -224,3 +229,65 @@ async def get(self): ---------- ''' self.render("stochss-project-manager.html", server_path=self.get_server_path()) + + +class LoadingPageHandler(PageHandler): + ''' + ################################################################################################ + StochSS Loading Page Page Handler + ################################################################################################ + ''' + @web.authenticated + async def get(self): + ''' + Render the StochSS loading page. + + Attributes + ---------- + ''' + self.render("stochss-loading-page.html", server_path=self.get_server_path()) + + +class MultiplePlotsHandler(PageHandler): + ''' + ################################################################################################ + StochSS Multiple Plots Page Handler + ################################################################################################ + ''' + @web.authenticated + async def get(self): + ''' + Render the StochSS multiple plots page. + + Attributes + ---------- + ''' + self.render("multiple-plots-page.html", server_path=self.get_server_path()) + + +class UserLogsAPIHandler(APIHandler): + ''' + ################################################################################################ + Handler for getting the user logs + ################################################################################################ + ''' + @web.authenticated + async def get(self): + ''' + Return the contents of the user log file. + + Attributes + ---------- + ''' + self.set_header('Content-Type', 'application/json') + log_num = self.get_query_arguments(name="logNum")[0] + user_dir = os.path.expanduser("~") + path = os.path.join(user_dir, ".user-logs.txt") + try: + with open(path, "r") as log_file: + logs = log_file.read().strip().split("\n")[int(log_num):] + except FileNotFoundError: + open(path, "w").close() + logs = [] + self.write({"logs":logs}) + self.finish() diff --git a/stochss/handlers/project.py b/stochss/handlers/project.py index 8a91d9e691..b0b727364a 100644 --- a/stochss/handlers/project.py +++ b/stochss/handlers/project.py @@ -18,30 +18,28 @@ import os -import ast import json -import shutil import logging - -# from shutil import copyfile, copytree, rmtree from tornado import web from notebook.base.handlers import APIHandler +# APIHandler documentation: +# https://github.com/jupyter/notebook/blob/master/notebook/base/handlers.py#L583 +# Note APIHandler.finish() sets Content-Type handler to 'application/json' +# Use finish() for json, write() for text -# from .util.rename import get_unique_file_name, get_file_name -# from .util.workflow_status import get_status -# from .util.generate_zip_file import download_zip - -from .util import StochSSBase, StochSSAPIError, report_error +from .util import StochSSFolder, StochSSProject, StochSSModel, StochSSSpatialModel, \ + StochSSAPIError, report_error log = logging.getLogger('stochss') # pylint: disable=abstract-method +# pylint: disable=too-few-public-methods class LoadProjectBrowserAPIHandler(APIHandler): ''' - ############################################################################## + ################################################################################################ Handler for loading all of the users projects - ############################################################################## + ################################################################################################ ''' @web.authenticated async def get(self): @@ -51,44 +49,22 @@ async def get(self): Attributes ---------- ''' - user_dir = "/home/jovyan" - self.set_header('Content-Type', 'application/json') - projects = [] - self.get_projects_from_directory(user_dir, projects) - log.debug("List of projects: %s", projects) - resp = {"projects":projects} - self.write(resp) + try: + self.set_header('Content-Type', 'application/json') + folder = StochSSFolder(path="") + data = folder.get_project_list() + log.debug("List of projects: %s", data) + self.write(data) + except StochSSAPIError as err: + report_error(self, log, err) self.finish() - @classmethod - def get_projects_from_directory(cls, path, projects): - ''' - Get the projects in the directory if any exist. - - Attributes - ---------- - path : string - Path the target directory - projects : list - List of project dictionaries - ''' - for item in os.listdir(path): - new_path = os.path.join(path, item) - if item.endswith('.proj'): - projects.append({'directory': new_path.replace("/home/jovyan/", ""), - 'parentDir': os.path.dirname(new_path.replace("/home/jovyan/", - "")), - 'elementID': "p{}".format(len(projects) + 1)}) - elif not item.startswith('.') and os.path.isdir(new_path): - cls.get_projects_from_directory(new_path, projects) - - class LoadProjectAPIHandler(APIHandler): ''' - ############################################################################## + ################################################################################################ Handler for creating new StochSS Projects - ############################################################################## + ################################################################################################ ''' @web.authenticated def get(self): @@ -100,164 +76,23 @@ def get(self): ''' self.set_header('Content-Type', 'application/json') path = self.get_query_argument(name="path") - log.debug("The path to the new project directory: %s", path) + log.debug("The path to the project directory: %s", path) + log.info("Loading project data") try: - project = {"models": [], "workflowGroups": [], "trash_empty": True} - for item in os.listdir(path): - if item == "README.md": - readme_path = os.path.join(path, item) - with open(readme_path, 'r') as readme_file: - project['annotation'] = readme_file.read() - elif item.endswith('.mdl') or item.endswith('.smdl'): - mdl_dir = os.path.join(path, item) - with open(mdl_dir, 'r') as mdl_file: - model = json.load(mdl_file) - base = StochSSBase(path=item) - model['name'] = base.get_name() - model['directory'] = mdl_dir - self.update_model_data(model) - project['models'].append(model) - elif item.endswith('.wkgp'): - name = item.split('.')[0] - workflows = [] - for workflow in os.listdir(os.path.join(path, item)): - if workflow.endswith('.wkfl'): - self.get_stochss_workflow(project, workflows, - os.path.join(path, item, workflow), - workflow) - elif workflow.endswith('.ipynb'): - self.get_notebook_workflow(workflows, - os.path.join(path, item, workflow), - workflow) - project['workflowGroups'].append({"name":name, "workflows":workflows}) - elif item == "trash": - project['trash_empty'] = len(os.listdir(os.path.join(path, item))) == 0 - log.debug("Contents of the project: %s", project) - self.write(project) + project = StochSSProject(path=path) + s_project = project.load() + log.debug("Contents of the project: %s", s_project) + self.write(s_project) except StochSSAPIError as err: report_error(self, log, err) self.finish() - @classmethod - def update_model_data(cls, data): - param_ids = [] - for param in data['parameters']: - param_ids.append(param['compID']) - if isinstance(param['expression'], str): - try: - param['expression'] = ast.literal_eval(param['expression']) - except ValueError: - pass - for reaction in data['reactions']: - if reaction['rate'].keys() and isinstance(reaction['rate']['expression'], str): - try: - value = ast.literal_eval(reaction['rate']['expression']) - reaction['rate']['expression'] = value - except ValueError: - pass - for event in data['eventsCollection']: - for assignment in event['eventAssignments']: - if assignment['variable']['compID'] in param_ids: - try: - value = ast.literal_eval(assignment['variable']['expression']) - assignment['variable']['expression'] = value - except ValueError: - pass - for rule in data['rules']: - if rule['variable']['compID'] in param_ids: - try: - value = ast.literal_eval(rule['variable']['expression']) - rule['variable']['expression'] = value - except ValueError: - pass - - - @classmethod - def get_workflow_info(cls, wkfl_dict): - ''' - Add the necessary workflow info elements to the workflow model - - Attributes - ---------- - wkfl_dict : dict - JSON representation of a workflow - ''' - with open(os.path.join(wkfl_dict["path"], "info.json"), 'r') as info_file: - info = json.load(info_file) - types = {'gillespy': 'Ensemble Simulation', 'parameterSweep':'Parameter Sweep'} - wkfl_dict['type'] = types[info['type']] - if not 'annotation' in info.keys(): - wkfl_dict['annotation'] = "" - else: - wkfl_dict['annotation'] = info['annotation'] - - - @classmethod - def get_notebook_workflow(cls, workflows, path, workflow): - ''' - Get the info for the notebook workflow - - Attributes - ---------- - workflows: list - List of workflows - path : string - Path to the workflow - workflow : string - Name of the workflow directory - ''' - wkfl_dict = {"path":path, "name":workflow.split('.')[0], - "status":"", "outputs":[], "annotation":""} - with open(path, "r") as nb_file: - file_data = nb_file.read() - if "Traceback (most recent call last)" in file_data: - wkfl_dict['status'] = 'error' - else: - wkfl_dict['status'] = 'ready' - wkfl_dict['type'] = "notebook" - workflows.append(wkfl_dict) - - - def get_stochss_workflow(self, project, workflows, path, workflow): - ''' - Get the info for the StochSS Workflow - - Attributes - ---------- - project : dict - Dictionary representation of the stochss project - workflows: list - List of workflows - path : string - Path to the workflow - workflow : string - Name of the workflow directory - ''' - wkfl_dict = {"path":path, "name":workflow.split('.')[0]} - base = StochSSBase(path=wkfl_dict['path']) - wkfl_dict['status'] = base.get_status() - with open(os.path.join(wkfl_dict['path'], - 'settings.json'), 'r') as settings_file: - outputs = json.load(settings_file)['resultsSettings']['outputs'] - if outputs: - output = max(outputs, key=lambda output: output['stamp']) - if "plot" in project.keys(): - if output['stamp'] > project['plot']['output']['stamp']: - project['plot']['path'] = wkfl_dict['path'] - project['plot']['output'] = output - else: - project['plot'] = {"path":wkfl_dict['path'], "output":output} - wkfl_dict['outputs'] = outputs - self.get_workflow_info(wkfl_dict) - workflows.append(wkfl_dict) - - class NewProjectAPIHandler(APIHandler): ''' - ############################################################################## + ################################################################################################ Handler for creating new StochSS Projects - ############################################################################## + ################################################################################################ ''' @web.authenticated def get(self): @@ -270,60 +105,48 @@ def get(self): self.set_header('Content-Type', 'application/json') path = self.get_query_argument(name="path") log.debug("The path to the new project directory: %s", path) + log.info("Creating %s project", path.split('/').pop()) try: - os.makedirs(path) - os.mkdir(os.path.join(path, "trash")) - os.mkdir(os.path.join(path, "WorkflowGroup1.wkgp")) - resp = {"message":"Successfully created the project: {0}\ - ".format(path.split('/').pop()), - "path":path} + project = StochSSProject(path=path, new=True) + resp = {"message":f"Successfully created the project: {project.get_file()}", + "path":project.path} + log.debug("Response: %s", resp) + log.info("Successfully created %s project", project.get_file()) self.write(resp) - except FileExistsError as err: - self.set_status(406) - error = {"Reason":"Project Already Exists", - "Message":"Could not create your project: {0}".format(err)} - log.error("Exception Information: %s", error) - self.write(error) + except StochSSAPIError as err: + report_error(self, log, err) self.finish() -class NewWorkflowGroupAPIHandler(APIHandler): +class NewModelAPIHandler(APIHandler): ''' - ############################################################################## - Handler for creating new StochSS Workflow Groups - ############################################################################## + ################################################################################################ + Handler for creating new StochSS Models in StochSS Projects + ################################################################################################ ''' @web.authenticated def get(self): ''' - Create a new workflow group directory. + Create a new model in the project. Attributes ---------- ''' + log.setLevel(logging.DEBUG) self.set_header('Content-Type', 'application/json') path = self.get_query_argument(name="path") - log.debug("The path to the new workflow group directory: %s", path) + log.debug("Path to the project: %s", path) + file = self.get_query_argument(name="mdlFile") + log.debug("Name to the file: %s", file) try: - os.mkdir(path) - proj_file = os.path.dirname(path).split('/').pop() - exp_file = path.split('/').pop() - resp = {"message":"The {} was successfully created in {}".format(exp_file, proj_file), - "path":path} + project = StochSSProject(path=path) + resp = project.add_model(file=file, new=True) + project.print_logs(log) + log.debug("Response: %s", resp) self.write(resp) - except FileExistsError as err: - self.set_status(406) - error = {"Reason":"Workflow Group Already Exists", - "Message":"Could not create your workflow group: {0}".format(err)} - log.error("Exception Information: %s", error) - self.write(error) - except FileNotFoundError as err: - self.set_status(404) - error = {"Reason":"Dirctory Not Found", - "Message":"Workflow Groups can only be created in a StochSS Project: \ - {0}".format(err)} - log.error("Exception Information: %s", error) - self.write(error) + except StochSSAPIError as err: + report_error(self, log, err) + log.setLevel(logging.WARNING) self.finish() @@ -341,23 +164,19 @@ def get(self): Attributes ---------- ''' - user_dir = "/home/jovyan" self.set_header('Content-Type', 'application/json') - path = os.path.join(user_dir, self.get_query_argument(name="path")) + path = self.get_query_argument(name="path") log.debug("Path to the model: %s", path) - models = [] - for root, _, files in os.walk("/home/jovyan"): - if path not in root and "/." not in root and ".wkfl" not in root: - root = root.replace(user_dir+"/", "") - files = list(filter(lambda file: (file.endswith(".smdl") or - file.endswith(".mdl")), files)) - for file in files: - if root == user_dir: - models.append(file) - else: - models.append(os.path.join(root, file)) - log.debug("List of model that can be added to the project: %s", models) - self.write({"models": models}) + try: + folder = StochSSFolder(path="") + # file will be excluded if test passes + test = lambda ext, root, file: bool(".wkfl" in root or f"{path}" in root or \ + "trash" in root.split("/")) + data = folder.get_file_list(ext=[".mdl", ".smdl"], test=test) + log.debug("List of models: %s", data) + self.write(data) + except StochSSAPIError as err: + report_error(self, log, err) self.finish() @@ -369,49 +188,32 @@ def post(self): Attributes ---------- ''' - user_dir = "/home/jovyan" self.set_header('Content-Type', 'application/json') - path = os.path.join(user_dir, self.get_query_argument(name="path")) - mdl_path = os.path.join(user_dir, self.get_query_argument(name="mdlPath")) + path = self.get_query_argument(name="path") log.debug("Path to the project: %s", path) + mdl_path = self.get_query_argument(name="mdlPath") log.debug("Path to the model: %s", mdl_path) - if mdl_path.endswith('.mdl') or mdl_path.endswith('.smdl'): - try: - base = StochSSBase(path=os.path.join(path, mdl_path.split("/").pop())) - unique_path, changed = base.get_unique_path(mdl_path.split("/").pop()) - shutil.copyfile(mdl_path, unique_path) - resp = {"message": "The model {0} was successfully move into \ - {1}".format(mdl_path.split('/').pop(), path.split("/").pop())} - if changed: - resp['message'] += " as {0}".format(unique_path.split('/').pop()) - log.debug("Response message: %s", resp) - self.write(resp) - except IsADirectoryError as err: - self.set_status(406) - error = {"Reason":"Not A Model", - "Message":"Cannot move directories into StochSS Projects: {0}".format(err)} - log.error("Exception Information: %s", error) - self.write(error) - except FileNotFoundError as err: - self.set_status(404) - error = {"Reason":"Model Not Found", - "Message":"Could not find the model: {0}".format(err)} - log.error("Exception Information: %s", error) - self.write(error) - else: - self.set_status(406) - error = {"Reason":"Not A Model", - "Message":"Cannot move non-model files into StochSS Projects"} - log.error("Exception Information: %s", error) - self.write(error) + try: + project = StochSSProject(path=path) + log.info("Loading model data") + model_class = StochSSModel if mdl_path.endswith(".mdl") else StochSSSpatialModel + model = model_class(path=mdl_path) + log.info("Adding %s to %s", model.get_file(), project.get_file()) + resp = project.add_model(file=model.get_file(), model=model.load()) + project.print_logs(log) + log.info("Successfully added %s to %s", model.get_file(), project.get_file()) + log.debug("Response: %s", resp) + self.write(resp) + except StochSSAPIError as err: + report_error(self, log, err) self.finish() class ExtractModelAPIHandler(APIHandler): ''' - ############################################################################## + ################################################################################################ Handler for extracting models from a project - ############################################################################## + ################################################################################################ ''' @web.authenticated def get(self): @@ -421,38 +223,33 @@ def get(self): Attributes ---------- ''' - user_dir = "/home/jovyan" self.set_header('Content-Type', 'application/json') - src_path = os.path.join(user_dir, self.get_query_argument(name="srcPath")) + src_path = self.get_query_argument(name="srcPath") log.debug("Path to the target model: %s", src_path) - dst_path = os.path.join(user_dir, self.get_query_argument(name="dstPath")) + dst_path = self.get_query_argument(name="dstPath") log.debug("Destination path for the target model: %s", dst_path) try: - base = StochSSBase(path=dst_path) - unique_path, changed = base.get_unique_path(dst_path.split('/').pop()) - shutil.copyfile(src_path, unique_path) - export_path = (os.path.dirname(unique_path).replace(user_dir+"/", "") - if os.path.dirname(unique_path) != user_dir else "/") - resp = "The Model {0} was extracted to {1} in files\ - ".format(src_path.split('/').pop(), export_path) - if changed: - resp += " as {0}".format(unique_path.split('/').pop()) - log.debug("Response message: %s", resp) - self.write(resp) - except FileNotFoundError as err: - self.set_status(404) - error = {"Reason":"Model Not Found", - "Message":"Could not find the model: {0}".format(err)} - log.error("Exception Information: %s", error) - self.write(error) + src_model = StochSSModel(path=src_path) + log.info("Extracting %s", src_model.get_file()) + dst_model = StochSSModel(path=dst_path, new=True, model=src_model.load()) + dirname = dst_model.get_dir_name() + if not dirname: + dirname = "/" + message = f"The Model {src_model.get_file()} was extracted to " + message += f"{dirname} in files as {dst_model.get_file()}" + log.debug("Response message: %s", message) + log.info("Successfully extracted %s to %s", src_model.get_file(), dirname) + self.write(message) + except StochSSAPIError as err: + report_error(self, log, err) self.finish() class ExtractWorkflowAPIHandler(APIHandler): ''' - ############################################################################## + ################################################################################################ Handler for extracting workflows from a project - ############################################################################## + ################################################################################################ ''' @web.authenticated def get(self): @@ -462,94 +259,20 @@ def get(self): Attributes ---------- ''' - user_dir = "/home/jovyan" - src_path = os.path.join(user_dir, self.get_query_argument(name="srcPath")) + self.set_header('Content-Type', 'application/json') + src_path = self.get_query_argument(name="srcPath") log.debug("Path to the target model: %s", src_path) - dst_path = os.path.join(user_dir, self.get_query_argument(name="dstPath")) + dst_path = self.get_query_argument(name="dstPath") log.debug("Destination path for the target model: %s", dst_path) try: - base = StochSSBase(path=src_path) - if base.get_status() != "running": - base.path = dst_path - unique_path, changed = base.get_unique_path(dst_path.split('/').pop()) - shutil.copytree(src_path, unique_path) - base.path = unique_path - if base.get_status() != "ready": - self.update_workflow_path(unique_path) - export_path = (os.path.dirname(unique_path).replace(user_dir+"/", "") - if os.path.dirname(unique_path) != user_dir else "/") - resp = "The Workflow {0} was exported to {1} in files\ - ".format(src_path.split('/').pop(), export_path) - if changed: - resp += " as {0}".format(unique_path.split('/').pop()) - log.debug("Response message: %s", resp) - self.write(resp) - except FileNotFoundError as err: - self.set_status(404) - self.set_header('Content-Type', 'application/json') - error = {"Reason":"Workflow Not Found", - "Message":"Could not find the workflow: {0}".format(err)} - log.error("Exception Information: %s", error) - self.write(error) - except StochSSAPIError as err: - report_error(self, log, err) - self.finish() - - - @classmethod - def update_workflow_path(cls, dst): - ''' - Update the path to the workflows model - - Attributes - ---------- - dst : string - Destination path for the workflow - ''' - with open(os.path.join(dst, "info.json"), "r+") as info_file: - info = json.load(info_file) - log.debug("Old workflow info: %s", info) - new_path = os.path.join(dst, info['wkfl_model'].split('/').pop()) - info['wkfl_model'] = new_path.replace("/home/jovyan/", "") - log.debug("New workflow info: %s", info) - info_file.seek(0) - json.dump(info, info_file) - info_file.truncate() - - -class EmptyTrashAPIHandler(APIHandler): - ''' - ############################################################################## - Handler for a projects trash directory - ############################################################################## - ''' - @web.authenticated - def get(self): - ''' - Empty the trash directory. - - Attributes - ---------- - ''' - user_dir = "/home/jovyan" - self.set_header('Content-Type', 'application/json') - path = os.path.join(user_dir, self.get_query_argument(name="path")) - log.debug("Path to the trash directory: %s", path) - try: - for item in os.listdir(path): - item_path = os.path.join(path, item) - if os.path.isdir(item_path): - shutil.rmtree(item_path) - else: - os.remove(item_path) - resp = "Successfully emptied the trash" - log.debug("Response message: %s", resp) - self.write(resp) - except FileNotFoundError: - os.mkdir(path) - resp = "The trash directory was removed." + log.info("Extracting %s", src_path.split('/').pop()) + project = StochSSProject(path=os.path.dirname(os.path.dirname(src_path))) + resp = project.extract_workflow(src=src_path, dst=dst_path) + project.print_logs(log) log.debug("Response message: %s", resp) self.write(resp) + except StochSSAPIError as err: + report_error(self, log, err) self.finish() @@ -559,42 +282,6 @@ class ProjectMetaDataAPIHandler(APIHandler): Handler for a projects meta data ############################################################################## ''' - @web.authenticated - def get(self): - ''' - Get the projects meta data if it exists else create a meta data dictionary. - - Attributes - ---------- - ''' - user_dir = "/home/jovyan" - self.set_header('Content-Type', 'application/json') - path = os.path.join(user_dir, self.get_query_argument(name="path")) - log.debug("Path to the project directory: %s", path) - files = self.get_query_argument(name="files").split(',') - log.debug("List of files: %s", files) - md_path = os.path.join(path, ".meta-data.json") - log.debug("Path to the meta-data file: %s", md_path) - if os.path.exists(md_path): - with open(md_path, "r") as md_file: - data = json.load(md_file) - meta_data = data['meta-data'] - creators = data['creators'] - else: - meta_data = {} - creators = {} - - for file in files: - if file not in meta_data.keys(): - meta_data[file] = {"description":"", "creators":[]} - log.debug("Meta-data for the project: %s", meta_data) - log.debug("Creators for the project: %s", creators) - resp = {"meta_data":meta_data, "creators":creators} - log.debug("Response Message: %s", resp) - self.write(resp) - self.finish() - - @web.authenticated def post(self): ''' @@ -603,14 +290,18 @@ def post(self): Attributes ---------- ''' - user_dir = "/home/jovyan" self.set_header('Content-Type', 'application/json') - path = os.path.join(user_dir, self.get_query_argument(name="path")) + path = self.get_query_argument(name="path") log.debug("Path to the project directory: %s", path) - data = self.request.body.decode() + data = json.loads(self.request.body.decode()) log.debug("Meta-data to be saved: %s", data) - with open(os.path.join(path, ".meta-data.json"), "w") as md_file: - md_file.write(data) + try: + log.info("Saving metadata for %s", path.split('/').pop()) + project = StochSSProject(path=path) + project.update_meta_data(data=data) + log.info("Successfully saved the metadata") + except StochSSAPIError as err: + report_error(self, log, err) self.finish() @@ -628,6 +319,8 @@ def get(self): Attributes ---------- ''' + log.warning("Export as combine function has not been cleaned up") + self.finish() @web.authenticated @@ -638,6 +331,8 @@ def post(self): Attributes ---------- ''' + log.warning("Export as combine w/meta data function has not been cleaned up") + self.finish() class UpdateAnnotationAPIHandler(APIHandler): @@ -654,12 +349,39 @@ def post(self): Attributes ---------- ''' - user_dir = "/home/jovyan" - path = os.path.join(user_dir, self.get_query_argument(name="path"), "README.md") + path = self.get_query_argument(name="path") log.debug("Path to the project directory: %s", path) data = json.loads(self.request.body.decode())['annotation'].strip() log.debug("Annotation to be saved: %s", data) - log.debug(type(data)) - with open(path, 'w') as readme_file: - readme_file.write(data) + try: + log.info("Saving the annotation for %s", path.split('/').pop()) + project = StochSSProject(path=path) + project.update_annotation(annotation=data) + log.info("Successfully saved the annotation") + except StochSSAPIError as err: + report_error(self, log, err) + self.finish() + + +class UpadteProjectAPIHandler(APIHandler): + ''' + ################################################################################################ + Handler for updating project format. + ################################################################################################ + ''' + @web.authenticated + async def get(self): + ''' + Updates the project and its workflows to the new format. + + Attributes + ---------- + ''' + path = self.get_query_argument(name="path") + log.debug("The path to the project: %s", path) + try: + proj = StochSSProject(path=path) + proj.update_project_format() + except StochSSAPIError as err: + report_error(self, log, err) self.finish() diff --git a/stochss/handlers/util/__init__.py b/stochss/handlers/util/__init__.py index e9e0e4bc78..eda8912745 100644 --- a/stochss/handlers/util/__init__.py +++ b/stochss/handlers/util/__init__.py @@ -24,6 +24,8 @@ from .stochss_sbml import StochSSSBMLModel from .stochss_notebook import StochSSNotebook from .stochss_workflow import StochSSWorkflow +from .stochss_job import StochSSJob +from .stochss_project import StochSSProject from .ensemble_simulation import EnsembleSimulation from .parameter_sweep import ParameterSweep from .stochss_errors import StochSSAPIError, report_error diff --git a/stochss/handlers/util/ensemble_simulation.py b/stochss/handlers/util/ensemble_simulation.py index 0df4e8e379..2b220e21fb 100644 --- a/stochss/handlers/util/ensemble_simulation.py +++ b/stochss/handlers/util/ensemble_simulation.py @@ -20,16 +20,22 @@ import os import json import pickle +import logging +import traceback + +import numpy import plotly +from gillespy2 import TauHybridSolver -from gillespy2 import TauLeapingSolver, TauHybridSolver, SSACSolver +from .stochss_job import StochSSJob +from .stochss_errors import StochSSAPIError, StochSSJobResultsError -from .stochss_workflow import StochSSWorkflow +log = logging.getLogger("stochss") -class EnsembleSimulation(StochSSWorkflow): +class EnsembleSimulation(StochSSJob): ''' ################################################################################################ - StochSS ensemble simulation workflow object + StochSS ensemble simulation job object ################################################################################################ ''' @@ -37,51 +43,88 @@ class EnsembleSimulation(StochSSWorkflow): def __init__(self, path, preview=False): ''' - Intitialize an ensemble simulation workflow object + Intitialize an ensemble simulation job object Attributes ---------- path : str - Path to the ensemble simulation workflow + Path to the ensemble simulation job ''' super().__init__(path=path) if not preview: - self.settings = self.load_settings() - self.g_model, self.s_model = self.load_models() + try: + self.settings = self.load_settings() + self.g_model, self.s_model = self.load_models() + except StochSSAPIError as err: + log.error(str(err)) def __get_run_settings(self): - solver_map = {"SSA":SSACSolver(model=self.g_model), "Tau-Leaping":TauLeapingSolver, - "ODE":TauHybridSolver, "Hybrid-Tau-Leaping":TauHybridSolver} - return self.get_run_settings(settings=self.settings, solver_map=solver_map) + solver_map = {"ODE":self.g_model.get_best_solver_algo("ODE"), + "SSA":self.g_model.get_best_solver_algo("SSA"), + "Tau-Leaping":self.g_model.get_best_solver_algo("Tau-Leaping"), + "Hybrid-Tau-Leaping":TauHybridSolver} + run_settings = self.get_run_settings(settings=self.settings, solver_map=solver_map) + instance_solvers = ["SSACSolver", "TauLeapingCSolver", "ODECSolver"] + if run_settings['solver'].name in instance_solvers : + run_settings['solver'] = run_settings['solver'](model=self.g_model) + return run_settings + + + def __store_csv_results(self, results): + try: + results.to_csv(path="results", nametag="results_csv", stamp=self.get_time_stamp()) + except Exception as err: + log.error("Error storing csv results: %s\n%s", + str(err), traceback.format_exc()) @classmethod - def __plot_results(cls, results): - plots = {"trajectories":results.plotplotly(return_plotly_figure=True)} - if len(results) > 1: - plots['stddevran'] = results.plotplotly_std_dev_range(return_plotly_figure=True) - std_res = results.stddev_ensemble() - plots['stddev'] = std_res.plotplotly(return_plotly_figure=True) - avg_res = results.average_ensemble() - plots['avg'] = avg_res.plotplotly(return_plotly_figure=True) - for _, plot in plots.items(): - plot["config"] = {"responsive":True} - with open('results/plots.json', 'w') as plots_file: - json.dump(plots, plots_file, cls=plotly.utils.PlotlyJSONEncoder) - - - def __store_results(self, results): - if not 'results' in os.listdir(): - os.mkdir('results') - with open('results/results.p', 'wb') as results_file: - pickle.dump(results, results_file) - results.to_csv(path="results", nametag="results_csv", stamp=self.get_time_stamp()) + def __store_pickled_results(cls, results): + try: + with open('results/results.p', 'wb') as results_file: + pickle.dump(results, results_file) + except Exception as err: + message = f"Error storing pickled results: {err}\n{traceback.format_exc()}" + log.error(message) + return message + return False - def run(self, preview=False, verbose=False): + @classmethod + def __store_result_plots(cls, results): + try: + plots = {"trajectories":results.plotplotly(return_plotly_figure=True)} + if len(results) > 1: + plots['stddevran'] = results.plotplotly_std_dev_range(return_plotly_figure=True) + std_res = results.stddev_ensemble() + plots['stddev'] = std_res.plotplotly(return_plotly_figure=True) + avg_res = results.average_ensemble() + plots['avg'] = avg_res.plotplotly(return_plotly_figure=True) + for _, plot in plots.items(): + plot["config"] = {"responsive":True} + with open('results/plots.json', 'w') as plots_file: + json.dump(plots, plots_file, cls=plotly.utils.PlotlyJSONEncoder, + indent=4, sort_keys=True) + except Exception as err: + message = f"Error storing result plots: {err}\n{traceback.format_exc()}" + log.error(message) + return message + return False + + + def __update_timespan(self): + if "timespanSettings" in self.settings.keys(): + keys = self.settings['timespanSettings'].keys() + if "endSim" in keys and "timeStep" in keys: + end = self.settings['timespanSettings']['endSim'] + step_size = self.settings['timespanSettings']['timeStep'] + self.g_model.timespan(numpy.arange(0, end + step_size, step_size)) + + + def run(self, preview=False, verbose=True): ''' - Run a GillesPy2 ensemble simulation workflow + Run a GillesPy2 ensemble simulation job Attributes ---------- @@ -92,26 +135,37 @@ def run(self, preview=False, verbose=False): ''' if preview: if verbose: - self.log("info", "Running a preview ensemble simulation") + log.info("Running %s preview simulation", self.g_model.name) results = self.g_model.run(timeout=5) + if verbose: + log.info("%s preview simulation has completed", self.g_model.name) + log.info("Generate result plot for %s preview", self.g_model.name) plot = results.plotplotly(return_plotly_figure=True) plot["layout"]["autosize"] = True plot["config"] = {"responsive": True, "displayModeBar": True} return plot + if verbose: + log.info("Running the ensemble simulation") if self.settings['simulationSettings']['isAutomatic']: - if verbose: - self.log("info", "Running an ensemble simulation with automatic solver") - is_ode = self.g_model.get_best_solver(precompile=False).name == "ODESolver" + self.__update_timespan() + is_ode = self.g_model.get_best_solver().name in ["ODESolver", "ODECSolver"] results = self.g_model.run(number_of_trajectories=1 if is_ode else 100) else: - if verbose: - self.log("info", "Running an ensemble simulation with manual solver") kwargs = self.__get_run_settings() + self.__update_timespan() results = self.g_model.run(**kwargs) if verbose: - self.log("info", "Storing the results as pickle and csv") - self.__store_results(results=results) + log.info("The ensemble simulation has completed") + log.info("Storing the results as pickle and csv") + if not 'results' in os.listdir(): + os.mkdir('results') + self.__store_csv_results(results=results) + pkl_err = self.__store_pickled_results(results=results) if verbose: - self.log("info", "Storing the polts of the results") - self.__plot_results(results=results) + log.info("Storing the polts of the results") + plt_err = self.__store_result_plots(results=results) + if pkl_err and plt_err: + message = "An unexpected error occured with the result object" + trace = f"{pkl_err}\n{plt_err}" + raise StochSSJobResultsError(message, trace) return None diff --git a/stochss/handlers/util/parameter_scan.py b/stochss/handlers/util/parameter_scan.py new file mode 100644 index 0000000000..be84dd7ef4 --- /dev/null +++ b/stochss/handlers/util/parameter_scan.py @@ -0,0 +1,102 @@ +''' +StochSS is a platform for simulating biochemical systems +Copyright (C) 2019-2020 StochSS developers. + +This program is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with this program. If not, see . +''' + +import copy +import logging +import traceback + +log = logging.getLogger("stochss") + +class ParameterScan(): + ''' + ################################################################################################ + StochSS parameter scan job object + ################################################################################################ + ''' + name = "ParameterScan" + + def __init__(self, model, settings, params): + ''' + initialize a Parameter Scan object + + Attributes + ---------- + model : obj + GillesPy2 Model + settings : dict + GillesPy2 simulation settings dictionary + params : list + list containing dictionaries of parameters + ''' + self.model = model + self.settings = settings + self.params = params + self.ts_results = {} + + + @classmethod + def __get_result_key(cls, variables): + elements = [] + for name, value in variables.items(): + elements.append(f"{name}:{value}") + return ",".join(elements) + + + def __run(self, job_id, index, variables, verbose): + if index < len(self.params): + param = self.params[index] + index += 1 + for val in param['range']: + variables[param['parameter']] = val + self.__run(job_id=job_id, index=index, variables=variables, verbose=verbose) + else: + tmp_mdl = self.__setup_model(variables=variables) + result_key = self.__get_result_key(variables=variables) + if verbose: + message = f'{job_id} --> running: ' + message += f'{result_key.replace(":", "=").replace(",", ", ")}' + log.info(message) + try: + tmp_result = tmp_mdl.run(**self.settings) + except Exception as err: + log.error("%s\n%s", err, traceback.format_exc()) + else: + self.ts_results[result_key] = tmp_result + + + def __setup_model(self, variables): + if "solver" in self.settings.keys() and \ + self.settings['solver'].name == "SSACSolver": + self.settings['variables'] = variables + return self.model + tmp_mdl = copy.deepcopy(self.model) + for name, value in variables.items(): + tmp_mdl.listOfParameters[name].set_expression(value) + return tmp_mdl + + + def run(self, job_id, verbose=False): + ''' + Run a parameter scan job + + Attributes + ---------- + ''' + index = 0 + variables = {} + self.__run(job_id=job_id, index=index, variables=variables, verbose=verbose) diff --git a/stochss/handlers/util/parameter_sweep.py b/stochss/handlers/util/parameter_sweep.py index b8e836b564..d1a4a909c2 100644 --- a/stochss/handlers/util/parameter_sweep.py +++ b/stochss/handlers/util/parameter_sweep.py @@ -20,21 +20,39 @@ import csv import json import pickle +import logging import itertools +import traceback import numpy import plotly -from gillespy2 import TauLeapingSolver, TauHybridSolver, VariableSSACSolver +from gillespy2 import TauHybridSolver -from .stochss_workflow import StochSSWorkflow +from .stochss_job import StochSSJob from .parameter_sweep_1d import ParameterSweep1D from .parameter_sweep_2d import ParameterSweep2D +from .parameter_scan import ParameterScan +from .stochss_errors import StochSSJobResultsError, StochSSJobError -class ParameterSweep(StochSSWorkflow): +log = logging.getLogger("stochss") + +class NumpyEncoder(json.JSONEncoder): + ''' + ################################################################################################ + Custom json encoder for numpy ndarrays + ################################################################################################ + ''' + def default(self, o): + if isinstance(o, numpy.ndarray): + return o.tolist() + return json.JSONEncoder.default(self, o) + + +class ParameterSweep(StochSSJob): ''' ################################################################################################ - StochSS parameter sweep workflow object + StochSS parameter sweep job object ################################################################################################ ''' @@ -42,120 +60,194 @@ class ParameterSweep(StochSSWorkflow): def __init__(self, path): ''' - Intitialize an parameter sweep workflow object + Intitialize an parameter sweep job object Attributes ---------- path : str - Path to the parameter sweep workflow + Path to the parameter sweep job ''' super().__init__(path=path) self.g_model, self.s_model = self.load_models() self.settings = self.load_settings() - def __get_run_settings(self, verbose=False): - solver_map = {"SSA":VariableSSACSolver(model=self.g_model), "Tau-Leaping":TauLeapingSolver, - "ODE":TauHybridSolver, "Hybrid-Tau-Leaping":TauHybridSolver} + def __get_run_settings(self): + instance_solvers = ["SSACSolver", "TauLeapingCSolver", "ODECSolver"] if self.settings['simulationSettings']['isAutomatic']: - if verbose: - self.log("info", "Running a parameter sweep with automatic solver") - solver_name = self.g_model.get_best_solver().name - kwargs = {"number_of_trajectories":1 if solver_name == "ODESolver" else 20} - if solver_name != "VariableSSACSolver": + solver = self.g_model.get_best_solver() + kwargs = {"number_of_trajectories":1 if "ODE" in solver.name else 20} + if solver.name not in instance_solvers: return kwargs - kwargs['solver'] = solver_map['SSA'] + kwargs['solver'] = solver(model=self.g_model) return kwargs - return self.get_run_settings(settings=self.settings, solver_map=solver_map) - - - def __store_csv_results(self, wkfl): - if wkfl.settings['number_of_trajectories'] > 1: - csv_keys = list(itertools.product(["min", "max", "avg", "var", "final"], - ["min", "max", "avg", "var"])) - else: - csv_keys = [["min"], ["max"], ["avg"], ["var"], ["final"]] - stamp = self.get_time_stamp() - dirname = f"results/results_csv{stamp}" - if not os.path.exists(dirname): - os.mkdir(dirname) - for key in csv_keys: - if not isinstance(key, list): - key = list(key) - path = os.path.join(dirname, f"{'-'.join(key)}.csv") - with open(path, "w", newline="") as csv_file: - csv_writer = csv.writer(csv_file) - wkfl.to_csv(keys=key, csv_writer=csv_writer) + solver_map = {"SSA":self.g_model.get_best_solver_algo("SSA"), + "Tau-Leaping":self.g_model.get_best_solver_algo("Tau-Leaping"), + "ODE":self.g_model.get_best_solver_algo("ODE"), + "Hybrid-Tau-Leaping":TauHybridSolver} + run_settings = self.get_run_settings(settings=self.settings, solver_map=solver_map) + if run_settings['solver'].name in instance_solvers: + run_settings['solver'] = run_settings['solver'](model=self.g_model) + return run_settings @classmethod - def __store_plots(cls, wkfl): - mappers = ["min", "max", "avg", "var", "final"] - if wkfl.settings['number_of_trajectories'] > 1: - keys = list(itertools.product(wkfl.list_of_species, mappers, - ["min", "max", "avg", "var"])) - else: - keys = list(itertools.product(wkfl.list_of_species, mappers)) - plot_figs = {} - for key in keys: - key = list(key) - trace_list = wkfl.get_plotly_traces(keys=key) - plt_data = {'title':f"Parameter Sweep - Variable: {key[0]}"} - wkfl.get_plotly_layout_data(plt_data=plt_data) - layout = plotly.graph_objs.Layout(title=dict(text=plt_data['title'], x=0.5), - xaxis=dict(title=plt_data['xaxis_label']), - yaxis=dict(title=plt_data['yaxis_label'])) + def __report_result_error(cls, trace): + message = "An unexpected error occured with the result object" + raise StochSSJobResultsError(message, trace) + + + def __store_csv_results(self, job): + try: + if "solver" in job.settings.keys(): + solver_name = job.settings['solver'].name + else: + solver_name = job.model.get_best_solver().name + if "ODE" not in solver_name and job.settings['number_of_trajectories'] > 1: + csv_keys = list(itertools.product(["min", "max", "avg", "var", "final"], + ["min", "max", "avg", "var"])) + else: + csv_keys = [["min"], ["max"], ["avg"], ["var"], ["final"]] + stamp = self.get_time_stamp() + dirname = f"results/results_csv{stamp}" + if not os.path.exists(dirname): + os.mkdir(dirname) + for key in csv_keys: + if not isinstance(key, list): + key = list(key) + path = os.path.join(dirname, f"{'-'.join(key)}.csv") + with open(path, "w", newline="") as csv_file: + csv_writer = csv.writer(csv_file) + job.to_csv(keys=key, csv_writer=csv_writer) + except Exception as err: + log.error("Error storing csv results: %s\n%s", + str(err), traceback.format_exc()) - fig = dict(data=trace_list, layout=layout, config={"responsive": True}) - plot_figs['-'.join(key)] = fig - with open('results/plots.json', 'w') as plots_file: - json.dump(plot_figs, plots_file, cls=plotly.utils.PlotlyJSONEncoder) + @classmethod + def __store_pickled_results(cls, job): + try: + with open('results/results.p', 'wb') as results_file: + pickle.dump(job.ts_results, results_file) + except Exception as err: + message = f"Error storing pickled results: {err}\n{traceback.format_exc()}" + log.error(message) + return message + return False - def __store_results(self, wkfl): - if not 'results' in os.listdir(): - os.mkdir('results') - with open('results/results.p', 'wb') as results_file: - pickle.dump(wkfl.ts_results, results_file) - with open('results/results.json', 'w') as json_file: - json_file.write(json.dumps(str(wkfl.results))) - self.__store_csv_results(wkfl) + @classmethod + def __store_result_plots(cls, job): + try: + mappers = ["min", "max", "avg", "var", "final"] + if "solver" in job.settings.keys(): + solver_name = job.settings['solver'].name + else: + solver_name = job.model.get_best_solver().name + if "ODE" not in solver_name and job.settings['number_of_trajectories'] > 1: + keys = list(itertools.product(job.list_of_species, mappers, + ["min", "max", "avg", "var"])) + else: + keys = list(itertools.product(job.list_of_species, mappers)) + plot_figs = {} + for key in keys: + key = list(key) + trace_list = job.get_plotly_traces(keys=key) + plt_data = {'title':f"Parameter Sweep - Variable: {key[0]}"} + job.get_plotly_layout_data(plt_data=plt_data) + layout = plotly.graph_objs.Layout(title=dict(text=plt_data['title'], x=0.5), + xaxis=dict(title=plt_data['xaxis_label']), + yaxis=dict(title=plt_data['yaxis_label'])) + + fig = dict(data=trace_list, layout=layout, config={"responsive": True}) + plot_figs['-'.join(key)] = fig + + with open('results/plots.json', 'w') as plots_file: + json.dump(plot_figs, plots_file, cls=plotly.utils.PlotlyJSONEncoder, + indent=4, sort_keys=True) + except Exception as err: + message = f"Error storing result plots: {err}\n{traceback.format_exc()}" + log.error(message) + return message + return False - def configure(self, verbose=False): + @classmethod + def __store_results(cls, job): + try: + with open('results/results.json', 'w') as json_file: + json.dump(job.results, json_file, indent=4, sort_keys=True, cls=NumpyEncoder) + except Exception as err: + message = f"Error storing results dictionary: {err}\n{traceback.format_exc()}" + log.err(message) + return message + return False + + + def configure(self): ''' Get the configuration arguments for 1D or 2D parameter sweep Attributes ---------- ''' - run_settings = self.__get_run_settings(verbose=verbose) + run_settings = self.__get_run_settings() + if "timespanSettings" in self.settings.keys(): + keys = self.settings['timespanSettings'].keys() + if "endSim" in keys and "timeStep" in keys: + end = self.settings['timespanSettings']['endSim'] + step_size = self.settings['timespanSettings']['timeStep'] + self.g_model.timespan(numpy.arange(0, end + step_size, step_size)) kwargs = {"model":self.g_model, "settings":run_settings} - settings = self.settings['parameterSweepSettings'] - p1_range = numpy.linspace(settings['p1Min'], settings['p1Max'], settings['p1Steps']) - param_one = {"parameter":settings['parameterOne']['name'], "range":p1_range} - if settings['is1D']: - kwargs['param'] = param_one + parameters = [] + for param in self.settings['parameterSweepSettings']['parameters']: + p_range = numpy.linspace(param['min'], param['max'], param['steps']) + parameters.append({"parameter":param['name'], "range":p_range}) + if len(parameters) > 1: + kwargs['params'] = parameters return kwargs - p2_range = numpy.linspace(settings['p2Min'], settings['p2Max'], settings['p2Steps']) - param_two = {"parameter":settings['parameterTwo']['name'], "range":p2_range} - kwargs["params"] = [param_one, param_two] + kwargs["param"] = parameters[0] return kwargs - def run(self, verbose=False): + def run(self, verbose=True): ''' - Run a 1D or 2D parameter sweep workflow + Run a 1D or 2D parameter sweep job Attributes ---------- verbose : bool Indicates whether or not to print debug statements ''' - is_1d = self.settings['parameterSweepSettings']['is1D'] - kwargs = self.configure(verbose=verbose) - wkfl = ParameterSweep1D(**kwargs) if is_1d else ParameterSweep2D(**kwargs) - wkfl.run(verbose=verbose) - self.__store_results(wkfl=wkfl) - self.__store_plots(wkfl=wkfl) + kwargs = self.configure() + if "param" in kwargs.keys(): + job = ParameterSweep1D(**kwargs) + sim_type = "1D parameter sweep" + elif len(kwargs['params']) > 2: + sim_type = "parameter scan" + job = ParameterScan(**kwargs) + else: + sim_type = "2D parameter sweep" + job = ParameterSweep2D(**kwargs) + if verbose: + log.info("Running the %s", sim_type) + job.run(job_id=self.get_file(), verbose=verbose) + if not job.ts_results: + message = "All simulations failed to complete." + raise StochSSJobError(message) + if verbose: + log.info("The %s has completed", sim_type) + log.info("Storing the results as pickle and csv") + if not 'results' in os.listdir(): + os.mkdir('results') + pkl_err = self.__store_pickled_results(job=job) + if job.name != "ParameterScan": + if verbose: + log.info("Storing the polts of the results") + res_err = self.__store_results(job=job) + self.__store_csv_results(job=job) + plt_err = self.__store_result_plots(job=job) + if pkl_err and res_err and plt_err: + self.__report_result_error(trace=f"{res_err}\n{pkl_err}\n{plt_err}") + elif pkl_err: + self.__report_result_error(trace=pkl_err) diff --git a/stochss/handlers/util/parameter_sweep_1d.py b/stochss/handlers/util/parameter_sweep_1d.py index 6fe062d867..33c580e115 100644 --- a/stochss/handlers/util/parameter_sweep_1d.py +++ b/stochss/handlers/util/parameter_sweep_1d.py @@ -17,17 +17,22 @@ ''' import copy +import logging +import traceback import numpy import plotly import matplotlib +log = logging.getLogger("stochss") + class ParameterSweep1D(): ''' ################################################################################################ - StochSS 1D parameter sweep workflow object + StochSS 1D parameter sweep job object ################################################################################################ ''' + name = "ParameterSweep1D" MAPPER_KEYS = ["min", "max", "avg", "var", "final"] REDUCER_KEYS = ["min", "max", "avg", "var"] @@ -50,8 +55,7 @@ def __init__(self, model, settings, param): self.param = param self.list_of_species = model.get_all_species().keys() self.results = {} - self.ts_results = [] - self.logs = [] + self.ts_results = {} def __ensemble_feature_extraction(self, results, index, verbose=False): @@ -63,14 +67,14 @@ def __ensemble_feature_extraction(self, results, index, verbose=False): else: m_data = [func_map[m_key](x[species]) for x in results] if verbose: - print(f' {m_key} population {species}={m_data}') + log.debug(' %s population %s=%s', m_key, species, m_data) std = numpy.std(m_data) for r_key in self.REDUCER_KEYS: r_data = func_map[r_key](m_data) self.results[species][m_key][r_key][index, 0] = r_data self.results[species][m_key][r_key][index, 1] = std if verbose: - print(f' {r_key} std of ensemble m:{r_data} s:{std}') + log.debug(' %s std of ensemble m:%s s:%s', r_key, r_data, std) def __feature_extraction(self, results, index, verbose=False): @@ -84,13 +88,13 @@ def __feature_extraction(self, results, index, verbose=False): data = func_map[key](spec_res) self.results[species][key][index, 0] = data if verbose: - print(f' {key} population {species}={data}') + log.debug(' %s population %s=%s', key, species, data) - def __setup_results(self): + def __setup_results(self, solver_name): for species in self.list_of_species: spec_res = {} - if self.settings['number_of_trajectories'] > 1: + if "ODE" not in solver_name and self.settings['number_of_trajectories'] > 1: for m_key in self.MAPPER_KEYS: spec_res[m_key] = {} for r_key in self.REDUCER_KEYS: @@ -113,7 +117,7 @@ def get_plotly_layout_data(self, plt_data): if "xaxis_label" not in plt_data: plt_data['xaxis_label'] = f"{self.param['parameter']}" if "yaxis_label" not in plt_data: - plt_data['xaxis_label'] = "Population" + plt_data['yaxis_label'] = "Population" def get_plotly_traces(self, keys): @@ -130,7 +134,8 @@ def get_plotly_traces(self, keys): else: results = self.results[keys[0]][keys[1]] - visible = self.settings['number_of_trajectories'] > 1 + visible = "number_of_trajectories" in self.settings.keys() and \ + self.settings['number_of_trajectories'] > 1 error_y = dict(type="data", array=results[:, 1], visible=visible) trace_list = [plotly.graph_objs.Scatter(x=self.param['range'], @@ -138,20 +143,6 @@ def get_plotly_traces(self, keys): return trace_list - def log(self, level, message): - ''' - Add a log to the objects internal logs - - Attribute - --------- - level : str - Level of the log - message : string - Message to be logged - ''' - self.logs.append({"level":level, "message":message}) - - def plot(self, keys=None): ''' Plot the results based on the keys using matplotlib @@ -174,30 +165,38 @@ def plot(self, keys=None): matplotlib.pyplot.ylabel("Population", fontsize=16, fontweight='bold') - def run(self, verbose=False): + def run(self, job_id, verbose=False): ''' - Run a 1D parameter sweep workflow + Run a 1D parameter sweep job Attributes ---------- ''' - self.__setup_results() + if "solver" in self.settings.keys(): + solver_name = self.settings['solver'].name + else: + solver_name = self.model.get_best_solver().name + self.__setup_results(solver_name=solver_name) for i, val in enumerate(self.param['range']): - if "solver" in self.settings.keys() and \ - self.settings['solver'].name == "VariableSSACSolver": + if solver_name in ["SSACSolver", "TauLeapingCSolver", "ODECSolver"]: tmp_mdl = self.model self.settings['variables'] = {self.param['parameter']:val} else: tmp_mdl = copy.deepcopy(self.model) tmp_mdl.listOfParameters[self.param['parameter']].set_expression(val) if verbose: - print(f"running {self.param['parameter']}={val}") - tmp_res = tmp_mdl.run(**self.settings) - self.ts_results.append(tmp_res) - if self.settings['number_of_trajectories'] > 1: - self.__ensemble_feature_extraction(results=tmp_res, index=i, verbose=verbose) + log.info("%s --> running: %s=%s", job_id, self.param['parameter'], val) + try: + tmp_res = tmp_mdl.run(**self.settings) + except Exception as err: + log.error("%s\n%s", err, traceback.format_exc()) else: - self.__feature_extraction(results=tmp_res, index=i, verbose=verbose) + key = f"{self.param['parameter']}:{val}" + self.ts_results[key] = tmp_res + if "ODE" not in solver_name and self.settings['number_of_trajectories'] > 1: + self.__ensemble_feature_extraction(results=tmp_res, index=i, verbose=verbose) + else: + self.__feature_extraction(results=tmp_res, index=i, verbose=verbose) def to_csv(self, keys, csv_writer): diff --git a/stochss/handlers/util/parameter_sweep_2d.py b/stochss/handlers/util/parameter_sweep_2d.py index b2b57abda3..0c909181de 100644 --- a/stochss/handlers/util/parameter_sweep_2d.py +++ b/stochss/handlers/util/parameter_sweep_2d.py @@ -17,18 +17,23 @@ ''' import copy +import logging +import traceback import numpy import plotly import matplotlib import mpl_toolkits +log = logging.getLogger("stochss") + class ParameterSweep2D(): ''' ################################################################################################ - StochSS 2D parameter sweep workflow object + StochSS 2D parameter sweep job object ################################################################################################ ''' + name = "ParameterSweep2D" MAPPER_KEYS = ["min", "max", "avg", "var", "final"] REDUCER_KEYS = ["min", "max", "avg", "var"] @@ -50,8 +55,7 @@ def __init__(self, model, settings, params): self.settings = settings self.list_of_species = model.get_all_species().keys() self.params = params - self.logs = [] - self.ts_results = [] + self.ts_results = {} self.results = {} @@ -64,12 +68,12 @@ def __ensemble_feature_extraction(self, results, i_ndx, j_ndx, verbose=False): else: m_data = [func_map[m_key](x[species]) for x in results] if verbose: - print(f' {m_key} population {species}={m_data}') + log.debug(' %s population %s=%s', m_key, species, m_data) for r_key in self.REDUCER_KEYS: r_data = func_map[r_key](m_data) self.results[species][m_key][r_key][i_ndx, j_ndx] = r_data if verbose: - print(f' {r_key} of ensemble = {r_data}') + log.debug(' %s of ensemble = %s', r_key, r_data) def __feature_extraction(self, results, i_ndx, j_ndx, verbose=False): @@ -83,13 +87,13 @@ def __feature_extraction(self, results, i_ndx, j_ndx, verbose=False): data = func_map[key](spec_res) self.results[species][key][i_ndx, j_ndx] = data if verbose: - print(f' {key} population {species}={data}') + log.debug(' %s population %s=%s', key, species, data) - def __setup_results(self): + def __setup_results(self, solver_name): for species in self.list_of_species: spec_res = {} - if self.settings['number_of_trajectories'] > 1: + if "ODE" not in solver_name and self.settings['number_of_trajectories'] > 1: for m_key in self.MAPPER_KEYS: spec_res[m_key] = {} for r_key in self.REDUCER_KEYS: @@ -136,20 +140,6 @@ def get_plotly_traces(self, keys): return trace_list - def log(self, level, message): - ''' - Add a log to the objects internal logs - - Attribute - --------- - level : str - Level of the log - message : string - Message to be logged - ''' - self.logs.append({"level":level, "message":message}) - - def plot(self, keys=None): ''' Plot the results based on the keys using matplotlib @@ -178,18 +168,21 @@ def plot(self, keys=None): _ = matplotlib.pyplot.colorbar(ax=axis, cax=cax) - def run(self, verbose=False): + def run(self, job_id, verbose=False): ''' - Run a 2D parameter sweep workflow + Run a 2D parameter sweep job Attributes ---------- ''' - self.__setup_results() + if "solver" in self.settings.keys(): + solver_name = self.settings['solver'].name + else: + solver_name = self.model.get_best_solver().name + self.__setup_results(solver_name=solver_name) for i, val1 in enumerate(self.params[0]['range']): for j, val2 in enumerate(self.params[1]['range']): - if "solver" in self.settings.keys() and \ - self.settings['solver'].name == "VariableSSACSolver": + if solver_name in ["SSACSolver", "TauLeapingCSolver", "ODECSolver"]: tmp_mdl = self.model variables = {self.params[0]['parameter']:val1, self.params[1]['parameter']:val2} self.settings['variables'] = variables @@ -198,16 +191,23 @@ def run(self, verbose=False): tmp_mdl.listOfParameters[self.params[0]['parameter']].set_expression(val1) tmp_mdl.listOfParameters[self.params[1]['parameter']].set_expression(val2) if verbose: - message = f"running {self.params[0]['parameter']}={val1}, " + message = f"{job_id} --> running: {self.params[0]['parameter']}={val1}, " message += f"{self.params[1]['parameter']}={val2}" - print(message) - tmp_res = tmp_mdl.run(**self.settings) - self.ts_results.append(tmp_res) - if self.settings['number_of_trajectories'] > 1: - self.__ensemble_feature_extraction(results=tmp_res, i_ndx=i, j_ndx=j, - verbose=verbose) + log.info(message) + try: + tmp_res = tmp_mdl.run(**self.settings) + except Exception as err: + log.error("%s\n%s", err, traceback.format_exc()) else: - self.__feature_extraction(results=tmp_res, i_ndx=i, j_ndx=j, verbose=verbose) + key = f"{self.params[0]['parameter']}:{val1}," + key += f"{self.params[1]['parameter']}:{val2}" + self.ts_results[key] = tmp_res + if "ODE" not in solver_name and self.settings['number_of_trajectories'] > 1: + self.__ensemble_feature_extraction(results=tmp_res, i_ndx=i, j_ndx=j, + verbose=verbose) + else: + self.__feature_extraction(results=tmp_res, i_ndx=i, j_ndx=j, + verbose=verbose) def to_csv(self, keys, csv_writer): diff --git a/stochss/handlers/util/scripts/run_preview.py b/stochss/handlers/util/scripts/run_preview.py index 32db9a4975..013f2b3d91 100755 --- a/stochss/handlers/util/scripts/run_preview.py +++ b/stochss/handlers/util/scripts/run_preview.py @@ -27,14 +27,20 @@ import warnings import plotly -from gillespy2.core import log +from tornado.log import LogFormatter +from gillespy2.core import log as gillespy2_log from gillespy2 import ModelError, SimulationError sys.path.append("/stochss/stochss/handlers/") # pylint: disable=wrong-import-position +sys.path.append("/stochss/stochss/") # pylint: disable=wrong-import-position from util.stochss_model import StochSSModel from util.stochss_spatial_model import StochSSSpatialModel from util.ensemble_simulation import EnsembleSimulation from util.spatial_simulation import SpatialSimulation +from handlers.log import init_log + +init_log() +log = logging.getLogger("stochss") def setup_logger(): ''' @@ -45,10 +51,16 @@ def setup_logger(): ''' warnings.simplefilter("ignore") log_stream = io.StringIO() - for handler in log.handlers: + for handler in gillespy2_log.handlers: if isinstance(handler, logging.StreamHandler): handler.stream = log_stream - return log_stream + handler = logging.FileHandler(".user-logs.txt") + fmt = '%(color)s%(asctime)s%(end_color)s$ %(message)s' + formatter = LogFormatter(fmt=fmt, datefmt="%b %d, %Y %I:%M %p UTC") + handler.setFormatter(formatter) + handler.setLevel(logging.INFO) + gillespy2_log.addHandler(handler) + return log_stream, handler def get_parsed_args(): @@ -63,33 +75,34 @@ def get_parsed_args(): parser = argparse.ArgumentParser(description=description) parser.add_argument('path', help="The path from the user directory to the model.") parser.add_argument('outfile', help="The temp file used to hold the results.") - parser.add_argument('species', help="Spatial species to preview.", default=None) + parser.add_argument('--species', help="Spatial species to preview.", default=None) return parser.parse_args() -def run_preview(wkfl): +def run_preview(job): ''' Run the preview simulation - wkfl : StochSSWorkflow instance + wkfl : StochSSJob instance The wkfl used for the preview simulation ''' - resp = {"timeout": False} + response = {"timeout": False} try: - plot = wkfl.run(preview=True) - resp["results"] = plot + plot = job.run(preview=True) + response["results"] = plot except ModelError as error: - resp['errors'] = f"{error}" + response['errors'] = f"{error}" except SimulationError as error: - resp['errors'] = f"{error}" + response['errors'] = f"{error}" except ValueError as error: - resp['errors'] = f"{error}" + response['errors'] = f"{error}" except Exception as error: - resp['errors'] = f"{error}" - return resp + response['errors'] = f"{error}" + return response if __name__ == "__main__": + log.info("Initializing the preview simulation") args = get_parsed_args() is_spatial = args.path.endswith(".smdl") if is_spatial: @@ -98,18 +111,20 @@ def run_preview(wkfl): wkfl.s_py_model = model.convert_to_spatialpy() wkfl.s_model = model.model else: - log_stm = setup_logger() + log_stm, f_handler = setup_logger() model = StochSSModel(path=args.path) wkfl = EnsembleSimulation(path="", preview=True) wkfl.g_model = model.convert_to_gillespy2() - resp = run_preview(wkfl) if not is_spatial: if 'GillesPy2 simulation exceeded timeout.' in log_stm.getvalue(): resp['timeout'] = True log_stm.close() - + f_handler.close() + outfile = os.path.join(model.user_dir, f".{args.outfile}.tmp") with open(outfile, "w") as file: - json.dump(resp, file, cls=plotly.utils.PlotlyJSONEncoder) + json.dump(resp, file, cls=plotly.utils.PlotlyJSONEncoder, + indent=4, sort_keys=True) open(f"{outfile}.done", "w").close() + log.info("Preview complete") diff --git a/stochss/handlers/util/scripts/start_job.py b/stochss/handlers/util/scripts/start_job.py index a1a1ba73da..fa880431a8 100755 --- a/stochss/handlers/util/scripts/start_job.py +++ b/stochss/handlers/util/scripts/start_job.py @@ -24,11 +24,17 @@ import argparse import traceback -from gillespy2.core import log +from tornado.log import LogFormatter +from gillespy2.core import log as gillespy2_log +sys.path.append("/stochss/stochss/") # pylint: disable=wrong-import-position sys.path.append("/stochss/stochss/handlers/") # pylint: disable=wrong-import-position from util.ensemble_simulation import EnsembleSimulation from util.parameter_sweep import ParameterSweep +from handlers.log import init_log + +init_log() +log = logging.getLogger("stochss") def get_parsed_args(): ''' @@ -38,10 +44,10 @@ def get_parsed_args(): Attributes ---------- ''' - description = "Start a job from an existing workflow." + description = "Start a job from an existing job." parser = argparse.ArgumentParser(description=description) - parser.add_argument('path', help="The path to the workflow.") - parser.add_argument('type', help="The type of the workflow.") + parser.add_argument('path', help="The path to the job.") + parser.add_argument('type', help="The type of the job.") parser.add_argument('-v', '--verbose', action="store_true", help="Print results as they are stored.") return parser.parse_args() @@ -54,12 +60,13 @@ def report_error(err): Attributes ---------- path : str - Path to the workflow + Path to the job err : Exception Obj Error caught in the except block ''' - log.error("Workflow errors: %s", err) - log.error("Traceback:\n%s", traceback.format_exc()) + message = f"Job errors: {str(err)}\n{traceback.format_exc()}" + gillespy2_log.error(message) + log.error(message) open('ERROR', 'w').close() @@ -67,47 +74,47 @@ def setup_logger(log_path): ''' Changer the GillesPy2 logger to record only error level logs and higher to the console and to log warning level logs and higher to a log file in - the workflow directory. + the job directory. Attributes ---------- log_path : str - Path to the workflows log file + Path to the jobs log file ''' - formatter = log.handlers[0].formatter # gillespy2 log formatter - fh_is_needed = True - for handler in log.handlers: + formatter = gillespy2_log.handlers[0].formatter # gillespy2 log formatter + for handler in gillespy2_log.handlers: if isinstance(handler, logging.StreamHandler): # Reset the stream to stderr handler.stream = sys.stderr # Only log error and critical logs to console handler.setLevel(logging.ERROR) - elif isinstance(handler, logging.FileHandler): - # File Handler was already added to the log - fh_is_needed = False - # Add the file handler if it not in the log already - if fh_is_needed: - # initialize file handler - file_handler = logging.FileHandler(log_path) - # log warning, error, and critical logs to file - file_handler.setLevel(logging.WARNING) - # add gillespy2 log formatter - file_handler.setFormatter(formatter) - # add file handler to log - log.addHandler(file_handler) + # Add the file handler for job logs + file_handler = logging.FileHandler(log_path) + file_handler.setLevel(logging.WARNING) + file_handler.setFormatter(formatter) + gillespy2_log.addHandler(file_handler) + # Add the file handler for user logs + handler = logging.FileHandler(".user-logs.txt") + fmt = '%(color)s%(asctime)s%(end_color)s$ %(message)s' + formatter = LogFormatter(fmt=fmt, datefmt="%b %d, %Y %I:%M %p UTC") + handler.setFormatter(formatter) + handler.setLevel(logging.INFO) + gillespy2_log.addHandler(handler) + return file_handler, handler if __name__ == "__main__": args = get_parsed_args() - workflows = {"gillespy":EnsembleSimulation, "parameterSweep":ParameterSweep} - wkfl = workflows[args.type](path=args.path) - os.chdir(wkfl.get_path(full=True)) - setup_logger("logs.txt") + jobs = {"gillespy":EnsembleSimulation, "parameterSweep":ParameterSweep} try: - wkfl.run(verbose=args.verbose) + os.chdir(args.path) + job = jobs[args.type](path=args.path) + job_handler, user_handler = setup_logger("logs.txt") + job.run(verbose=args.verbose) except Exception as error: - wkfl.print_logs(log) report_error(err=error) else: + job_handler.close() + user_handler.close() # update status to complete open('COMPLETE', 'w').close() diff --git a/stochss/handlers/util/spatial_simulation.py b/stochss/handlers/util/spatial_simulation.py index 43b28311b1..c2fd231b00 100644 --- a/stochss/handlers/util/spatial_simulation.py +++ b/stochss/handlers/util/spatial_simulation.py @@ -19,12 +19,12 @@ import os from spatialpy import Solver -from .stochss_workflow import StochSSWorkflow +from .stochss_job import StochSSJob -class SpatialSimulation(StochSSWorkflow): +class SpatialSimulation(StochSSJob): ''' ################################################################################################ - StochSS spatial ensemble simulation workflow object + StochSS spatial ensemble simulation job object ################################################################################################ ''' @@ -32,12 +32,12 @@ class SpatialSimulation(StochSSWorkflow): def __init__(self, path, preview=False, species=None): ''' - Intitialize a spatial ensemble simulation workflow object + Intitialize a spatial ensemble simulation job object Attributes ---------- path : str - Path to the spatial ensemble simulation workflow + Path to the spatial ensemble simulation job ''' super().__init__(path=path) if not preview: @@ -54,7 +54,7 @@ def __get_run_settings(self): def run(self, preview=False, verbose=False): ''' - Run a SpatialPy ensemble simulation workflow + Run a SpatialPy ensemble simulation job Attributes ---------- diff --git a/stochss/handlers/util/stochss_base.py b/stochss/handlers/util/stochss_base.py index 7f8f567827..c17075e87f 100644 --- a/stochss/handlers/util/stochss_base.py +++ b/stochss/handlers/util/stochss_base.py @@ -46,6 +46,47 @@ def __init__(self, path): self.logs = [] + @classmethod + def check_project_format(cls, path): + ''' + Determine if the format of the project is out of date + + Attributes + ---------- + ''' + files = os.listdir(path) + model_test = lambda file: file.endswith(".mdl") or file.endswith(".smdl") + wkgp_test = lambda file: file.endswith(".wkgp") + models = list(filter(model_test, files)) + wkgps = list(filter(wkgp_test, files)) + if len(models) > 0: + return False + if len(wkgps) == 1 and wkgps[0] == "WorkflowGroup1.wkgp": + return False + return True + + + @classmethod + def check_workflow_format(cls, path): + ''' + Determine if the format of the workflow is out of date + + Attributes + ---------- + path : str + Path to the workflow. + ''' + path = os.path.join(cls.user_dir, path) + files = os.listdir(path) + old_files = ["info.json", "logs.txt", "results", "RUNNING", "ERROR", "COMPLETE"] + for file in old_files: + if file in files: + return False + if len(list(filter(lambda file: file.endswith(".mdl"), files))) > 0: + return False + return True + + def get_new_path(self, dst_path): ''' Gets the proper destination path for the file object to be moved @@ -56,6 +97,8 @@ def get_new_path(self, dst_path): New path for the file object from the users home directory ''' new_path = os.path.join(self.user_dir, dst_path) + if dst_path.startswith("trash/") and not "trash" in os.listdir(self.user_dir): + os.mkdir(os.path.join(self.user_dir, "trash")) if new_path.split().pop().replace('.', '', 5).isdigit(): return new_path.replace(new_path.split().pop(), "").strip() if "trash/" in new_path and os.path.exists(new_path): @@ -95,10 +138,10 @@ def get_model_template(self, as_string=False): return json.load(template) except FileNotFoundError as err: message = f"Could not find the model template file: {str(err)}" - raise StochSSFileNotFoundError(message, traceback.format_exc()) + raise StochSSFileNotFoundError(message, traceback.format_exc()) from err except json.decoder.JSONDecodeError as err: message = f"Model template data is not JSON decodeable: {str(err)}" - raise FileNotJSONFormatError(message, traceback.format_exc()) + raise FileNotJSONFormatError(message, traceback.format_exc()) from err def get_settings_template(self, as_string=False): @@ -119,10 +162,10 @@ def get_settings_template(self, as_string=False): return json.load(template) except FileNotFoundError as err: message = f"Could not find the settings template file: {str(err)}" - raise StochSSFileNotFoundError(message, traceback.format_exc()) + raise StochSSFileNotFoundError(message, traceback.format_exc()) from err except json.decoder.JSONDecodeError as err: message = f"Settings template data is not JSON decodeable: {str(err)}" - raise FileNotJSONFormatError(message, traceback.format_exc()) + raise FileNotJSONFormatError(message, traceback.format_exc()) from err def get_name(self, path=None): @@ -194,10 +237,10 @@ def get_status(self, path=None): return "ready" except FileNotFoundError as err: message = f"Could not find the workflow: {str(err)}" - raise StochSSFileNotFoundError(message, traceback.format_exc()) + raise StochSSFileNotFoundError(message, traceback.format_exc()) from err - def get_unique_path(self, name): + def get_unique_path(self, name, dirname=None): ''' Get a unique path for the file object with the target name @@ -206,8 +249,9 @@ def get_unique_path(self, name): name : str New name for the target file ''' - dirname = self.get_dir_name(full=True) - exists = name in os.listdir(dirname) + if dirname is None: + dirname = self.get_dir_name(full=True) + exists = name in os.listdir(dirname if dirname else self.user_dir) i = 1 if exists: @@ -221,7 +265,7 @@ def get_unique_path(self, name): i = 2 while exists: proposed_name = ''.join([name, f"({i})", ext]) - exists = proposed_name in os.listdir(dirname) + exists = proposed_name in os.listdir(dirname if dirname else self.user_dir) i += 1 changed = i > 1 @@ -230,18 +274,20 @@ def get_unique_path(self, name): return os.path.join(dirname, name), changed - def get_unique_copy_path(self): + def get_unique_copy_path(self, path=None): ''' Gets a unique name for the file object being copied. Accounts for files that are already copies. Attributes ---------- + path : str + Path to the file object ''' - file = self.get_file() - dirname = self.get_dir_name() + file = self.get_file(path=path) + dirname = self.get_dir_name() if path is None else os.path.dirname(path) ext = '.' + file.split('.').pop() if '.' in file else '' - name = file.split('-copy')[0] if '-copy' in file else self.get_name() + name = file.split('-copy')[0] if '-copy' in file else self.get_name(path=path) # Check if the file object is an original or at least the second copy if not '-copy' in file or '-copy(' in file: @@ -316,8 +362,8 @@ def rename(self, name): file = self.get_file() new_path, changed = self.get_unique_path(name) try: - dst = shutil.move(path, new_path) - self.path = dst.replace(self.user_dir + '/', '') + shutil.move(path, new_path) + self.path = new_path.replace(self.user_dir + '/', '') new_file = self.get_file() if changed: message = f"A file already exists with that name, {file} was renamed to " @@ -327,7 +373,7 @@ def rename(self, name): return {"message":message, "_path":self.path, "changed":changed} except FileNotFoundError as err: message = f"Could not find the file or directory: {str(err)}" - raise StochSSFileNotFoundError(message, traceback.format_exc()) + raise StochSSFileNotFoundError(message, traceback.format_exc()) from err except PermissionError as err: message = f"You don not have permission to rename this file or directory: {str(err)}" - raise StochSSPermissionsError(message, traceback.format_exc()) + raise StochSSPermissionsError(message, traceback.format_exc()) from err diff --git a/stochss/handlers/util/stochss_errors.py b/stochss/handlers/util/stochss_errors.py index 58a2b04610..3ee1cbd411 100644 --- a/stochss/handlers/util/stochss_errors.py +++ b/stochss/handlers/util/stochss_errors.py @@ -69,6 +69,10 @@ def __init__(self, status_code, reason, msg, trace): self.traceback = trace + def __str__(self): + return f"{self.message}: \n{self.traceback}" + + #################################################################################################### # File System Errors @@ -136,6 +140,27 @@ def __init__(self, msg, trace=None): ''' super().__init__(403, "Permission Denied", msg, trace) + +class StochSSUnzipError(StochSSAPIError): + ''' + ################################################################################################ + StochSS Un-Zip Zip Archive API Handler Error + ################################################################################################ + ''' + + def __init__(self, msg, trace=None): + ''' + Indicates that a problem occured during the extraction process for the zip archive + + Attributes + ---------- + msg : str + Details on what caused the error + trace : str + Error traceback for the error + ''' + super().__init__(403, "Unable to Extract Contents", msg, trace) + #################################################################################################### # Model Errors #################################################################################################### @@ -203,19 +228,19 @@ def __init__(self, msg, trace=None): super().__init__(406, "Domain File Not In Proper Format", msg, trace) #################################################################################################### -# Workflow Errors +# Job Errors #################################################################################################### -class StochSSWorkflowError(StochSSAPIError): +class StochSSJobError(StochSSAPIError): ''' ################################################################################################ - StochSS Workflow Errored During Run Time + StochSS Job Errored During Run Time ################################################################################################ ''' def __init__(self, msg, trace=None): ''' - Indicates that the workflow experienced an error during run + Indicates that the job experienced an error during run Attributes ---------- @@ -224,19 +249,19 @@ def __init__(self, msg, trace=None): trace : str Error traceback for the error ''' - super().__init__(403, "Workflow Errored on Run", msg, trace) + super().__init__(403, "Job Errored on Run", msg, trace) -class StochSSWorkflowNotCompleteError(StochSSAPIError): +class StochSSJobNotCompleteError(StochSSAPIError): ''' ################################################################################################ - StochSS Workflow Has Not Completed + StochSS Job Has Not Completed ################################################################################################ ''' def __init__(self, msg, trace=None): ''' - Indicates that the action requires a workflow to finish running before it can be executed + Indicates that the action requires a job to finish running before it can be executed Attributes ---------- @@ -245,7 +270,7 @@ def __init__(self, msg, trace=None): trace : str Error traceback for the error ''' - super().__init__(403, "Workflow Run Not Complete", msg, trace) + super().__init__(403, "Job Run Not Complete", msg, trace) class PlotNotAvailableError(StochSSAPIError): @@ -267,3 +292,24 @@ def __init__(self, msg, trace=None): Error traceback for the error ''' super().__init__(406, "Plot Figure Not Available", msg, trace) + + +class StochSSJobResultsError(StochSSAPIError): + ''' + ################################################################################################ + StochSS Job Results Error + ################################################################################################ + ''' + + def __init__(self, msg, trace=None): + ''' + Indicates that the job results object was corrupted + + Attributes + ---------- + msg : str + Details on what caused the error + trace : str + Error traceback for the error + ''' + super().__init__(500, "Job Results Error", msg, trace) diff --git a/stochss/handlers/util/stochss_file.py b/stochss/handlers/util/stochss_file.py index 429e23f7e5..fbe99c91d3 100644 --- a/stochss/handlers/util/stochss_file.py +++ b/stochss/handlers/util/stochss_file.py @@ -23,7 +23,7 @@ from .stochss_base import StochSSBase from .stochss_errors import StochSSFileNotFoundError, StochSSPermissionsError, \ - StochSSFileExistsError + StochSSFileExistsError, StochSSUnzipError class StochSSFile(StochSSBase): ''' @@ -64,10 +64,10 @@ def delete(self): return "The file {0} was successfully deleted.".format(self.get_file()) except FileNotFoundError as err: message = f"Could not find the file: {str(err)}" - raise StochSSFileNotFoundError(message, traceback.format_exc()) + raise StochSSFileNotFoundError(message, traceback.format_exc()) from err except PermissionError as err: message = f"You do not have permission to delete this file: {str(err)}" - raise StochSSPermissionsError(message, traceback.format_exc()) + raise StochSSPermissionsError(message, traceback.format_exc()) from err def duplicate(self): @@ -79,7 +79,12 @@ def duplicate(self): ''' src_path = self.get_path(full=True) self.log("debug", f"Full path to the file: {src_path}") - dst_path = self.get_unique_copy_path() + if ".proj" in src_path and ".wkgp" in src_path and not src_path.endswith(".ipynb"): + wkgp = self.get_unique_copy_path(path=self.get_dir_name()) + os.mkdir(wkgp) + dst_path = os.path.join(wkgp, f"{self.get_name(path=wkgp)}.{src_path.split('.').pop()}") + else: + dst_path = self.get_unique_copy_path() self.log("debug", f"Full destination path: {dst_path}") try: shutil.copyfile(src_path, dst_path) @@ -88,10 +93,10 @@ def duplicate(self): return {"Message":message, "File":cp_name} except FileNotFoundError as err: message = f"Could not find the file: {str(err)}" - raise StochSSFileNotFoundError(message, traceback.format_exc()) + raise StochSSFileNotFoundError(message, traceback.format_exc()) from err except PermissionError as err: message = f"You do not have permission to copy this file: {str(err)}" - raise StochSSPermissionsError(message, traceback.format_exc()) + raise StochSSPermissionsError(message, traceback.format_exc()) from err def move(self, location): @@ -113,10 +118,10 @@ def move(self, location): return f"Success! {self.get_file()} was moved to {self.get_dir_name()}." except FileNotFoundError as err: message = f"Could not find the file: {str(err)}" - raise StochSSFileNotFoundError(message, traceback.format_exc) + raise StochSSFileNotFoundError(message, traceback.format_exc) from err except PermissionError as err: message = f"You do not have permission to move this file: {str(err)}" - raise StochSSPermissionsError(message, traceback.format_exc()) + raise StochSSPermissionsError(message, traceback.format_exc()) from err def read(self): @@ -134,10 +139,10 @@ def read(self): return resp except FileNotFoundError as err: message = f"Could not find the file: {str(err)}" - raise StochSSFileNotFoundError(message, traceback.format_exc()) + raise StochSSFileNotFoundError(message, traceback.format_exc()) from err - def unzip(self): + def unzip(self, from_upload=True): ''' Extract the contents of a zip archive @@ -146,7 +151,6 @@ def unzip(self): ''' if not self.path.endswith(".zip"): return [] - try: path = self.get_path(full=True) dirname = self.get_dir_name(full=True) @@ -162,6 +166,12 @@ def unzip(self): zip_file.extractall(dirname) if "__MACOSX" in os.listdir(dirname): shutil.rmtree(os.path.join(dirname, "__MACOSX")) - return [] + if from_upload: + return [] + message = "Successfully extracted the contents of" + return {"message": f"{message} {self.get_file()} to {self.get_dir_name()}"} except zipfile.BadZipFile as err: - return [str(err)] + message = f"{str(err)} so it could not be unzipped." + if not from_upload: + raise StochSSUnzipError(message, traceback.format_exc()) from err + return [message] diff --git a/stochss/handlers/util/stochss_folder.py b/stochss/handlers/util/stochss_folder.py index eb52873dcc..d9dbc44d4c 100644 --- a/stochss/handlers/util/stochss_folder.py +++ b/stochss/handlers/util/stochss_folder.py @@ -57,7 +57,7 @@ def __init__(self, path, new=False): os.makedirs(new_path) except FileExistsError as err: message = f"Could not create your directory: {str(err)}" - raise StochSSFileExistsError(message, traceback.format_exc()) + raise StochSSFileExistsError(message, traceback.format_exc()) from err def __get_rmt_upld_path(self, file): @@ -79,7 +79,12 @@ def __build_jstree_node(self, path, file): file_type = types[ext] node['type'] = file_type if file_type == "workflow": - node['_status'] = self.get_status(path=path) + node['_newFormat'] = self.check_workflow_format(path=_path) + if node['_newFormat']: + node['_hasJobs'] = len(list(filter(lambda file: "job" in file, + os.listdir(_path)))) > 0 + else: + node['_status'] = self.get_status(path=_path) elif file_type == "workflow-group": node['children'] = True elif os.path.isdir(os.path.join(path, file)): @@ -95,8 +100,6 @@ def __upload_file(self, file, body, new_name=None): path = os.path.join(self.path, file) new_file = StochSSFile(path=path, new=True, body=body) error = new_file.unzip() - if error: - error[0] += " so it could not be unzipped." file = new_file.get_file() dirname = new_file.get_dir_name() message = f"{file} was successfully uploaded to {dirname}" @@ -106,8 +109,7 @@ def __upload_file(self, file, body, new_name=None): def __upload_model(self, file, body, new_name=None): is_valid, error = self.__validate_model(body, file) if is_valid: - is_spatial = json.loads(body)['is_spatial'] - ext = "smdl" if is_spatial else "mdl" + ext = "smdl" if json.loads(body)['is_spatial'] else "mdl" else: ext = "json" if new_name is not None: @@ -115,7 +117,15 @@ def __upload_model(self, file, body, new_name=None): elif not file.endswith(ext): _ext = file.split('.').pop() file = file.replace(_ext, ext) - path = os.path.join(self.path, file) + if self.path.endswith(".proj") and ext != "json" and \ + self.check_project_format(path=self.path): + wkgp_file = f"{self.get_name(path=file)}.wkgp" + wkgp_path, changed = self.get_unique_path(name=wkgp_file, dirname=self.path) + if changed: + file = f"{self.get_name(path=wkgp_path)}.{ext}" + path = os.path.join(wkgp_path, file) + else: + path = os.path.join(self.path, file) new_file = StochSSFile(path=path, new=True, body=body) file = new_file.get_file() dirname = new_file.get_dir_name() @@ -137,7 +147,12 @@ def __upload_sbml(self, file, body, new_name=None): dirname = sbml.get_dir_name() is_valid, errors = self.__validate_sbml(sbml=sbml) if is_valid: - convert_resp = sbml.convert_to_model(name=sbml.get_name()) + if self.path.endswith(".proj") and self.check_project_format(path=self.path): + wkgp_path, _ = self.get_unique_path(name=f"{sbml.get_name()}.wkgp", + dirname=self.path) + convert_resp = sbml.convert_to_model(name=self.get_name(wkgp_path), wkgp=True) + else: + convert_resp = sbml.convert_to_model(name=sbml.get_name()) _ = StochSSModel(path=convert_resp['path'], new=True, model=convert_resp['model']) message = f"{sbml.get_file()} was successfully uploaded to {dirname}" else: @@ -175,57 +190,6 @@ def __validate_sbml(cls, sbml): return bool(not errors), errors - def get_file_list(self, ext): - ''' - Get the list of files matching the ext in this directory and all sub-directories - - Attributes - ---------- - ''' - domain_paths = {} - domain_files = {} - for root, _, files in os.walk(self.get_path(full=True)): - dirname = root.replace(self.user_dir+"/", "") - for file in files: - if file.endswith(ext): - path = os.path.join(dirname, file) if dirname else file - if file in domain_files.keys(): - domain_paths[domain_files[file]].append(path) - else: - index = str(len(domain_files.keys())) - domain_files[file] = index - domain_paths[index] = [path] - options = [[index, file] for file, index in domain_files.items()] - return {"files":options, "paths":domain_paths} - - - def get_jstree_node(self, is_root=False): - ''' - Build and return a JSTree node object the represents the file object - - Attributes - ---------- - is_root : bool - Indicates whether or not a folder is to be treated as the root - ''' - path = self.user_dir if self.path == "none" else self.get_path(full=True) - try: - files = list(filter(lambda file: not file.startswith('.'), os.listdir(path=path))) - nodes = list(map(lambda file: self.__build_jstree_node(path, file), files)) - if self.path == "none": - state = {"opened":True} - root = {"text":"/", "type":"root", "_path":"/", "children":nodes, "state":state} - return json.dumps([root]) - if is_root: - root = {"text":self.get_name(), "type":"root", "_path":self.path, "children":nodes, - "state":{"opened":True}} - return json.dumps([root]) - return json.dumps(nodes) - except FileNotFoundError as err: - message = f"Could not find the directory: {str(err)}" - raise StochSSFileNotFoundError(message, traceback.format_exc()) - - def delete(self): ''' Delete the directory from the file system @@ -239,10 +203,10 @@ def delete(self): return f"The directory {self.get_file()} was successfully deleted." except FileNotFoundError as err: message = f"Could not find the directory: {str(err)}" - raise StochSSFileNotFoundError(message, traceback.format_exc()) + raise StochSSFileNotFoundError(message, traceback.format_exc()) from err except PermissionError as err: message = f"You do not have permission to delete this directory: {str(err)}" - raise StochSSPermissionsError(message, traceback.format_exc()) + raise StochSSPermissionsError(message, traceback.format_exc()) from err def duplicate(self): @@ -263,10 +227,28 @@ def duplicate(self): return {"Message":message, "File":cp_name} except FileNotFoundError as err: message = f"Could not find the directory: {str(err)}" - raise StochSSFileNotFoundError(message, traceback.format_exc()) + raise StochSSFileNotFoundError(message, traceback.format_exc()) from err except PermissionError as err: message = f"You do not have permission to copy this directory: {str(err)}" - raise StochSSPermissionsError(message, traceback.format_exc()) + raise StochSSPermissionsError(message, traceback.format_exc()) from err + + + def empty(self): + ''' + Delete the contents of the folder + + Attribites + ---------- + ''' + path = self.get_path(full=True) + if not os.path.exists(path): + os.mkdir(path) + return "The trash directory was removed." + for item in os.listdir(path): + item_path = os.path.join(self.path, item) + item_class = StochSSFolder if os.path.isdir(item_path) else StochSSFile + item_class(path=item_path).delete() + return "Successfully emptied the trash." def generate_zip_file(self): @@ -292,6 +274,82 @@ def generate_zip_file(self): return {"Message":message, "Path":zip_path} + def get_file_list(self, ext, folder=False, test=None): + ''' + Get the list of files matching the ext in this directory and all sub-directories + + Attributes + ---------- + ext : str or list + Extension of file object to search for + folder : bool + Indicates whether or not the file object is a folder + test : func + Function that determines if a file object should be excluded + ''' + domain_paths = {} + domain_files = {} + for root, folders, files in os.walk(self.get_path(full=True)): + root = root.replace(self.user_dir+"/", "") + file_list = folders if folder else files + for file in file_list: + exclude = False if test is None else test(ext, root, file) + if not exclude and '.' in file and f".{file.split('.').pop()}" in ext: + path = os.path.join(root, file) if root else file + if file in domain_files.keys(): + domain_paths[domain_files[file]].append(path) + else: + index = str(len(domain_files.keys())) + domain_files[file] = index + domain_paths[index] = [path] + options = [[index, file] for file, index in domain_files.items()] + return {"files":options, "paths":domain_paths} + + + def get_jstree_node(self, is_root=False): + ''' + Build and return a JSTree node object the represents the file object + + Attributes + ---------- + is_root : bool + Indicates whether or not a folder is to be treated as the root + ''' + path = self.user_dir if self.path == "none" else self.get_path(full=True) + try: + files = list(filter(lambda file: not file.startswith('.'), os.listdir(path=path))) + nodes = list(map(lambda file: self.__build_jstree_node(path, file), files)) + if self.path == "none": + state = {"opened":True} + root = {"text":"/", "type":"root", "_path":"/", "children":nodes, "state":state} + return json.dumps([root]) + if is_root: + root = {"text":self.get_name(), "type":"root", "_path":self.path, "children":nodes, + "state":{"opened":True}} + return json.dumps([root]) + return json.dumps(nodes) + except FileNotFoundError as err: + message = f"Could not find the directory: {str(err)}" + raise StochSSFileNotFoundError(message, traceback.format_exc()) from err + + + def get_project_list(self): + ''' + Get the list of project on the users disk + + Attributes + ---------- + ''' + test = lambda ext, root, file: bool("trash" in root.split("/")) + data = self.get_file_list(ext=".proj", folder=True, test=test) + projects = [] + for file in data['files']: + for path in data['paths'][file[0]]: + projects.append({"directory":path, "dirname":os.path.dirname(path), + "name":self.get_name(path=path)}) + return {"projects":projects} + + def move(self, location): ''' Moves a directory and its contents to a new location. @@ -311,9 +369,10 @@ def move(self, location): return f"Success! {self.get_file()} was moved to {self.get_dir_name()}." except FileNotFoundError as err: message = f"Could not find the directory: {str(err)}" - raise StochSSFileNotFoundError(message) + raise StochSSFileNotFoundError(message, traceback.format_exc()) from err except PermissionError as err: message = f"You do not have permission to move this directory: {str(err)}" + raise StochSSPermissionsError(message, traceback.format_exc()) from err def upload(self, file_type, file, body, new_name=None): diff --git a/stochss/handlers/util/stochss_job.py b/stochss/handlers/util/stochss_job.py new file mode 100644 index 0000000000..612c513b62 --- /dev/null +++ b/stochss/handlers/util/stochss_job.py @@ -0,0 +1,669 @@ +''' +StochSS is a platform for simulating biochemical systems +Copyright (C) 2019-2020 StochSS developers. + +This program is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with this program. If not, see . +''' + +import os +import json +import shutil +import pickle + +import datetime +import traceback +import numpy +import plotly + +from .stochss_base import StochSSBase +from .stochss_folder import StochSSFolder +from .stochss_model import StochSSModel +from .stochss_spatial_model import StochSSSpatialModel +from .stochss_errors import StochSSJobError, StochSSJobNotCompleteError, \ + StochSSFileNotFoundError, StochSSFileExistsError, \ + FileNotJSONFormatError, PlotNotAvailableError + +class StochSSJob(StochSSBase): + ''' + ################################################################################################ + StochSS job object + ################################################################################################ + ''' + + TYPES = {"gillespy":"_ES", "parameterSweep":"_PS"} + TITLES = {"gillespy":"Ensemble Simulation", "parameterSweep":"Parameter Sweep"} + + def __init__(self, path, new=False, data=None): + ''' + Intitialize a job object and if its new create it on the users file system + + Attributes + ---------- + path : str + Path to the job + new : bool + Indicates whether or not the job is new + data : dict + Load data needed for loading a job + ''' + super().__init__(path=path) + self.job = {} + self.type = None + self.time_stamp = None + if new: + self.type = data['type'] + self.__create_new_job(mdl_path=data['mdl_path'], settings=data['settings']) + + + def __create_new_job(self, mdl_path, settings=None): + path = self.get_path(full=True) + try: + os.mkdir(path) + os.mkdir(self.get_results_path(full=True)) + info = {"source_model":mdl_path, "wkfl_model":None, "type":self.type, "start_time":None} + self.update_info(new_info=info, new=True) + open(os.path.join(path, "logs.txt"), "w").close() + shutil.copyfile(os.path.join(self.user_dir, mdl_path), + self.get_model_path(full=True)) + if settings is None: + self.__create_settings() + else: + with open(self.__get_settings_path(full=True), "w") as settings_file: + json.dump(settings, settings_file) + except FileExistsError as err: + message = f"Could not create your job: {str(err)}" + raise StochSSFileExistsError(message, traceback.format_exc()) from err + except FileNotFoundError as err: + message = f"Could not find the file: {str(err)}" + raise StochSSFileNotFoundError(message, traceback.format_exc()) from err + + + def __create_settings(self): + if self.type == "parameterSweep": + settings = self.get_settings_template() + settings['simulationSettings']['realizations'] = 20 + with open(self.__get_settings_path(full=True), "w") as file: + json.dump(settings, file, indent=4, sort_keys=True) + else: + shutil.copyfile('/stochss/stochss_templates/workflowSettingsTemplate.json', + self.__get_settings_path(full=True)) + + + def __get_settings_path(self, full=False): + return os.path.join(self.get_path(full=full), "settings.json") + + + def __get_extract_dst_path(self, mdl_file): + if ".proj" not in self.path: + wkfl_dirname = os.path.dirname(self.path.replace(self.path.partition(".wkfl")[2], "")) + return os.path.join(wkfl_dirname, mdl_file) + proj_path = self.path.replace(self.path.partition(".proj")[2], "") + if "WorkflowGroup1.wkgp" in self.path: + return os.path.join(proj_path, mdl_file) + wkgp_path = self.path.replace(self.path.partition(".wkgp")[2], "") + has_mdl = len(list(filter(lambda file: file.endswith(".mdl"), os.listdir(wkgp_path)))) > 0 + if has_mdl: + wkgp_file = f"{self.get_name(path=mdl_file)}.wkgp" + path, changed = self.get_unique_path(name=wkgp_file, dirname=proj_path) + if changed: + mdl_file = f"{self.get_name(path=path)}.{mdl_file.split('.').pop()}" + return os.path.join(path, mdl_file) + wkgp_name = self.get_name(path=wkgp_path) + if wkgp_name != self.get_name(path=mdl_file): + mdl_file = f"{wkgp_name}.{mdl_file.split('.').pop()}" + return os.path.join(wkgp_path, mdl_file) + + + def __is_csv_dir(self, file): + if "results_csv" not in file: + return False + path = os.path.join(self.get_results_path(), file) + if not os.path.isdir(path): + return False + return True + + + def __update_settings(self): + settings = self.job['settings']['parameterSweepSettings'] + if "parameters" not in settings.keys(): + parameters = [] + if "paramID" in settings['parameterOne']: + p1_range = list(numpy.linspace(settings['p1Min'], settings['p1Max'], + settings['p1Steps'])) + param1 = {"paramID": settings['parameterOne']['paramID'], + "min": settings['p1Min'], + "max": settings['p1Max'], + "name": settings['parameterOne']['name'], + "range" : p1_range, + "steps": settings['p1Steps'], + "hasChangedRanged": False} + parameters.append(param1) + if "paramID" in settings['parameterTwo']: + p2_range = list(numpy.linspace(settings['p2Min'], settings['p2Max'], + settings['p2Steps'])) + param2 = {"paramID": settings['parameterTwo']['paramID'], + "min": settings['p2Min'], + "max": settings['p2Max'], + "name": settings['parameterTwo']['name'], + "range" : p2_range, + "steps": settings['p2Steps'], + "hasChangedRanged": False} + parameters.append(param2) + soi = settings['speciesOfInterest'] + self.job['settings']['parameterSweepSettings'] = {"speciesOfInterest": soi, + "parameters": parameters} + + + def duplicate_as_new(self, stamp): + ''' + Get all data needed to create a new job that + is a copy of this job in ready state. + + Attributes + ---------- + ''' + wkfl = self.load() + if wkfl['status'] != "ready": + mdl_path = self.get_model_path(external=True) + else: + mdl_path = wkfl['mdlPath'] + if self.get_time_stamp(): + path = self.path.replace(self.get_time_stamp(), stamp) + else: + dirname = self.get_dir_name() + mdl_name = self.get_name(path=mdl_path) + path = os.path.join(dirname, f"{mdl_name}{self.TYPES[self.type]}{stamp}.wkfl") + data = {"type":self.type, "mdl_path":self.get_model_path(), "settings":wkfl['settings']} + kwargs = {"path": path, "new":True, "data":data} + resp = {"message":f"A new job has been created from {self.path}", + "mdlPath":mdl_path, + "mdl_file":self.get_file(path=mdl_path)} + return resp, kwargs + + + def extract_model(self): + ''' + Get all data needed to create a new model that is a copy of the jobs model + + Attributes + ---------- + ''' + src_path = self.get_model_path() + model = StochSSModel(path=src_path).load() + dst_path = self.__get_extract_dst_path(mdl_file=self.get_file(path=src_path)) + kwargs = {"path":dst_path, "new":True, "model":model} + resp = {"message":f"A copy of the model in {self.path} has been created"} + return resp, kwargs + + + def generate_csv_zip(self): + ''' + Create a zip archive of the csv results for download + + Atrributes + ---------- + ''' + status = self.get_status() + if status == "error": + message = f"The job experienced an error during run: {status}" + raise StochSSJobError(message, traceback.format_exc()) + if status != "complete": + message = f"The job has not finished running: {status}." + raise StochSSJobNotCompleteError(message, traceback.format_exc()) + + csv_path = self.get_csv_path(full=True) + if os.path.exists(csv_path + ".zip"): + message = f"{csv_path}.zip already exists." + return {"Message":message, "Path":csv_path.replace(self.user_dir+"/", "") + ".zip"} + csv_folder = StochSSFolder(path=csv_path) + return csv_folder.generate_zip_file() + + + def get_csv_path(self, full=False): + ''' + Return the path to the csv directory + + Attributes + ---------- + ''' + res_path = self.get_results_path(full=full) + if not os.path.exists(res_path): + message = f"Could not find the results directory: {res_path}" + raise StochSSFileNotFoundError(message, traceback.format_exc()) + + try: + res_files = os.listdir(res_path) + csv_path = list(filter(lambda file: self.__is_csv_dir(file=file), res_files))[0] + return os.path.join(res_path, csv_path) + except IndexError as err: + message = f"Could not find the job results csv directory: {str(err)}" + raise StochSSFileNotFoundError(message, traceback.format_exc()) from err + + + def get_info_path(self, full=False): + ''' + Return the path to the info.json file + + Attributes + ---------- + full : bool + Indicates whether or not to get the full path or local path + ''' + return os.path.join(self.get_path(full=full), "info.json") + + + def get_model_path(self, full=False, external=False): + ''' + Return the path to the model file + + Attributes + ---------- + full : bool + Indicates whether or not to get the full path or local path + external : bool + Indicates whether or not to consider the path to the internal model + ''' + info = self.load_info() + self.log("debug", f"Job info: {info}") + if external: + if '.proj' not in self.path: + return info['source_model'] + file = self.get_file(path=info['source_model']) + proj_path = f"{self.path.split('.proj')[0]}.proj" + if self.check_project_format(path=proj_path): + return os.path.join(self.get_dir_name(), file) + return os.path.join(proj_path, file) + if info['wkfl_model'] is None: + file = self.get_file(path=info['source_model']) + return os.path.join(self.get_path(full=full), file) + file = self.get_file(path=info['wkfl_model']) + return os.path.join(self.get_path(full=full), file) + + + def get_notebook_data(self): + ''' + Get the needed data for converting to notebook + + Attributes + ---------- + ''' + info = self.load_info() + file = f"{self.get_name()}.ipynb" + dirname = self.get_dir_name() + if ".wkfl" in dirname: + code = "_ES" if info['type'] == "gillespy" else "_PS" + wkfl_name = self.get_name(path=dirname).replace(code, "_NB") + file = f"{wkfl_name}_{file}" + dirname = os.path.dirname(dirname) + path = os.path.join(dirname, file) + g_model, s_model = self.load_models() + settings = self.load_settings() + if info['type'] == "gillespy": + wkfl_type = info['type'] + elif info['type'] == "parameterSweep" and \ + len(settings['parameterSweepSettings']['parameters']) == 1: + wkfl_type = "1d_parameter_sweep" + else: + wkfl_type = "2d_parameter_sweep" + kwargs = {"path":path, "new":True, "settings":settings, + "models":{"s_model":s_model, "model":g_model}} + return {"kwargs":kwargs, "type":wkfl_type} + + + def get_plot_from_results(self, plt_key, plt_data, plt_type): + ''' + Get the plotly figure for the results of a job + + Attributes + ---------- + plt_key : str + Indentifier for the requested plot figure + plt_data : dict + Title and axes data for the plot + plt_type : str + Type of plot to generate. + ''' + self.log("debug", f"Key identifying the plot to generate: {plt_type}") + path = os.path.join(self.get_results_path(full=True), "results.p") + try: + self.log("info", "Loading the results...") + with open(path, "rb") as results_file: + result = pickle.load(results_file) + if plt_key is not None: + result = result[plt_key] + self.log("info", "Generating the plot...") + if plt_type == "mltplplt": + fig = result.plotplotly(return_plotly_figure=True, multiple_graphs=True) + elif plt_type == "stddevran": + fig = result.plotplotly_std_dev_range(return_plotly_figure=True) + else: + if plt_type == "stddev": + result = result.stddev_ensemble() + elif plt_type == "avg": + result = result.average_ensemble() + fig = result.plotplotly(return_plotly_figure=True) + if plt_type != "mltplplt": + fig["config"] = {"responsive":True} + self.log("info", "Loading the plot...") + fig = json.loads(json.dumps(fig, cls=plotly.utils.PlotlyJSONEncoder)) + return self.get_results_plot(plt_key=None, plt_data=plt_data, fig=fig) + except FileNotFoundError as err: + message = f"Could not find the results pickle file: {str(err)}" + raise StochSSFileNotFoundError(message, traceback.format_exc()) from err + except KeyError as err: + message = f"The requested plot is not available: {str(err)}" + raise PlotNotAvailableError(message, traceback.format_exc()) from err + + + def get_results_path(self, full=False): + ''' + Return the path to the results directory + + Attributes + ---------- + full : bool + Indicates whether or not to get the full path or local path + ''' + return os.path.join(self.get_path(full=full), "results") + + + def get_results_plot(self, plt_key, plt_data, fig=None): + ''' + Get the plotly figure for the results of a job + + Attributes + ---------- + plt_key : str + Indentifier for the requested plot figure + plt_data : dict + Title and axes data for the plot + ''' + self.log("debug", f"Key identifying the requested plot: {plt_key}") + self.log("debug", f"Title and axis data for the plot: {plt_data}") + path = os.path.join(self.get_results_path(full=True), "plots.json") + self.log("debug", f"Path to the job result plot file: {path}") + try: + if fig is None: + with open(path, "r") as plot_file: + fig = json.load(plot_file)[plt_key] + if plt_data is None: + return fig + for key in plt_data.keys(): + if key == "title": + fig['layout']['title']['text'] = plt_data[key] + else: + fig['layout'][key]['title']['text'] = plt_data[key] + return fig + except FileNotFoundError as err: + message = f"Could not find the plots file: {str(err)}" + raise StochSSFileNotFoundError(message, traceback.format_exc()) from err + except json.decoder.JSONDecodeError as err: + message = f"The plots file is not JSON decodable: {str(err)}" + raise FileNotJSONFormatError(message, traceback.format_exc()) from err + except KeyError as err: + message = f"The requested plot is not available: {str(err)}" + raise PlotNotAvailableError(message, traceback.format_exc()) from err + + + def get_run_logs(self): + ''' + Return the contents of the log file' + + Attributes + ---------- + ''' + path = os.path.join(self.get_path(full=True), "logs.txt") + try: + with open(path, "r") as file: + logs = file.read() + self.log("debug", f"Contents of the log file: {logs}") + if logs: + return logs + return "No logs were recoded for this job." + except FileNotFoundError as err: + message = f"Could not find the log file: {str(err)}" + raise StochSSFileNotFoundError(message, traceback.format_exc()) from err + + + @classmethod + def get_run_settings(cls, settings, solver_map): + ''' + Get the gillespy2 run settings for model.run() + + Attributes + ---------- + settings : dict + StochSS simulation settings dict + solver_map : dict + Dictionary mapping algorithm to solver + ''' + settings = settings['simulationSettings'] + kwargs = {"solver":solver_map[settings['algorithm']]} + if settings['algorithm'] in ("ODE", "Hybrid-Tau-Leaping"): + integrator_options = {"atol":settings['absoluteTol'], "rtol":settings['relativeTol']} + kwargs["integrator_options"] = integrator_options + if settings['algorithm'] == "ODE": + return kwargs + kwargs["number_of_trajectories"] = settings['realizations'] + if settings['seed'] != -1: + kwargs['seed'] = settings['seed'] + if settings['algorithm'] == "SSA": + return kwargs + kwargs['tau_tol'] = settings['tauTol'] + return kwargs + + + def get_time_stamp(self): + ''' + Get the time stamp from the job name + + Attributes + ---------- + ''' + name = self.get_name() + time_stamp = "_"+"_".join(name.split('_')[-2:]) + if time_stamp.replace('_', '').isdigit(): + return time_stamp + return None + + + def load(self, new=False): + ''' + Reads in all relavent data for a job and stores it in self.job. + + Attributes + ---------- + ''' + error = None + info = self.load_info() + self.type = info['type'] + status = "new" if new else self.get_status() + if status in ("new", "ready"): + if ".proj" in self.path: + mdl_dirname = self.get_dir_name() + if "WorkflowGroup1" in self.path: + mdl_dirname = os.path.dirname(mdl_dirname) + mdl_path = os.path.join(mdl_dirname, self.get_file(path=info['source_model'])) + else: + mdl_path = info['source_model'] + else: + mdl_path = self.get_model_path() + try: + model = StochSSModel(path=mdl_path).load() + except StochSSFileNotFoundError as err: + model = None + error = {"Reason":err.reason, "Message":err.message, "traceback":err.traceback} + self.log("error", f"Exception information: {error}") + finally: + settings = self.load_settings(model=model) + if os.path.exists(os.path.join(self.path, "logs.txt")): + logs = self.get_run_logs() + else: + logs = "" + self.job = {"mdlPath":mdl_path, "model":model, "settings":settings, + "startTime":info['start_time'], "status":status, + "timeStamp":self.time_stamp, "titleType":self.TITLES[info['type']], + "type":self.type, "directory":self.path, "logs":logs} + self.__update_settings() + if error is not None: + self.job['error'] = error + return self.job + + + def load_info(self): + ''' + Reads the jobs load function + + Attributes + ---------- + ''' + try: + path = self.get_info_path(full=True) + self.log("debug", f"The path to the job's info file: {path}") + with open(path, "r") as info_file: + info = json.load(info_file) + if "annotation" not in info: + info['annotation'] = "" + return info + except FileNotFoundError as err: + message = f"Could not find the info file: {str(err)}" + raise StochSSFileNotFoundError(message, traceback.format_exc()) from err + except json.decoder.JSONDecodeError as err: + message = f"The info file is not JSON decobable: {str(err)}" + raise FileNotJSONFormatError(message, traceback.format_exc()) from err + + + def load_models(self): + ''' + Load GillesPy2 and StochSS models for running + + Atrributes + ---------- + ''' + path = self.get_model_path() + if path.endswith('.mdl'): + model_obj = StochSSModel(path=path) + model = model_obj.convert_to_gillespy2() + else: + model_obj = StochSSSpatialModel(path=path) + model = model_obj.convert_to_spatialpy() + return model, model_obj.model + + + def load_settings(self, model=None): + ''' + Load the job settings from the settings file + + Attributes + ---------- + model : dict + Stochss model dict (used to backwards compatability) + ''' + try: + path = self.__get_settings_path(full=True) + with open(path, "r") as settings_file: + return json.load(settings_file) + except FileNotFoundError as err: + if model is None: + message = f"Could not find the settings file: {str(err)}" + raise StochSSFileNotFoundError(message, traceback.format_exc()) from err + settings = self.get_settings_template() + if "simulationSettings" in model.keys(): + settings['simulationSettings'] = model['simulationSettings'] + elif self.type == "parameterSweep": + settings['simulationSettings']['realizations'] = 20 + if "parameterSweepSettings" in model.keys(): + settings['parameterSweepSettings'] = model['parameterSweepSettings'] + return settings + except json.decoder.JSONDecodeError as err: + message = f"The settings file is not JSON decobable: {str(err)}" + raise FileNotJSONFormatError(message, traceback.format_exc()) from err + + + def save(self, mdl_path, settings, initialize=False): + ''' + Save the data for a new or ready state job + + Attributes + ---------- + ''' + path = self.get_model_path(full=True) + new_info = {"source_model":mdl_path} + if initialize: + # If this format is not something Javascript's Date.parse() method + # understands then the job status page will be unable to correctly create a + # Date object from the datestring parsed from the job's info.json file + new_info['start_time'] = datetime.datetime.now().strftime("%b %d, %Y %I:%M %p UTC") + new_info['wkfl_model'] = self.get_file(path=mdl_path) + open(os.path.join(self.path, 'RUNNING'), 'w').close() + self.update_info(new_info=new_info) + with open(self.__get_settings_path(full=True), "w") as file: + json.dump(settings, file, indent=4, sort_keys=True) + try: + os.remove(path) + shutil.copyfile(os.path.join(self.user_dir, mdl_path), + self.get_model_path(full=True)) + return f"Successfully saved the job: {self.path}" + except FileNotFoundError as err: + message = f"Could not find the model file: {str(err)}" + raise StochSSFileNotFoundError(message, traceback.format_exc()) from err + + + def save_plot(self, plot): + ''' + Save a plot to the output settings (for projects only) + + Attributes + ---------- + plot : dict + plot data used needed to look up the plot + ''' + settings = self.load_settings() + self.log("debug", f"Original settings: {settings}") + settings['resultsSettings']['outputs'].append(plot) + self.log("debug", f"New settings: {settings}") + with open(self.__get_settings_path(full=True), "w") as settings_file: + json.dump(settings, settings_file, indent=4, sort_keys=True) + return {"message":"The plot was successfully saved", "data":plot} + + + def update_info(self, new_info, new=False): + ''' + Updates the contents of the info file. If source model is updated, + checks if the model exists at that path + + Attributes + ---------- + new_info : dict + Contains all data to be updated under the correct key + new : bool + Indicates whether or not an info file needs to be created + ''' + if new: + info = new_info + else: + info = self.load_info() + if "source_model" in new_info.keys(): + info['source_model'] = new_info['source_model'] + if "wkfl_model" in new_info.keys(): + info['wkfl_model'] = new_info['wkfl_model'] + if "type" in new_info.keys(): + info['type'] = new_info['type'] + if "start_time" in new_info.keys(): + info['start_time'] = new_info['start_time'] + if "annotation" in new_info.keys(): + info['annotation'] = new_info['annotation'] + self.log("debug", f"New info: {info}") + with open(self.get_info_path(full=True), "w") as file: + json.dump(info, file, indent=4, sort_keys=True) diff --git a/stochss/handlers/util/stochss_model.py b/stochss/handlers/util/stochss_model.py index 3e168b63ec..bb2b9ba9d9 100644 --- a/stochss/handlers/util/stochss_model.py +++ b/stochss/handlers/util/stochss_model.py @@ -28,7 +28,7 @@ RateRule, AssignmentRule, FunctionDefinition from .stochss_base import StochSSBase -from .stochss_errors import StochSSFileNotFoundError, FileNotJSONFormatError, \ +from .stochss_errors import StochSSAPIError, StochSSFileNotFoundError, FileNotJSONFormatError, \ StochSSModelFormatError class StochSSModel(StochSSBase): @@ -63,7 +63,7 @@ def __init__(self, path, new=False, model=None): if changed: self.path = new_path.replace(self.user_dir + '/', "") with open(new_path, "w") as mdl_file: - json.dump(model, mdl_file) + json.dump(model, mdl_file, indent=4, sort_keys=True) else: self.model = None @@ -81,10 +81,11 @@ def __convert_event_assignments(cls, model, event): g_assignment = EventAssignment(variable=var, expression=assignment['expression']) assignments.append(g_assignment) + return assignments except KeyError as err: message = "Event assignments are not properly formatted or " message += f"are referenced incorrectly: {str(err)}" - raise StochSSModelFormatError(message, traceback.format_exc()) + raise StochSSModelFormatError(message, traceback.format_exc()) from err @classmethod @@ -113,7 +114,7 @@ def __convert_events(self, model): except KeyError as err: message = "Events are not properly formatted or " message += f"are referenced incorrectly: {str(err)}" - raise StochSSModelFormatError(message, traceback.format_exc()) + raise StochSSModelFormatError(message, traceback.format_exc()) from err def __convert_function_definitions(self, model): @@ -126,18 +127,18 @@ def __convert_function_definitions(self, model): except KeyError as err: message = "Function definitions are not properly formatted or " message += f"are referenced incorrectly: {str(err)}" - raise StochSSModelFormatError(message, traceback.format_exc()) + raise StochSSModelFormatError(message, traceback.format_exc()) from err def __convert_model_settings(self): try: end = self.model['modelSettings']['endSim'] step_size = self.model['modelSettings']['timeStep'] - return numpy.arange(0, end, step_size) + return numpy.arange(0, end + step_size, step_size) except KeyError as err: message = "Model settings are not properly formatted or " message += f"are referenced incorrectly: {str(err)}" - raise StochSSModelFormatError(message, traceback.format_exc()) + raise StochSSModelFormatError(message, traceback.format_exc()) from err def __convert_parameters(self, model): @@ -149,7 +150,7 @@ def __convert_parameters(self, model): except KeyError as err: message = "Parameters are not properly formatted or " message += f"are referenced incorrectly: {str(err)}" - raise StochSSModelFormatError(message, traceback.format_exc()) + raise StochSSModelFormatError(message, traceback.format_exc()) from err def __convert_reactions(self, model): @@ -172,15 +173,15 @@ def __convert_reactions(self, model): except KeyError as err: message = "Reactions are not properly formatted or " message += f"are referenced incorrectly: {str(err)}" - raise StochSSModelFormatError(message, traceback.format_exc()) + raise StochSSModelFormatError(message, traceback.format_exc()) from err def __convert_rules(self, model): try: for rule in self.model['rules']: if rule['expression'].strip() != "": - G_Rule = RateRule if rule['type'] == "Rate Rule" else AssignmentRule - g_rule = G_Rule(name=rule['name'].strip(), + rule_class = RateRule if rule['type'] == "Rate Rule" else AssignmentRule + g_rule = rule_class(name=rule['name'].strip(), variable=rule['variable']['name'], formula=rule['expression'].strip()) if rule['type'] == "Rate Rule": @@ -190,7 +191,7 @@ def __convert_rules(self, model): except KeyError as err: message = "Rules are not properly formatted or " message += f"are referenced incorrectly: {str(err)}" - raise StochSSModelFormatError(message, traceback.format_exc()) + raise StochSSModelFormatError(message, traceback.format_exc()) from err def __convert_species(self, model): @@ -208,7 +209,7 @@ def __convert_species(self, model): except KeyError as err: message = "Species are not properly formatted or " message += f"are referenced incorrectly: {str(err)}" - raise StochSSModelFormatError(message, traceback.format_exc()) + raise StochSSModelFormatError(message, traceback.format_exc()) from err @classmethod @@ -232,7 +233,7 @@ def __convert_stoich_species(cls, reaction): except KeyError as err: message = "Reactants or products are not properly formatted or " message += f"are referenced incorrectly: {str(err)}" - raise StochSSModelFormatError(message, traceback.format_exc()) + raise StochSSModelFormatError(message, traceback.format_exc()) from err def __read_model_file(self): @@ -241,10 +242,10 @@ def __read_model_file(self): self.model = json.load(mdl_file) except FileNotFoundError as err: message = f"Could not find the model file: {str(err)}" - raise StochSSFileNotFoundError(message, traceback.format_exc()) + raise StochSSFileNotFoundError(message, traceback.format_exc()) from err except json.decoder.JSONDecodeError as err: message = f"The model is not JSON decobable: {str(err)}" - raise FileNotJSONFormatError(message, traceback.format_exc()) + raise FileNotJSONFormatError(message, traceback.format_exc()) from err @classmethod @@ -320,25 +321,29 @@ def convert_to_gillespy2(self): Attributes ---------- ''' - if self.model is None: - _ = self.load() - name = self.get_name() - tspan = self.__convert_model_settings() try: - g_model = Model(name=name, volume=self.model['volume'], tspan=tspan, - annotation=self.model['annotation']) - except KeyError as err: - message = "Model properties are not properly formatted or " - message += f"are referenced incorrectly: {str(err)}" - raise StochSSModelFormatError(message, traceback.format_exc()) - self.__convert_species(model=g_model) - self.__convert_parameters(model=g_model) - self.__convert_reactions(model=g_model) - self.__convert_events(model=g_model) - self.__convert_rules(model=g_model) - self.__convert_function_definitions(model=g_model) - self.log("debug", str(g_model)) - return g_model + if self.model is None: + _ = self.load() + name = self.get_name() + tspan = self.__convert_model_settings() + try: + g_model = Model(name=name, volume=self.model['volume'], tspan=tspan, + annotation=self.model['annotation']) + except KeyError as err: + message = "Model properties are not properly formatted or " + message += f"are referenced incorrectly: {str(err)}" + raise StochSSModelFormatError(message, traceback.format_exc()) from err + self.__convert_species(model=g_model) + self.__convert_parameters(model=g_model) + self.__convert_reactions(model=g_model) + self.__convert_events(model=g_model) + self.__convert_rules(model=g_model) + self.__convert_function_definitions(model=g_model) + self.log("debug", str(g_model)) + return g_model + except Exception as err: + message = f"An un-expected error occured: {str(err)}" + raise StochSSAPIError(500, "Server Error", message, traceback.format_exc()) from err def convert_to_sbml(self): @@ -350,7 +355,10 @@ def convert_to_sbml(self): ''' name = self.get_name() s_file = f"{name}.sbml" - s_path = os.path.join(self.get_dir_name(), s_file) + dirname = self.get_dir_name() + if ".proj" in dirname and ".wkgp" in dirname: + dirname = os.path.dirname(dirname) + s_path = os.path.join(dirname, s_file) g_model = self.convert_to_gillespy2() tmp_path = export(g_model, path=tempfile.NamedTemporaryFile().name) @@ -376,12 +384,19 @@ def convert_to_spatial(self): model['domain'] = self.get_model_template()['domain'] for species in model['species']: if "types" not in species.keys(): - species['types'] = list(range(1, len(model['domain']['type_names']))) + species['types'] = list(range(1, len(model['domain']['types']))) for reaction in model['reactions']: if "types" not in reaction.keys(): - reaction['types'] = list(range(1, len(model['domain']['type_names']))) - s_path = self.path.replace(".mdl", ".smdl") - s_file = self.get_file(path=s_path) + reaction['types'] = list(range(1, len(model['domain']['types']))) + if ".wkgp" in self.path: + wkgp_path = self.get_dir_name() + wkgp_path, _ = self.get_unique_path(name=self.get_file(path=wkgp_path), + dirname=os.path.dirname(wkgp_path)) + s_file = self.get_file(path=wkgp_path).replace(".wkgp", ".smdl") + s_path = os.path.join(wkgp_path, s_file) + else: + s_path = self.path.replace(".mdl", ".smdl") + s_file = self.get_file(path=s_path) message = f"{self.get_file()} was successfully convert to {s_file}!" return {"Message":message, "File":s_file}, {"spatial":model, "path":s_path} @@ -439,6 +454,8 @@ def load(self): self.__update_reactions() self.__update_events(param_ids=param_ids) self.__update_rules(param_ids=param_ids) + self.model['name'] = self.get_name() + self.model['directory'] = self.path return self.model diff --git a/stochss/handlers/util/stochss_notebook.py b/stochss/handlers/util/stochss_notebook.py index 710abd7233..baaadd017b 100644 --- a/stochss/handlers/util/stochss_notebook.py +++ b/stochss/handlers/util/stochss_notebook.py @@ -39,32 +39,39 @@ class StochSSNotebook(StochSSBase): PARAMETER_SWEEP_2D = 4 MODEL_EXPLORATION = 5 MODEL_INFERENCE = 6 - SOLVER_MAP = {"SSACSolver":"SSA", "NumPySSASolver":"SSA", "VariableSSACSolver":"V-SSA", + SOLVER_MAP = {"SSACSolver":"SSA", "NumPySSASolver":"SSA", "ODESolver":"ODE", "Solver":"SSA", "TauLeapingSolver":"Tau-Leaping", "TauHybridSolver":"Hybrid-Tau-Leaping", - "ODESolver":"ODE", "Solver":"SSA"} + "ODECSolver":"ODE", "TauLeapingCSolver":"Tau-Leaping"} def __init__(self, path, new=False, models=None, settings=None): - ''' - Intitialize a notebook object and if its new create it on the users file system + '''Intitialize a notebook object and if its new create it on the users file system Attributes ---------- path : str - Path to the notebook - ''' + Path to the notebook''' super().__init__(path=path) if new: self.is_ssa_c = check_cpp_support() self.nb_type = 0 self.s_model = models["s_model"] self.model = models["model"] - self.settings = self.get_settings_template() if settings is None else settings + if settings is None: + self.settings = self.get_settings_template() + else: + self.settings = settings + if "timespanSettings" in settings.keys(): + keys = settings['timespanSettings'].keys() + if "endSim" in keys and "timeStep" in keys: + end = settings['timespanSettings']['endSim'] + step_size = settings['timespanSettings']['timeStep'] + self.s_model['modelSettings']['endSim'] = end + self.s_model['modelSettings']['timeStep'] = step_size self.make_parent_dirs() n_path, changed = self.get_unique_path(name=self.get_file()) if changed: self.path = n_path.replace(self.user_dir + '/', "") - def __create_common_cells(self, interactive_backend=False): cells = [self.__create_import_cell(interactive_backend=interactive_backend), nbf.new_markdown_cell(f"# {self.get_name()}"), @@ -78,10 +85,15 @@ def __create_configuration_cell(self): pad = " " config = ["def configure_simulation():"] # Add solver instantiation line if the c solver are available - instance_solvers = ["SSACSolver", "VariableSSACSolver"] + instance_solvers = ["SSACSolver", "ODECSolver", "TauLeapingCSolver"] is_automatic = self.settings['simulationSettings']['isAutomatic'] - if self.is_ssa_c and self.settings['solver'] in instance_solvers: - commented = is_automatic and self.settings['solver'] != "VariableSSACSolver" + if self.settings['solver'] in instance_solvers: + if is_automatic and self.nb_type <= self.ENSEMBLE_SIMULATION: + commented = True + elif is_automatic and self.settings['solver'] not in instance_solvers: + commented = True + else: + commented = False start = f"{pad}# " if commented else pad config.append(f"{start}solver = {self.settings['solver']}(model=model)") config.append(pad + "kwargs = {") @@ -91,7 +103,6 @@ def __create_configuration_cell(self): settings = self.__get_gillespy2_run_settings() settings_lists = {"ODE":['"solver"', '"integrator_options"'], "SSA":['"solver"', '"seed"', '"number_of_trajectories"'], - "V-SSA":['"solver"', '"seed"', '"number_of_trajectories"'], "Tau-Leaping":['"solver"', '"seed"', '"number_of_trajectories"', '"tau_tol"'], "Hybrid-Tau-Leaping":['"solver"', '"seed"', '"number_of_trajectories"', @@ -100,7 +111,8 @@ def __create_configuration_cell(self): is_spatial = self.s_model['is_spatial'] for setting in settings: key = setting.split(':')[0] - if self.settings['solver'] == "VariableSSACSolver" and key == '"solver"': + if self.nb_type > self.ENSEMBLE_SIMULATION and key == '"solver"' and \ + self.settings['solver'] in instance_solvers: start = pad*2 elif key not in settings_lists[algorithm]: start = f"{pad*2}# " @@ -125,10 +137,10 @@ def __create_event_strings(self, model, pad): pad=pad) a_names = self.__create_event_assignment_strings(assignments=assignments, event=event, pad=pad) - delay = event['delay'] if event['delay'] else None + delay = f"{event['delay']}" if event['delay'] else None ev_str = f'{pad}self.add_event(Event(name="{event["name"]}", ' ev_str += f'trigger={t_name}, assignments=[{a_names}], ' - ev_str += f'delay="{delay}", priority="{event["priority"]}", ' + ev_str += f'delay={delay}, priority="{event["priority"]}", ' ev_str += f'use_values_from_trigger_time={event["useValuesFromTriggerTime"]}))' events.append(ev_str) model.extend(triggers) @@ -137,7 +149,7 @@ def __create_event_strings(self, model, pad): except KeyError as err: message = "Events are not properly formatted or " message += f"are referenced incorrectly for notebooks: {str(err)}" - raise StochSSModelFormatError(message, traceback.format_exc()) + raise StochSSModelFormatError(message, traceback.format_exc()) from err @classmethod def __create_event_assignment_strings(cls, assignments, event, pad): @@ -171,7 +183,7 @@ def __create_function_definition_strings(self, model, pad): except KeyError as err: message = "Function definitions are not properly formatted or " message += f"are referenced incorrectly for notebooks: {str(err)}" - raise StochSSModelFormatError(message, traceback.format_exc()) + raise StochSSModelFormatError(message, traceback.format_exc()) from err def __create_import_cell(self, interactive_backend=False): try: @@ -193,19 +205,18 @@ def __create_import_cell(self, interactive_backend=False): imports.append("from gillespy2 import Model, Species, Parameter, Reaction, Event, \\") imports.append(" EventTrigger, EventAssignment, RateRule, \\") imports.append(" AssignmentRule, FunctionDefinition") - ssa = "SSACSolver" if self.is_ssa_c else "NumPySSASolver" - algorithm_map = {'SSA': f'from gillespy2 import {ssa}', - 'V-SSA': 'from gillespy2 import VariableSSACSolver', - 'Tau-Leaping': 'from gillespy2 import TauLeapingSolver', - 'Hybrid-Tau-Leaping': 'from gillespy2 import TauHybridSolver', - 'ODE': 'from gillespy2 import ODESolver'} + ssa_import = f'from gillespy2 import {self.model.get_best_solver_algo("SSA").name}' + tau_import = 'from gillespy2 import ' + tau_import += f'{self.model.get_best_solver_algo("Tau-Leaping").name}' + ode_import = f'from gillespy2 import {self.model.get_best_solver_algo("ODE").name}' + algorithm_map = {'SSA': ssa_import, 'Tau-Leaping': tau_import, 'ODE': ode_import, + 'Hybrid-Tau-Leaping': 'from gillespy2 import TauHybridSolver'} algorithm = self.settings['simulationSettings']['algorithm'] - if self.nb_type > self.ENSEMBLE_SIMULATION and algorithm == "SSA": - algorithm = "V-SSA" for name, alg_import in algorithm_map.items(): if not is_automatic and name == algorithm: imports.append(alg_import) - elif name == algorithm and algorithm == "V-SSA": + elif name == algorithm and self.nb_type > self.ENSEMBLE_SIMULATION and \ + name == "SSA": imports.append(alg_import) else: imports.append(f"# {alg_import}") @@ -213,7 +224,7 @@ def __create_import_cell(self, interactive_backend=False): except KeyError as err: message = "Workflow settings are not properly formatted or " message += f"are referenced incorrectly for notebooks: {str(err)}" - raise StochSSModelFormatError(message, traceback.format_exc()) + raise StochSSModelFormatError(message, traceback.format_exc()) from err def __create_initial_condition_strings(self, model, pad): if self.s_model['initialConditions']: @@ -234,12 +245,13 @@ def __create_initial_condition_strings(self, model, pad): except KeyError as err: message = "Initial conditions are not properly formatted or " message += f"are referenced incorrectly for notebooks: {str(err)}" - raise StochSSModelFormatError(message, traceback.format_exc()) + raise StochSSModelFormatError(message, traceback.format_exc()) from err def __create_mesh_string(self, model, pad): mesh = ["", f"{pad}# Domain", f"{pad}mesh = Mesh.read_stochss_domain('{self.s_model['path']}')", - f"{pad}self.add_mesh(mesh)"] + f"{pad}self.add_mesh(mesh)", + "", f"{pad}self.staticDomain = {self.s_model['domain']['static']}"] model.extend(mesh) def __create_model_cell(self): @@ -253,7 +265,6 @@ def __create_model_cell(self): self.__create_initial_condition_strings(model=model, pad=pad) self.__create_parameter_strings(model=model, pad=pad) self.__create_reaction_strings(model=model, pad=pad) - self.__create_tspan_string(model=model, pad=pad) else: model = [f"class {self.__get_class_name()}(Model):", " def __init__(self, parameter_values=None):", @@ -265,7 +276,7 @@ def __create_model_cell(self): self.__create_event_strings(model=model, pad=pad) self.__create_rules_strings(model=model, pad=pad) self.__create_function_definition_strings(model=model, pad=pad) - self.__create_tspan_string(model=model, pad=pad) + self.__create_tspan_string(model=model, pad=pad) return nbf.new_code_cell("\n".join(model)) def __create_parameter_strings(self, model, pad): @@ -289,7 +300,7 @@ def __create_parameter_strings(self, model, pad): except KeyError as err: message = "Parameters are not properly formatted or " message += f"are referenced incorrectly for notebooks: {str(err)}" - raise StochSSModelFormatError(message, traceback.format_exc()) + raise StochSSModelFormatError(message, traceback.format_exc()) from err def __create_ps_post_process_cells(self): pad = " " @@ -337,7 +348,7 @@ def __create_ps1d_class_cell(self): def __create_ps1d_config_cell(self): pad = " " - if self.settings['solver'] == "VariableSSACSolver": + if self.settings['solver'] == "SSACSolver": model_str = f"{pad}model = {self.__get_class_name()}()" else: model_str = f"{pad}ps_class = {self.__get_class_name()}" @@ -346,21 +357,23 @@ def __create_ps1d_config_cell(self): settings = self.settings['parameterSweepSettings'] eval_str = "float(eval(model.get_parameter(p1).expression))" number_of_trajectories = self.settings['simulationSettings']['realizations'] - if not settings['parameterOne']: + if not settings['parameters']: param = self.s_model['parameters'][0] p_min = f"0.5 * {eval_str}" p_max = f"1.5 * {eval_str}" + p_steps = "11" spec_of_interest = self.s_model['species'][0] else: - param = settings['parameterOne'] - p_min = settings['p1Min'] - p_max = settings['p1Max'] + param = settings['parameters'][0] + p_min = param['min'] + p_max = param['max'] + p_steps = param['steps'] spec_of_interest = settings['speciesOfInterest'] config_cell.extend([f"{pad}# ENTER PARAMETER HERE", f"{pad}p1 = '{param['name']}'", f"{pad}# ENTER START VALUE FOR P1 RANGE HERE", f"{pad}p1_min = {p_min}", f"{pad}# ENTER END VALUE FOR P1 RANGE HERE", f"{pad}p1_max = {p_max}", f"{pad}# ENTER THE NUMBER OF STEPS FOR P1 HERE", - f"{pad}p1_steps = {settings['p1Steps']}", + f"{pad}p1_steps = {p_steps}", f"{pad}p1_range = np.linspace(p1_min, p1_max, p1_steps)", f"{pad}# ENTER VARIABLE OF INTEREST HERE", f"{pad}variable_of_interest = '{spec_of_interest['name']}'", @@ -401,7 +414,7 @@ def __create_ps1d_run_str(self): f"{pad*2}data = np.zeros((len(c.p1_range), 2)) # mean and std", f"{pad*2}for i, v1 in enumerate(c.p1_range):"] res_str = f"{pad*4}tmp_results = " - if self.settings['solver'] == "VariableSSACSolver": + if self.settings['solver'] == "SSACSolver": res_str += "model.run(**kwargs, variables={c.p1:v1})" else: res_str += "tmp_model.run(**kwargs)" @@ -444,7 +457,7 @@ def __create_ps2d_class_cell(self): def __create_ps2d_config_cell(self): pad = " " - if self.settings['solver'] == "VariableSSACSolver": + if self.settings['solver'] == "SSACSolver": model_str = f"{pad}model = {self.__get_class_name()}()" else: model_str = f"{pad}ps_class = {self.__get_class_name()}" @@ -454,7 +467,7 @@ def __create_ps2d_config_cell(self): p1_eval_str = "float(eval(model.get_parameter(p1).expression))" p2_eval_str = "float(eval(model.get_parameter(p2).expression))" number_of_trajectories = self.settings['simulationSettings']['realizations'] - if not settings['parameterOne']: + if not settings['parameters']: param1 = self.s_model['parameters'][0] p1_min = f"0.5 * {p1_eval_str}" p1_max = f"1.5 * {p1_eval_str}" @@ -463,12 +476,12 @@ def __create_ps2d_config_cell(self): p2_max = f"1.5 * {p2_eval_str}" spec_of_interest = self.s_model['species'][0] else: - param1 = settings['parameterOne'] - p1_min = settings['p1Min'] - p1_max = settings['p1Max'] - param2 = settings['parameterTwo'] - p2_min = settings['p2Min'] - p2_max = settings['p2Max'] + param1 = settings['parameters'][0] + p1_min = param1['min'] + p1_max = param1['max'] + param2 = settings['parameters'][1] + p2_min = param2['min'] + p2_max = param2['max'] spec_of_interest = settings['speciesOfInterest'] config_cell.extend([f"{pad}# ENTER PARAMETER 1 HERE", f"{pad}p1 = '{param1['name']}'", f"{pad}# ENTER PARAMETER 2 HERE", f"{pad}p2 = '{param2['name']}'", @@ -476,13 +489,13 @@ def __create_ps2d_config_cell(self): f"{pad}p1_min = {p1_min}", f"{pad}# ENTER END VALUE FOR P1 RANGE HERE", f"{pad}p1_max = {p1_max}", f"{pad}# ENTER THE NUMBER OF STEPS FOR P1 HERE", - f"{pad}p1_steps = {settings['p1Steps']}", + f"{pad}p1_steps = {param1['steps'] if settings['parameters'] else 11}", f"{pad}p1_range = np.linspace(p1_min, p1_max, p1_steps)", f"{pad}# ENTER START VALUE FOR P2 RANGE HERE", f"{pad}p2_min = {p2_min}", f"{pad}# ENTER END VALUE FOR P2 RANGE HERE", f"{pad}p2_max = {p2_max}", f"{pad}# ENTER THE NUMBER OF STEPS FOR P2 HERE", - f"{pad}p2_steps = {settings['p2Steps']}", + f"{pad}p2_steps = {param2['steps'] if settings['parameters'] else 11}", f"{pad}p2_range = np.linspace(p2_min, p2_max, p2_steps)", f"{pad}# ENTER VARIABLE OF INTEREST HERE", f"{pad}variable_of_interest = '{spec_of_interest['name']}'", @@ -521,7 +534,7 @@ def __create_ps2d_run_str(self): f"{pad*2}for i, v1 in enumerate(c.p1_range):", f"{pad*3}for j, v2 in enumerate(c.p2_range):"] res_str = f"{pad*5}tmp_results = " - if self.settings['solver'] == "VariableSSACSolver": + if self.settings['solver'] == "SSACSolver": res_str += "model.run(**kwargs, variables={c.p1:v1, c.p2:v2})" else: res_str += "tmp_model.run(**kwargs)" @@ -569,7 +582,7 @@ def __create_reaction_strings(self, model, pad): except KeyError as err: message = "Reactions are not properly formatted or " message += f"are referenced incorrectly for notebooks: {str(err)}" - raise StochSSModelFormatError(message, traceback.format_exc()) + raise StochSSModelFormatError(message, traceback.format_exc()) from err def __create_rules_strings(self, model, pad): if self.s_model['rules']: @@ -593,7 +606,7 @@ def __create_rules_strings(self, model, pad): except KeyError as err: message = "Rules are not properly formatted or " message += f"are referenced incorrectly for notebooks: {str(err)}" - raise StochSSModelFormatError(message, traceback.format_exc()) + raise StochSSModelFormatError(message, traceback.format_exc()) from err @classmethod def __create_sme_expres_cells(cls): @@ -684,7 +697,7 @@ def __create_smi_simulator_cell(self): pad = " " comment = f"{pad}# params - array, need to have the same order as model.listOfParameters" loop = f"{pad}for e, pname in enumerate(model.listOfParameters.keys()):" - if self.settings['solver'] == "VariableSSACSolver": + if self.settings['solver'] == "SSACSolver": comment += "\n"+ pad +"variables = {}" func_def = "def get_variables(params, model):" body = f"{pad*2}variables[pname] = params[e]" @@ -737,7 +750,7 @@ def __create_species_strings(self, model, pad): except KeyError as err: message = "Species are not properly formatted or " message += f"are referenced incorrectly for notebooks: {str(err)}" - raise StochSSModelFormatError(message, traceback.format_exc()) + raise StochSSModelFormatError(message, traceback.format_exc()) from err def __create_stoich_spec_string(self, stoich_species): species = {} @@ -758,7 +771,7 @@ def __create_tspan_string(self, model, pad): end = self.s_model['modelSettings']['endSim'] step = self.s_model['modelSettings']['timeStep'] tspan = ["", f"{pad}# Timespan"] - ts_str = f'{pad}self.timespan(np.arange(0, {end}, {step})' + ts_str = f'{pad}self.timespan(np.arange(0, {end + step}, {step})' if self.s_model['is_spatial']: ts_str += f", timestep_size={step})" else: @@ -787,10 +800,11 @@ def __get_gillespy2_run_settings(self): settings['realizations'] = 1 # Map algorithm for GillesPy2 ssa_solver = "solver" if self.is_ssa_c else "NumPySSASolver" + ode_solver = "solver" if self.is_ssa_c else "ODESolver" + tau_solver = "solver" if self.is_ssa_c else "TauLeapingSolver" solver_map = {"SSA":f'"solver":{ssa_solver}', - "V-SSA":'"solver":solver', - "ODE":'"solver":ODESolver', - "Tau-Leaping":'"solver":TauLeapingSolver', + "ODE":f'"solver":{ode_solver}', + "Tau-Leaping":f'"solver":{tau_solver}', "Hybrid-Tau-Leaping":'"solver":TauHybridSolver'} # Map algorithm settings for GillesPy2. GillesPy2 requires snake case, remap camelCase settings_map = {"number_of_trajectories":settings['realizations'], @@ -812,18 +826,14 @@ def __get_spatialpy_run_setting(self): return [f'"{key}":{val}' for key, val in settings_map.items()] def __get_gillespy2_solver_name(self): - precompile = self.nb_type > self.ENSEMBLE_SIMULATION if self.settings['simulationSettings']['isAutomatic']: - solver = self.model.get_best_solver(precompile=precompile).name + solver = self.model.get_best_solver().name self.settings['simulationSettings']['algorithm'] = self.SOLVER_MAP[solver] return solver - algorithm_map = {'SSA': "SSACSolver" if self.is_ssa_c else "NumPySSASolver", - 'V-SSA': 'VariableSSACSolver', - 'Tau-Leaping': 'TauLeapingSolver', + algorithm_map = {'SSA': self.model.get_best_solver_algo("SSA").name, + 'Tau-Leaping': self.model.get_best_solver_algo("Tau-Leaping").name, 'Hybrid-Tau-Leaping': 'TauHybridSolver', - 'ODE': 'ODESolver'} - if precompile and self.settings['simulationSettings']['algorithm'] == "SSA": - return algorithm_map["V-SSA"] + 'ODE': self.model.get_best_solver_algo("ODE").name} return algorithm_map[self.settings['simulationSettings']['algorithm']] def create_1dps_notebook(self): @@ -966,16 +976,13 @@ def create_smi_notebook(self): return {"Message":message, "FilePath":self.get_path(), "File":self.get_file()} def load(self): - '''Read the notebook file and return as a dict - - Attributes - ----------''' + '''Read the notebook file and return as a dict''' try: with open(self.get_path(full=True), "r") as notebook_file: return json.load(notebook_file) except FileNotFoundError as err: message = f"Could not find the notebook file: {str(err)}" - raise StochSSFileNotFoundError(message, traceback.format_exc()) + raise StochSSFileNotFoundError(message, traceback.format_exc()) from err def write_notebook_file(self, cells): '''Write the new notebook file to disk diff --git a/stochss/handlers/util/stochss_project.py b/stochss/handlers/util/stochss_project.py new file mode 100644 index 0000000000..3b2c9327a4 --- /dev/null +++ b/stochss/handlers/util/stochss_project.py @@ -0,0 +1,388 @@ +''' +StochSS is a platform for simulating biochemical systems +Copyright (C) 2019-2020 StochSS developers. + +This program is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with this program. If not, see . +''' + +import os +import json +import shutil +import traceback + +from .stochss_base import StochSSBase +from .stochss_model import StochSSModel +from .stochss_spatial_model import StochSSSpatialModel +from .stochss_workflow import StochSSWorkflow +from .stochss_job import StochSSJob +from .stochss_notebook import StochSSNotebook +from .stochss_errors import StochSSFileExistsError, StochSSFileNotFoundError, \ + StochSSPermissionsError + +class StochSSProject(StochSSBase): + ''' + ################################################################################################ + StochSS project object + ################################################################################################ + ''' + + MODEL_TEST = lambda self, file: file.endswith(".mdl") or file.endswith(".smdl") + + def __init__(self, path, new=False): + ''' + Intitialize a project object and if its new create it on the users file system + + Attributes + ---------- + path : str + Path to the project + new : bool + Indicates whether or not the workflow is new + ''' + super().__init__(path=path) + self.project = None + if new: + try: + os.makedirs(os.path.join(self.get_path(full=True), "trash")) + except FileExistsError as err: + message = f"Could not create your project: {self.path}" + raise StochSSFileExistsError(message, traceback.format_exc()) from err + + + def __get_meta_data(self, path=None): + if path is None: + path = os.path.join(self.get_path(full=True), ".metadata.json") + if not os.path.exists(path): + return {"description":"", "creators":[]}, [] + with open(path, "r") as md_file: + data = json.load(md_file) + creators = [] + metadata = data['meta_data'] if "meta_data" in data.keys() else data['metadata'] + if "creators" in data.keys(): + if isinstance(data['creators'], dict): + for _, info in data['creators'].items(): + creators.append(info) + else: + creators = data['creators'] + return metadata, creators + + + def __get_old_model_data(self): + wkgps = {} + for file in os.listdir(self.get_path(full=True)): + ext = file.split('.').pop() + if ext in ("mdl", "smdl"): + name = self.get_name(path=file) + wkgp = {"file":f"{name}.wkgp", + "model":file, + "workflows":[]} + wkgps[name] = wkgp + return wkgps + + + def __get_old_workflow_data(self, data): + has_notebook = False + wkgp_path = os.path.join(self.get_path(), "WorkflowGroup1.wkgp") + for file in os.listdir(wkgp_path): + if file.endswith(".wkfl"): + path = os.path.join(wkgp_path, file) + wkfl = StochSSWorkflow(path=path) + mdl_file = wkfl.get_file(path=wkfl.get_model_path()) + mdl_name = wkfl.get_name(path=mdl_file) + if mdl_name not in data.keys(): + try: + _, kwargs = wkfl.extract_model() + StochSSModel(**kwargs) + except StochSSFileNotFoundError: + mdl_file = None + wkgp = {"file":f"{mdl_name}.wkgp", + "model":mdl_file, + "workflows":[file]} + data[mdl_name] = wkgp + else: + data[mdl_name]['workflows'].append(file) + if data[mdl_name]['model'] is None: + try: + _, kwargs = wkfl.extract_model() + StochSSModel(**kwargs) + data[mdl_name]['model'] = mdl_file + except StochSSFileNotFoundError: + pass + elif not has_notebook and file.endswith(".ipynb"): + has_notebook = True + return has_notebook + + + def __load_annotation(self): + path = os.path.join(self.get_path(full=True), "README.md") + if not os.path.exists(path): + return "" + with open(path, "r") as rdme_file: + return rdme_file.read() + + + def __load_model(self, dirname, file): + classes = {"mdl":StochSSModel, "smdl":StochSSSpatialModel} + model_class = classes[file.split('.').pop()] + mdl_path = os.path.join(dirname, file) + model = model_class(path=mdl_path).load() + model['name'] = self.get_name(path=file) + model['directory'] = mdl_path.replace(self.user_dir + "/", "") + return model + + + def __load_notebook(self, dirname, file): + path = os.path.join(dirname, file) + notebook = json.dumps(StochSSNotebook(path=path).load()) + status = "error" if "Traceback (most recent call last)" in notebook else "ready" + nb_wkfl = {"directory":path.replace(self.user_dir + "/", ""), "annotation":"", + "name":self.get_name(path=path), "status":status, "type":"Notebook"} + return nb_wkfl + + + def __load_workflow(self, dirname, folder): + path = os.path.join(dirname, folder) + wkfl = {"directory":path.replace(self.user_dir + "/", ""), "name":self.get_name(path=path)} + if self.check_workflow_format(path=path): + workflow = StochSSWorkflow(path=path) + workflow.load() + wkfl['annotation'] = workflow.workflow['annotation'] + wkfl['type'] = workflow.workflow['type'] + wkfl['status'] = None + else: + workflow = StochSSJob(path=path) + info = workflow.load_info() + wkfl["annotation"] = info['annotation'] + wkfl["status"] = workflow.get_status() + wkfl["type"] = workflow.TITLES[info['type']] + return wkfl + + + def __load_workflow_group(self, current_format, file, metadata=None): + path = os.path.join(self.get_path(full=True), file) + if metadata is None: + metadata, _ = self.__get_meta_data(path=os.path.join(path, ".metadata.json")) + wkgp = {"name": self.get_name(path=file), "workflows": [], "model": None, + "metadata": metadata} + for file_obj in os.listdir(path): + if current_format and self.MODEL_TEST(file_obj): + wkgp['model'] = self.__load_model(dirname=path, file=file_obj) + elif file_obj.endswith(".wkfl"): + wkgp['workflows'].append(self.__load_workflow(dirname=path, folder=file_obj)) + elif file_obj.endswith(".ipynb"): + wkgp['workflows'].append(self.__load_notebook(dirname=path, file=file_obj)) + if current_format and wkgp['model'] is None: + self.project['archive'].append(wkgp) + else: + self.project['workflowGroups'].append(wkgp) + + + def __update_all_workflows(self): + wkgp = os.path.join(self.path, "WorkflowGroup1.wkgp") + for file in os.listdir(wkgp): + if file.endswith(".wkfl"): + path = os.path.join(wkgp, file) + if not self.check_workflow_format(path=path): + wkfl = StochSSWorkflow(path=path) + if "error" in wkfl.check_for_external_model().keys(): + wkfl.extract_model() + wkfl.update_wkfl_format() + + + @classmethod + def __update_metadata(cls, metadata, creators): + creator_ids = [] + for email in metadata['creators']: + for i, creator in enumerate(creators): + if creator['email'] == email: + creator_ids.append(f"C{i + 1}") + metadata['creators'] = creator_ids + return metadata + + + def add_model(self, file, model=None, new=False): + ''' + Add a model to the project + + Attributes + ---------- + file : str + Name for the model file + model : dict + Model data + new : bool + Indicates whether or not the model is new + ''' + try: + self.log("debug", f"Original file name: {file}") + if self.check_project_format(path=self.path): + wkgp_file = f"{self.get_name(path=file)}.wkgp" + self.log("debug", f"Original workflow group folder name: {wkgp_file}") + if new: + wkgp_path = os.path.join(self.get_path(full=True), wkgp_file) + else: + wkgp_path, changed = self.get_unique_path(name=wkgp_file, dirname=self.path) + if changed: + wkgp_file = self.get_file(path=wkgp_path) + file = f"{self.get_name(path=wkgp_path)}.{file.split('.').pop()}" + self.log("debug", f"Final file name: {file}") + self.log("debug", f"Final workflow group folder name: {wkgp_file}") + self.log("debug", f"Workflow group path: {wkgp_path}") + path = os.path.join(self.path, wkgp_file, file) + else: + path = os.path.join(self.path, file) + if new and os.path.exists(path): + message = f"Could not create your model: {file}" + raise StochSSFileExistsError(message, traceback.format_exc()) + self.log("debug", f"Path to the model: {path}") + if model is None: + model = self.get_model_template() + model_class = StochSSModel if path.endswith(".mdl") else StochSSSpatialModel + model = model_class(path=path, new=True, model=model) + if new: + return {"path":path} + message = f"{file} was successfully added to the project." + return {"message":message} + except FileExistsError as err: + message = f"Could not create your model: {file}" + raise StochSSFileExistsError(message, traceback.format_exc()) from err + + + def extract_workflow(self, src, dst): + ''' + Make a copy of the target workflow and place it in the parent directory of the project. + + Attributes + ---------- + src : str + Path to the target workflow + dst : str + Proposed path for the workflows copy + ''' + dirname = os.path.dirname(dst) + dst, _ = self.get_unique_path(name=self.get_file(path=dst), dirname=dirname) + try: + shutil.copytree(src, dst) + if not dirname: + dirname = "/" + self.log("info", f"Successfully extracted {self.get_file(path=src)} to {dirname}") + resp = f"The Workflow {self.get_file(path=src)} was exported to {dirname}" + resp += f" in files as {self.get_file(path=dst)}" + return resp + except FileNotFoundError as err: + message = f"Could not find the directory: {str(err)}" + raise StochSSFileNotFoundError(message, traceback.format_exc()) from err + except PermissionError as err: + message = f"You do not have permission to copy this directory: {str(err)}" + raise StochSSPermissionsError(message, traceback.format_exc()) from err + + + def load(self): + ''' + Determines the project format, gets all models and workflows + in the project based on the format. + + Attributes + ---------- + ''' + current_format = self.check_project_format(path=self.path) + trash_path = os.path.join(self.get_path(full=True), "trash") + annotation = self.__load_annotation() + metadata, creators = self.__get_meta_data() + self.project = {"name":self.get_name(), "directory":self.path, "annotation":annotation, + "dirname":self.get_dir_name(), "newFormat": current_format, + "creators": creators, "workflowGroups": [], "archive":[]} + if "description" in metadata.keys(): + self.project['metadata'] = metadata + else: + new_metadata = self.__update_metadata(metadata=metadata[self.get_file()], + creators=creators) + self.project['metadata'] = new_metadata + if os.path.exists(trash_path): + self.project['trash_empty'] = len(os.listdir(trash_path)) == 0 + else: + self.project['trash_empty'] = True + os.mkdir(trash_path) + wkgp_test = lambda folder: folder.endswith(".wkgp") + for wkgp in filter(wkgp_test, os.listdir(self.get_path(full=True))): + if wkgp in metadata.keys(): + wkgp_md = self.__update_metadata(metadata=metadata[wkgp], creators=creators) + else: + wkgp_md = None + self.__load_workflow_group(current_format=current_format, file=wkgp, metadata=wkgp_md) + if not current_format: + self.project["models"] = [] + for mdl in filter(self.MODEL_TEST, os.listdir(self.get_path(full=True))): + self.project['models'].append(self.__load_model(dirname=self.path, file=mdl)) + return self.project + + + def update_annotation(self, annotation): + ''' + Updates the projects annotation file + + Attributes + ---------- + annotation : str + The annotations to be saved. + ''' + path = os.path.join(self.get_path(full=True), "README.md") + with open(path, 'w') as readme_file: + readme_file.write(annotation) + + + def update_meta_data(self, data): + ''' + Updates the projects meta-data file. + + Attributes + ---------- + meta-data : str + Meta-Data to be saved + ''' + for file, metadata in data.items(): + if file.endswith(".proj"): + path = os.path.join(self.get_path(full=True), ".metadata.json") + else: + path = os.path.join(self.get_path(full=True), file, ".metadata.json") + with open(path, "w") as metadata_file: + json.dump(metadata, metadata_file, indent=4, sort_keys=True) + + + def update_project_format(self): + ''' + Update a project to the new format + + Attributes + ---------- + ''' + self.__update_all_workflows() + data = self.__get_old_model_data() + has_notebook = self.__get_old_workflow_data(data=data) + os.chdir(self.path) + for _, wkgp in data.items(): + if wkgp['model'] is not None: + os.mkdir(wkgp['file']) + shutil.move(wkgp['model'], os.path.join(wkgp['file'], wkgp['model'])) + for workflow in wkgp['workflows']: + dst = os.path.join(wkgp['file'], workflow) + shutil.move(os.path.join("WorkflowGroup1.wkgp", workflow), dst) + else: + for workflow in wkgp['workflows']: + shutil.rmtree(os.path.join("WorkflowGroup1.wkgp", workflow)) + if has_notebook: + shutil.move("WorkflowGroup1.wkgp", "Notebooks") + else: + shutil.rmtree("WorkflowGroup1.wkgp") + os.chdir(self.user_dir) diff --git a/stochss/handlers/util/stochss_sbml.py b/stochss/handlers/util/stochss_sbml.py index ff59b8a03d..7f3cf29486 100644 --- a/stochss/handlers/util/stochss_sbml.py +++ b/stochss/handlers/util/stochss_sbml.py @@ -275,7 +275,7 @@ def convert_to_gillespy(self): return g_model, errors - def convert_to_model(self, name=None): + def convert_to_model(self, name=None, wkgp=False): ''' Convert the sbml model to a stochss model and return it with mdl path @@ -291,7 +291,14 @@ def convert_to_model(self, name=None): return {"message":message, "errors":errors, "model":None} s_file = f"{g_model.name}.mdl" if name is None else f"{name}.mdl" - s_path = os.path.join(self.get_dir_name(), s_file) + if wkgp: + wkgp_path, changed = self.get_unique_path(name=f"{self.get_name(path=s_file)}.wkgp", + dirname=self.get_dir_name()) + if changed: + s_file = s_file.replace(self.get_name(path=s_file), self.get_name(path=wkgp_path)) + s_path = os.path.join(wkgp_path, s_file) + else: + s_path = os.path.join(self.get_dir_name(), s_file) self.__convert_species(model=s_model, species=g_model.get_all_species()) self.__convert_parameters(model=s_model, parameters=g_model.get_all_parameters()) diff --git a/stochss/handlers/util/stochss_spatial_model.py b/stochss/handlers/util/stochss_spatial_model.py index d38964a051..1c930fed1e 100644 --- a/stochss/handlers/util/stochss_spatial_model.py +++ b/stochss/handlers/util/stochss_spatial_model.py @@ -54,6 +54,7 @@ def __init__(self, path, new=False, model=None): if new: if model is None: model = self.get_model_template() + if not model['is_spatial']: model['is_spatial'] = True if isinstance(model, str): model = json.loads(model) @@ -63,7 +64,7 @@ def __init__(self, path, new=False, model=None): if changed: self.path = new_path.replace(self.user_dir + '/', "") with open(new_path, "w") as smdl_file: - json.dump(model, smdl_file) + json.dump(model, smdl_file, indent=4, sort_keys=True) else: self.model = None @@ -134,10 +135,11 @@ def __convert_domain(self, model): mesh = Mesh(0, xlim, ylim, zlim, rho0=rho0, c0=c_0, P0=p_0, gravity=gravity) self.__convert_particles(mesh=mesh) model.add_mesh(mesh) + model.staticDomain = self.model['domain']['static'] except KeyError as err: message = "Spatial model domain properties are not properly formatted or " message += f"are referenced incorrectly: {str(err)}" - raise StochSSModelFormatError(message, traceback.format_exc()) + raise StochSSModelFormatError(message, traceback.format_exc()) from err def __convert_initial_conditions(self, model): @@ -161,19 +163,19 @@ def __convert_initial_conditions(self, model): except KeyError as err: message = "Spatial model domain properties are not properly formatted or " message += f"are referenced incorrectly: {str(err)}" - raise StochSSModelFormatError(message, traceback.format_exc()) + raise StochSSModelFormatError(message, traceback.format_exc()) from err def __convert_model_settings(self, model): try: end = self.model['modelSettings']['endSim'] step_size = self.model['modelSettings']['timeStep'] - tspan = numpy.arange(0, end, step_size) + tspan = numpy.arange(0, end + step_size, step_size) model.timespan(tspan, timestep_size=step_size) except KeyError as err: message = "Spatial model settings are not properly formatted or " message += f"are referenced incorrectly: {str(err)}" - raise StochSSModelFormatError(message, traceback.format_exc()) + raise StochSSModelFormatError(message, traceback.format_exc()) from err def __convert_parameters(self, model): @@ -184,7 +186,7 @@ def __convert_parameters(self, model): except KeyError as err: message = "Spatial model parameters are not properly formatted or " message += f"are referenced incorrectly: {str(err)}" - raise StochSSModelFormatError(message, traceback.format_exc()) + raise StochSSModelFormatError(message, traceback.format_exc()) from err def __convert_particles(self, mesh): @@ -195,7 +197,7 @@ def __convert_particles(self, mesh): except KeyError as err: message = "Spatial model domain particle properties are not properly formatted or " message += f"are referenced incorrectly: {str(err)}" - raise StochSSModelFormatError(message, traceback.format_exc()) + raise StochSSModelFormatError(message, traceback.format_exc()) from err def __convert_reactions(self, model): @@ -223,7 +225,7 @@ def __convert_reactions(self, model): except KeyError as err: message = "Spatial model reactions are not properly formatted or " message += f"are referenced incorrectly: {str(err)}" - raise StochSSModelFormatError(message, traceback.format_exc()) + raise StochSSModelFormatError(message, traceback.format_exc()) from err def __convert_species(self, model): @@ -236,7 +238,7 @@ def __convert_species(self, model): except KeyError as err: message = "Spatial model species are not properly formatted or " message += f"are referenced incorrectly: {str(err)}" - raise StochSSModelFormatError(message, traceback.format_exc()) + raise StochSSModelFormatError(message, traceback.format_exc()) from err @classmethod @@ -263,7 +265,7 @@ def __convert_stoich_species(cls, model, reaction): except KeyError as err: message = "Spatial model stoich species are not properly formatted or " message += f"are referenced incorrectly: {str(err)}" - raise StochSSModelFormatError(message, traceback.format_exc()) + raise StochSSModelFormatError(message, traceback.format_exc()) from err @classmethod @@ -291,13 +293,13 @@ def __load_domain_from_file(self, path): return self.__build_stochss_domain(s_domain=s_domain) except FileNotFoundError as err: message = f"Could not find the domain file: {str(err)}" - raise StochSSFileNotFoundError(message, traceback.format_exc()) + raise StochSSFileNotFoundError(message, traceback.format_exc()) from err except json.decoder.JSONDecodeError as err: message = f"The domain file is not JSON decobable: {str(err)}" - raise FileNotJSONFormatError(message, traceback.format_exc()) + raise FileNotJSONFormatError(message, traceback.format_exc()) from err except MeshError as err: message = f"The domain file is not in proper format: {str(err)}" - raise DomainFormatError(message, traceback.format_exc()) + raise DomainFormatError(message, traceback.format_exc()) from err def __read_model_file(self): @@ -306,10 +308,10 @@ def __read_model_file(self): self.model = json.load(smdl_file) except FileNotFoundError as err: message = f"Could not find the spatial model file: {str(err)}" - raise StochSSFileNotFoundError(message, traceback.format_exc()) + raise StochSSFileNotFoundError(message, traceback.format_exc()) from err except json.decoder.JSONDecodeError as err: message = f"The spatial model is not JSON decobable: {str(err)}" - raise FileNotJSONFormatError(message, traceback.format_exc()) + raise FileNotJSONFormatError(message, traceback.format_exc()) from err def convert_to_model(self): @@ -322,8 +324,15 @@ def convert_to_model(self): if self.model is None: s_model = self.load() s_model['is_spatial'] = False - m_path = self.path.replace(".smdl", ".mdl") - m_file = self.get_file(path=m_path) + if ".wkgp" in self.path: + wkgp_path = self.get_dir_name() + wkgp_path, _ = self.get_unique_path(name=self.get_file(path=wkgp_path), + dirname=os.path.dirname(wkgp_path)) + m_file = self.get_file(path=wkgp_path).replace(".wkgp", ".mdl") + m_path = os.path.join(wkgp_path, m_file) + else: + m_path = self.path.replace(".smdl", ".mdl") + m_file = self.get_file(path=m_path) message = f"{self.get_file()} was successfully convert to {m_file}!" return {"Message":message, "File":m_file}, {"model":s_model, "path":m_path} @@ -440,7 +449,7 @@ def get_particles_from_3d_domain(cls, data): @classmethod - def get_particles_from_remote(cls, mesh, data): + def get_particles_from_remote(cls, mesh, data, types): ''' Get a list of stochss particles from a mesh @@ -450,17 +459,28 @@ def get_particles_from_remote(cls, mesh, data): Mesh containing particle data data : dict Property and location data to be applied to each particle + types : list + List of type discriptions (lines from an uploaded file) ''' file = tempfile.NamedTemporaryFile() with open(file.name, "w") as mesh_file: mesh_file.write(mesh) s_domain = Mesh.read_xml_mesh(filename=file.name) domain = cls.__build_stochss_domain(s_domain=s_domain, data=data) + if types is not None: + type_data = cls.get_types_from_file(lines=types) + for t_data in type_data['types']: + if t_data['particle_id'] < len(domain['particles']): + domain['particles'][t_data['particle_id']]['type'] = t_data['typeID'] limits = {"x_lim":domain['x_lim'], "y_lim":domain['y_lim'], "z_lim":domain['z_lim']} - return {"particles":domain['particles'], "limits":limits} + resp = {"particles":domain['particles'], "limits":limits} + if types is not None: + resp['types'] = type_data['names'] + return resp - def get_types_from_file(self, path): + @classmethod + def get_types_from_file(cls, path=None, lines=None): ''' Get the type descriptions from the .txt file @@ -468,10 +488,13 @@ def get_types_from_file(self, path): ---------- path : str Path to the types description file + lines : list + Lines from an uploaded file ''' - path = os.path.join(self.user_dir, path) - with open(path, "r") as types_file: - lines = types_file.readlines() + if lines is None: + path = os.path.join(cls.user_dir, path) + with open(path, "r") as types_file: + lines = types_file.readlines() types = [] names = [] for line in lines: @@ -500,13 +523,18 @@ def load(self): if self.model is None: self.__read_model_file() self.model['name'] = self.get_name() - if "domain" not in self.model.keys(): + if not self.model['defaultMode']: + self.model['defaultMode'] = "discrete" + if "domain" not in self.model.keys() or len(self.model['domain'].keys()) < 6: self.model['domain'] = self.get_model_template()['domain'] + elif "static" not in self.model['domain'].keys(): + self.model['domain']['static'] = True for species in self.model['species']: if "types" not in species.keys(): species['types'] = list(range(1, len(self.model['domain']['types']))) if "diffusionConst" not in species.keys(): - species['diffusionConst'] = species['diffusionCoeff'] + diff = 0.0 if "diffusionCoeff" not in species.keys() else species['diffusionCoeff'] + species['diffusionConst'] = diff for reaction in self.model['reactions']: if "types" not in reaction.keys(): reaction['types'] = list(range(1, len(self.model['domain']['types']))) diff --git a/stochss/handlers/util/stochss_workflow.py b/stochss/handlers/util/stochss_workflow.py index b63da0372e..c4646e5304 100644 --- a/stochss/handlers/util/stochss_workflow.py +++ b/stochss/handlers/util/stochss_workflow.py @@ -22,13 +22,13 @@ import datetime import traceback +import numpy + from .stochss_base import StochSSBase from .stochss_folder import StochSSFolder from .stochss_model import StochSSModel -from .stochss_spatial_model import StochSSSpatialModel -from .stochss_errors import StochSSWorkflowError, StochSSWorkflowNotCompleteError, \ - StochSSFileNotFoundError, StochSSFileExistsError, \ - FileNotJSONFormatError, PlotNotAvailableError +from .stochss_job import StochSSJob +from .stochss_errors import StochSSFileNotFoundError class StochSSWorkflow(StochSSBase): ''' @@ -37,10 +37,7 @@ class StochSSWorkflow(StochSSBase): ################################################################################################ ''' - TYPES = {"gillespy":"_ES", "parameterSweep":"_PS"} - TITLES = {"gillespy":"Ensemble Simulation", "parameterSweep":"Parameter Sweep"} - - def __init__(self, path, new=False, data=None): + def __init__(self, path, new=False, mdl_path=None, wkfl_type=None): ''' Intitialize a workflow object and if its new create it on the users file system @@ -50,88 +47,153 @@ def __init__(self, path, new=False, data=None): Path to the workflow new : bool Indicates whether or not the workflow is new - data : dict - Load data needed for loading a workflow + mdl_path : str + Path to model for the workflow + wkfl_type : str + Type of workflow ''' super().__init__(path=path) self.workflow = {} - self.type = None - self.time_stamp = None - if data is not None: - self.type = data['type'] - self.time_stamp = data['stamp'] if new else self.get_time_stamp() if new: - file = f"{self.get_name()}{self.TYPES[self.type]}{self.time_stamp}.wkfl" - self.path = file if data['dirname'] is None else os.path.join(data['dirname'], file) - settings = data['settings'] if "settings" in data.keys() else None - self.__create_new_workflow(mdl_path=path, settings=settings) + unique_path, changed = self.get_unique_path(name=self.get_file()) + if changed: + self.path = unique_path.replace(self.user_dir + '/', "") + os.mkdir(unique_path) + settings = self.get_settings_template() + if wkfl_type == "Parameter Sweep": + settings['simulationSettings']['realizations'] = 20 + if os.path.exists(mdl_path): + with open(mdl_path, "r") as mdl_file: + timespan_settings = json.load(mdl_file)['modelSettings'] + settings['timespanSettings'] = timespan_settings + self.workflow['settings'] = {"settings": settings, "model": mdl_path, "type":wkfl_type} + settings_path = os.path.join(self.get_path(full=True), "settings.json") + with open(settings_path, "w") as settings_file: + json.dump(self.workflow['settings'], settings_file, indent=4, sort_keys=True) + else: + self.workflow['settings'] = None + + + def __get_old_wkfl_data(self): + job = StochSSJob(path=self.path) + wkfl = job.load() + if wkfl['model'] is None: + mdl_path = job.get_model_path() + wkfl['model'] = StochSSModel(path=mdl_path).load() + wkfl['settings']['timespanSettings'] = wkfl['model']['modelSettings'] + info = job.load_info() + settings = {"settings":wkfl['settings'], "model":info['source_model'], + "type":wkfl['titleType']} + time_stamp = job.get_time_stamp() + if time_stamp is None: + wkfl_file = job.get_file() + if wkfl['status'] != "ready": + ctime = os.path.getctime(job.path) + time_stamp = datetime.datetime.fromtimestamp(ctime).strftime("_%m%d%Y_%H%M%S") + else: + wkfl_file = job.get_file(path=job.path.replace(time_stamp, "")) + job_file = None if wkfl['status'] == "ready" else f"job{time_stamp}" + return {"wkfl":wkfl_file, "job":job_file, "settings":settings, + "status":wkfl['status'], "annotation":info['annotation']} - def __create_new_workflow(self, mdl_path, settings=None): - path = self.get_path(full=True) + def __load_annotation(self): + path = os.path.join(self.get_path(full=True), "README.md") try: - if not os.path.exists(self.get_dir_name(full=True)): - os.makedirs(path) - else: - os.mkdir(path) - os.mkdir(self.get_results_path(full=True)) - info = {"source_model":mdl_path, "wkfl_model":None, "type":self.type, "start_time":None} - self.update_info(new_info=info, new=True) - open(os.path.join(path, "logs.txt"), "w").close() - shutil.copyfile(os.path.join(self.user_dir, mdl_path), - self.get_model_path(full=True)) - if settings is None: - self.__create_settings() - except FileExistsError as err: - message = f"Could not create your workflow: {str(err)}" - raise StochSSFileExistsError(message, traceback.format_exc()) - except FileNotFoundError as err: - message = f"Could not find the file: {str(err)}" - raise StochSSFileNotFoundError(message, traceback.format_exc()) + with open(path, "r") as annotation_file: + annotation = annotation_file.read() + except FileNotFoundError: + annotation = "" + self.workflow['annotation'] = annotation + + + def __load_jobs(self): + self.workflow['jobs'] = [] + time = 0 + last_job = None + for file_obj in os.listdir(self.get_path(full=True)): + if file_obj.startswith("job_"): + path = os.path.join(self.path, file_obj) + job = StochSSJob(path=path).load() + self.workflow['jobs'].append(job) + if os.path.getmtime(path) > time and job['status'] != "running": + time = os.path.getmtime(path) + last_job = job + if last_job is None: + self.workflow['activeJob'] = None + else: + self.workflow['activeJob'] = last_job - def __create_settings(self): - if self.type == "parameterSweep": - settings = self.get_settings_template() - settings['simulationSettings']['realizations'] = 20 - with open(self.get_settings_path(full=True), "w") as file: - json.dump(settings, file) - else: - shutil.copyfile('/stochss/stochss_templates/workflowSettingsTemplate.json', - self.get_settings_path(full=True)) + def __load_settings(self): + path = os.path.join(self.get_path(full=True), "settings.json") + try: + with open(path, "r") as settings_file: + settings = json.load(settings_file) + self.workflow['model'] = settings['model'] + self.workflow['settings'] = settings['settings'] + self.workflow['type'] = settings['type'] + except FileNotFoundError as err: + message = f"Could not find the settings file: {str(err)}" + raise StochSSFileNotFoundError(message, traceback.format_exc) from err - def __is_csv_dir(self, file): - if "results_csv" not in file: - return False - path = os.path.join(file, self.get_results_path()) - if not os.path.isdir(path): - return False - return True + @classmethod + def __update_results_settings(cls, settings): + for param in settings['parameterSweepSettings']['parameters']: + p_range = list(numpy.linspace(param['min'], param['max'], param['steps'])) + param['range'] = p_range + + + def __update_settings(self): + settings = self.workflow['settings']['parameterSweepSettings'] + parameters = [] + if "parameters" not in settings.keys(): + if "paramID" in settings['parameterOne']: + param1 = {"paramID": settings['parameterOne']['paramID'], + "min": settings['p1Min'], + "max": settings['p1Max'], + "name": settings['parameterOne']['name'], + "steps": settings['p1Steps'], + "hasChangedRanged": False} + parameters.append(param1) + if "paramID" in settings['parameterTwo']: + param2 = {"paramID": settings['parameterTwo']['paramID'], + "min": settings['p2Min'], + "max": settings['p2Max'], + "name": settings['parameterTwo']['name'], + "steps": settings['p2Steps'], + "hasChangedRanged": False} + parameters.append(param2) + soi = settings['speciesOfInterest'] + self.workflow['settings']['parameterSweepSettings'] = {"speciesOfInterest": soi, + "parameters": parameters} - def __load_info(self): - try: - path = self.get_info_path(full=True) - self.log("debug", f"The path to the workflow's info file: {path}") - with open(path, "r") as info_file: - return json.load(info_file) - except FileNotFoundError as err: - message = f"Could not find the info file: {str(err)}" - raise StochSSFileNotFoundError(message, traceback.format_exc()) - except json.decoder.JSONDecodeError as err: - message = f"The info file is not JSON decobable: {str(err)}" - raise FileNotJSONFormatError(message, traceback.format_exc()) + @classmethod + def __write_new_files(cls, settings, annotation): + with open("settings.json", "w") as settings_file: + json.dump(settings, settings_file, indent=4, sort_keys=True) + with open("README.md", "w") as rdme_file: + rdme_file.write(annotation) def check_for_external_model(self, path=None): ''' - Check if the workflows model exists outside of the workflow and return it path + Check if the jobs model exists outside of the job and return it path + + Attributes + ---------- + path : str + Path to the external model ''' if path is None: - path = self.get_model_path(full=True, external=True) - self.log("debug", - f"Path to the workflow's model: {path}") + if self.check_workflow_format(path=self.path): + path = self.get_model_path() + else: + job = StochSSJob(path=self.path) + path = job.get_model_path(full=True, external=True) + self.log("debug", f"Path to the job's model: {path}") resp = {"file":path.replace(self.user_dir + '/', '')} if not os.path.exists(path): file = self.get_file(path=path) @@ -142,26 +204,21 @@ def check_for_external_model(self, path=None): return resp - def duplicate_as_new(self, stamp): + def duplicate_as_new(self): ''' - Get all data needed to create a new workflow that - is a copy of this workflow in ready state. + Create a clean copy of the workflow and its settings with no jobs. Attributes ---------- ''' - wkfl = self.load() - if wkfl['status'] != "ready": - mdl_path = self.__load_info()['source_model'] - else: - mdl_path = wkfl['mdlPath'] - data = {"type":self.type, "stamp":stamp, - "dirname":self.get_dir_name(), "settings":wkfl['settings']} - kwargs = {"path":self.get_model_path(), "new":True, "data":data} - resp = {"message":f"A new workflow has been created from {self.path}", - "mdlPath":mdl_path, - "mdl_file":self.get_file(path=mdl_path)} - c_resp = self.check_for_external_model(path=os.path.join(self.user_dir, mdl_path)) + self.load() + path = self.get_unique_copy_path(path=self.path) + kwargs = {"path": path, "new": True, "mdl_path": self.workflow['model'], + "wkfl_type": self.workflow['type']} + message = f"A new workflow has been created from {self.path}" + resp = {"message": message, "mdlPath": self.workflow['model'], + "mdl_file": self.get_file(path=self.workflow['model'])} + c_resp = self.check_for_external_model(path=self.workflow['model']) if "error" in c_resp.keys(): resp['error'] = c_resp['error'] return resp, kwargs @@ -169,395 +226,196 @@ def duplicate_as_new(self, stamp): def extract_model(self): ''' - Get all data needed to create a new model that is a copy of the workflows model - - Attributes - ---------- - ''' - src_path = self.get_model_path() - model = StochSSModel(path=src_path).load() - file = self.get_file(path=src_path) - dst_dirname = self.get_dir_name() - if ".proj" in dst_dirname: - dst_dirname = os.path.dirname(dst_dirname) - dst_path = os.path.join(dst_dirname, file) - kwargs = {"path":dst_path, "new":True, "model":model} - resp = {"message":f"A copy of the model in {self.path} has been created"} - return resp, kwargs - - - def generate_csv_zip(self): - ''' - Create a zip archive of the csv results for download - - Atrributes - ---------- - ''' - status = self.get_status() - if status == "error": - message = f"The workflow experienced an error during run: {status}" - raise StochSSWorkflowError(message, traceback.format_exc()) - if status != "complete": - message = f"The workflow has not finished running: {status}." - raise StochSSWorkflowNotCompleteError(message, traceback.format_exc()) - - csv_path = self.get_csv_path(full=True) - if os.path.exists(csv_path + ".zip"): - message = f"{csv_path}.zip already exists." - return {"Message":message, "Path":csv_path.replace(self.user_dir+"/", "") + ".zip"} - csv_folder = StochSSFolder(path=csv_path) - return csv_folder.generate_zip_file() - - - def get_csv_path(self, full=False): - ''' - Return the path to the csv directory - - Attributes - ---------- - ''' - res_path = self.get_results_path(full=full) - if not os.path.exists(res_path): - message = f"Could not find the results directory: {res_path}" - raise StochSSFileNotFoundError(message, traceback.format_exc()) - - try: - res_files = os.listdir(res_path) - csv_path = list(filter(lambda file: self.__is_csv_dir(file=file), res_files))[0] - return os.path.join(res_path, csv_path) - except IndexError as err: - message = f"Could not find the workflow results csv directory: {str(err)}" - raise StochSSFileNotFoundError(message, traceback.format_exc()) - - - def get_info_path(self, full=False): - ''' - Return the path to the info.json file + Extract the model from the most recently created job. Attributes ---------- - full : bool - Indicates whether or not to get the full path or local path ''' - return os.path.join(self.get_path(full=full), "info.json") - - - def get_model_path(self, full=False, external=False): - ''' - Return the path to the model file - - Attributes - ---------- - full : bool - Indicates whether or not to get the full path or local path - external : bool - Indicates whether or not to consider the path to the internal model - ''' - info = self.__load_info() - self.log("debug", f"Workflow info: {info}") - if external or info['wkfl_model'] is None: - file = self.get_file(path=info['source_model']) - return os.path.join(self.get_path(full=full), file) - file = self.get_file(path=info['wkfl_model']) - return os.path.join(self.get_path(full=full), file) - - - def get_notebook_data(self): - ''' - Get the needed data for converting to notebook - - Attributes - ---------- - ''' - info = self.__load_info() - file = f"{self.get_name()}.ipynb" - path = os.path.join(self.get_dir_name(), file) - g_model, s_model = self.load_models() - settings = self.load_settings() - if info['type'] == "gillespy": - wkfl_type = info['type'] - elif info['type'] == "parameterSweep" and settings['parameterSweepSettings']['is1D']: - wkfl_type = "1d_parameter_sweep" + new_format = self.check_workflow_format(path=self.path) + if new_format: + os.chdir(self.path) + files = list(filter(lambda file: file.startswith("job_"), os.listdir())) + if len(files) <= 0: + os.chdir(self.user_dir) + message = "There are no jobs to extract a model from." + raise StochSSFileNotFoundError(message) + files.sort(reverse=True, key=os.path.getctime) + os.chdir(self.user_dir) + path = os.path.join(self.path, files[0]) else: - wkfl_type = "2d_parameter_sweep" - kwargs = {"path":path, "new":True, "settings":settings, - "models":{"s_model":s_model, "model":g_model}} - return {"kwargs":kwargs, "type":wkfl_type} - + path = self.path + job = StochSSJob(path=path) + return job.extract_model() - def get_results_path(self, full=False): - ''' - Return the path to the results directory - - Attributes - ---------- - full : bool - Indicates whether or not to get the full path or local path - ''' - return os.path.join(self.get_path(full=full), "results") - - - def get_results_plot(self, plt_key, plt_data): - ''' - Get the plotly figure for the results of a workflow - - Attributes - ---------- - plt_key : str - Indentifier for the requested plot figure - plt_data : dict - Title and axes data for the plot - ''' - self.log("debug", f"Key identifying the requested plot: {plt_key}") - self.log("debug", f"Title and axis data for the plot: {plt_data}") - path = os.path.join(self.get_results_path(full=True), "plots.json") - self.log("debug", f"Path to the workflow result plot file: {path}") - try: - with open(path, "r") as plot_file: - fig = json.load(plot_file)[plt_key] - if plt_data is None: - return fig - for key in plt_data.keys(): - if key == "title": - fig['layout']['title']['text'] = plt_data[key] - else: - fig['layout'][key]['title']['text'] = plt_data[key] - return fig - except FileNotFoundError as err: - message = f"Could not find the plots file: {str(err)}" - raise StochSSFileNotFoundError(message, traceback.format_exc()) - except json.decoder.JSONDecodeError as err: - message = f"The plots file is not JSON decodable: {str(err)}" - raise FileNotJSONFormatError(message, traceback.format_exc()) - except KeyError as err: - message = f"The requested plot is not available: {str(err)}" - raise PlotNotAvailableError(message, traceback.format_exc()) - - def get_run_logs(self): + def get_model_path(self): ''' - Return the contents of the log file' + Return the path to the external model file Attributes ---------- ''' - path = os.path.join(self.get_path(full=True), "logs.txt") try: - with open(path, "r") as file: - logs = file.read() - self.log("debug", f"Contents of the log file: {logs}") - if logs: - return logs - return "No logs were recoded for this workflow." + with open(os.path.join(self.path, "settings.json")) as settings_file: + path = json.load(settings_file)['model'] + if ".proj" not in self.path: + return path + file = self.get_file(path=path) + proj_path = f"{self.path.split('.proj')[0]}.proj" + if self.check_project_format(path=proj_path): + return os.path.join(self.get_dir_name(), file) + return os.path.join(proj_path, file) except FileNotFoundError as err: - message = f"Could not find the log file: {str(err)}" - raise StochSSFileNotFoundError(message, traceback.format_exc()) + message = f"Could not find settings file: {str(err)}" + raise StochSSFileNotFoundError(message, traceback.format_exc()) from err - @classmethod - def get_run_settings(cls, settings, solver_map): + def initialize_job(self, settings, mdl_path, time_stamp, wkfl_type): ''' - Get the gillespy2 run settings for model.run() + Initialize a new job for this workflow. Attributes ---------- settings : dict - StochSS simulation settings dict - need_variable_ssa : bool - Indicates whether or not the VariableSSACSolver is needed - ''' - settings = settings['simulationSettings'] - kwargs = {"solver":solver_map[settings['algorithm']]} - if settings['algorithm'] in ("ODE", "Hybrid-Tau-Leaping"): - integrator_options = {"atol":settings['absoluteTol'], "rtol":settings['relativeTol']} - kwargs["integrator_options"] = integrator_options - if settings['algorithm'] == "ODE": - return kwargs - kwargs["number_of_trajectories"] = settings['realizations'] - if settings['seed'] != -1: - kwargs['seed'] = settings['seed'] - if settings['algorithm'] == "SSA": - return kwargs - kwargs['tau_tol'] = settings['tauTol'] - return kwargs - - - def get_settings_path(self, full=False): - ''' - Return the path to the settings.json file - - Attributes - ---------- - full : bool - Indicates whether or not to get the full path or local path - ''' - return os.path.join(self.get_path(full=full), "settings.json") - - - def get_time_stamp(self): - ''' - Get the time stamp from the workflow name - - Attributes - ---------- - ''' - name = self.get_name() - return "_"+"_".join(name.split('_')[-2:]) + Workflow settings dictionary + mdl_path : str + Path to the model of the workflow + time_stamp : str + Datetime stamp for the new job + wkfl_type : str + Type of workflow + ''' + self.log("info", f"Saving {self.get_file()}") + self.save(new_settings=settings, mdl_path=mdl_path) + if wkfl_type == "parameterSweep": + self.__update_results_settings(settings=settings) + self.log("info", f"Successfully saved {self.get_file()}") + if self.check_workflow_format(path=self.path): + self.log("info", f"Creating job{time_stamp} job") + path = os.path.join(self.path, f"job{time_stamp}") + data = {"mdl_path": mdl_path, "settings": settings, "type":wkfl_type} + job = StochSSJob(path=path, new=True, data=data) + self.log("info", f"Successfully created {job.get_file()} job") + else: + job = StochSSJob(path=self.path) + self.log("info", f"Initializing {job.get_file()}") + job.save(mdl_path=mdl_path, settings=settings, initialize=True) + return job.path - def load(self, new=False): + def load(self): ''' - Reads in all relavent data for a workflow and stores it in self.workflow. + Load a StochSS Workflow object. Attributes ---------- ''' - error = None - info = self.__load_info() - self.type = info['type'] - status = "new" if new else self.get_status() - if status in ("new", "ready"): - mdl_path = info['source_model'] + self.workflow['directory'] = self.path + self.workflow['name'] = self.get_name() + self.workflow['newFormat'] = self.check_workflow_format(path=self.path) + if self.workflow['newFormat']: + if self.workflow['settings'] is None: + self.__load_settings() + self.__load_annotation() + self.__load_jobs() + oldfmtrdy = False else: - mdl_path = self.get_model_path() - try: - model = StochSSModel(path=mdl_path).load() - except StochSSFileNotFoundError as err: - model = None - error = {"Reason":err.reason, "Message":err.message, "traceback":err.traceback} - self.log("error", f"Exception information: {error}") - finally: - settings = self.load_settings(model=model) - self.workflow = {"mdlPath":mdl_path, "model":model, "settings":settings, - "startTime":info['start_time'], "status":status, - "timeStamp":self.time_stamp, "titleType":self.TITLES[info['type']], - "type":self.type, "wkflDir":self.get_file(), - "wkflName":self.get_name(), "wkflParPath":self.get_dir_name()} - if error is not None: - self.workflow['error'] = error + self.workflow['jobs'] = [] + job = StochSSJob(path=self.path) + jobdata = job.load() + self.workflow['activeJob'] = jobdata + self.workflow['model'] = job.get_model_path(external=True) + self.workflow['settings'] = jobdata['settings'] + self.workflow['type'] = jobdata['titleType'] + oldfmtrdy = jobdata['status'] == "ready" + self.__update_settings() + if not os.path.exists(self.workflow['model']) and (oldfmtrdy or self.workflow['newFormat']): + if ".proj" in self.path: + if "WorkflowGroup1.wkgp" in self.path: + proj = StochSSFolder(path=os.path.dirname(self.get_dir_name(full=True))) + test = lambda ext, root, file: ".wkfl" in root or "trash" in root.split("/") + models = proj.get_file_list(ext=[".mdl"], test=test) + else: + wkgp = StochSSFolder(path=self.get_dir_name(full=True)) + test = lambda ext, root, file: ".wkfl" in root + models = wkgp.get_file_list(ext=[".mdl"], test=test) + if models['files']: + self.workflow['model'] = models["paths"]["0"][0] + models = None + else: + self.workflow['model'] = None + else: + root = StochSSFolder(path="") + test = lambda ext, root, file: ".wkfl" in root or ".proj" in root or \ + "trash" in root.split("/") + models = root.get_file_list(ext=[".mdl"], test=test) + if models is not None: + self.workflow['models'] = models return self.workflow - def load_models(self): + def save(self, new_settings, mdl_path): ''' - Load GillesPy2 and StochSS models for running - - Atrributes - ---------- - ''' - path = self.get_model_path() - if path.endswith('.mdl'): - model_obj = StochSSModel(path=path) - model = model_obj.convert_to_gillespy2() - else: - model_obj = StochSSSpatialModel(path=path) - model = model_obj.convert_to_spatialpy() - return model, model_obj.model - - - def load_settings(self, model=None): - ''' - Load the workflow settings from the settings file + Save the settings and model path for the workflow to the settings file. Attributes ---------- - model : dict - Stochss model dict (used to backwards compatability) + new_settings : dict + Settings used for initializing jobs. + mdl_path : str + Path to the model used for jobs. ''' - try: - path = self.get_settings_path(full=True) + if self.check_workflow_format(path=self.path): + path = os.path.join(self.get_path(full=True), "settings.json") with open(path, "r") as settings_file: - return json.load(settings_file) - except FileNotFoundError as err: - if model is None: - message = f"Could not find the settings file: {str(err)}" - raise StochSSFileNotFoundError(message, traceback.format_exc()) - settings = self.get_settings_template() - if "simulationSettings" in model.keys(): - settings['simulationSettings'] = model['simulationSettings'] - elif self.type == "parameterSweep": - settings['simulationSettings']['realizations'] = 20 - if "parameterSweepSettings" in model.keys(): - settings['parameterSweepSettings'] = model['parameterSweepSettings'] - return settings - except json.decoder.JSONDecodeError as err: - message = f"The settings file is not JSON decobable: {str(err)}" - raise FileNotJSONFormatError(message, traceback.format_exc()) - - - def save(self, mdl_path, settings, initialize): - ''' - Save the data for a new or ready state workflow - - Attributes - ---------- - ''' - path = self.get_model_path(full=True) - new_info = {"source_model":mdl_path} - if initialize: - # If this format is not something Javascript's Date.parse() method - # understands then the workflow status page will be unable to correctly create a - # Date object from the datestring parsed from the workflow's info.json file - new_info['start_time'] = datetime.datetime.now().strftime("%b %d, %Y %I:%M %p UTC") - new_info['wkfl_model'] = self.get_file(path=mdl_path) - open(os.path.join(self.path, 'RUNNING'), 'w').close() - self.update_info(new_info=new_info) - with open(self.get_settings_path(full=True), "w") as file: - json.dump(settings, file) - try: - os.remove(path) - shutil.copyfile(os.path.join(self.user_dir, mdl_path), - self.get_model_path(full=True)) + settings = json.load(settings_file) + settings['settings'] = new_settings + settings['model'] = mdl_path + with open(path, "w") as settings_file: + json.dump(settings, settings_file, indent=4, sort_keys=True) return f"Successfully saved the workflow: {self.path}" - except FileNotFoundError as err: - message = f"Could not find the model file: {str(err)}" - raise StochSSFileNotFoundError(message, traceback.format_exc()) + job = StochSSJob(path=self.path) + return job.save(mdl_path=mdl_path, settings=new_settings) - def save_plot(self, plot): + def save_annotation(self, annotation): ''' - Save a plot to the output settings (for projects only) + Save the workflows annotation. - Attributes - ---------- - plot : dict - plot data used needed to look up the plot + annotation : str + Annotation to be saved ''' - settings = self.load_settings() - self.log("debug", f"Original settings: {settings}") - settings['resultsSettings']['outputs'].append(plot) - self.log("debug", f"New settings: {settings}") - with open(self.get_settings_path(full=True), "w") as settings_file: - json.dump(settings, settings_file) - return {"message":"The plot was successfully saved", "data":plot} + with open(os.path.join(self.path, "README.md"), "w") as rdme_file: + rdme_file.write(annotation) - def update_info(self, new_info, new=False): + def update_wkfl_format(self): ''' - Updates the contents of the info file. If source model is updated, - checks if the model exists at that path + Update a workflow to the new workflow/job format Attributes ---------- - new_info : dict - Contains all data to be updated under the correct key - new : bool - Indicates whether or not an info file needs to be created ''' - if new: - info = new_info + data = self.__get_old_wkfl_data() + os.chdir(self.path) + if data['status'] == "ready": + for file in os.listdir(): + if os.path.isdir(file): + shutil.rmtree(file) + else: + os.remove(file) + self.__write_new_files(data['settings'], data['annotation']) + if data['wkfl'] != self.get_file(): + self.rename(name=data['wkfl']) else: - info = self.__load_info() - if "source_model" in new_info.keys(): - info['source_model'] = new_info['source_model'] - if "wkfl_model" in new_info.keys(): - info['wkfl_model'] = new_info['wkfl_model'] - if "type" in new_info.keys(): - info['type'] = new_info['type'] - if "start_time" in new_info.keys(): - info['start_time'] = new_info['start_time'] - if "annotation" in new_info.keys(): - info['annotation'] = new_info['annotation'] - self.log("debug", f"New info: {info}") - with open(self.get_info_path(full=True), "w") as file: - json.dump(info, file) + with open("settings.json", "w") as settings_file: + json.dump(data['settings']['settings'], settings_file, indent=4, sort_keys=True) + self.rename(name=data['job']) + path, _ = self.get_unique_path(name=data['wkfl'], dirname=self.get_dir_name(full=True)) + os.mkdir(path) + shutil.move(self.get_path(full=True), os.path.join(path, data['job'])) + os.chdir(path) + self.__write_new_files(data['settings'], data['annotation']) + self.path = os.path.join(self.get_dir_name(), self.get_file(path=path)) + os.chdir(self.user_dir) + return self.path diff --git a/stochss/handlers/workflows.py b/stochss/handlers/workflows.py index 70b7d3834d..cb37ad715a 100644 --- a/stochss/handlers/workflows.py +++ b/stochss/handlers/workflows.py @@ -27,13 +27,46 @@ # Note APIHandler.finish() sets Content-Type handler to 'application/json' # Use finish() for json, write() for text -from .util import StochSSWorkflow, StochSSModel, StochSSSpatialModel, StochSSNotebook, \ +from .util import StochSSJob, StochSSModel, StochSSSpatialModel, StochSSNotebook, StochSSWorkflow, \ StochSSAPIError, report_error log = logging.getLogger('stochss') # pylint: disable=abstract-method +# pylint: disable=too-few-public-methods +class NewWorkflowAPIHandler(APIHandler): + ''' + ################################################################################################ + Handler for creating a new workflow + ################################################################################################ + ''' + @web.authenticated + async def get(self): + ''' + Creates a new workflow of the given type for the given model. + + Attributes + ---------- + ''' + self.set_header('Content-Type', 'application/json') + path = self.get_query_argument(name="path") + log.debug("The path to the workflow: %s", path) + mdl_path = self.get_query_argument(name="model") + log.debug("The path to the model: %s", mdl_path) + wkfl_type = self.get_query_argument(name="type") + log.debug("Type of the workflow: %s", wkfl_type) + try: + log.info("Creating %s workflow", path.split('/').pop()) + wkfl = StochSSWorkflow(path=path, new=True, mdl_path=mdl_path, wkfl_type=wkfl_type) + resp = {"path": wkfl.path} + log.info("Successfully created %s workflow", wkfl.get_file()) + self.write(resp) + except StochSSAPIError as err: + report_error(self, log, err) + self.finish() + + class LoadWorkflowAPIHandler(APIHandler): ''' ################################################################################################ @@ -51,16 +84,9 @@ async def get(self): self.set_header('Content-Type', 'application/json') path = self.get_query_argument(name="path") log.debug("The path to the workflow/model: %s", path) - wkfl_type = self.get_query_argument(name="type") - dirname = self.get_query_argument(name='parentPath', default=os.path.dirname(path)) - data = {"type":wkfl_type if wkfl_type != "none" else None, - "stamp": self.get_query_argument(name="stamp"), - "dirname": None if not dirname or dirname == "." else dirname} - log.debug("Load data for the workflow: %s", data) try: - new = path.endswith(".mdl") - wkfl = StochSSWorkflow(path=path, new=new, data=data) - resp = wkfl.load(new=new) + log.info("Loading workflow data") + resp = StochSSWorkflow(path=path).load() log.debug("Response: %s", resp) self.write(resp) except StochSSAPIError as err: @@ -68,68 +94,94 @@ async def get(self): self.finish() -class RunWorkflowAPIHandler(APIHandler): + @web.authenticated + async def post(self): + ''' + Start saving the workflow. Creates the workflow directory and workflow_info file if + saving a new workflow. Copys model into the workflow directory. + + Attributes + ---------- + ''' + path = self.get_query_argument(name="path") + log.debug("Path to the workflow: %s", path) + data = json.loads(self.request.body.decode()) + log.debug("Workflow Data: %s", data) + log.debug("Path to the model: %s", data['model']) + try: + wkfl = StochSSWorkflow(path=path) + log.info("Saving %s", wkfl.get_file()) + resp = wkfl.save(new_settings=data['settings'], mdl_path=data['model']) + log.debug("Response: %s", resp) + log.info("Successfully saved %s", wkfl.get_file()) + self.write(resp) + except StochSSAPIError as err: + report_error(self, log, err) + self.finish() + + +class InitializeJobAPIHandler(APIHandler): ''' ################################################################################################ - Handler for running workflows. + Handler for initializing jobs. ################################################################################################ ''' @web.authenticated async def get(self): ''' - Start running a workflow and record the time in UTC in the workflow_info file. - Creates workflow directory and workflow_info file if running a new workflow. Copys - model into the workflow directory. + Initialize a new job or an existing old format workflow. Attributes ---------- ''' + path = self.get_query_argument(name="path") + log.debug("Path to the workflow: %s", path) data = json.loads(self.get_query_argument(name="data")) log.debug("Handler query string: %s", data) - path = data['wkflPath'] - log.debug("Path to the workflow: %s", path) - wkfl_type = data['type'] - log.debug("Type of workflow: %s", wkfl_type) try: - # nav = f"cd {StochSSWorkflow(path=path).get_path(full=True)}" - script = "/stochss/stochss/handlers/util/scripts/start_job.py" - exec_cmd = [f"{script}", f"{path}", f"{wkfl_type}"] - if "v" in data['optType']: - exec_cmd.append("-v") - log.debug("Exec command sent to the subprocess: %s", exec_cmd) - log.debug('Sending the workflow run cmd') - subprocess.Popen(exec_cmd) - log.debug('The workflow has started') + wkfl = StochSSWorkflow(path=path) + resp = wkfl.initialize_job(settings=data['settings'], mdl_path=data['mdl_path'], + wkfl_type=data['type'], time_stamp=data['time_stamp']) + wkfl.print_logs(log) + log.debug("Response message: %s", resp) + self.write(resp) except StochSSAPIError as err: report_error(self, log, err) self.finish() -class SaveWorkflowAPIHandler(APIHandler): +class RunWorkflowAPIHandler(APIHandler): ''' ################################################################################################ - Handler for saving workflows. + Handler for running workflows. ################################################################################################ ''' @web.authenticated async def get(self): ''' - Start saving the workflow. Creates the workflow directory and workflow_info file if - saving a new workflow. Copys model into the workflow directory. + Start running a workflow and record the time in UTC in the workflow_info file. + Creates workflow directory and workflow_info file if running a new workflow. Copys + model into the workflow directory. Attributes ---------- ''' + path = self.get_query_argument(name="path") + log.debug("Path to the workflow: %s", path) + wkfl_type = self.get_query_argument(name="type") + log.debug("Type of workflow: %s", wkfl_type) + verbose = self.get_query_argument(name="verbose", default=False) try: - data = json.loads(self.get_query_argument(name="data")) - log.debug("Handler query string: %s", data) - model_path = data['mdlPath'] - log.debug("Path to the model: %s", model_path) - wkfl = StochSSWorkflow(path=data['wkflPath']) - resp = wkfl.save(mdl_path=model_path, settings=data['settings'], - initialize="r" in data['optType']) - log.debug("Response: %s", resp) - self.write(resp) + script = "/stochss/stochss/handlers/util/scripts/start_job.py" + exec_cmd = [f"{script}", f"{path}", f"{wkfl_type}", "-v"] + if verbose: + exec_cmd.append("-v") + log.debug("Exec command sent to the subprocess: %s", exec_cmd) + log.debug('Sending the workflow run cmd') + job = subprocess.Popen(exec_cmd) + with open(os.path.join(path, "RUNNING"), "w") as file: + file.write(f"Subprocess id: {job.pid}") + log.debug('The workflow has started') except StochSSAPIError as err: report_error(self, log, err) self.finish() @@ -153,7 +205,7 @@ async def get(self): log.debug('path to the workflow: %s', path) log.debug('Getting the status of the workflow') try: - wkfl = StochSSWorkflow(path=path) + wkfl = StochSSJob(path=path) status = wkfl.get_status() log.debug('The status of the workflow is: %s', status) self.write(status) @@ -185,8 +237,13 @@ async def get(self): body['plt_data'] = None log.debug("Plot args passed to the plot: %s", body) try: - wkfl = StochSSWorkflow(path=path) - fig = wkfl.get_results_plot(**body) + wkfl = StochSSJob(path=path) + if "plt_type" in body.keys(): + fig = wkfl.get_plot_from_results(**body) + wkfl.print_logs(log) + else: + log.info("Loading the plot...") + fig = wkfl.get_results_plot(**body) log.debug("Plot figure: %s", fig) self.write(fig) except StochSSAPIError as err: @@ -194,33 +251,6 @@ async def get(self): self.finish() -class WorkflowLogsAPIHandler(APIHandler): - ''' - ################################################################################################ - Handler for getting Workflow logs. - ################################################################################################ - ''' - @web.authenticated - async def get(self): - ''' - Retrieve workflow logs from User's file system. - - Attributes - ---------- - ''' - path = os.path.dirname(self.get_query_argument(name="path")) - log.debug("Path to the workflow logs file: %s", path) - try: - wkfl = StochSSWorkflow(path=path) - logs = wkfl.get_run_logs() - wkfl.print_logs(log) - log.debug("Response: %s", logs) - self.write(logs) - except StochSSAPIError as err: - report_error(self, log, err) - self.finish() - - class WorkflowNotebookHandler(APIHandler): ''' ################################################################################################ @@ -245,11 +275,15 @@ async def get(self): elif path.endswith(".smdl"): file_obj = StochSSSpatialModel(path=path) else: - file_obj = StochSSWorkflow(path=path) + file_obj = StochSSJob(path=path) + log.info("Loading data for %s", file_obj.get_file()) kwargs = file_obj.get_notebook_data() if "type" in kwargs.keys(): wkfl_type = kwargs['type'] kwargs = kwargs['kwargs'] + log.info("Converting %s to notebook", file_obj.get_file()) + else: + log.info("Creating notebook workflow for %s", file_obj.get_file()) log.debug("Type of workflow to be run: %s", wkfl_type) notebook = StochSSNotebook(**kwargs) notebooks = {"gillespy":notebook.create_es_notebook, @@ -261,6 +295,7 @@ async def get(self): resp = notebooks[wkfl_type]() notebook.print_logs(log) log.debug("Response: %s", resp) + log.info("Successfully created the notebook for %s", file_obj.get_file()) self.write(resp) except StochSSAPIError as err: report_error(self, log, err) @@ -288,7 +323,7 @@ async def post(self): plot = json.loads(self.request.body.decode()) log.debug("The plot to be saved: %s", plot) try: - wkfl = StochSSWorkflow(path=path) + wkfl = StochSSJob(path=path) resp = wkfl.save_plot(plot=plot) wkfl.print_logs(log) log.debug("Response message: %s", resp) @@ -318,12 +353,44 @@ async def post(self): info = json.loads(self.request.body.decode()) log.debug("The annotation to be saved: %s", info['annotation']) try: - wkfl = StochSSWorkflow(path=path) - wkfl.update_info(new_info=info) - wkfl.print_logs(log) + log.info("Saving annotation for %s", path.split('/').pop()) + if StochSSWorkflow.check_workflow_format(path=path): + wkfl = StochSSWorkflow(path=path) + wkfl.save_annotation(info['annotation']) + else: + wkfl = StochSSJob(path=path) + wkfl.update_info(new_info=info) + wkfl.print_logs(log) resp = {"message":"The annotation was successfully saved", "data":info['annotation']} + log.info("Successfully saved the annotation") log.debug("Response message: %s", resp) self.write(resp) except StochSSAPIError as err: report_error(self, log, err) self.finish() + + +class UpadteWorkflowAPIHandler(APIHandler): + ''' + ################################################################################################ + Handler for updating workflow format. + ################################################################################################ + ''' + @web.authenticated + async def get(self): + ''' + Updates the workflow to the new format. + + Attributes + ---------- + ''' + path = self.get_query_argument(name="path") + log.debug("The path to the workflow: %s", path) + try: + wkfl = StochSSWorkflow(path=path) + resp = wkfl.update_wkfl_format() + log.debug("Response Message: %s", resp) + self.write(resp) + except StochSSAPIError as err: + report_error(self, log, err) + self.finish() diff --git a/stochss/tests/run_tests.py b/stochss/tests/run_tests.py index d989178642..5aa6cce0f0 100755 --- a/stochss/tests/run_tests.py +++ b/stochss/tests/run_tests.py @@ -1,5 +1,25 @@ #!/usr/bin/env python3 +''' +StochSS is a platform for simulating biochemical systems +Copyright (C) 2019-2020 StochSS developers. + +This program is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with this program. If not, see . +''' + + + import unittest import sys import os diff --git a/stochss_templates/nonSpatialModelTemplate.json b/stochss_templates/nonSpatialModelTemplate.json index 6c5c393151..248896e2cc 100644 --- a/stochss_templates/nonSpatialModelTemplate.json +++ b/stochss_templates/nonSpatialModelTemplate.json @@ -17,6 +17,7 @@ "x_lim": [0, 0], "y_lim": [0, 0], "z_lim": [0, 0], + "static": true, "boundary_condition": { "reflect_x": true, "reflect_y": true, diff --git a/stochss_templates/workflowSettingsTemplate.json b/stochss_templates/workflowSettingsTemplate.json index fe88916077..85bfd2de1a 100644 --- a/stochss_templates/workflowSettingsTemplate.json +++ b/stochss_templates/workflowSettingsTemplate.json @@ -9,20 +9,16 @@ "tauTol": 0.03 }, "parameterSweepSettings":{ - "is1D":true, - "p1Min":0, - "p1Max":0, - "p1Steps":11, - "p2Min":0, - "p2Max":0, - "p2Steps":11, - "parameterOne": {}, - "parameterTwo": {}, + "parameters": [], "speciesOfInterest": {} }, "resultsSettings":{ "mapper":"final", "reducer":"avg", "outputs": [] + }, + "timespanSettings": { + "endSim": 20, + "timeStep": 0.05 } } \ No newline at end of file diff --git a/webpack.config.js b/webpack.config.js index 13892d30b5..440717e916 100644 --- a/webpack.config.js +++ b/webpack.config.js @@ -12,7 +12,9 @@ module.exports = { workflowSelection: './client/pages/workflow-selection.js', workflowEditor: './client/pages/workflow-manager.js', projectBrowser: './client/pages/project-browser.js', - projectManager: './client/pages/project-manager.js' + projectManager: './client/pages/project-manager.js', + loadingPage: './client/pages/loading-page.js', + multiplePlots: './client/pages/multiple-plots.js' }, output: { filename: 'stochss-[name].bundle.js', @@ -82,6 +84,20 @@ module.exports = { template: 'page_template.pug', name: 'projectManager', inject: false + }), + new HtmlWebpackPlugin({ + title: "StochSS | Loading Page", + filename: 'stochss-loading-page.html', + template: 'page_template.pug', + name: 'loadingPage', + inject: false + }), + new HtmlWebpackPlugin({ + title: "StochSS | Multiple Plots Page", + filename: 'multiple-plots-page.html', + template: 'page_template.pug', + name: 'multiplePlots', + inject: false }) ], optimization: {