From cc63e2c3f65d0faa6426169e322d4ab3ee3cef4c Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Thu, 27 May 2021 13:02:44 -0400 Subject: [PATCH 001/192] Added function to publish model presentations to the .presentations directory. --- stochss/handlers/util/stochss_file.py | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/stochss/handlers/util/stochss_file.py b/stochss/handlers/util/stochss_file.py index fbe99c91d3..425182d8e1 100644 --- a/stochss/handlers/util/stochss_file.py +++ b/stochss/handlers/util/stochss_file.py @@ -17,6 +17,7 @@ ''' import os +import stat import shutil import zipfile import traceback @@ -99,6 +100,30 @@ def duplicate(self): raise StochSSPermissionsError(message, traceback.format_exc()) from err + def publish_presentation(self): + ''' + Publish a model or spatial model presentation + + Attributes + ---------- + ''' + present_dir = os.path.join(self.user_dir, ".presentations") + if not os.path.exists(present_dir): + os.mkdir(present_dir) + dst = os.path.join(present_dir, self.get_file()) + if os.path.exists(dst): + message = "A publication with this name already exists" + raise StochSSFileExistsError(message) + src = self.get_path(full=True) + try: + shutil.copyfile(src, dst) + os.chmod(dst, stat.S_IREAD) + return {"message": f"Successfully published the {self.get_name()} presentation"} + except PermissionError as err: + message = f"You do not have permission to copy this file: {str(err)}" + raise StochSSPermissionsError(message, traceback.format_exc()) from err + + def move(self, location): ''' Moves a file to a new location. From 4852ef0787dfa6ff9807a192bf78352c1e6e8ef5 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Thu, 27 May 2021 13:04:03 -0400 Subject: [PATCH 002/192] Added api handler and route for publising model presentations. --- stochss/handlers/__init__.py | 1 + stochss/handlers/models.py | 31 ++++++++++++++++++++++++++++++- 2 files changed, 31 insertions(+), 1 deletion(-) diff --git a/stochss/handlers/__init__.py b/stochss/handlers/__init__.py index f52ecc0747..635faa897c 100644 --- a/stochss/handlers/__init__.py +++ b/stochss/handlers/__init__.py @@ -73,6 +73,7 @@ def get_page_handlers(route_start): (r"/stochss/api/model/to-sbml\/?", ModelToSBMLAPIHandler), (r"/stochss/api/model/run\/?", RunModelAPIHandler), (r"/stochss/api/model/exists\/?", ModelExistsAPIHandler), + (r"/stochss/api/model/presentation\/?", ModelPresentationAPIHandler), (r"/stochss/api/spatial-model/domain-list\/?", LoadExternalDomains), (r"/stochss/api/spatial-model/types-list\/?", LoadParticleTypesDescriptions), (r"/stochss/api/spatial-model/domain-plot\/?", LoadDomainAPIHandler), diff --git a/stochss/handlers/models.py b/stochss/handlers/models.py index ee9c9284e1..988e486bce 100644 --- a/stochss/handlers/models.py +++ b/stochss/handlers/models.py @@ -28,7 +28,7 @@ # Use finish() for json, write() for text from .util import StochSSFolder, StochSSModel, StochSSSpatialModel, StochSSNotebook, \ - StochSSAPIError, report_error + StochSSFile, StochSSAPIError, report_error log = logging.getLogger('stochss') @@ -403,3 +403,32 @@ async def get(self): except StochSSAPIError as err: report_error(self, log, err) self.finish() + + +class ModelPresentationAPIHandler(APIHandler): + ''' + ################################################################################################ + Handler publishing model presentations. + ################################################################################################ + ''' + @web.authenticated + async def get(self): + ''' + Publish a model or spatial model presentation. + + Attributes + ---------- + ''' + self.set_header('Content-Type', 'application/json') + path = self.get_query_argument(name="path") + log.debug("Path to the file: %s", path) + try: + file = StochSSFile(path=path) + log.info("Publishing the %s presentation", file.get_name()) + resp = file.publish_presentation() + log.info(resp['message']) + log.debug("Response Message: %s", resp) + self.write(resp) + except StochSSAPIError as err: + report_error(self, log, err) + self.finish() From 2ffcbf2594432de8bd0b4a7a5494c083b35ab987 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Thu, 27 May 2021 14:41:37 -0400 Subject: [PATCH 003/192] removed the chmod block. --- stochss/handlers/util/stochss_file.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/stochss/handlers/util/stochss_file.py b/stochss/handlers/util/stochss_file.py index 425182d8e1..83f49388ec 100644 --- a/stochss/handlers/util/stochss_file.py +++ b/stochss/handlers/util/stochss_file.py @@ -117,7 +117,7 @@ def publish_presentation(self): src = self.get_path(full=True) try: shutil.copyfile(src, dst) - os.chmod(dst, stat.S_IREAD) + # INSERT JUPYTER HUB CODE HERE return {"message": f"Successfully published the {self.get_name()} presentation"} except PermissionError as err: message = f"You do not have permission to copy this file: {str(err)}" From 39d578c6542941a20ec84389579ea22b5133bc20 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Thu, 27 May 2021 15:51:46 -0400 Subject: [PATCH 004/192] Setup the user interface to allow users to publish a model presentation. --- .../templates/includes/modelStateButtons.pug | 18 +++- client/views/model-state-buttons.js | 84 +++++++++++++++---- 2 files changed, 82 insertions(+), 20 deletions(-) diff --git a/client/templates/includes/modelStateButtons.pug b/client/templates/includes/modelStateButtons.pug index e5f340e678..32d0ce7f0d 100644 --- a/client/templates/includes/modelStateButtons.pug +++ b/client/templates/includes/modelStateButtons.pug @@ -1,14 +1,22 @@ div.mdl-edit-btn - div.mdl-edit-btn.saving-status(data-hook="saving-mdl") + div.mdl-edit-btn.saving-status(data-hook="mdl-action-start") div.spinner-grow - span Saving... + span(data-hook="saving" style="display: none") Saving ... - div.mdl-edit-btn.saved-status(data-hook="saved-mdl") + span(data-hook="publishing" style="display: none") Publishing ... - span Saved + div.mdl-edit-btn.saved-status(data-hook="mdl-action-end") + + span(data-hook="saved" style="display: none") Saved + + span(data-hook="published" style="display: none") Published + + div.mdl-edit-btn.save-error-status(data-hook="mdl-action-err") + + span Error button.btn.btn-primary.box-shadow(data-hook="save") Save @@ -29,4 +37,6 @@ div.mdl-edit-btn li.dropdown-item(id="stochss-es" data-hook="stochss-es" data-type="ensemble") Ensemble Simulation li.dropdown-item(id="stochss-ps" data-hook="stochss-ps" data-type="psweep") Parameter Sweep li.dropdown-item(data-hook="new-workflow" data-type="notebook") Jupyter Notebook + + button.btn.btn-primary.box-shadow(data-hook="presentation") Publish Presentation \ No newline at end of file diff --git a/client/views/model-state-buttons.js b/client/views/model-state-buttons.js index f7d5bebf8a..79fc02b4bb 100644 --- a/client/views/model-state-buttons.js +++ b/client/views/model-state-buttons.js @@ -19,6 +19,7 @@ along with this program. If not, see . var path = require('path'); var Plotly = require('../lib/plotly'); var $ = require('jquery'); +let _ = require('underscore'); //support file var app = require('../app'); var modals = require('../modals'); @@ -35,7 +36,8 @@ module.exports = View.extend({ "click [data-hook=stochss-es]" : "handleSimulateClick", "click [data-hook=stochss-ps]" : "handleSimulateClick", 'click [data-hook=new-workflow]' : 'handleSimulateClick', - 'click [data-hook=return-to-project-btn]' : 'clickReturnToProjectHandler' + 'click [data-hook=return-to-project-btn]' : 'clickReturnToProjectHandler', + 'click [data-hook=presentation]' : 'handlePresentationClick' }, initialize: function (attrs, options) { View.prototype.initialize.apply(this, arguments); @@ -51,7 +53,8 @@ module.exports = View.extend({ } }, clickSaveHandler: function (e) { - this.saveModel(this.saved.bind(this)); + let self = this; + this.saveModel(_.bind(self.endAction, self, "save")); }, clickRunHandler: function (e) { if(this.model.is_spatial && $(this.queryByHook("domain-plot-viewer-container")).css("display") !== "none") { @@ -71,7 +74,7 @@ module.exports = View.extend({ clickReturnToProjectHandler: function (e) { let self = this this.saveModel(function () { - self.saved() + self.endAction("save") var dirname = path.dirname(self.model.directory) if(dirname.endsWith(".wkgp")) { dirname = path.dirname(dirname) @@ -83,7 +86,7 @@ module.exports = View.extend({ clickNewWorkflowHandler: function (e) { let self = this this.saveModel(function () { - self.saved() + self.endAction("save") var queryString = "?path="+self.model.directory if(self.model.directory.includes('.proj')) { let wkgp = self.model.directory.includes('.wkgp') ? self.model.name + ".wkgp" : "WorkflowGroup1.wkgp" @@ -95,7 +98,7 @@ module.exports = View.extend({ }) }, getPreviewSpecies: function () { - this.saved(); + this.endAction("save"); let species = this.model.species.map(function (species) { return species.name }); @@ -125,7 +128,7 @@ module.exports = View.extend({ } }, saveModel: function (cb) { - this.saving(); + this.startAction("save"); // this.model is a ModelVersion, the parent of the collection is Model var model = this.model; if (cb) { @@ -134,24 +137,50 @@ module.exports = View.extend({ model.saveModel(); } }, - saving: function () { - var saving = this.queryByHook('saving-mdl'); - var saved = this.queryByHook('saved-mdl'); + startAction: function (action) { + if(action === "save") { + msg = $(this.queryByHook("saving")); + }else{ + msg = $(this.queryByHook("publishing")); + } + msg.css("display", "inline-block"); + var saving = this.queryByHook('mdl-action-start'); + var saved = this.queryByHook('mdl-action-end'); saved.style.display = "none"; saving.style.display = "inline-block"; }, - saved: function () { - var saving = this.queryByHook('saving-mdl'); - var saved = this.queryByHook('saved-mdl'); + errorAction: function () { + oldMsg = $(this.queryByHook("publishing")).css("display", "none"); + var saving = this.queryByHook('mdl-action-start'); + var error = this.queryByHook('mdl-action-err'); + saving.style.display = "none"; + error.style.display = "inline-block"; + setTimeout(function () { + error.style.display = "none"; + }, 5000); + }, + endAction: function (action) { + if(action === "save") { + oldMsg = $(this.queryByHook("saving")); + msg = $(this.queryByHook("saved")); + }else{ + oldMsg = $(this.queryByHook("publishing")); + msg = $(this.queryByHook("published")); + } + oldMsg.css("display", "none"); + msg.css("display", "inline-block"); + var saving = this.queryByHook('mdl-action-start'); + var saved = this.queryByHook('mdl-action-end'); saving.style.display = "none"; saved.style.display = "inline-block"; setTimeout(function () { saved.style.display = "none"; + msg.css("display", "none"); }, 5000); }, runModel: function (species=null) { if(typeof species !== "string") { - this.saved(); + this.endAction("save"); } this.running(); $(this.parent.queryByHook('model-run-container')).css("display", "block") @@ -238,12 +267,15 @@ module.exports = View.extend({ Plotly.newPlot(el, data); window.scrollTo(0, document.body.scrollHeight) }, + displayError: function (errorMsg, e) { + $(this.parent.queryByHook('toggle-preview-plot')).click() + errorMsg.css('display', 'block') + this.focusOnError(e) + }, handleSimulateClick: function (e) { var errorMsg = $(this.parent.queryByHook("error-detected-msg")) if(!this.model.valid) { - $(this.parent.queryByHook('toggle-preview-plot')).click() - errorMsg.css('display', 'block') - this.focusOnError(e) + this.displayError(errorMsg, e); }else{ errorMsg.css('display', 'none') let simType = e.target.dataset.type @@ -260,6 +292,26 @@ module.exports = View.extend({ } } }, + handlePresentationClick: function (e) { + var errorMsg = $(this.parent.queryByHook("error-detected-msg")); + if(!this.model.valid) { + this.displayError(errorMsg, e); + }else{ + let self = this; + this.startAction("publish") + let queryStr = "?path=" + this.model.directory; + let endpoint = path.join(app.getApiPath(), "model/presentation") + queryStr; + app.getXHR(endpoint, { + success: function (err, response, body) { + self.endAction("publish"); + }, + error: function (err, response, body) { + self.errorAction(); + $(modals.newProjectModelErrorHtml(body.Reason, body.Message)).modal(); + } + }); + } + }, focusOnError: function (e) { if(this.model.error) { let self = this From 89b677f8a31439e30b709fddf87ec7cfd6936e8c Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Thu, 27 May 2021 16:17:01 -0400 Subject: [PATCH 005/192] Added function to publish job, workflow, and project presentations. --- stochss/handlers/util/stochss_folder.py | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/stochss/handlers/util/stochss_folder.py b/stochss/handlers/util/stochss_folder.py index 8d9200e65b..2639a772a9 100644 --- a/stochss/handlers/util/stochss_folder.py +++ b/stochss/handlers/util/stochss_folder.py @@ -374,6 +374,30 @@ def move(self, location): raise StochSSPermissionsError(message, traceback.format_exc()) from err + def publish_presentation(self): + ''' + Publish a job, workflow, or project presentation. + + Attributes + ---------- + ''' + present_dir = os.path.join(self.user_dir, ".presentations") + if not os.path.exists(present_dir): + os.mkdir(present_dir) + dst = os.path.join(present_dir, self.get_file()) + if os.path.exists(dst): + message = "A presentation with this name already exists" + raise StochSSFileExistsError(message) + src = self.get_path(full=True) + try: + shutil.copytree(src, dst) + # INSERT JUPYTER HUB CODE HERE + return {"message": f"Successfully published the {self.get_name()} presentation"} + except PermissionError as err: + message = f"You do not have permission to publish this directory: {str(err)}" + raise StochSSPermissionsError(message, traceback.format_exc()) from err + + def upload(self, file_type, file, body, new_name=None): ''' Upload a file from a remote location to the users file system From 7f0c17d0224d90a7c26fbbc666efe657be363ecb Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Thu, 27 May 2021 16:18:21 -0400 Subject: [PATCH 006/192] Added api handler and routes for publishing job presentations. --- stochss/handlers/__init__.py | 3 ++- stochss/handlers/workflows.py | 31 ++++++++++++++++++++++++++++++- 2 files changed, 32 insertions(+), 2 deletions(-) diff --git a/stochss/handlers/__init__.py b/stochss/handlers/__init__.py index f52ecc0747..c686c013b5 100644 --- a/stochss/handlers/__init__.py +++ b/stochss/handlers/__init__.py @@ -103,7 +103,8 @@ def get_page_handlers(route_start): (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/update-format\/?", UpadteWorkflowAPIHandler) + (r"/stochss/api/workflow/update-format\/?", UpadteWorkflowAPIHandler), + (r"/stochss/api/job/presentation\/?", JobPresentationAPIHandler) ] full_handlers = list(map(lambda h: (url_path_join(route_start, h[0]), h[1]), handlers)) return full_handlers diff --git a/stochss/handlers/workflows.py b/stochss/handlers/workflows.py index cb37ad715a..92eab198cb 100644 --- a/stochss/handlers/workflows.py +++ b/stochss/handlers/workflows.py @@ -28,7 +28,7 @@ # Use finish() for json, write() for text from .util import StochSSJob, StochSSModel, StochSSSpatialModel, StochSSNotebook, StochSSWorkflow, \ - StochSSAPIError, report_error + StochSSFolder, StochSSAPIError, report_error log = logging.getLogger('stochss') @@ -394,3 +394,32 @@ async def get(self): except StochSSAPIError as err: report_error(self, log, err) self.finish() + + +class JobPresentationAPIHandler(APIHandler): + ''' + ################################################################################################ + Handler for publishing job presentations. + ################################################################################################ + ''' + @web.authenticated + async def get(self): + ''' + Publish a job presentation. + + Attributes + ---------- + ''' + self.set_header('Content-Type', 'application/json') + path = self.get_query_argument(name="path") + log.debug("The path to the job: %s", path) + try: + folder = StochSSFolder(path=path) + log.info("Publishing the %s presentation", folder.get_name()) + resp = folder.publish_presentation() + log.info(resp['message']) + log.debug("Response Message: %s", resp) + self.write(resp) + except StochSSAPIError as err: + report_error(self, log, err) + self.finish() From d02eafc8c0b869c5378c942e168aa703c3678fa9 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Thu, 27 May 2021 16:22:30 -0400 Subject: [PATCH 007/192] Fixed the error messages and removed the stat import. --- stochss/handlers/util/stochss_file.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/stochss/handlers/util/stochss_file.py b/stochss/handlers/util/stochss_file.py index 83f49388ec..695b442ef4 100644 --- a/stochss/handlers/util/stochss_file.py +++ b/stochss/handlers/util/stochss_file.py @@ -17,7 +17,6 @@ ''' import os -import stat import shutil import zipfile import traceback @@ -112,7 +111,7 @@ def publish_presentation(self): os.mkdir(present_dir) dst = os.path.join(present_dir, self.get_file()) if os.path.exists(dst): - message = "A publication with this name already exists" + message = "A presentation with this name already exists" raise StochSSFileExistsError(message) src = self.get_path(full=True) try: @@ -120,7 +119,7 @@ def publish_presentation(self): # INSERT JUPYTER HUB CODE HERE return {"message": f"Successfully published the {self.get_name()} presentation"} except PermissionError as err: - message = f"You do not have permission to copy this file: {str(err)}" + message = f"You do not have permission to publish this file: {str(err)}" raise StochSSPermissionsError(message, traceback.format_exc()) from err From 57146a4bef108d4d7bdffca4eb9b4a0466688bec Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Thu, 27 May 2021 17:14:15 -0400 Subject: [PATCH 008/192] Added arguments that will allow the job presentation to have the correct name. --- stochss/handlers/util/stochss_folder.py | 5 +++-- stochss/handlers/workflows.py | 4 +++- 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/stochss/handlers/util/stochss_folder.py b/stochss/handlers/util/stochss_folder.py index 2639a772a9..3bac89337f 100644 --- a/stochss/handlers/util/stochss_folder.py +++ b/stochss/handlers/util/stochss_folder.py @@ -374,7 +374,7 @@ def move(self, location): raise StochSSPermissionsError(message, traceback.format_exc()) from err - def publish_presentation(self): + def publish_presentation(self, name=None): ''' Publish a job, workflow, or project presentation. @@ -384,7 +384,8 @@ def publish_presentation(self): present_dir = os.path.join(self.user_dir, ".presentations") if not os.path.exists(present_dir): os.mkdir(present_dir) - dst = os.path.join(present_dir, self.get_file()) + file = self.get_file() if name is None else name + dst = os.path.join(present_dir, file) if os.path.exists(dst): message = "A presentation with this name already exists" raise StochSSFileExistsError(message) diff --git a/stochss/handlers/workflows.py b/stochss/handlers/workflows.py index 92eab198cb..f5c3b3e06a 100644 --- a/stochss/handlers/workflows.py +++ b/stochss/handlers/workflows.py @@ -413,10 +413,12 @@ async def get(self): self.set_header('Content-Type', 'application/json') path = self.get_query_argument(name="path") log.debug("The path to the job: %s", path) + name = self.get_query_argument(name="name") + log.debug("Name of the job presentation: %s", name) try: folder = StochSSFolder(path=path) log.info("Publishing the %s presentation", folder.get_name()) - resp = folder.publish_presentation() + resp = folder.publish_presentation(name=name) log.info(resp['message']) log.debug("Response Message: %s", resp) self.write(resp) From 559d33eebef86c3b34e3bb42306a1405e2fc7aba Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Thu, 27 May 2021 17:15:31 -0400 Subject: [PATCH 009/192] Added the user interface that will allow user to publish job presentations. --- client/templates/includes/gillespyResults.pug | 16 ++++++++ .../includes/gillespyResultsEnsemble.pug | 16 ++++++++ .../includes/parameterScanResults.pug | 15 +++++++ .../includes/parameterSweepResults.pug | 16 ++++++++ client/views/workflow-results.js | 41 ++++++++++++++++++- 5 files changed, 103 insertions(+), 1 deletion(-) diff --git a/client/templates/includes/gillespyResults.pug b/client/templates/includes/gillespyResults.pug index 354ec74d2a..a37a6c6858 100644 --- a/client/templates/includes/gillespyResults.pug +++ b/client/templates/includes/gillespyResults.pug @@ -63,3 +63,19 @@ div#workflow-results.card.card-body 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 + + button.btn.btn-primary.box-shadow(id="job-presentation" data-hook="job-presentation") Publish Presentation + + div.saving-status(data-hook="job-action-start") + + div.spinner-grow + + span Publishing ... + + div.saved-status(data-hook="job-action-end") + + span Published + + div.save-error-status(data-hook="job-action-err") + + span Error diff --git a/client/templates/includes/gillespyResultsEnsemble.pug b/client/templates/includes/gillespyResultsEnsemble.pug index ada2db9858..be9fa68f37 100644 --- a/client/templates/includes/gillespyResultsEnsemble.pug +++ b/client/templates/includes/gillespyResultsEnsemble.pug @@ -174,3 +174,19 @@ div#workflow-results.card.card-body 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 + + button.btn.btn-primary.box-shadow(id="job-presentation" data-hook="job-presentation") Publish Presentation + + div.saving-status(data-hook="job-action-start") + + div.spinner-grow + + span Publishing ... + + div.saved-status(data-hook="job-action-end") + + span Published + + div.save-error-status(data-hook="job-action-err") + + span Error diff --git a/client/templates/includes/parameterScanResults.pug b/client/templates/includes/parameterScanResults.pug index 4b76a7a150..a6284002fe 100644 --- a/client/templates/includes/parameterScanResults.pug +++ b/client/templates/includes/parameterScanResults.pug @@ -78,3 +78,18 @@ div#workflow-results.card.card-body div.mt-2(data-hook="parameter-ranges") + button.btn.btn-primary.box-shadow(id="job-presentation" data-hook="job-presentation") Publish Presentation + + div.saving-status(data-hook="job-action-start") + + div.spinner-grow + + span Publishing ... + + div.saved-status(data-hook="job-action-end") + + span Published + + div.save-error-status(data-hook="job-action-err") + + span Error diff --git a/client/templates/includes/parameterSweepResults.pug b/client/templates/includes/parameterSweepResults.pug index 135f7f9121..ce1724f36c 100644 --- a/client/templates/includes/parameterSweepResults.pug +++ b/client/templates/includes/parameterSweepResults.pug @@ -158,3 +158,19 @@ div#workflow-results.card.card-body 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 + + button.btn.btn-primary.box-shadow(id="job-presentation" data-hook="job-presentation") Publish Presentation + + div.saving-status(data-hook="job-action-start") + + div.spinner-grow + + span Publishing ... + + div.saved-status(data-hook="job-action-end") + + span Published + + div.save-error-status(data-hook="job-action-err") + + span Error diff --git a/client/views/workflow-results.js b/client/views/workflow-results.js index 7bcf2fe2f7..c28245c5d3 100644 --- a/client/views/workflow-results.js +++ b/client/views/workflow-results.js @@ -20,6 +20,7 @@ let $ = require('jquery'); let path = require('path'); //support files let app = require('../app'); +let modals = require('../modals'); let Tooltips = require('../tooltips'); let Plotly = require('../lib/plotly'); //views @@ -48,7 +49,8 @@ module.exports = View.extend({ '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' + 'click [data-hook=download-results-csv]' : 'handleDownloadResultsCsvClick', + 'click [data-hook=job-presentation]' : 'handlePresentationClick' }, initialize: function (attrs, options) { View.prototype.initialize.apply(this, arguments); @@ -95,6 +97,22 @@ module.exports = View.extend({ changeCollapseButtonText: function (e) { app.changeCollapseButtonText(this, e); }, + endAction: function () { + $(this.queryByHook("job-action-start")).css("display", "none"); + let saved = $(this.queryByHook("job-action-end")); + saved.css("display", "inline-block"); + setTimeout(function () { + saved.css("display", "none"); + }, 5000); + }, + errorAction: function () { + $(this.queryByHook("job-action-start")).css("display", "none"); + let error = $(this.queryByHook("job-action-err")); + error.css("display", "inline-block"); + setTimeout(function () { + error.css("display", "none"); + }, 5000); + }, getPlot: function (type) { let self = this; let el = this.queryByHook(type + "-plot"); @@ -233,6 +251,22 @@ module.exports = View.extend({ } }); }, + handlePresentationClick: function (e) { + let self = this; + this.startAction(); + let name = this.parent.model.name + "_" + this.model.name; + let queryStr = "?path=" + this.model.directory + "&name=" + name; + let endpoint = path.join(app.getApiPath(), "job/presentation") + queryStr; + app.getXHR(endpoint, { + success: function (err, response, body) { + self.endAction(); + }, + error: function (err, response, body) { + self.errorAction(); + $(modals.newProjectModelErrorHtml(body.Reason, body.Message)).modal(); + } + }); + }, openPlotArgsSection: function (e) { $(this.queryByHook("edit-plot-args")).collapse("show"); $(document).ready(function () { @@ -342,6 +376,11 @@ module.exports = View.extend({ this.plotFigure(fig, type) } }, + startAction: function () { + $(this.queryByHook("job-action-start")).css("display", "inline-block"); + $(this.queryByHook("job-action-end")).css("display", "none"); + $(this.queryByHook("job-action-err")).css("display", "none"); + }, update: function () {}, updateValid: function () {}, subviews: { From bcaadbe156d03b56d32b03abbb06c255f8368842 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 28 May 2021 11:40:59 -0400 Subject: [PATCH 010/192] Setup the base page for job presentations. --- client/pages/job-presentation.js | 93 ++++++++++++++++++++++ client/templates/pages/jobPresentation.pug | 22 +++++ 2 files changed, 115 insertions(+) create mode 100644 client/pages/job-presentation.js create mode 100644 client/templates/pages/jobPresentation.pug diff --git a/client/pages/job-presentation.js b/client/pages/job-presentation.js new file mode 100644 index 0000000000..1cd52015ad --- /dev/null +++ b/client/pages/job-presentation.js @@ -0,0 +1,93 @@ +/* +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 domReady = require('domready'); +let bootstrap = require('bootstrap'); +//support files +let app = require("../app"); +//models +let Job = require("../models/job"); +//views +let PageView = require('./base'); +let ModelView = require('../views/model-viewer'); +let ResultsView = require('../views/workflow-results'); +let SettingsView = require('../views/settings-viewer'); +//templates +let template = require('../templates/pages/jobPresentation.pug'); + +import bootstrapStyles from '../styles/bootstrap.css'; +import styles from '../styles/styles.css'; +import fontawesomeStyles from '@fortawesome/fontawesome-free/css/svg-with-js.min.css' + +let JobPresentationPage = PageView.extend({ + template: template, + initialize: function () { + PageView.prototype.initialize.apply(this, arguments); + console.log("TODO: get the path to the job from the url") + // let urlParams = new URLSearchParams(window.location.search) + // this.model = new Job({ + // directory: urlParams.get("path") + // }); + console.log("TODO: get job from file system using the app.getXHR function") + // let self = this; + // let queryStr = "?path=" + this.model.directory; + // let endpoint = path.join(); + // app.getXHR(endpoint, { + // success: function (err, response, body) { + // self.model.set(body); + // self.renderSubviews(); + // } + // }); + console.log("TODO: generate the open link and store in this.open") + }, + renderSubviews: function () { + PageView.prototype.render.apply(this, arguments); + this.renderResultsContainer(); + this.renderSettingsContainer(); + this.renderModelContainer(); + }, + renderModelContainer: function () { + let modelView = new ModelView({ + model: this.model.model, + mode: "presentation" + }); + app.registerRenderSubview(this, modelView, "job-model"); + }, + renderResultsContainer: function () { + let resultsView = new ResultsView({ + model: this.model, + mode: "presentation" + }); + app.registerRenderSubview(this, resultsView, "job-results"); + }, + renderSettingsContainer: function () { + let settingsView = new SettingsView({ + model: this.model.settings, + mode: "presentation" + }); + app.registerRenderSubview(this, settingsView, "job-settings"); + } +}); + +domReady(() => { + let p = new JobPresentationPage({ + el: document.body + }); + p.render(); +}); \ No newline at end of file diff --git a/client/templates/pages/jobPresentation.pug b/client/templates/pages/jobPresentation.pug new file mode 100644 index 0000000000..bd2980d202 --- /dev/null +++ b/client/templates/pages/jobPresentation.pug @@ -0,0 +1,22 @@ +html + + head + meta(charset="utf-8") + title StochSS: Stochastic Simulation Service + meta(name="viewport", content="width=device-width, initial-scale=1.0") + meta(name="description", content="") + meta(name="author", content="") + + body + + div#job-presentation.container + + h2=this.model.name + + div(data-hook="job-results") + + div(data-hook="job-settings") + + div(data-hook="job-model") + + a.btn.btn-outline-secondary.box-shadow.text-break(href=this.open role="button") Open in StochSS \ No newline at end of file From c72b100c432fc1a3a276064802b9b31cc8b203a2 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 28 May 2021 11:55:50 -0400 Subject: [PATCH 011/192] Added a check for a mode attribute that will hide elements that are not wanted for job presentations. --- client/views/workflow-results.js | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/client/views/workflow-results.js b/client/views/workflow-results.js index 7bcf2fe2f7..6655cef574 100644 --- a/client/views/workflow-results.js +++ b/client/views/workflow-results.js @@ -55,6 +55,7 @@ module.exports = View.extend({ this.tooltips = Tooltips.parameterSweepResults; this.plots = {}; this.plotArgs = {}; + this.mode = Boolean(attrs.mode) ? attrs.mode : "edit"; }, render: function (attrs, options) { let isEnsemble = this.model.settings.simulationSettings.realizations > 1 && @@ -66,6 +67,12 @@ module.exports = View.extend({ this.template = isEnsemble ? gillespyResultsEnsembleTemplate : gillespyResultsTemplate; } View.prototype.render.apply(this, arguments); + if(this.mode === "presentation") { + $(this.queryByHook("job-presentation")).css("display", "none"); + if(!isParameterScan){ + $(this.queryByHook("convert-to-notebook")).css("display", "none"); + } + } if(this.parent.model.type === "Ensemble Simulation") { var type = isEnsemble ? "stddevran" : "trajectories"; }else{ From 8adefe739a4a2c932dc90fdbafddf4f32c830afc Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 28 May 2021 12:01:21 -0400 Subject: [PATCH 012/192] Added a data hook to the section header to allow it to be changed. --- client/templates/includes/modelViewer.pug | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/client/templates/includes/modelViewer.pug b/client/templates/includes/modelViewer.pug index 9559e2a1f8..cab8cb6844 100644 --- a/client/templates/includes/modelViewer.pug +++ b/client/templates/includes/modelViewer.pug @@ -2,7 +2,7 @@ div.card.card-body div(id="model-viewer-header") - h3.inline="Review Model: "+this.model.name + h3.inline(data-hook="job-model-name")="Review Model: "+this.model.name button.btn.btn-outline-collapse(data-toggle="collapse" data-target="#collapse-model" data-hook="collapse-model") + From f28f8156d8736d349fb57463a92cea5fb36624db Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 28 May 2021 12:02:40 -0400 Subject: [PATCH 013/192] Added check for a mode attribute that will alter the section header for job presentations. --- client/views/model-viewer.js | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/client/views/model-viewer.js b/client/views/model-viewer.js index d35fe7885a..fec00e9ebc 100644 --- a/client/views/model-viewer.js +++ b/client/views/model-viewer.js @@ -16,6 +16,7 @@ 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 @@ -36,9 +37,13 @@ module.exports = View.extend({ }, initialize: function (attrs, options) { View.prototype.initialize.apply(this, arguments); + this.mode = Boolean(attrs.mode) ? attrs.mode : "edit"; }, render: function () { View.prototype.render.apply(this, arguments); + if(this.mode === "presentation") { + $(this.queryByHook("job-model-name")).html("Model: " + this.model.name) + } this.renderSpeciesView(); this.renderParametersView(); this.renderReactionsView(); From 703974b0a44e7bc5161cb2a89cc23b7486b10054 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 28 May 2021 12:09:01 -0400 Subject: [PATCH 014/192] Added data hook to the section header to allow it to be changed. --- client/templates/includes/settingsViewer.pug | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/client/templates/includes/settingsViewer.pug b/client/templates/includes/settingsViewer.pug index 90ba4f0528..b4875f85a5 100644 --- a/client/templates/includes/settingsViewer.pug +++ b/client/templates/includes/settingsViewer.pug @@ -2,7 +2,7 @@ div#workflow-settings-viewer.card.card-body div - h3.inline Review Settings + h3.inline(data-hook="job-settings-header") Review Settings button.btn.btn-outline-collapse(data-toggle="collapse" data-target="#collapse-wkfl-settings-viewer" data-hook="collapse-settings-viewer") + From 2a062290a78e230590840fdafa3620951f91f31d Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 28 May 2021 12:33:46 -0400 Subject: [PATCH 015/192] Added check for a mode attribute that will alter the section header for job presentations. --- client/views/settings-viewer.js | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/client/views/settings-viewer.js b/client/views/settings-viewer.js index 918bfddf2b..f9312d7c1f 100644 --- a/client/views/settings-viewer.js +++ b/client/views/settings-viewer.js @@ -37,9 +37,13 @@ module.exports = View.extend({ this.algorithm = this.model.simulationSettings.isAutomatic ? "The algorithm was chosen based on your model." : this.model.simulationSettings.algorithm + this.mode = Boolean(attrs.mode) ? attrs.mode : "edit"; }, render: function (attrs, options) { View.prototype.render.apply(this, arguments); + if(this.mode === "presentation") { + $(this.queryByHook("job-settings-header")).html("Settings") + } if(!this.parent.model.newFormat) { $(this.queryByHook("timespan-settings-viewer-container")).css("display", "none"); } From 1657543c5a305bfa77822e24de78573e67227fa3 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 28 May 2021 13:14:29 -0400 Subject: [PATCH 016/192] Added line to set the job models type to allow the current workflow results file to be compatable with the presentation page. --- client/pages/job-presentation.js | 1 + 1 file changed, 1 insertion(+) diff --git a/client/pages/job-presentation.js b/client/pages/job-presentation.js index 1cd52015ad..1ee8e38f0a 100644 --- a/client/pages/job-presentation.js +++ b/client/pages/job-presentation.js @@ -51,6 +51,7 @@ let JobPresentationPage = PageView.extend({ // app.getXHR(endpoint, { // success: function (err, response, body) { // self.model.set(body); + // self.model.type = body.titleType; // self.renderSubviews(); // } // }); From 29fa9332ce616a1c61daa76453a84d3b266c1c36 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 28 May 2021 13:15:54 -0400 Subject: [PATCH 017/192] Added the page api handler for the job presentation page. --- jupyterhub/handlers.py | 7 +++++++ jupyterhub/jupyterhub_config.py | 3 ++- webpack.hub.config.js | 8 ++++++++ 3 files changed, 17 insertions(+), 1 deletion(-) diff --git a/jupyterhub/handlers.py b/jupyterhub/handlers.py index cd74cfb679..9b79473575 100644 --- a/jupyterhub/handlers.py +++ b/jupyterhub/handlers.py @@ -5,3 +5,10 @@ class HomeHandler(BaseHandler): async def get(self): html = self.render_template("stochss-home.html") self.finish(html) + + +class JobPresentationHandler(BaseHandler): + + async def get(self): + html = self.render_template("stochss-job-presentation.html") + self.finish(html) diff --git a/jupyterhub/jupyterhub_config.py b/jupyterhub/jupyterhub_config.py index 6b4103d270..0659af2c93 100644 --- a/jupyterhub/jupyterhub_config.py +++ b/jupyterhub/jupyterhub_config.py @@ -71,11 +71,12 @@ c.JupyterHub.default_url = '/stochss' # Page handlers -from handlers import HomeHandler +from handlers import HomeHandler, JobPresentationHandler # StochSS request handlers c.JupyterHub.extra_handlers = [ (r"/stochss\/?", HomeHandler), + (r"/stochss/job-presentation\/?", JobPresentationHandler) ] ## Paths to search for jinja templates, before using the default templates. diff --git a/webpack.hub.config.js b/webpack.hub.config.js index 99119e673d..77d0d2de4f 100644 --- a/webpack.hub.config.js +++ b/webpack.hub.config.js @@ -5,6 +5,7 @@ module.exports = { mode: 'development', entry: { home: './client/pages/home.js', + jobPresentation: './client/pages.job-presentation.js' }, output: { filename: 'stochss-[name].bundle.js', @@ -18,6 +19,13 @@ module.exports = { template: 'jupyterhub/home_template.pug', name: 'home', inject: false + }), + new HtmlWebpackPlugin({ + title: 'StochSS | Job Presentation', + filename: '../templates/stochss-job-presentation.html', + template: 'jupyterhub/home_template.pug', + name: 'jobPresentation', + inject: false }) ], module: { From 3250362e233e4b486dfbd2311b0c1a62007cd6c8 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 28 May 2021 13:19:12 -0400 Subject: [PATCH 018/192] Added blank model presentation pug file. --- client/templates/pages/modelPresetation.pug | 0 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 client/templates/pages/modelPresetation.pug diff --git a/client/templates/pages/modelPresetation.pug b/client/templates/pages/modelPresetation.pug new file mode 100644 index 0000000000..e69de29bb2 From 9e51e07430dc450965c6c9dd14ab036625152edd Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 28 May 2021 13:32:30 -0400 Subject: [PATCH 019/192] pylint changes. --- jupyterhub/handlers.py | 24 ++++++++++++++++-------- 1 file changed, 16 insertions(+), 8 deletions(-) diff --git a/jupyterhub/handlers.py b/jupyterhub/handlers.py index 9b79473575..51903a707d 100644 --- a/jupyterhub/handlers.py +++ b/jupyterhub/handlers.py @@ -1,14 +1,22 @@ from jupyterhub.handlers.base import BaseHandler class HomeHandler(BaseHandler): - - async def get(self): - html = self.render_template("stochss-home.html") - self.finish(html) + ''' + ################################################################################################ + Handler for rendering jupyterhub home page. + ################################################################################################ + ''' + async def get(self): + html = self.render_template("stochss-home.html") + self.finish(html) class JobPresentationHandler(BaseHandler): - - async def get(self): - html = self.render_template("stochss-job-presentation.html") - self.finish(html) + ''' + ################################################################################################ + Handler for rendering jupyterhub job presentation page. + ################################################################################################ + ''' + async def get(self): + html = self.render_template("stochss-job-presentation.html") + self.finish(html) From 8816cd732d7b56bebda867da31756b8ae9745de3 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 28 May 2021 13:46:24 -0400 Subject: [PATCH 020/192] More pylint changes. --- jupyterhub/handlers.py | 32 ++++ jupyterhub/jupyterhub_config.py | 306 ++++++++++++++++---------------- 2 files changed, 185 insertions(+), 153 deletions(-) diff --git a/jupyterhub/handlers.py b/jupyterhub/handlers.py index 51903a707d..e6023700f8 100644 --- a/jupyterhub/handlers.py +++ b/jupyterhub/handlers.py @@ -1,5 +1,25 @@ +''' +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 . +''' + from jupyterhub.handlers.base import BaseHandler +# pylint: disable=abstract-method +# pylint: disable=too-few-public-methods class HomeHandler(BaseHandler): ''' ################################################################################################ @@ -7,6 +27,12 @@ class HomeHandler(BaseHandler): ################################################################################################ ''' async def get(self): + ''' + Render the jupyterhub home page. + + Attributes + ---------- + ''' html = self.render_template("stochss-home.html") self.finish(html) @@ -18,5 +44,11 @@ class JobPresentationHandler(BaseHandler): ################################################################################################ ''' async def get(self): + ''' + Render the jupyterhub job presentation page. + + Attributes + ---------- + ''' html = self.render_template("stochss-job-presentation.html") self.finish(html) diff --git a/jupyterhub/jupyterhub_config.py b/jupyterhub/jupyterhub_config.py index 0659af2c93..9128aea405 100644 --- a/jupyterhub/jupyterhub_config.py +++ b/jupyterhub/jupyterhub_config.py @@ -22,22 +22,22 @@ import sys, os, os.path, shutil, logging ## Class for authenticating users. -# +# # This should be a subclass of :class:`jupyterhub.auth.Authenticator` -# +# # with an :meth:`authenticate` method that: -# +# # - is a coroutine (asyncio or tornado) # - returns username on success, None on failure # - takes two arguments: (handler, data), # where `handler` is the calling web.RequestHandler, # and `data` is the POST form data from the login page. -# +# # .. versionchanged:: 1.0 # authenticators may be registered via entry points, # e.g. `c.JupyterHub.authenticator_class = 'pam'` -# -# Currently installed: +# +# Currently installed: # - default: jupyterhub.auth.PAMAuthenticator # - dummy: jupyterhub.auth.DummyAuthenticator # - pam: jupyterhub.auth.PAMAuthenticator @@ -51,12 +51,12 @@ data_dir = os.environ.get('DATA_VOLUME_CONTAINER', '/data') c.JupyterHub.cookie_secret_file = os.path.join(data_dir, - 'jupyterhub_cookie_secret') + 'jupyterhub_cookie_secret') c.JupyterHub.db_url = 'postgresql://postgres:{password}@{host}/{db}'.format( - host=os.environ['POSTGRES_HOST'], - password=os.environ['POSTGRES_PASSWORD'], - db=os.environ['POSTGRES_DB'], + host=os.environ['POSTGRES_HOST'], + password=os.environ['POSTGRES_PASSWORD'], + db=os.environ['POSTGRES_DB'], ) ## An Application for starting a Multi-User Jupyter Notebook server. @@ -66,7 +66,7 @@ c.JupyterHub.log_level = 'DEBUG' ## The default URL for users when they arrive (e.g. when user directs to "/") -# +# # By default, redirects users to their own server. c.JupyterHub.default_url = '/stochss' @@ -75,57 +75,57 @@ # StochSS request handlers c.JupyterHub.extra_handlers = [ - (r"/stochss\/?", HomeHandler), - (r"/stochss/job-presentation\/?", JobPresentationHandler) + (r"/stochss\/?", HomeHandler), + (r"/stochss/job-presentation\/?", JobPresentationHandler) ] ## Paths to search for jinja templates, before using the default templates. c.JupyterHub.template_paths = [ - '/srv/jupyterhub/templates' + '/srv/jupyterhub/templates' ] ## The class to use for spawning single-user servers. -# +# # Should be a subclass of :class:`jupyterhub.spawner.Spawner`. -# +# # .. versionchanged:: 1.0 # spawners may be registered via entry points, # e.g. `c.JupyterHub.spawner_class = 'localprocess'` -# -# Currently installed: +# +# Currently installed: # - default: jupyterhub.spawner.LocalProcessSpawner # - localprocess: jupyterhub.spawner.LocalProcessSpawner # - simple: jupyterhub.spawner.SimpleLocalProcessSpawner c.JupyterHub.spawner_class = 'dockerspawner.DockerSpawner' ## The ip address for the Hub process to *bind* to. -# +# # By default, the hub listens on localhost only. This address must be accessible # from the proxy and user servers. You may need to set this to a public ip or '' # for all interfaces if the proxy or user servers are in containers or on a # different host. -# +# # See `hub_connect_ip` for cases where the bind and connect address should # differ, or `hub_bind_url` for setting the full bind URL. c.JupyterHub.hub_ip = os.environ.get('DOCKER_HUB_IMAGE') ## The internal port for the Hub process. -# +# # This is the internal port of the hub itself. It should never be accessed # directly. See JupyterHub.port for the public port to use when accessing # jupyterhub. It is rare that this port should be set except in cases of port # conflict. -# +# # See also `hub_ip` for the ip and `hub_bind_url` for setting the full bind URL. c.JupyterHub.hub_port = 8080 ## Services managed by JupyterHub c.JupyterHub.services = [ - { - 'name': 'cull-idle', - 'admin': True, - 'command': [sys.executable, '/srv/jupyterhub/cull_idle_servers.py', '--timeout=28800'], - } + { + 'name': 'cull-idle', + 'admin': True, + 'command': [sys.executable, '/srv/jupyterhub/cull_idle_servers.py', '--timeout=28800'], + } ] #------------------------------------------------------------------------------ @@ -147,7 +147,7 @@ # Pass the network name as argument to spawned containers # Pass cpu limit as extra config since dockerspawner does not natively support it c.DockerSpawner.extra_host_config = { - 'network_mode': network_name, + 'network_mode': network_name, } # Explicitly set notebook directory because we'll be mounting a host volume to # it. Most jupyter/docker-stacks *-notebook images run the Notebook server as @@ -160,7 +160,7 @@ c.DockerSpawner.volumes = { 'jupyterhub-user-{username}': notebook_dir } # Set extra environment variables c.DockerSpawner.environment = { - 'JUPYTER_CONFIG_DIR': os.environ['JUPYTER_CONFIG_DIR'] + 'JUPYTER_CONFIG_DIR': os.environ['JUPYTER_CONFIG_DIR'] } # Remove containers once they are stopped c.DockerSpawner.remove_containers = True @@ -172,123 +172,123 @@ #------------------------------------------------------------------------------ def get_user_cpu_count_or_fail(): - log = logging.getLogger() - reserve_count = int(os.environ['RESERVED_CPUS']) - log.info("RESERVED_CPUS environment variable is set to {}".format(reserve_count)) - # Round up to an even number of reserved cpus - if reserve_count % 2 > 0: - log.warn("Increasing reserved cpu count by one so it's an even number. This helps allocate logical cpus to users more easily.") - reserve_count += 1 - total_cpus = os.cpu_count() - log.info("Total cpu count as reported by os.count: {}".format(total_cpus)) - if reserve_count >= total_cpus: - e_message = "RESERVED_CPUS environment cannot be greater than or equal to the number of cpus returned by os.cpu_count()" - log.error(e_message) - raise ValueError(e_message) - user_cpu_count = total_cpus - reserve_count - # If (num logical cpus) - (num reserved cpus) is odd, - # use one less logical cpu for allocating user cpus - if user_cpu_count % 2 > 0 and user_cpu_count > 1: - user_cpu_count -= 1 - c.StochSS.reserved_cpu_count = reserve_count - log.info('Using {} logical cpus for user containers...'.format(user_cpu_count)) - log.info('Reserving {} logical cpus for hub container and underlying OS'.format(reserve_count)) - return user_cpu_count + log = logging.getLogger() + reserve_count = int(os.environ['RESERVED_CPUS']) + log.info("RESERVED_CPUS environment variable is set to {}".format(reserve_count)) + # Round up to an even number of reserved cpus + if reserve_count % 2 > 0: + log.warn("Increasing reserved cpu count by one so it's an even number. This helps allocate logical cpus to users more easily.") + reserve_count += 1 + total_cpus = os.cpu_count() + log.info("Total cpu count as reported by os.count: {}".format(total_cpus)) + if reserve_count >= total_cpus: + e_message = "RESERVED_CPUS environment cannot be greater than or equal to the number of cpus returned by os.cpu_count()" + log.error(e_message) + raise ValueError(e_message) + user_cpu_count = total_cpus - reserve_count + # If (num logical cpus) - (num reserved cpus) is odd, + # use one less logical cpu for allocating user cpus + if user_cpu_count % 2 > 0 and user_cpu_count > 1: + user_cpu_count -= 1 + c.StochSS.reserved_cpu_count = reserve_count + log.info('Using {} logical cpus for user containers...'.format(user_cpu_count)) + log.info('Reserving {} logical cpus for hub container and underlying OS'.format(reserve_count)) + return user_cpu_count c.StochSS.user_cpu_count = get_user_cpu_count_or_fail() c.StochSS.user_cpu_alloc = [0] * c.StochSS.user_cpu_count def get_power_users(): - power_users_file = os.environ.get('POWER_USERS_FILE') - log = logging.getLogger() - if not os.path.exists(power_users_file): - log.warn('No power users defined!') - return [] - with open(power_users_file) as f: - power_users = [ x.rstrip() for x in f.readlines() ] - return power_users + power_users_file = os.environ.get('POWER_USERS_FILE') + log = logging.getLogger() + if not os.path.exists(power_users_file): + log.warn('No power users defined!') + return [] + with open(power_users_file) as f: + power_users = [ x.rstrip() for x in f.readlines() ] + return power_users c.StochSS.power_users = get_power_users() def pre_spawn_hook(spawner): - '''Function that runs before DockerSpawner spawns a user container. - Limits the resources available to user containers, excluding a list of power users. - ''' - log = logging.getLogger() - # Remove the memory limit for power users - if spawner.user.name in c.StochSS.power_users: - spawner.mem_limit = None - return - palloc = c.StochSS.user_cpu_alloc - div = len(palloc) // 2 - reserved = c.StochSS.reserved_cpu_count - log.warn('Reserved CPUs: {}'.format(reserved)) - log.warn('Number of user containers using each logical core: {}'.format(palloc)) - # We want to allocate logical cores that are on the same physical core - # whenever possible. - # - # A hyper-threaded 4-core processor has 8 logical cpus, with - # two logical cpus per core. Logical cpus on the same cpu core are grouped - # such that if (#, #) represents two logical cpus on a single physical core, - # then the logical cores in this case are indexed on the system like this: - # - # (1, 5), (2, 6), (3, 7), (4, 8) - # - # To allocate two logical cpus per user container, we find the logical cpu that - # is being used by the least number of users in the first half of an - # array tracking which users are using what logical cores. - # - # The general formula for finding the index of the second logical core - # on the same physical core is then: - # - # index(matching logical core) = - # index(chosen logical core) + ( (number of logical cores) / 2 ) - # - avail_cpus = palloc[div:] - # If <= 4 cpus available then use 1 cpu for each user instead of 2 - if not len(avail_cpus): - log.warn("The host system only has 4 logical cpus, so we'll only reserve one logical cpu per user container, instead of the normal 2") - avail_cpus = palloc - least_used_cpu = min(avail_cpus) - cpu1_index = avail_cpus.index(least_used_cpu) - log.info("User {} to use logical cpu {}".format(spawner.user.name, str(cpu1_index))) - palloc[cpu1_index] += 1 - spawner.extra_host_config['cpuset_cpus'] = '{}'.format(cpu1_index) - else: - least_used_cpu = min(avail_cpus) - cpu1_index = avail_cpus.index(least_used_cpu) - palloc[cpu1_index] += 1 - cpu2_index = cpu1_index+div - palloc[cpu2_index] += 1 - log.info("User {} to use logical cpus {} and {}".format( - spawner.user.name, str(cpu1_index), str(cpu2_index))) - spawner.extra_host_config['cpuset_cpus'] = '{},{}'.format(cpu1_index, cpu2_index) + '''Function that runs before DockerSpawner spawns a user container. + Limits the resources available to user containers, excluding a list of power users. + ''' + log = logging.getLogger() + # Remove the memory limit for power users + if spawner.user.name in c.StochSS.power_users: + spawner.mem_limit = None + return + palloc = c.StochSS.user_cpu_alloc + div = len(palloc) // 2 + reserved = c.StochSS.reserved_cpu_count + log.warn('Reserved CPUs: {}'.format(reserved)) + log.warn('Number of user containers using each logical core: {}'.format(palloc)) + # We want to allocate logical cores that are on the same physical core + # whenever possible. + # + # A hyper-threaded 4-core processor has 8 logical cpus, with + # two logical cpus per core. Logical cpus on the same cpu core are grouped + # such that if (#, #) represents two logical cpus on a single physical core, + # then the logical cores in this case are indexed on the system like this: + # + # (1, 5), (2, 6), (3, 7), (4, 8) + # + # To allocate two logical cpus per user container, we find the logical cpu that + # is being used by the least number of users in the first half of an + # array tracking which users are using what logical cores. + # + # The general formula for finding the index of the second logical core + # on the same physical core is then: + # + # index(matching logical core) = + # index(chosen logical core) + ( (number of logical cores) / 2 ) + # + avail_cpus = palloc[div:] + # If <= 4 cpus available then use 1 cpu for each user instead of 2 + if not len(avail_cpus): + log.warn("The host system only has 4 logical cpus, so we'll only reserve one logical cpu per user container, instead of the normal 2") + avail_cpus = palloc + least_used_cpu = min(avail_cpus) + cpu1_index = avail_cpus.index(least_used_cpu) + log.info("User {} to use logical cpu {}".format(spawner.user.name, str(cpu1_index))) + palloc[cpu1_index] += 1 + spawner.extra_host_config['cpuset_cpus'] = '{}'.format(cpu1_index) + else: + least_used_cpu = min(avail_cpus) + cpu1_index = avail_cpus.index(least_used_cpu) + palloc[cpu1_index] += 1 + cpu2_index = cpu1_index+div + palloc[cpu2_index] += 1 + log.info("User {} to use logical cpus {} and {}".format( + spawner.user.name, str(cpu1_index), str(cpu2_index))) + spawner.extra_host_config['cpuset_cpus'] = '{},{}'.format(cpu1_index, cpu2_index) def post_stop_hook(spawner): - log = logging.getLogger() - reserved = c.StochSS.reserved_cpu_count - palloc = c.StochSS.user_cpu_alloc - try: - cpu1_index, cpu2_index = spawner.extra_host_config['cpuset_cpus'].split(',') - palloc[int(cpu1_index)] -= 1 - palloc[int(cpu2_index)] -= 1 - log.warn('Reserved CPUs: {}'.format(reserved)) - log.warn('Number of user containers using each logical core: {}'.format(palloc)) - except: - # Exception thrown due to cpuset_cpus not being set (power user) - pass + log = logging.getLogger() + reserved = c.StochSS.reserved_cpu_count + palloc = c.StochSS.user_cpu_alloc + try: + cpu1_index, cpu2_index = spawner.extra_host_config['cpuset_cpus'].split(',') + palloc[int(cpu1_index)] -= 1 + palloc[int(cpu2_index)] -= 1 + log.warn('Reserved CPUs: {}'.format(reserved)) + log.warn('Number of user containers using each logical core: {}'.format(palloc)) + except: + # Exception thrown due to cpuset_cpus not being set (power user) + pass c.Spawner.pre_spawn_hook = pre_spawn_hook c.Spawner.post_stop_hook = post_stop_hook ## The URL the single-user server should start in. -# +# # `{username}` will be expanded to the user's username -# +# # Example uses: -# +# # - You can set `notebook_dir` to `/` and `default_url` to `/tree/home/{username}` to allow people to # navigate the whole filesystem from their notebook server, but still start in their home directory. # - Start with `/notebooks` instead of `/tree` if `default_url` points to a notebook instead of a directory. @@ -296,17 +296,17 @@ def post_stop_hook(spawner): c.Spawner.default_url = '/stochss/models' ## Maximum number of bytes a single-user notebook server is allowed to use. -# +# # Allows the following suffixes: # - K -> Kilobytes # - M -> Megabytes # - G -> Gigabytes # - T -> Terabytes -# +# # If the single user server tries to allocate more memory than this, it will # fail. There is no guarantee that the single-user notebook server will be able # to allocate this much memory - only that it can not allocate more than this. -# +# # **This is a configuration setting. Your spawner must implement support for the # limit to work.** The default spawner, `LocalProcessSpawner`, does **not** # implement this support. A custom spawner **must** add support for this setting @@ -314,14 +314,14 @@ def post_stop_hook(spawner): c.Spawner.mem_limit = '4G' ## Maximum number of cpu-cores a single-user notebook server is allowed to use. -# +# # If this value is set to 0.5, allows use of 50% of one CPU. If this value is # set to 2, allows use of up to 2 CPUs. -# +# # The single-user notebook server will never be scheduled by the kernel to use # more cpu-cores than this. There is no guarantee that it can access this many # cpu-cores. -# +# # **This is a configuration setting. Your spawner must implement support for the # limit to work.** The default spawner, `LocalProcessSpawner`, does **not** # implement this support. A custom spawner **must** add support for this setting @@ -329,20 +329,20 @@ def post_stop_hook(spawner): #c.Spawner.cpu_limit = 2 ## Extra arguments to be passed to the single-user server. -# +# # Some spawners allow shell-style expansion here, allowing you to use # environment variables here. Most, including the default, do not. Consult the # documentation for your spawner to verify! #c.Spawner.args = [] ## The command used for starting the single-user server. -# +# # Provide either a string or a list containing the path to the startup script # command. Extra arguments, other than this path, should be provided via `args`. -# +# # This is usually set if you want to start the single-user server in a different # python environment (with virtualenv/conda) than JupyterHub itself. -# +# # Some spawners allow shell-style expansion here, allowing you to use # environment variables. Most, including the default, do not. Consult the # documentation for your spawner to verify! @@ -350,10 +350,10 @@ def post_stop_hook(spawner): ## Minimum number of cpu-cores a single-user notebook server is guaranteed to # have available. -# +# # If this value is set to 0.5, allows use of 50% of one CPU. If this value is # set to 2, allows use of up to 2 CPUs. -# +# # **This is a configuration setting. Your spawner must implement support for the # limit to work.** The default spawner, `LocalProcessSpawner`, does **not** # implement this support. A custom spawner **must** add support for this setting @@ -363,13 +363,13 @@ def post_stop_hook(spawner): ## Minimum number of bytes a single-user notebook server is guaranteed to have # available. -# +# # Allows the following suffixes: # - K -> Kilobytes # - M -> Megabytes # - G -> Gigabytes # - T -> Terabytes -# +# # **This is a configuration setting. Your spawner must implement support for the # limit to work.** The default spawner, `LocalProcessSpawner`, does **not** # implement this support. A custom spawner **must** add support for this setting @@ -383,28 +383,28 @@ def post_stop_hook(spawner): ## Base class for implementing an authentication provider for JupyterHub ## Set of users that will have admin rights on this JupyterHub. -# +# # Admin users have extra privileges: # - Use the admin panel to see list of users logged in # - Add / remove users in some authenticators # - Restart / halt the hub # - Start / stop users' single-user servers # - Can access each individual users' single-user server (if configured) -# +# # Admin access should be treated the same way root access is. -# +# # Defaults to an empty set, in which case no user has admin access. c.Authenticator.admin_users = admin = set([]) pwd = os.path.dirname(__file__) with open(os.path.join(pwd, 'userlist')) as f: - for line in f: - if not line: - continue - parts = line.split() - # in case of newline at the end of userlist file - if len(parts) >= 1: - name = parts[0] - #whitelist.add(name) - if len(parts) > 1 and parts[1] == 'admin': - admin.add(name) + for line in f: + if not line: + continue + parts = line.split() + # in case of newline at the end of userlist file + if len(parts) >= 1: + name = parts[0] + #whitelist.add(name) + if len(parts) > 1 and parts[1] == 'admin': + admin.add(name) From a84f80cfe00fc6444515c8566299dc89b0d9de86 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 28 May 2021 15:11:28 -0400 Subject: [PATCH 021/192] Setup the base page for model presentations. --- client/pages/model-presentation.js | 117 +++++++++++++++++++ client/templates/pages/modelPresentation.pug | 30 +++++ client/templates/pages/modelPresetation.pug | 0 3 files changed, 147 insertions(+) create mode 100644 client/pages/model-presentation.js create mode 100644 client/templates/pages/modelPresentation.pug delete mode 100644 client/templates/pages/modelPresetation.pug diff --git a/client/pages/model-presentation.js b/client/pages/model-presentation.js new file mode 100644 index 0000000000..eb40d97a5e --- /dev/null +++ b/client/pages/model-presentation.js @@ -0,0 +1,117 @@ +/* +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 domReady = require('domready'); +let bootstrap = require('bootstrap'); +//support files +let app = require('../app'); +//models +let Model = require('../models/model'); +//views +let PageView = require('./base'); +let Rules = require('./rules-viewer'); +let Events = require('./events-viewer'); +let Species = require('./species-viewer'); +let Reactions = require('./reactions-viewer'); +let Parameters = require('./parameters-viewer'); +let SBMLComponents = require('./sbml-component-editor'); +//templates +let template = require('../templates/pages/modelPresentation.pug'); + +import bootstrapStyles from '../styles/bootstrap.css'; +import styles from '../styles/styles.css'; +import fontawesomeStyles from '@fortawesome/fontawesome-free/css/svg-with-js.min.css' + +let ModelPresentationPage = PageView.extend({ + template: template, + initialize: function (attrs, arguments) { + PageView.prototype.initialize.apply(this, arguments); + console.log("TODO: get the path to the model from the url") + // let urlParams = new URLSearchParams(window.location.search) + // this.model = new Model({ + // directory: urlParams.get("path"), + // for: "presentation" + // }); + console.log("TODO: get model from file system using the app.getXHR function") + // let self = this; + // let queryStr = "?path=" + this.model.directory; + // let endpoint = path.join(); + // app.getXHR(endpoint, { + // success: function (err, response, body) { + // self.model.set(body); + // self.renderSubviews(); + // } + // }); + console.log("TODO: generate the open link and store in this.open") + }, + renderSubviews: function () { + PageView.prototype.render.apply(this, arguments); + this.renderSpeciesContainer(); + this.renderParametersContainer(); + this.renderReactionsContainer(); + this.renderEventsContainer(); + this.renderRulesContainer(); + this.renderSBMLComponents(); + }, + renderEventsContainer: function () { + let events = new Events({ + collection: this.model.eventsCollection + }); + app.registerRenderSubview(this, events, "model-events"); + }, + renderParametersContainer: function () { + let parameters = new Parameters({ + collection: this.model.parameters + }); + app.registerRenderSubview(this, parameters, "model-parameters"); + }, + renderReactionsContainer: function () { + let reactions = new Reactions({ + collection: this.model.reactions + }); + app.registerRenderSubview(this, reactions, "model-reactions"); + }, + renderRulesContainer: function () { + let rules = new Rules({ + collection: this.model.rules + }); + app.registerRenderSubview(this, rules, "model-rules"); + }, + renderSBMLComponents: function () { + let sbmlComponents = new SBMLComponentsView({ + functionDefinitions: this.model.functionDefinitions, + viewMode: true + }); + app.registerRenderSubview(this, sbmlComponents, "model-sbml-components"); + }, + renderSpeciesContainer: function () { + let species = new Species({ + collection: this.model.species + }); + app.registerRenderSubview(this, species, "model-species"); + } +}); + +domReady(() => { + let p = new ModelPresentationPage({ + el: document.body + }); + p.render(); +}); diff --git a/client/templates/pages/modelPresentation.pug b/client/templates/pages/modelPresentation.pug new file mode 100644 index 0000000000..65b571444c --- /dev/null +++ b/client/templates/pages/modelPresentation.pug @@ -0,0 +1,30 @@ +html + + head + meta(charset="utf-8") + title StochSS: Stochastic Simulation Service + meta(name="viewport", content="width=device-width, initial-scale=1.0") + meta(name="description", content="") + meta(name="author", content="") + + body + + div#model-presentation.container + + h2=this.model.name + + div(data-hook="model-species") + + div(data-hook="model-parameters") + + div(data-hook="model-reactions") + + div(data-hook="model-events") + + div(data-hook="model-rules") + + div(data-hook="model-sbml-components") + + div.card.card-body="System Volume: "+this.model.volume + + a.btn.btn-outline-secondary.box-shadow.text-break(href=this.open role="button") Open in StochSS diff --git a/client/templates/pages/modelPresetation.pug b/client/templates/pages/modelPresetation.pug deleted file mode 100644 index e69de29bb2..0000000000 From eaf0b9a4cab70abd4fd1b024bf3b2cb5c88fe4d6 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 28 May 2021 15:15:06 -0400 Subject: [PATCH 022/192] Added the page handler for model presentations. --- client/pages/job-presentation.js | 1 + jupyterhub/handlers.py | 17 +++++++++++++++++ jupyterhub/jupyterhub_config.py | 5 +++-- webpack.hub.config.js | 10 +++++++++- 4 files changed, 30 insertions(+), 3 deletions(-) diff --git a/client/pages/job-presentation.js b/client/pages/job-presentation.js index 1ee8e38f0a..b38c7c7fa6 100644 --- a/client/pages/job-presentation.js +++ b/client/pages/job-presentation.js @@ -17,6 +17,7 @@ along with this program. If not, see . */ let $ = require('jquery'); +let path = require('path'); let domReady = require('domready'); let bootstrap = require('bootstrap'); //support files diff --git a/jupyterhub/handlers.py b/jupyterhub/handlers.py index e6023700f8..b98c406d1d 100644 --- a/jupyterhub/handlers.py +++ b/jupyterhub/handlers.py @@ -52,3 +52,20 @@ async def get(self): ''' html = self.render_template("stochss-job-presentation.html") self.finish(html) + + +class ModelPresentationHandler(BaseHandler): + ''' + ################################################################################################ + Handler for rendering jupyterhub model presentation page. + ################################################################################################ + ''' + async def get(self): + ''' + Render the jupyterhub model presentation page. + + Attributes + ---------- + ''' + html = self.render_template("stochss-model-presentation.html") + self.finish(html) diff --git a/jupyterhub/jupyterhub_config.py b/jupyterhub/jupyterhub_config.py index 9128aea405..93998b6e88 100644 --- a/jupyterhub/jupyterhub_config.py +++ b/jupyterhub/jupyterhub_config.py @@ -71,12 +71,13 @@ c.JupyterHub.default_url = '/stochss' # Page handlers -from handlers import HomeHandler, JobPresentationHandler +from handlers import * # StochSS request handlers c.JupyterHub.extra_handlers = [ (r"/stochss\/?", HomeHandler), - (r"/stochss/job-presentation\/?", JobPresentationHandler) + (r"/stochss/job-presentation\/?", JobPresentationHandler), + (r"/stochss/model-presentation\/?", ModelPresentationHandler) ] ## Paths to search for jinja templates, before using the default templates. diff --git a/webpack.hub.config.js b/webpack.hub.config.js index 77d0d2de4f..658b62b9ff 100644 --- a/webpack.hub.config.js +++ b/webpack.hub.config.js @@ -5,7 +5,8 @@ module.exports = { mode: 'development', entry: { home: './client/pages/home.js', - jobPresentation: './client/pages.job-presentation.js' + jobPresentation: './client/pages/job-presentation.js', + modelPresentation: './client/pages/model-presentation.js' }, output: { filename: 'stochss-[name].bundle.js', @@ -26,6 +27,13 @@ module.exports = { template: 'jupyterhub/home_template.pug', name: 'jobPresentation', inject: false + }), + new HtmlWebpackPlugin({ + title: 'StochSS | Model Presentation', + filename: '../templates/stochss-model-presentation.html', + template: 'jupyterhub/home_template.pug', + name: 'modelPresentation', + inject: false }) ], module: { From dc902351a8417d9274e8e7a124fe7c877947f415 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Thu, 3 Jun 2021 15:08:40 -0400 Subject: [PATCH 023/192] updated the gillespy2 version to 1.6.0. --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index eb3d418969..64cdace781 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==1.5.11 +gillespy2==1.6.0 sciope==0.4 pygmsh==5.0.2 meshio==2.3.10 From f3883a0be1c75128ab31110295b47e8495006e67 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Thu, 3 Jun 2021 15:41:09 -0400 Subject: [PATCH 024/192] Refactored the sbml convert-to-model function to use the new gillespy2 model-to-stochss export function. --- stochss/handlers/util/stochss_sbml.py | 218 +------------------------- 1 file changed, 4 insertions(+), 214 deletions(-) diff --git a/stochss/handlers/util/stochss_sbml.py b/stochss/handlers/util/stochss_sbml.py index 7f3cf29486..ff0fa7d67c 100644 --- a/stochss/handlers/util/stochss_sbml.py +++ b/stochss/handlers/util/stochss_sbml.py @@ -21,8 +21,7 @@ import traceback from gillespy2.sbml.SBMLimport import convert -from gillespy2.sbml.SBMLimport import __read_sbml_model as _read_sbml_model -from gillespy2.sbml.SBMLimport import __get_math as _get_math +from gillespy2.stochss.StochSSexport import export from .stochss_base import StochSSBase from .stochss_errors import StochSSFileNotFoundError @@ -57,205 +56,6 @@ def __init__(self, path, new=False, document=None): sbml_file.write(document) - @classmethod - def __build_element(cls, stoich_species): - if not stoich_species: - return "\\emptyset" - - elements = [] - for species in stoich_species: - name = species['specie']['name'] - ratio = species['ratio'] - element = f"{ratio}{name}" if ratio > 1 else name - elements.append(element) - return '+'.join(elements) - - - @classmethod - def __convert_assignments(cls, model, event, assignments): - for assignment in assignments: - name = assignment.variable.name - try: - variable = cls.__get_species(species=model['species'], name=name) - except IndexError: - variable = cls.__get_parameter(parameters=model['parameters'], name=name) - - s_assignment = {"variable": variable, - "expression": assignment.expression} - event['eventAssignments'].append(s_assignment) - - - @classmethod - def __convert_events(cls, model, events): - for name, event in events.items(): - s_event = {"compID":model['defaultID'], - "name": name, - "annotation": "", - "delay": event.delay, - "priority": event.priority, - "triggerExpression": event.trigger.expression, - "initialValue": event.trigger.value, - "persistent": event.trigger.persistent, - "useValuesFromTriggerTime": event.use_values_from_trigger_time, - "eventAssignments": []} - - cls.__convert_assignments(model=model, event=s_event, assignments=event.assignments) - - model['eventsCollection'].append(s_event) - model['defaultID'] += 1 - - - @classmethod - def __convert_function_definition(cls, model, function_definitions): - for function_definition in function_definitions: - name = function_definition["name"] - variables = ', '.join(function_definition["args"]) - expression = function_definition["function"] - function = "lambda({0}, {1})".format(variables, expression) - signature = "{0}({1})".format(name, variables) - - s_function_definition = {"compID":model['defaultID'], - "name":name, - "function":function, - "expression":expression, - "variables":variables, - "signature":signature, - "annotation": ""} - model['functionDefinitions'].append(s_function_definition) - model['defaultID'] += 1 - - - @classmethod - def __convert_parameters(cls, model, parameters): - for name, parameter in parameters.items(): - s_parameter = {"compID":model['defaultID'], - "name":name, - "expression":str(parameter.expression), - "annotation": ""} - model['parameters'].append(s_parameter) - model['defaultID'] += 1 - - - @classmethod - def __convert_stoich_species(cls, s_reaction, reaction, key, species): - source = reaction.reactants if key == "reactants" else reaction.products - for specie, ratio in source.items(): - stoich_species = {"ratio":ratio, - "specie":cls.__get_species(species=species, name=specie.name)} - s_reaction[key].append(stoich_species) - - - @classmethod - def __convert_reactions(cls, model, reactions): - for name, reaction in reactions.items(): - s_reaction = {"compID":model['defaultID'], - "name":name, - "reactionType": "custom-propensity", - "massaction": False, - "propensity": reaction.propensity_function, - "annotation": "", - "rate": {}, - "subdomains": [ - "subdomain 1: ", - "subdomain 2: " - ], - "reactants": [], - "products": []} - - for key in ['reactants', 'products']: - cls.__convert_stoich_species(s_reaction=s_reaction, reaction=reaction, - key=key, species=model['species']) - cls.__get_summary(reaction=s_reaction) - - model['reactions'].append(s_reaction) - model['defaultID'] += 1 - - - @classmethod - def __convert_rules(cls, model, r_type, rules): - for name, rule in rules.items(): - try: - variable = cls.__get_species(species=model['species'], name=rule.variable) - except IndexError: - variable = cls.__get_parameter(parameters=model['parameters'], name=rule.variable) - - s_rule = {"compID":model['defaultID'], - "name":name, - "expression":rule.formula, - "type":r_type, - "variable":variable, - "annotation": ""} - model['rules'].append(s_rule) - model['defaultID'] += 1 - - - @classmethod - def __convert_species(cls, model, species): - mode = "dynamic" - - # Get the model for all species - for _, specie in species.items(): - if specie.mode != mode: - mode = "continuous" - break - - for name, specie in species.items(): - s_species = {"compID":model['defaultID'], - "name":name, - "value":specie.initial_value, - "mode":mode, - "switchTol": 0.03, - "switchMin": 100, - "isSwitchTol": True, - "annotation": "", - "diffusionConst":0, - "subdomains": [ - "subdomain 1: ", - "subdomain 2: " - ]} - model['species'].append(s_species) - model['defaultID'] += 1 - - model['defaultMode'] = mode - - - def __get_function_definitions(self): - path = self.get_path(full=True) - sb_model = _read_sbml_model(path)[0] - function_definitions = [] - - for i in range(sb_model.getNumFunctionDefinitions()): - function = sb_model.getFunctionDefinition(i) - function_name = function.getId() - function_tree = function.getMath() - num_nodes = function_tree.getNumChildren() - function_args = [function_tree.getChild(i).getName() for i in range(num_nodes-1)] - function_string = _get_math(function_tree.getChild(num_nodes-1)) - s_function_definition = {"name":function_name, - "function":function_string, - "args":function_args} - function_definitions.append(s_function_definition) - - return function_definitions - - - @classmethod - def __get_parameter(cls, parameters, name): - return list(filter(lambda parameter: parameter['name'] == name, parameters))[0] - - - @classmethod - def __get_summary(cls, reaction): - r_summary = cls.__build_element(reaction['reactants']) - p_summary = cls.__build_element(reaction['products']) - reaction['summary'] = f"{r_summary} \\rightarrow {p_summary}" - - - @classmethod - def __get_species(cls, species, name): - return list(filter(lambda specie: specie['name'] == name, species))[0] - - def convert_to_gillespy(self): ''' Convert the sbml model to a gillespy model and return it @@ -282,14 +82,14 @@ def convert_to_model(self, name=None, wkgp=False): Attributes ---------- ''' - s_model = self.get_model_template() # StochSS Model in json format - self.log("debug", f"Model template: \n{json.dumps(s_model)}") - g_model, errors = self.convert_to_gillespy() # GillesPy2 Model object if g_model is None: message = "ERROR! We were unable to convert the SBML Model into a StochSS Model." return {"message":message, "errors":errors, "model":None} + s_model = export(model=g_model, return_stochss_model=True) # StochSS Model in json format + self.log("debug", f"Model: \n{json.dumps(s_model)}") + s_file = f"{g_model.name}.mdl" if name is None else f"{name}.mdl" if wkgp: wkgp_path, changed = self.get_unique_path(name=f"{self.get_name(path=s_file)}.wkgp", @@ -300,15 +100,5 @@ def convert_to_model(self, name=None, wkgp=False): 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()) - self.__convert_reactions(model=s_model, reactions=g_model.get_all_reactions()) - self.__convert_events(model=s_model, events=g_model.get_all_events()) - self.__convert_rules(model=s_model, r_type='Rate Rule', rules=g_model.get_all_rate_rules()) - self.__convert_rules(model=s_model, r_type='Assignment Rule', - rules=g_model.get_all_assignment_rules()) - self.__convert_function_definition(model=s_model, - function_definitions=self.__get_function_definitions()) - message = "The SBML Model was successfully converted to a StochSS Model." return {"message":message, "errors":errors, "model":s_model, "path":s_path} From ad0d1d157f84a830986e5c968d55495e23ef2154 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Wed, 9 Jun 2021 14:30:58 -0400 Subject: [PATCH 025/192] Added the presentation base class to handle common backend functions for presentations. Added the presentation error module to hold all of the presentation system backend errors. --- jupyterhub/presentation_base.py | 57 +++++++++++++++ jupyterhub/presentation_error.py | 118 +++++++++++++++++++++++++++++++ 2 files changed, 175 insertions(+) create mode 100644 jupyterhub/presentation_base.py create mode 100644 jupyterhub/presentation_error.py diff --git a/jupyterhub/presentation_base.py b/jupyterhub/presentation_base.py new file mode 100644 index 0000000000..bf201c867a --- /dev/null +++ b/jupyterhub/presentation_base.py @@ -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 . +''' + +import os + +class StochSSBase(): + ''' + ################################################################################################ + StochSS base object + ################################################################################################ + ''' + user_dir = os.path.expanduser("~") # returns the path to the users home directory + + def __init__(self, path): + ''' + Intitialize a file object + + Attributes + ---------- + path : str + Path to the folder + ''' + self.path = path + self.logs = [] + + + def get_name(self, path=None): + ''' + Get the name from the file object's path or provided path + + Attributes + ---------- + path : str + Path to a file object + ''' + name = self.path if path is None else path + if name.endswith("/"): + name = name[:-1] + name = name.split('/').pop() + if "." not in name: + return name + return '.'.join(name.split('.')[:-1]) diff --git a/jupyterhub/presentation_error.py b/jupyterhub/presentation_error.py new file mode 100644 index 0000000000..ead4cbb8ef --- /dev/null +++ b/jupyterhub/presentation_error.py @@ -0,0 +1,118 @@ +''' +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 traceback + +def report_error(handler, log, err): + ''' + Report a stochss error to the front end + + Attributes + ---------- + handler : obj + Jupyter Notebook API Handler + log : obj + StochSS log + ''' + handler.set_status(err.status_code) + error = {"Reason":err.reason, "Message":err.message} + if err.traceback is None: + trace = traceback.format_exc() + else: + trace = err.traceback + log.error("Exception information: %s\n%s", error, trace) + error['Traceback'] = trace + handler.write(error) + + +class StochSSAPIError(Exception): + ''' + ################################################################################################ + StochSS Base Api Handler Error + ################################################################################################ + ''' + + def __init__(self, status_code, reason, msg, trace): + ''' + Base error for all stochss api errors + + Attributes + ---------- + status_code : int + XML request status code + reason : str + Reason for the error + msg : str + Details on what caused the error + trace : str + Error traceback for the error + ''' + super().__init__() + self.status_code = status_code + self.reason = reason + self.message = msg + self.traceback = trace + + +#################################################################################################### +# File System Errors +#################################################################################################### + +class StochSSFileNotFoundError(StochSSAPIError): + ''' + ################################################################################################ + StochSS File/Folder Not Found API Handler Error + ################################################################################################ + ''' + + def __init__(self, msg, trace=None): + ''' + Indicates that the file/folder with the given path does not exist + + Attributes + ---------- + msg : str + Details on what caused the error + trace : str + Error traceback for the error + ''' + super().__init__(404, "StochSS File or Directory Not Found", msg, trace) + +#################################################################################################### +# Model Errors +#################################################################################################### + +class FileNotJSONFormatError(StochSSAPIError): + ''' + ################################################################################################ + StochSS Model/Template Not In JSON Format + ################################################################################################ + ''' + + def __init__(self, msg, trace=None): + ''' + Indicates that the model or template file is not in proper JSON format + + Attributes + ---------- + msg : str + Details on what caused the error + trace : str + Error traceback for the error + ''' + super().__init__(406, "File Data Not JSON Format", msg, trace) From 15d414544f3c6d4d4e89451da94857bb92be5739 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Wed, 9 Jun 2021 14:33:22 -0400 Subject: [PATCH 026/192] Added the load model api handler to load models and spatial models for presentation. Added the model and spatial model presentation classes to load the models form disc. --- jupyterhub/model_presentation.py | 235 +++++++++++++++++++++++++++++++ 1 file changed, 235 insertions(+) create mode 100644 jupyterhub/model_presentation.py diff --git a/jupyterhub/model_presentation.py b/jupyterhub/model_presentation.py new file mode 100644 index 0000000000..3c5108f57a --- /dev/null +++ b/jupyterhub/model_presentation.py @@ -0,0 +1,235 @@ +''' +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 ast +import json +import logging +import traceback +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 presentation_base import StochSSBase +from presentation_error import StochSSAPIError, report_error, \ + StochSSFileNotFoundError, FileNotJSONFormatError + +log = logging.getLogger('stochss') + +# pylint: disable=abstract-method +# pylint: disable=too-few-public-methods +class JsonFileAPIHandler(APIHandler): + ''' + ################################################################################################ + Base Handler for interacting with Model file Get/Post Requests and + downloading json formatted files. + ################################################################################################ + ''' + @web.authenticated + async def get(self): + ''' + Retrieve model data from User's file system if it exists and + create new models using a model template if they don't. Also + retrieves JSON files for download. + + Attributes + ---------- + ''' + purpose = self.get_query_argument(name="for") + log.debug("Purpose of the handler: %s", purpose) + path = self.get_query_argument(name="path") + log.debug("Path to the file: %s", path) + self.set_header('Content-Type', 'application/json') + file_objs = {"mdl":StochSSModel, "smdl":StochSSSpatialModel} + ext = path.split(".").pop() + try: + file = file_objs[ext](path=path) + data = file.load() + log.debug("Contents of the json file: %s", data) + file.print_logs(log) + self.write(data) + except StochSSAPIError as load_err: + report_error(self, log, load_err) + self.finish() + + +def __read_model_file(model): + try: + with open(model.get_path(full=True), "r") as mdl_file: + return json.load(mdl_file) + except FileNotFoundError as err: + message = f"Could not find the model file: {str(err)}" + 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()) from err + + +class StochSSModel(StochSSBase): + ''' + ################################################################################################ + StochSS model object + ################################################################################################ + ''' + + def __init__(self, path): + ''' + Intitialize a model object + + Attributes + ---------- + path : str + Path to the model + ''' + super().__init__(path=path) + self.model = __read_model_file(self) + + + @classmethod + def __update_event_assignments(cls, event, param_ids): + if "eventAssignments" not in event.keys(): + return + for assignment in event['eventAssignments']: + try: + if assignment['variable']['compID'] in param_ids: + expression = ast.literal_eval(assignment['variable']['expression']) + assignment['variable']['expression'] = expression + except KeyError: + pass + except ValueError: + pass + + + def __update_events(self, param_ids): + if "eventsCollection" not in self.model.keys() or not param_ids: + return + for event in self.model['eventsCollection']: + self.__update_event_assignments(event=event, param_ids=param_ids) + + + def __update_parameters(self): + if "parameters" not in self.model.keys(): + return [] + param_ids = [] + for param in self.model['parameters']: + try: + param_ids.append(param['compID']) + if isinstance(param['expression'], str): + param['expression'] = ast.literal_eval(param['expression']) + except KeyError: + pass + except ValueError: + pass + return param_ids + + + def __update_reactions(self): + if "reactions" not in self.model.keys(): + return + for reaction in self.model['reactions']: + try: + if reaction['rate'].keys() and isinstance(reaction['rate']['expression'], str): + expression = ast.literal_eval(reaction['rate']['expression']) + reaction['rate']['expression'] = expression + except KeyError: + pass + except ValueError: + pass + + + def __update_rules(self, param_ids): + if "rules" not in self.model.keys() or not param_ids: + return + for rule in self.model['rules']: + try: + if rule['variable']['compID'] in param_ids: + expression = ast.literal_eval(rule['variable']['expression']) + rule['variable']['expression'] = expression + except KeyError: + pass + except ValueError: + pass + + + def load(self): + ''' + Reads the model file, updates the model to the current format, and stores it in self.model + + Attributes + ---------- + ''' + if "annotation" not in self.model.keys(): + self.model['annotation'] = "" + if "volume" not in self.model.keys(): + if "volume" in self.model['modelSettings'].keys(): + self.model['volume'] = self.model['modelSettings']['volume'] + else: + self.model['volume'] = 1 + param_ids = self.__update_parameters() + 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 + + +class StochSSSpatialModel(StochSSBase): + ''' + ################################################################################################ + StochSS spatial model object + ################################################################################################ + ''' + + def __init__(self, path): + ''' + Intitialize a spatial model object + + Attributes + ---------- + path : str + Path to the spatial model + ''' + super().__init__(path=path) + self.model = __read_model_file(self) + + + def load(self): + ''' + Reads the spatial model file, updates it to the current format, and stores it in self.model + + Attributes + ---------- + ''' + self.model['name'] = self.get_name() + if not self.model['defaultMode']: + self.model['defaultMode'] = "discrete" + if "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(): + 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']))) + return self.model From 0b7a87e599eb203a8ede4bbd710dd084c8117cf4 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Wed, 9 Jun 2021 14:36:18 -0400 Subject: [PATCH 027/192] Added the api handler route for loading models. Pylint fixes. --- jupyterhub/jupyterhub_config.py | 81 +++++++++++++++++++-------------- 1 file changed, 48 insertions(+), 33 deletions(-) diff --git a/jupyterhub/jupyterhub_config.py b/jupyterhub/jupyterhub_config.py index 93998b6e88..df6b88a19c 100644 --- a/jupyterhub/jupyterhub_config.py +++ b/jupyterhub/jupyterhub_config.py @@ -18,8 +18,15 @@ #------------------------------------------------------------------------------ # JupyterHub(Application) configuration #------------------------------------------------------------------------------ +import os +import os.path +import sys +import logging -import sys, os, os.path, shutil, logging +# Page handlers +from handlers import * +# API Handlers +from model_presentation import JsonFileAPIHandler ## Class for authenticating users. # @@ -70,14 +77,12 @@ # By default, redirects users to their own server. c.JupyterHub.default_url = '/stochss' -# Page handlers -from handlers import * - # StochSS request handlers c.JupyterHub.extra_handlers = [ (r"/stochss\/?", HomeHandler), (r"/stochss/job-presentation\/?", JobPresentationHandler), - (r"/stochss/model-presentation\/?", ModelPresentationHandler) + (r"/stochss/model-presentation\/?", ModelPresentationHandler), + (r"/stochss/api/file/json-data\/?", JsonFileAPIHandler) ] ## Paths to search for jinja templates, before using the default templates. @@ -173,15 +178,18 @@ #------------------------------------------------------------------------------ def get_user_cpu_count_or_fail(): + ''' + Get the user cpu count or raise error + ''' log = logging.getLogger() reserve_count = int(os.environ['RESERVED_CPUS']) - log.info("RESERVED_CPUS environment variable is set to {}".format(reserve_count)) + log.info("RESERVED_CPUS environment variable is set to %s", reserve_count) # Round up to an even number of reserved cpus if reserve_count % 2 > 0: - log.warn("Increasing reserved cpu count by one so it's an even number. This helps allocate logical cpus to users more easily.") + log.warning("Increasing reserved cpu count by one so it's an even number. This helps allocate logical cpus to users more easily.") reserve_count += 1 total_cpus = os.cpu_count() - log.info("Total cpu count as reported by os.count: {}".format(total_cpus)) + log.info("Total cpu count as reported by os.count: %s", total_cpus) if reserve_count >= total_cpus: e_message = "RESERVED_CPUS environment cannot be greater than or equal to the number of cpus returned by os.cpu_count()" log.error(e_message) @@ -192,28 +200,32 @@ def get_user_cpu_count_or_fail(): if user_cpu_count % 2 > 0 and user_cpu_count > 1: user_cpu_count -= 1 c.StochSS.reserved_cpu_count = reserve_count - log.info('Using {} logical cpus for user containers...'.format(user_cpu_count)) - log.info('Reserving {} logical cpus for hub container and underlying OS'.format(reserve_count)) + log.info('Using %s logical cpus for user containers...', user_cpu_count) + log.info('Reserving %s logical cpus for hub container and underlying OS', reserve_count) return user_cpu_count c.StochSS.user_cpu_count = get_user_cpu_count_or_fail() c.StochSS.user_cpu_alloc = [0] * c.StochSS.user_cpu_count def get_power_users(): + ''' + Get the list of power users + ''' power_users_file = os.environ.get('POWER_USERS_FILE') log = logging.getLogger() if not os.path.exists(power_users_file): - log.warn('No power users defined!') + log.warning('No power users defined!') return [] - with open(power_users_file) as f: - power_users = [ x.rstrip() for x in f.readlines() ] + with open(power_users_file) as file: + power_users = [ x.rstrip() for x in file.readlines() ] return power_users c.StochSS.power_users = get_power_users() def pre_spawn_hook(spawner): - '''Function that runs before DockerSpawner spawns a user container. + ''' + Function that runs before DockerSpawner spawns a user container. Limits the resources available to user containers, excluding a list of power users. ''' log = logging.getLogger() @@ -224,8 +236,8 @@ def pre_spawn_hook(spawner): palloc = c.StochSS.user_cpu_alloc div = len(palloc) // 2 reserved = c.StochSS.reserved_cpu_count - log.warn('Reserved CPUs: {}'.format(reserved)) - log.warn('Number of user containers using each logical core: {}'.format(palloc)) + log.warning('Reserved CPUs: %s', reserved) + log.warning('Number of user containers using each logical core: %s', palloc) # We want to allocate logical cores that are on the same physical core # whenever possible. # @@ -248,12 +260,12 @@ def pre_spawn_hook(spawner): # avail_cpus = palloc[div:] # If <= 4 cpus available then use 1 cpu for each user instead of 2 - if not len(avail_cpus): - log.warn("The host system only has 4 logical cpus, so we'll only reserve one logical cpu per user container, instead of the normal 2") + if not avail_cpus: + log.warning("The host system only has 4 logical cpus, so we'll only reserve one logical cpu per user container, instead of the normal 2") avail_cpus = palloc least_used_cpu = min(avail_cpus) cpu1_index = avail_cpus.index(least_used_cpu) - log.info("User {} to use logical cpu {}".format(spawner.user.name, str(cpu1_index))) + log.info("User %s to use logical cpu %s", spawner.user.name, str(cpu1_index)) palloc[cpu1_index] += 1 spawner.extra_host_config['cpuset_cpus'] = '{}'.format(cpu1_index) else: @@ -262,12 +274,15 @@ def pre_spawn_hook(spawner): palloc[cpu1_index] += 1 cpu2_index = cpu1_index+div palloc[cpu2_index] += 1 - log.info("User {} to use logical cpus {} and {}".format( - spawner.user.name, str(cpu1_index), str(cpu2_index))) + log.info("User %s to use logical cpus %s and %s", + spawner.user.name, str(cpu1_index), str(cpu2_index)) spawner.extra_host_config['cpuset_cpus'] = '{},{}'.format(cpu1_index, cpu2_index) def post_stop_hook(spawner): + ''' + Post stop hook + ''' log = logging.getLogger() reserved = c.StochSS.reserved_cpu_count palloc = c.StochSS.user_cpu_alloc @@ -275,8 +290,8 @@ def post_stop_hook(spawner): cpu1_index, cpu2_index = spawner.extra_host_config['cpuset_cpus'].split(',') palloc[int(cpu1_index)] -= 1 palloc[int(cpu2_index)] -= 1 - log.warn('Reserved CPUs: {}'.format(reserved)) - log.warn('Number of user containers using each logical core: {}'.format(palloc)) + log.warning('Reserved CPUs: %s', reserved) + log.warning('Number of user containers using each logical core: %s', palloc) except: # Exception thrown due to cpuset_cpus not being set (power user) pass @@ -399,13 +414,13 @@ def post_stop_hook(spawner): pwd = os.path.dirname(__file__) with open(os.path.join(pwd, 'userlist')) as f: - for line in f: - if not line: - continue - parts = line.split() - # in case of newline at the end of userlist file - if len(parts) >= 1: - name = parts[0] - #whitelist.add(name) - if len(parts) > 1 and parts[1] == 'admin': - admin.add(name) + for line in f: + if not line: + continue + parts = line.split() + # in case of newline at the end of userlist file + if len(parts) >= 1: + name = parts[0] + #whitelist.add(name) + if len(parts) > 1 and parts[1] == 'admin': + admin.add(name) From 0baf9cd5d79bb5252bafb9f880d105c5d25b1eb6 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Wed, 9 Jun 2021 14:39:08 -0400 Subject: [PATCH 028/192] Finalized the initialize function for the model presentation page. --- client/pages/model-presentation.js | 32 ++++++++++++++---------------- 1 file changed, 15 insertions(+), 17 deletions(-) diff --git a/client/pages/model-presentation.js b/client/pages/model-presentation.js index eb40d97a5e..3a681b64ec 100644 --- a/client/pages/model-presentation.js +++ b/client/pages/model-presentation.js @@ -43,23 +43,21 @@ let ModelPresentationPage = PageView.extend({ template: template, initialize: function (attrs, arguments) { PageView.prototype.initialize.apply(this, arguments); - console.log("TODO: get the path to the model from the url") - // let urlParams = new URLSearchParams(window.location.search) - // this.model = new Model({ - // directory: urlParams.get("path"), - // for: "presentation" - // }); - console.log("TODO: get model from file system using the app.getXHR function") - // let self = this; - // let queryStr = "?path=" + this.model.directory; - // let endpoint = path.join(); - // app.getXHR(endpoint, { - // success: function (err, response, body) { - // self.model.set(body); - // self.renderSubviews(); - // } - // }); - console.log("TODO: generate the open link and store in this.open") + let urlParams = new URLSearchParams(window.location.search); + this.model = new Model({ + directory: urlParams.get("path"), + for: "presentation" + }); + let self = this; + let queryStr = "?path=" + this.model.directory; + let endpoint = path.join(); + app.getXHR(endpoint, { + success: function (err, response, body) { + self.model.set(body); + self.renderSubviews(); + } + }); + this.open = "open.stochss.org?open=" + this.model.directory; }, renderSubviews: function () { PageView.prototype.render.apply(this, arguments); From fddd31646aa5f99cb17db51493802eeeafcbee97 Mon Sep 17 00:00:00 2001 From: Matthew Geiger Date: Thu, 10 Jun 2021 11:27:35 -0400 Subject: [PATCH 029/192] Skeleton for copying files via docker from user container to jupyterhub --- client/pages/model-presentation.js | 16 ++++++------- jupyterhub/Dockerfile.jupyterhub | 3 ++- jupyterhub/handlers.py | 24 +++++++++++++++++++ jupyterhub/jupyterhub_config.py | 5 +++- .../templates/stochss-job-presentation.html | 1 + .../templates/stochss-model-presentation.html | 1 + 6 files changed, 40 insertions(+), 10 deletions(-) create mode 100644 jupyterhub/templates/stochss-job-presentation.html create mode 100644 jupyterhub/templates/stochss-model-presentation.html diff --git a/client/pages/model-presentation.js b/client/pages/model-presentation.js index 3a681b64ec..66f18cd24b 100644 --- a/client/pages/model-presentation.js +++ b/client/pages/model-presentation.js @@ -26,12 +26,12 @@ let app = require('../app'); let Model = require('../models/model'); //views let PageView = require('./base'); -let Rules = require('./rules-viewer'); -let Events = require('./events-viewer'); -let Species = require('./species-viewer'); -let Reactions = require('./reactions-viewer'); -let Parameters = require('./parameters-viewer'); -let SBMLComponents = require('./sbml-component-editor'); +let Rules = require('../views/rules-viewer'); +let Events = require('../views/events-viewer'); +let Species = require('../views/species-viewer'); +let Reactions = require('../views/reactions-viewer'); +let Parameters = require('../views/parameters-viewer'); +let SBMLComponents = require('../views/sbml-component-editor'); //templates let template = require('../templates/pages/modelPresentation.pug'); @@ -41,7 +41,7 @@ import fontawesomeStyles from '@fortawesome/fontawesome-free/css/svg-with-js.min let ModelPresentationPage = PageView.extend({ template: template, - initialize: function (attrs, arguments) { + initialize: function (attrs, options) { PageView.prototype.initialize.apply(this, arguments); let urlParams = new URLSearchParams(window.location.search); this.model = new Model({ @@ -60,7 +60,7 @@ let ModelPresentationPage = PageView.extend({ this.open = "open.stochss.org?open=" + this.model.directory; }, renderSubviews: function () { - PageView.prototype.render.apply(this, arguments); + PageView.prototype.render.apply(this, options); this.renderSpeciesContainer(); this.renderParametersContainer(); this.renderReactionsContainer(); diff --git a/jupyterhub/Dockerfile.jupyterhub b/jupyterhub/Dockerfile.jupyterhub index ab0119b137..38df4d10b2 100644 --- a/jupyterhub/Dockerfile.jupyterhub +++ b/jupyterhub/Dockerfile.jupyterhub @@ -39,7 +39,8 @@ RUN python3 -m pip install --no-cache-dir \ jupyterhub==1.1.0 \ oauthenticator==0.11.* \ dockerspawner==0.11.* \ - psycopg2==2.7.* + psycopg2==2.7.* \ + notebook COPY static/* /usr/local/share/jupyterhub/static/ diff --git a/jupyterhub/handlers.py b/jupyterhub/handlers.py index b98c406d1d..3b7da6f570 100644 --- a/jupyterhub/handlers.py +++ b/jupyterhub/handlers.py @@ -37,6 +37,30 @@ async def get(self): self.finish(html) +class PublishUserModel(BaseHandler): + ''' + ################################################################################################ + Handler for copying a user model from a user container into a presentations folder + managed by jupyterhub. + ################################################################################################ + ''' + async def get(self): + pass + # Pass the username as a query parameter + # username = + # Pass the model filename as a query parameter + # filename = + client = docker.from_env() + containers = client.containers.list() + user_container = [ c in containers if c.name == f'jupyter-{username}' ][0] + user_model_path = f'/home/jovyan/.presentations/{filename}' + jupyterhub_tar_path = f'/srv/jupyterhub/.presentations/{filename}.tar' + bits, stat = user_container.get_archive(user_model_path) + with open(jupyterhub_tar_path, 'w') as tar_file: + for chunk in bits: + tar_file.write(chunk) + + class JobPresentationHandler(BaseHandler): ''' ################################################################################################ diff --git a/jupyterhub/jupyterhub_config.py b/jupyterhub/jupyterhub_config.py index df6b88a19c..aa4ef947e8 100644 --- a/jupyterhub/jupyterhub_config.py +++ b/jupyterhub/jupyterhub_config.py @@ -23,6 +23,8 @@ import sys import logging +sys.path.append('/srv/jupyterhub/') + # Page handlers from handlers import * # API Handlers @@ -82,7 +84,8 @@ (r"/stochss\/?", HomeHandler), (r"/stochss/job-presentation\/?", JobPresentationHandler), (r"/stochss/model-presentation\/?", ModelPresentationHandler), - (r"/stochss/api/file/json-data\/?", JsonFileAPIHandler) + (r"/stochss/api/file/json-data\/?", JsonFileAPIHandler), + (r"/stochss/api/publish/model\/?", PublishUserModel) ] ## Paths to search for jinja templates, before using the default templates. diff --git a/jupyterhub/templates/stochss-job-presentation.html b/jupyterhub/templates/stochss-job-presentation.html new file mode 100644 index 0000000000..47c4ea2ab8 --- /dev/null +++ b/jupyterhub/templates/stochss-job-presentation.html @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/jupyterhub/templates/stochss-model-presentation.html b/jupyterhub/templates/stochss-model-presentation.html new file mode 100644 index 0000000000..3092353528 --- /dev/null +++ b/jupyterhub/templates/stochss-model-presentation.html @@ -0,0 +1 @@ + \ No newline at end of file From 4c8adda0a3a22eb686d2af7992e29ce526054b4e Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 11 Jun 2021 11:55:11 -0400 Subject: [PATCH 030/192] Moved the publish presentation function to the stochss_model file. --- stochss/handlers/util/stochss_file.py | 24 --------------------- stochss/handlers/util/stochss_model.py | 30 ++++++++++++++++++++++++++ 2 files changed, 30 insertions(+), 24 deletions(-) diff --git a/stochss/handlers/util/stochss_file.py b/stochss/handlers/util/stochss_file.py index 695b442ef4..fbe99c91d3 100644 --- a/stochss/handlers/util/stochss_file.py +++ b/stochss/handlers/util/stochss_file.py @@ -99,30 +99,6 @@ def duplicate(self): raise StochSSPermissionsError(message, traceback.format_exc()) from err - def publish_presentation(self): - ''' - Publish a model or spatial model presentation - - Attributes - ---------- - ''' - present_dir = os.path.join(self.user_dir, ".presentations") - if not os.path.exists(present_dir): - os.mkdir(present_dir) - dst = os.path.join(present_dir, self.get_file()) - if os.path.exists(dst): - message = "A presentation with this name already exists" - raise StochSSFileExistsError(message) - src = self.get_path(full=True) - try: - shutil.copyfile(src, dst) - # INSERT JUPYTER HUB CODE HERE - return {"message": f"Successfully published the {self.get_name()} presentation"} - except PermissionError as err: - message = f"You do not have permission to publish this file: {str(err)}" - raise StochSSPermissionsError(message, traceback.format_exc()) from err - - def move(self, location): ''' Moves a file to a new location. diff --git a/stochss/handlers/util/stochss_model.py b/stochss/handlers/util/stochss_model.py index bb2b9ba9d9..b884dacc95 100644 --- a/stochss/handlers/util/stochss_model.py +++ b/stochss/handlers/util/stochss_model.py @@ -19,6 +19,7 @@ import os import ast import json +import haslib import tempfile import traceback @@ -459,6 +460,35 @@ def load(self): return self.model + def publish_presentation(self): + ''' + Publish a model or spatial model presentation + + Attributes + ---------- + ''' + present_dir = os.path.join(self.user_dir, ".presentations") + if not os.path.exists(present_dir): + os.mkdir(present_dir) + dst = os.path.join(present_dir, self.get_file()) + if os.path.exists(dst): + message = "A presentation with this name already exists" + raise StochSSFileExistsError(message) + src = self.get_path(full=True) + try: + shutil.copyfile(src, dst) + hostname = os.uname()[1] + model = json.jumps(self.load(), sort_keys=True) + file = f"{hashlib.md5(model.encode('utf-8')).hexdigest()}.mdl" # replace with gillespy2.Model.to_json + present_link = f"live.stochss.org/present-model?owner={hostname}&file={file}" + download_link = f"live.stochss.org/download_presentation?owner={hostname}&file={file}" + return {"message": f"Successfully published the {self.get_name()} presentation", + "links": {"presentation": present_link, "download": download_link}} + except PermissionError as err: + message = f"You do not have permission to publish this file: {str(err)}" + raise StochSSPermissionsError(message, traceback.format_exc()) from err + + def save(self, model): ''' Saves the model to an existing file From d12cd8ff3b3bf4d2e8c4478407a444efa2b25d01 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 11 Jun 2021 12:04:16 -0400 Subject: [PATCH 031/192] Generated links for presentation and download. --- stochss/handlers/util/stochss_model.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/stochss/handlers/util/stochss_model.py b/stochss/handlers/util/stochss_model.py index b884dacc95..361d138652 100644 --- a/stochss/handlers/util/stochss_model.py +++ b/stochss/handlers/util/stochss_model.py @@ -480,8 +480,8 @@ def publish_presentation(self): hostname = os.uname()[1] model = json.jumps(self.load(), sort_keys=True) file = f"{hashlib.md5(model.encode('utf-8')).hexdigest()}.mdl" # replace with gillespy2.Model.to_json - present_link = f"live.stochss.org/present-model?owner={hostname}&file={file}" - download_link = f"live.stochss.org/download_presentation?owner={hostname}&file={file}" + present_link = f"live.stochss.org/stochss/present-model?owner={hostname}&file={file}" + download_link = f"live.stochss.org/stochss/download_presentation?owner={hostname}&file={file}" return {"message": f"Successfully published the {self.get_name()} presentation", "links": {"presentation": present_link, "download": download_link}} except PermissionError as err: From 37d5bdc5a54ed3022e4d46633dd80658c14c499c Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 11 Jun 2021 12:49:34 -0400 Subject: [PATCH 032/192] Refactor the model presentation handler to load a model and presentation links, create a new model in the presentation directory and return the links. --- stochss/handlers/models.py | 24 +++++++++++++++--------- 1 file changed, 15 insertions(+), 9 deletions(-) diff --git a/stochss/handlers/models.py b/stochss/handlers/models.py index b2d5ec321d..603632aa77 100644 --- a/stochss/handlers/models.py +++ b/stochss/handlers/models.py @@ -425,13 +425,19 @@ async def get(self): self.set_header('Content-Type', 'application/json') path = self.get_query_argument(name="path") log.debug("Path to the file: %s", path) - try: - file = StochSSFile(path=path) - log.info("Publishing the %s presentation", file.get_name()) - resp = file.publish_presentation() - log.info(resp['message']) - log.debug("Response Message: %s", resp) - self.write(resp) - except StochSSAPIError as err: - report_error(self, log, err) + file_objs = {"mdl":StochSSModel, "smdl":StochSSSpatialModel} + ext = path.split(".").pop() + if ext == "mdl": + try: + model = file_objs[ext](path=path) + log.info("Publishing the %s presentation", file.get_name()) + links, data = model.publish_presentation() + presentation_model = file_objs[ext](**data) + resp = {"message": f"Successfully published the {self.get_name()} presentation", + "links": links} + log.info(resp['message']) + log.debug("Response Message: %s", resp) + self.write(resp) + except StochSSAPIError as err: + report_error(self, log, err) self.finish() From b66fd0d5ac5f9b0d02ea649a23c57937d4b5cc44 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 11 Jun 2021 12:52:34 -0400 Subject: [PATCH 033/192] Refactored the publish presentation function to generate presentation links, load the model, and generate a md5 hash file. --- stochss/handlers/util/stochss_model.py | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/stochss/handlers/util/stochss_model.py b/stochss/handlers/util/stochss_model.py index 361d138652..c9c1ceff39 100644 --- a/stochss/handlers/util/stochss_model.py +++ b/stochss/handlers/util/stochss_model.py @@ -470,20 +470,21 @@ def publish_presentation(self): present_dir = os.path.join(self.user_dir, ".presentations") if not os.path.exists(present_dir): os.mkdir(present_dir) - dst = os.path.join(present_dir, self.get_file()) - if os.path.exists(dst): - message = "A presentation with this name already exists" - raise StochSSFileExistsError(message) src = self.get_path(full=True) try: - shutil.copyfile(src, dst) + self.load() hostname = os.uname()[1] - model = json.jumps(self.load(), sort_keys=True) + model = json.jumps(self.model, sort_keys=True) file = f"{hashlib.md5(model.encode('utf-8')).hexdigest()}.mdl" # replace with gillespy2.Model.to_json + dst = os.path.join(present_dir, file) + if os.path.exists(dst): + message = "A presentation with this name already exists" + raise StochSSFileExistsError(message) present_link = f"live.stochss.org/stochss/present-model?owner={hostname}&file={file}" download_link = f"live.stochss.org/stochss/download_presentation?owner={hostname}&file={file}" - return {"message": f"Successfully published the {self.get_name()} presentation", - "links": {"presentation": present_link, "download": download_link}} + links = {"presentation": present_link, "download": download_link} + data = {"path": dst, "new":True, "model":self.model} + return links, data except PermissionError as err: message = f"You do not have permission to publish this file: {str(err)}" raise StochSSPermissionsError(message, traceback.format_exc()) from err From 3fc4d10e2ad2d97443c5120c289a2b61a8c82ffe Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 11 Jun 2021 12:54:24 -0400 Subject: [PATCH 034/192] Refactored the presentation page initialize function to pass on the ower and file query arguments to the load handler. --- client/pages/model-presentation.js | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/client/pages/model-presentation.js b/client/pages/model-presentation.js index 66f18cd24b..1d998e55c1 100644 --- a/client/pages/model-presentation.js +++ b/client/pages/model-presentation.js @@ -44,13 +44,15 @@ let ModelPresentationPage = PageView.extend({ initialize: function (attrs, options) { PageView.prototype.initialize.apply(this, arguments); let urlParams = new URLSearchParams(window.location.search); + let owner = urlParams.get("owner") + let file = urlParams.get("file"); this.model = new Model({ - directory: urlParams.get("path"), + directory: file, for: "presentation" }); let self = this; - let queryStr = "?path=" + this.model.directory; - let endpoint = path.join(); + let queryStr = "?file=" + this.model.directory + "&owner=" + owner; + let endpoint = "stochss/api/file/json-data" + queryStr; app.getXHR(endpoint, { success: function (err, response, body) { self.model.set(body); From e3db1687d1b95bd881e58812ad8f4df51c12a516 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 11 Jun 2021 12:55:57 -0400 Subject: [PATCH 035/192] Updated the page routes for the presentation pages. --- jupyterhub/jupyterhub_config.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/jupyterhub/jupyterhub_config.py b/jupyterhub/jupyterhub_config.py index aa4ef947e8..f9598a2053 100644 --- a/jupyterhub/jupyterhub_config.py +++ b/jupyterhub/jupyterhub_config.py @@ -82,8 +82,8 @@ # StochSS request handlers c.JupyterHub.extra_handlers = [ (r"/stochss\/?", HomeHandler), - (r"/stochss/job-presentation\/?", JobPresentationHandler), - (r"/stochss/model-presentation\/?", ModelPresentationHandler), + (r"/stochss/present-job\/?", JobPresentationHandler), + (r"/stochss/present-model\/?", ModelPresentationHandler), (r"/stochss/api/file/json-data\/?", JsonFileAPIHandler), (r"/stochss/api/publish/model\/?", PublishUserModel) ] From ff4e90c67dce2912f8496ea01c0bc832fa356f35 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 11 Jun 2021 13:00:48 -0400 Subject: [PATCH 036/192] Refactor the model presentation handler to load a model and presentation links, create a new model in the presentation directory and return the links. --- stochss/handlers/models.py | 25 ++++++++++++------------- 1 file changed, 12 insertions(+), 13 deletions(-) diff --git a/stochss/handlers/models.py b/stochss/handlers/models.py index 603632aa77..ff167604e5 100644 --- a/stochss/handlers/models.py +++ b/stochss/handlers/models.py @@ -427,17 +427,16 @@ async def get(self): log.debug("Path to the file: %s", path) file_objs = {"mdl":StochSSModel, "smdl":StochSSSpatialModel} ext = path.split(".").pop() - if ext == "mdl": - try: - model = file_objs[ext](path=path) - log.info("Publishing the %s presentation", file.get_name()) - links, data = model.publish_presentation() - presentation_model = file_objs[ext](**data) - resp = {"message": f"Successfully published the {self.get_name()} presentation", - "links": links} - log.info(resp['message']) - log.debug("Response Message: %s", resp) - self.write(resp) - except StochSSAPIError as err: - report_error(self, log, err) + try: + model = file_objs[ext](path=path) + log.info("Publishing the %s presentation", file.get_name()) + links, data = model.publish_presentation() + presentation_model = file_objs[ext](**data) + resp = {"message": f"Successfully published the {self.get_name()} presentation", + "links": links} + log.info(resp['message']) + log.debug("Response Message: %s", resp) + self.write(resp) + except StochSSAPIError as err: + report_error(self, log, err) self.finish() From a87dea472e46806fd09f03511e17ba0336783aa7 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 11 Jun 2021 15:09:42 -0400 Subject: [PATCH 037/192] Fixed bugs and did some pylint cleanup. --- stochss/handlers/models.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/stochss/handlers/models.py b/stochss/handlers/models.py index ff167604e5..de9c8aacf0 100644 --- a/stochss/handlers/models.py +++ b/stochss/handlers/models.py @@ -28,7 +28,7 @@ # Use finish() for json, write() for text from .util import StochSSFolder, StochSSModel, StochSSSpatialModel, StochSSNotebook, \ - StochSSFile, StochSSAPIError, report_error + StochSSAPIError, report_error log = logging.getLogger('stochss') @@ -429,9 +429,9 @@ async def get(self): ext = path.split(".").pop() try: model = file_objs[ext](path=path) - log.info("Publishing the %s presentation", file.get_name()) + log.info("Publishing the %s presentation", model.get_name()) links, data = model.publish_presentation() - presentation_model = file_objs[ext](**data) + file_objs[ext](**data) resp = {"message": f"Successfully published the {self.get_name()} presentation", "links": links} log.info(resp['message']) From be28bcdab233a744d7485213e48ee9354aea914d Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 11 Jun 2021 15:11:34 -0400 Subject: [PATCH 038/192] Finalized the return for the publish presentation function. Added missing imports. pylint cleanup. --- stochss/handlers/util/stochss_model.py | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/stochss/handlers/util/stochss_model.py b/stochss/handlers/util/stochss_model.py index c9c1ceff39..6fce11ca1d 100644 --- a/stochss/handlers/util/stochss_model.py +++ b/stochss/handlers/util/stochss_model.py @@ -19,7 +19,7 @@ import os import ast import json -import haslib +import hashlib import tempfile import traceback @@ -30,7 +30,7 @@ from .stochss_base import StochSSBase from .stochss_errors import StochSSAPIError, StochSSFileNotFoundError, FileNotJSONFormatError, \ - StochSSModelFormatError + StochSSModelFormatError, StochSSFileExistsError, StochSSPermissionsError class StochSSModel(StochSSBase): ''' @@ -470,18 +470,19 @@ def publish_presentation(self): present_dir = os.path.join(self.user_dir, ".presentations") if not os.path.exists(present_dir): os.mkdir(present_dir) - src = self.get_path(full=True) try: self.load() hostname = os.uname()[1] - model = json.jumps(self.model, sort_keys=True) - file = f"{hashlib.md5(model.encode('utf-8')).hexdigest()}.mdl" # replace with gillespy2.Model.to_json + model = json.dumps(self.model, sort_keys=True) + # replace with gillespy2.Model.to_json + file = f"{hashlib.md5(model.encode('utf-8')).hexdigest()}.mdl" dst = os.path.join(present_dir, file) if os.path.exists(dst): message = "A presentation with this name already exists" raise StochSSFileExistsError(message) - present_link = f"live.stochss.org/stochss/present-model?owner={hostname}&file={file}" - download_link = f"live.stochss.org/stochss/download_presentation?owner={hostname}&file={file}" + query_str = f"?owner={hostname}&file={file}" + present_link = f"live.stochss.org/stochss/present-model{query_str}" + download_link = f"live.stochss.org/stochss/download_presentation{query_str}" links = {"presentation": present_link, "download": download_link} data = {"path": dst, "new":True, "model":self.model} return links, data From 941e400b109acb10ec6765fcca867ddb189a958c Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 11 Jun 2021 15:14:21 -0400 Subject: [PATCH 039/192] Integrated the PublishUserModel handler code into the model presentation python file. --- jupyterhub/handlers.py | 24 ------------------------ 1 file changed, 24 deletions(-) diff --git a/jupyterhub/handlers.py b/jupyterhub/handlers.py index 3b7da6f570..b98c406d1d 100644 --- a/jupyterhub/handlers.py +++ b/jupyterhub/handlers.py @@ -37,30 +37,6 @@ async def get(self): self.finish(html) -class PublishUserModel(BaseHandler): - ''' - ################################################################################################ - Handler for copying a user model from a user container into a presentations folder - managed by jupyterhub. - ################################################################################################ - ''' - async def get(self): - pass - # Pass the username as a query parameter - # username = - # Pass the model filename as a query parameter - # filename = - client = docker.from_env() - containers = client.containers.list() - user_container = [ c in containers if c.name == f'jupyter-{username}' ][0] - user_model_path = f'/home/jovyan/.presentations/{filename}' - jupyterhub_tar_path = f'/srv/jupyterhub/.presentations/{filename}.tar' - bits, stat = user_container.get_archive(user_model_path) - with open(jupyterhub_tar_path, 'w') as tar_file: - for chunk in bits: - tar_file.write(chunk) - - class JobPresentationHandler(BaseHandler): ''' ################################################################################################ From 4ea24a085e5240fed7f11f1adf050a022a2f0d8a Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 11 Jun 2021 15:15:50 -0400 Subject: [PATCH 040/192] Removed the route for the PublishUserModel handler. --- jupyterhub/jupyterhub_config.py | 1 - 1 file changed, 1 deletion(-) diff --git a/jupyterhub/jupyterhub_config.py b/jupyterhub/jupyterhub_config.py index f9598a2053..10f2594d4f 100644 --- a/jupyterhub/jupyterhub_config.py +++ b/jupyterhub/jupyterhub_config.py @@ -85,7 +85,6 @@ (r"/stochss/present-job\/?", JobPresentationHandler), (r"/stochss/present-model\/?", ModelPresentationHandler), (r"/stochss/api/file/json-data\/?", JsonFileAPIHandler), - (r"/stochss/api/publish/model\/?", PublishUserModel) ] ## Paths to search for jinja templates, before using the default templates. From f45ecfbc6b047d3486dabb9c809f97e54254ea84 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 11 Jun 2021 15:21:55 -0400 Subject: [PATCH 041/192] Created a function to execute the docker commands to the get the presentation model from the user container. Added functions to extract the model presentation from the tar bits returned from the get_archive function. Refactored the StochSSModel and StochSSSpatialModel classes fit the new presentation functionality. --- jupyterhub/model_presentation.py | 98 +++++++++++++++++++------------- 1 file changed, 57 insertions(+), 41 deletions(-) diff --git a/jupyterhub/model_presentation.py b/jupyterhub/model_presentation.py index 3c5108f57a..7dfaaeb423 100644 --- a/jupyterhub/model_presentation.py +++ b/jupyterhub/model_presentation.py @@ -16,10 +16,14 @@ along with this program. If not, see . ''' +import os import ast import json import logging -import traceback +import tarfile +import tempfile + +import docker from tornado import web from notebook.base.handlers import APIHandler # APIHandler documentation: @@ -27,9 +31,7 @@ # Note APIHandler.finish() sets Content-Type handler to 'application/json' # Use finish() for json, write() for text -from presentation_base import StochSSBase -from presentation_error import StochSSAPIError, report_error, \ - StochSSFileNotFoundError, FileNotJSONFormatError +from presentation_error import StochSSAPIError, report_error log = logging.getLogger('stochss') @@ -52,54 +54,72 @@ async def get(self): Attributes ---------- ''' - purpose = self.get_query_argument(name="for") - log.debug("Purpose of the handler: %s", purpose) - path = self.get_query_argument(name="path") - log.debug("Path to the file: %s", path) + owner = self.get_query_argument(name="owner") + log.debug("Container id of the owner: %s", owner) + file = self.get_query_argument(name="file") + log.debug("Name to the file: %s", file) self.set_header('Content-Type', 'application/json') file_objs = {"mdl":StochSSModel, "smdl":StochSSSpatialModel} - ext = path.split(".").pop() + ext = file.split(".").pop() try: - file = file_objs[ext](path=path) - data = file.load() - log.debug("Contents of the json file: %s", data) - file.print_logs(log) - self.write(data) + model = get_presentation_from_user(owner=owner, file=file) + file_obj = file_objs[ext](model=model) + model = file_obj.load() + log.debug("Contents of the json file: %s", model) + file_obj.print_logs(log) + self.write(model) except StochSSAPIError as load_err: report_error(self, log, load_err) self.finish() -def __read_model_file(model): - try: - with open(model.get_path(full=True), "r") as mdl_file: - return json.load(mdl_file) - except FileNotFoundError as err: - message = f"Could not find the model file: {str(err)}" - 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()) from err - - -class StochSSModel(StochSSBase): +def get_presentation_from_user(owner, file): + ''' + Get the model presentation from the users container + + Attributes + ---------- + owner : str + Hostname of the user container + file : str + Name of the model presentation file + ''' + client = docker.from_env() + containers = client.containers.list() + user_container = list(filter(lambda container: container.id.startswith(owner), + containers))[0] + user_model_path = f'/home/jovyan/.presentations/{file}' + tar_mdl = tempfile.TemporaryFile() + bits, _ = user_container.get_archive(user_model_path) + for chunk in bits: + tar_mdl.write(chunk) + tar_mdl.seek(0) + tar_file = tarfile.TarFile(fileobj=tar_mdl) + tmp_dir = tempfile.TemporaryDirectory() + tar_file.extractall(tmp_dir.name) + tar_mdl.close() + mdl_path = os.path.join(tmp_dir.name, file) + with open(mdl_path, "r") as mdl_file: + return json.load(mdl_file) + + +class StochSSModel(): ''' ################################################################################################ StochSS model object ################################################################################################ ''' - def __init__(self, path): + def __init__(self, model): ''' Intitialize a model object Attributes ---------- - path : str - Path to the model + model : dict + Existing model data ''' - super().__init__(path=path) - self.model = __read_model_file(self) + self.model = model @classmethod @@ -186,29 +206,26 @@ 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 -class StochSSSpatialModel(StochSSBase): +class StochSSSpatialModel(): ''' ################################################################################################ StochSS spatial model object ################################################################################################ ''' - def __init__(self, path): + def __init__(self, model): ''' Intitialize a spatial model object Attributes ---------- - path : str - Path to the spatial model + model : dict + Existing model data ''' - super().__init__(path=path) - self.model = __read_model_file(self) + self.model = model def load(self): @@ -218,7 +235,6 @@ def load(self): Attributes ---------- ''' - self.model['name'] = self.get_name() if not self.model['defaultMode']: self.model['defaultMode'] = "discrete" if "static" not in self.model['domain'].keys(): From b4d26dcb63ed0eb0565f01e939299232089c7871 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 11 Jun 2021 15:35:42 -0400 Subject: [PATCH 042/192] removed the presentation buttons for local deployments of stochss. removed the model presentation button for spatial models. disabled the job presentation button. --- client/views/model-state-buttons.js | 3 +++ client/views/workflow-results.js | 4 ++++ 2 files changed, 7 insertions(+) diff --git a/client/views/model-state-buttons.js b/client/views/model-state-buttons.js index 79fc02b4bb..90474e6534 100644 --- a/client/views/model-state-buttons.js +++ b/client/views/model-state-buttons.js @@ -50,6 +50,9 @@ module.exports = View.extend({ if(this.model.is_spatial) { $(this.queryByHook("stochss-es")).addClass("disabled"); $(this.queryByHook("stochss-ps")).addClass("disabled"); + $(this.queryByHook("presentation")).css("display", "none"); + }else if(app.getBasePath() === "/") { + $(this.queryByHook("presentation")).css("display", "none"); } }, clickSaveHandler: function (e) { diff --git a/client/views/workflow-results.js b/client/views/workflow-results.js index 2dc10c1d3a..6fe988d7cb 100644 --- a/client/views/workflow-results.js +++ b/client/views/workflow-results.js @@ -75,6 +75,10 @@ module.exports = View.extend({ if(!isParameterScan){ $(this.queryByHook("convert-to-notebook")).css("display", "none"); } + }else if(app.getBasePath() === "/") { + $(this.queryByHook("job-presentation")).css("display", "none"); + }else{ + $(this.queryByHook("job-presentation")).prop("disabled", true); } if(this.parent.model.type === "Ensemble Simulation") { var type = isEnsemble ? "stddevran" : "trajectories"; From 2bcb890a54c514da71ebcd76295173d46f828c4d Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 11 Jun 2021 15:53:24 -0400 Subject: [PATCH 043/192] Created a model to present the presentation links to the user. --- client/modals.js | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/client/modals.js b/client/modals.js index c55db1f6b8..3c9ef0f7de 100644 --- a/client/modals.js +++ b/client/modals.js @@ -223,6 +223,30 @@ let templates = { ` + }, + presentationLinks : (modalID, title, name, headers, links) => { + return ` + ` } } @@ -530,5 +554,10 @@ module.exports = { ` + }, + presentationLinks : (title, name, headers, links) => { + let modalID = "presentationLinksModal" + + return templates.presentationLinks(modalID, title, name, headers, links); } } \ No newline at end of file From 6e31d9d570e3233c53f351984ec29e94ad64e2e9 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 11 Jun 2021 15:54:35 -0400 Subject: [PATCH 044/192] Added function to launch the presentation links modal when publishing is successful. --- client/views/model-state-buttons.js | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/client/views/model-state-buttons.js b/client/views/model-state-buttons.js index 90474e6534..6ab8276c85 100644 --- a/client/views/model-state-buttons.js +++ b/client/views/model-state-buttons.js @@ -307,6 +307,11 @@ module.exports = View.extend({ app.getXHR(endpoint, { success: function (err, response, body) { self.endAction("publish"); + let title = body.message; + let linkHeaders = ["Presentation Link", "Download Link"]; + let links = body.links; + let name = self.model.name + $(modals.presentationLinks(title, name, linkHeaders, links)).modal(); }, error: function (err, response, body) { self.errorAction(); From 6bb685e7f40f01a2b33fc643271092ccd645210c Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Sun, 13 Jun 2021 12:35:04 -0400 Subject: [PATCH 045/192] Added the download api handler for model presentations. --- jupyterhub/model_presentation.py | 38 +++++++++++++++++++++++++++----- 1 file changed, 33 insertions(+), 5 deletions(-) diff --git a/jupyterhub/model_presentation.py b/jupyterhub/model_presentation.py index 7dfaaeb423..1b31cd41db 100644 --- a/jupyterhub/model_presentation.py +++ b/jupyterhub/model_presentation.py @@ -40,16 +40,13 @@ class JsonFileAPIHandler(APIHandler): ''' ################################################################################################ - Base Handler for interacting with Model file Get/Post Requests and - downloading json formatted files. + Base Handler for getting model presentations from user containers. ################################################################################################ ''' @web.authenticated async def get(self): ''' - Retrieve model data from User's file system if it exists and - create new models using a model template if they don't. Also - retrieves JSON files for download. + Load the model presentation from User's presentations directory. Attributes ---------- @@ -73,6 +70,37 @@ async def get(self): self.finish() +class DownModelPresentationAPIHandler(APIHandler): + ''' + ################################################################################################ + Base Handler for downloading model presentations from user containers. + ################################################################################################ + ''' + @web.authenticated + async def get(self): + ''' + Download the model presentation from User's presentations directory. + + Attributes + ---------- + ''' + owner = self.get_query_argument(name="owner") + log.debug("Container id of the owner: %s", owner) + file = self.get_query_argument(name="file") + log.debug("Name to the file: %s", file) + self.set_header('Content-Type', 'application/json') + file_objs = {"mdl":StochSSModel, "smdl":StochSSSpatialModel} + ext = file.split(".").pop() + try: + model = get_presentation_from_user(owner=owner, file=file) + self.set_header('Content-Disposition', f'attachment; filename="{model["name"]}.{ext}"') + log.debug("Contents of the json file: %s", model) + self.write(model) + except StochSSAPIError as load_err: + report_error(self, log, load_err) + self.finish() + + def get_presentation_from_user(owner, file): ''' Get the model presentation from the users container From c7a3716317af79cf375933c263effddae74b818f Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Sun, 13 Jun 2021 12:45:18 -0400 Subject: [PATCH 046/192] Refactored the download model presentation link to use link args instead of query paramters. Added route for downloding presentations. --- jupyterhub/jupyterhub_config.py | 1 + jupyterhub/model_presentation.py | 4 +--- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/jupyterhub/jupyterhub_config.py b/jupyterhub/jupyterhub_config.py index 10f2594d4f..1b2626b315 100644 --- a/jupyterhub/jupyterhub_config.py +++ b/jupyterhub/jupyterhub_config.py @@ -85,6 +85,7 @@ (r"/stochss/present-job\/?", JobPresentationHandler), (r"/stochss/present-model\/?", ModelPresentationHandler), (r"/stochss/api/file/json-data\/?", JsonFileAPIHandler), + (r"/stochss/presentation-download/(\w+)/(.+)\/?", DownModelPresentationAPIHandler) ] ## Paths to search for jinja templates, before using the default templates. diff --git a/jupyterhub/model_presentation.py b/jupyterhub/model_presentation.py index 1b31cd41db..4a3b490e8f 100644 --- a/jupyterhub/model_presentation.py +++ b/jupyterhub/model_presentation.py @@ -77,16 +77,14 @@ class DownModelPresentationAPIHandler(APIHandler): ################################################################################################ ''' @web.authenticated - async def get(self): + async def get(self, owner, file): ''' Download the model presentation from User's presentations directory. Attributes ---------- ''' - owner = self.get_query_argument(name="owner") log.debug("Container id of the owner: %s", owner) - file = self.get_query_argument(name="file") log.debug("Name to the file: %s", file) self.set_header('Content-Type', 'application/json') file_objs = {"mdl":StochSSModel, "smdl":StochSSSpatialModel} From e62dd35bf0cc6e731cecd9069054fba32cf2f2cf Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Sun, 13 Jun 2021 14:19:26 -0400 Subject: [PATCH 047/192] Added missing import. Pylint fixes. --- jupyterhub/jupyterhub_config.py | 2 +- jupyterhub/model_presentation.py | 3 +-- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/jupyterhub/jupyterhub_config.py b/jupyterhub/jupyterhub_config.py index 1b2626b315..64c02e7605 100644 --- a/jupyterhub/jupyterhub_config.py +++ b/jupyterhub/jupyterhub_config.py @@ -28,7 +28,7 @@ # Page handlers from handlers import * # API Handlers -from model_presentation import JsonFileAPIHandler +from model_presentation import JsonFileAPIHandler, DownModelPresentationAPIHandler ## Class for authenticating users. # diff --git a/jupyterhub/model_presentation.py b/jupyterhub/model_presentation.py index 4a3b490e8f..a8e52ea197 100644 --- a/jupyterhub/model_presentation.py +++ b/jupyterhub/model_presentation.py @@ -87,10 +87,9 @@ async def get(self, owner, file): log.debug("Container id of the owner: %s", owner) log.debug("Name to the file: %s", file) self.set_header('Content-Type', 'application/json') - file_objs = {"mdl":StochSSModel, "smdl":StochSSSpatialModel} - ext = file.split(".").pop() try: model = get_presentation_from_user(owner=owner, file=file) + ext = file.split(".").pop() self.set_header('Content-Disposition', f'attachment; filename="{model["name"]}.{ext}"') log.debug("Contents of the json file: %s", model) self.write(model) From bf56951a8b4c0ee5a1a288b5ad875906dfc1cf54 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Sun, 13 Jun 2021 14:23:34 -0400 Subject: [PATCH 048/192] Open links are now generated when presentations are published. --- stochss/handlers/util/stochss_model.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/stochss/handlers/util/stochss_model.py b/stochss/handlers/util/stochss_model.py index 6fce11ca1d..63a620074c 100644 --- a/stochss/handlers/util/stochss_model.py +++ b/stochss/handlers/util/stochss_model.py @@ -482,8 +482,10 @@ def publish_presentation(self): raise StochSSFileExistsError(message) query_str = f"?owner={hostname}&file={file}" present_link = f"live.stochss.org/stochss/present-model{query_str}" - download_link = f"live.stochss.org/stochss/download_presentation{query_str}" - links = {"presentation": present_link, "download": download_link} + download_link = os.path.join("live.stochss.org/stochss/download_presentation", + hostname, file) + open_link = f"live.stochss.org?open={download_link}" + links = {"presentation": present_link, "download": download_link, "open": open_link} data = {"path": dst, "new":True, "model":self.model} return links, data except PermissionError as err: From cb3e33c122f36aa99d9ead0623df31c9a3a74c82 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Sun, 13 Jun 2021 14:42:05 -0400 Subject: [PATCH 049/192] Fixed issue with generating the response message. --- stochss/handlers/models.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/stochss/handlers/models.py b/stochss/handlers/models.py index de9c8aacf0..bca85af6ac 100644 --- a/stochss/handlers/models.py +++ b/stochss/handlers/models.py @@ -432,7 +432,7 @@ async def get(self): log.info("Publishing the %s presentation", model.get_name()) links, data = model.publish_presentation() file_objs[ext](**data) - resp = {"message": f"Successfully published the {self.get_name()} presentation", + resp = {"message": f"Successfully published the {model.get_name()} presentation", "links": links} log.info(resp['message']) log.debug("Response Message: %s", resp) From d171b52fca7dba1688713e9150499a2cebd1f843 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Sun, 13 Jun 2021 14:43:38 -0400 Subject: [PATCH 050/192] Added the open link block to the success modal and updated the styling. --- client/modals.js | 8 ++++++-- client/views/model-state-buttons.js | 10 +++++----- 2 files changed, 11 insertions(+), 7 deletions(-) diff --git a/client/modals.js b/client/modals.js index 3c9ef0f7de..aad8b627af 100644 --- a/client/modals.js +++ b/client/modals.js @@ -236,10 +236,14 @@ let templates = {
-

${headers[0]}

+

${headers[0]}

Open ${name} Presentation -

${headers[1]}

+
+

${headers[1]}

Download ${name} Presentation +
+

${headers[2]}

+ Open ${name} Presentation
diff --git a/client/views/model-state-buttons.js b/client/views/model-state-buttons.js index 6ab8276c85..b115684387 100644 --- a/client/views/model-state-buttons.js +++ b/client/views/model-state-buttons.js @@ -50,10 +50,10 @@ module.exports = View.extend({ if(this.model.is_spatial) { $(this.queryByHook("stochss-es")).addClass("disabled"); $(this.queryByHook("stochss-ps")).addClass("disabled"); - $(this.queryByHook("presentation")).css("display", "none"); - }else if(app.getBasePath() === "/") { - $(this.queryByHook("presentation")).css("display", "none"); - } + // $(this.queryByHook("presentation")).css("display", "none"); + }//else if(app.getBasePath() === "/") { + // $(this.queryByHook("presentation")).css("display", "none"); + // } }, clickSaveHandler: function (e) { let self = this; @@ -308,7 +308,7 @@ module.exports = View.extend({ success: function (err, response, body) { self.endAction("publish"); let title = body.message; - let linkHeaders = ["Presentation Link", "Download Link"]; + let linkHeaders = ["Presentation Link", "Download Link", "Open Link"]; let links = body.links; let name = self.model.name $(modals.presentationLinks(title, name, linkHeaders, links)).modal(); From b788291be79d3c9d32a5362c44e974d6abaf4890 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Sun, 13 Jun 2021 14:48:30 -0400 Subject: [PATCH 051/192] un-commented the checks that disable the publish presentation button. --- client/views/model-state-buttons.js | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/client/views/model-state-buttons.js b/client/views/model-state-buttons.js index b115684387..01d1283f75 100644 --- a/client/views/model-state-buttons.js +++ b/client/views/model-state-buttons.js @@ -50,10 +50,10 @@ module.exports = View.extend({ if(this.model.is_spatial) { $(this.queryByHook("stochss-es")).addClass("disabled"); $(this.queryByHook("stochss-ps")).addClass("disabled"); - // $(this.queryByHook("presentation")).css("display", "none"); - }//else if(app.getBasePath() === "/") { - // $(this.queryByHook("presentation")).css("display", "none"); - // } + $(this.queryByHook("presentation")).css("display", "none"); + }else if(app.getBasePath() === "/") { + $(this.queryByHook("presentation")).css("display", "none"); + } }, clickSaveHandler: function (e) { let self = this; From f57b24674b52cdaf556dd0b685dac0ca4096f768 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Sun, 13 Jun 2021 15:45:51 -0400 Subject: [PATCH 052/192] Refactored the upload from link function to allow it to upload presentations. --- stochss/handlers/util/stochss_folder.py | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/stochss/handlers/util/stochss_folder.py b/stochss/handlers/util/stochss_folder.py index 20841e4557..e18356ff58 100644 --- a/stochss/handlers/util/stochss_folder.py +++ b/stochss/handlers/util/stochss_folder.py @@ -19,9 +19,10 @@ import os import json import shutil -from urllib import request import traceback +import requests + from .stochss_base import StochSSBase from .stochss_file import StochSSFile from .stochss_model import StochSSModel @@ -442,17 +443,20 @@ def upload_from_link(self, remote_path): remote_path : str Path to the remote file ''' - response = request.urlopen(remote_path) - file = self.get_file(path=remote_path) + ext = remote_path.split('.').pop() + body = requests.get(remote_path, allow_redirects=True).content + if "presentation-download" in remote_path: + file = f"{json.loads(body)['name']}.{ext}" + else: + file = self.get_file(path=remote_path) path = self.get_new_path(dst_path=file) if os.path.exists(path): message = f"Could not upload this file as {file} already exists" return {"message":message, "reason":"File Already Exists"} try: file_types = {"mdl":"model", "smdl":"model", "sbml":"sbml"} - ext = file.split('.').pop() file_type = file_types[ext] if ext in file_types.keys() else "file" - _ = self.upload(file_type=file_type, file=file, body=response.read()) + _ = self.upload(file_type=file_type, file=file, body=body) new_path = self.__get_rmt_upld_path(file=file) message = f"Successfully uploaded the file {file} to {new_path}" return {"message":message, "file_path":new_path} From 92340d0e74a3d172adf69123eeeef42e397c21fe Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Sun, 13 Jun 2021 15:51:58 -0400 Subject: [PATCH 053/192] Updated the model-presentation page to work with the new parameters viewer. --- client/pages/model-presentation.js | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/client/pages/model-presentation.js b/client/pages/model-presentation.js index 1d998e55c1..df8a321232 100644 --- a/client/pages/model-presentation.js +++ b/client/pages/model-presentation.js @@ -30,7 +30,7 @@ let Rules = require('../views/rules-viewer'); let Events = require('../views/events-viewer'); let Species = require('../views/species-viewer'); let Reactions = require('../views/reactions-viewer'); -let Parameters = require('../views/parameters-viewer'); +let Parameters = require('../views/parameters-editor'); let SBMLComponents = require('../views/sbml-component-editor'); //templates let template = require('../templates/pages/modelPresentation.pug'); @@ -78,7 +78,8 @@ let ModelPresentationPage = PageView.extend({ }, renderParametersContainer: function () { let parameters = new Parameters({ - collection: this.model.parameters + collection: this.model.parameters, + readOnly: true }); app.registerRenderSubview(this, parameters, "model-parameters"); }, From bcbb103d332b5af9e7df4c403657efd68cf63da8 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 18 Jun 2021 14:20:49 -0400 Subject: [PATCH 054/192] Updated the jupyterhub page templates to remove the duplicated head and body tags. --- client/templates/pages/home.pug | 81 +++++++++----------- client/templates/pages/jobPresentation.pug | 11 +-- client/templates/pages/modelPresentation.pug | 11 +-- jupyterhub/home_template.pug | 4 + 4 files changed, 42 insertions(+), 65 deletions(-) diff --git a/client/templates/pages/home.pug b/client/templates/pages/home.pug index 49b2d48185..8b73387efb 100644 --- a/client/templates/pages/home.pug +++ b/client/templates/pages/home.pug @@ -1,58 +1,49 @@ -html +section.page + div#home-wrapper.container.card.card-body + + div.logo(id="stochss-logo" data-hook="stochss-logo") + img(src="/hub/static/stochss-logo.png") - head - meta(charset="utf-8") - title StochSS: Stochastic Simulation Service - meta(name="viewport", content="width=device-width, initial-scale=1.0") - meta(name="description", content="") - meta(name="author", content="") + div.centered + h1.display-5 Welcome to StochSS Live! - body - div#home-wrapper.container.card.card-body - - div.logo(id="stochss-logo" data-hook="stochss-logo") - img(src="/hub/static/stochss-logo.png") + p.home-p + | An accessible platform for modeling mathematical, biological, and biochemical systems. - div.centered - h1.display-5 Welcome to StochSS Live! + div.row.home-highlights + div.col-md-2 + div.col-md-5 - p.home-p - | An accessible platform for modeling mathematical, biological, and biochemical systems. + h5 Features + ul.home-list + li Discrete Stochastic Modeling + li Continuous ODE Modeling + li Convert Between Stochastic and ODE Models + li Import SBML Models + li Parameter Sweep Workflows + li Spatial Simulations + + div.col-md-5 - div.row.home-highlights - div.col-md-2 - div.col-md-5 + h5 Coming soon... + ul.home-list + li Sciope Integration + li Bring Your Own Cloud - h5 Features - ul.home-list - li Discrete Stochastic Modeling - li Continuous ODE Modeling - li Convert Between Stochastic and ODE Models - li Import SBML Models - li Parameter Sweep Workflows - li Spatial Simulations - - div.col-md-5 + div.centered + a.try-stochss-btn.btn.btn-primary.box-shadow(href="/hub/spawn" role="button") Click here to login - h5 Coming soon... - ul.home-list - li Sciope Integration - li Bring Your Own Cloud + div#registration-home.container.card.card-body - div.centered - a.try-stochss-btn.btn.btn-primary.box-shadow(href="/hub/spawn" role="button") Click here to login + div.centered - div#registration-home.container.card.card-body + p.home-p + | StochSS is open-source software. To obtain continued funding for sustained development, we must show that StochSS is making an impact in the scientific community. For this, we need to know who is using the software, and a bit about what they are using it for. Please consider registering StochSS to show your support. - div.centered + div.collapse(data-hook="registration-link") - p.home-p - | StochSS is open-source software. To obtain continued funding for sustained development, we must show that StochSS is making an impact in the scientific community. For this, we need to know who is using the software, and a bit about what they are using it for. Please consider registering StochSS to show your support. + button.btn.btn-primary.box-shadow(data-hook="registration-link-button" style="margin: 1.5rem;") Register Stochss - div.collapse(data-hook="registration-link") + div.collapse.show(data-hook="registration-form" id="registration-form") - button.btn.btn-primary.box-shadow(data-hook="registration-link-button" style="margin: 1.5rem;") Register Stochss - - div.collapse.show(data-hook="registration-form" id="registration-form") - - iframe(src="https://docs.google.com/forms/d/12tAH4f8CJ-3F-lK44Q9uQHFio_mGoK0oY829q5lD7i4/viewform?embedded=true" width="100%" height="800" frameborder="0") + iframe(src="https://docs.google.com/forms/d/12tAH4f8CJ-3F-lK44Q9uQHFio_mGoK0oY829q5lD7i4/viewform?embedded=true" width="100%" height="800" frameborder="0") diff --git a/client/templates/pages/jobPresentation.pug b/client/templates/pages/jobPresentation.pug index bd2980d202..34e51b0375 100644 --- a/client/templates/pages/jobPresentation.pug +++ b/client/templates/pages/jobPresentation.pug @@ -1,13 +1,4 @@ -html - - head - meta(charset="utf-8") - title StochSS: Stochastic Simulation Service - meta(name="viewport", content="width=device-width, initial-scale=1.0") - meta(name="description", content="") - meta(name="author", content="") - - body +section.page div#job-presentation.container diff --git a/client/templates/pages/modelPresentation.pug b/client/templates/pages/modelPresentation.pug index 65b571444c..0edbe87293 100644 --- a/client/templates/pages/modelPresentation.pug +++ b/client/templates/pages/modelPresentation.pug @@ -1,13 +1,4 @@ -html - - head - meta(charset="utf-8") - title StochSS: Stochastic Simulation Service - meta(name="viewport", content="width=device-width, initial-scale=1.0") - meta(name="description", content="") - meta(name="author", content="") - - body +section.page div#model-presentation.container diff --git a/jupyterhub/home_template.pug b/jupyterhub/home_template.pug index 8558e61851..334896fd28 100644 --- a/jupyterhub/home_template.pug +++ b/jupyterhub/home_template.pug @@ -5,6 +5,10 @@ html head meta(charset="UTF-8") link(rel="stylesheet", href="https://cdnjs.cloudflare.com/ajax/libs/jstree/3.3.8/themes/default/style.min.css") + title StochSS: Stochastic Simulation Service + meta(name="viewport", content="width=device-width, initial-scale=1.0") + meta(name="description", content="") + meta(name="author", content="") body script(type="text/javascript", src=bundleUrl) script(type="text/javascript", src=commonBundleUrl) From 1b9edd8c75534b0972b6d15fc62459f2f6be8ac5 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 18 Jun 2021 14:46:59 -0400 Subject: [PATCH 055/192] Fixed the endpoint for the model presentation load api handler. --- client/pages/model-presentation.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/client/pages/model-presentation.js b/client/pages/model-presentation.js index df8a321232..02dd4f2806 100644 --- a/client/pages/model-presentation.js +++ b/client/pages/model-presentation.js @@ -52,7 +52,7 @@ let ModelPresentationPage = PageView.extend({ }); let self = this; let queryStr = "?file=" + this.model.directory + "&owner=" + owner; - let endpoint = "stochss/api/file/json-data" + queryStr; + let endpoint = "api/file/json-data" + queryStr; app.getXHR(endpoint, { success: function (err, response, body) { self.model.set(body); From 0073f7393c70a1ba64091d8eeecabbf6f853d654 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 18 Jun 2021 15:30:13 -0400 Subject: [PATCH 056/192] Fixed the links for model presentations. --- stochss/handlers/util/stochss_model.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/stochss/handlers/util/stochss_model.py b/stochss/handlers/util/stochss_model.py index 63a620074c..2bf31060b1 100644 --- a/stochss/handlers/util/stochss_model.py +++ b/stochss/handlers/util/stochss_model.py @@ -481,10 +481,10 @@ def publish_presentation(self): message = "A presentation with this name already exists" raise StochSSFileExistsError(message) query_str = f"?owner={hostname}&file={file}" - present_link = f"live.stochss.org/stochss/present-model{query_str}" - download_link = os.path.join("live.stochss.org/stochss/download_presentation", + present_link = f"https://live.stochss.org/stochss/present-model{query_str}" + download_link = os.path.join("https://live.stochss.org/stochss/download_presentation", hostname, file) - open_link = f"live.stochss.org?open={download_link}" + open_link = f"https://live.stochss.org?open={download_link}" links = {"presentation": present_link, "download": download_link, "open": open_link} data = {"path": dst, "new":True, "model":self.model} return links, data From 280a750cca02b57c709d12111c7a169dd932006a Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 18 Jun 2021 15:35:56 -0400 Subject: [PATCH 057/192] Set the to true to allow the notebook container to get the published model. --- jupyterhub/jupyterhub_config.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/jupyterhub/jupyterhub_config.py b/jupyterhub/jupyterhub_config.py index 64c02e7605..372a435067 100644 --- a/jupyterhub/jupyterhub_config.py +++ b/jupyterhub/jupyterhub_config.py @@ -415,6 +415,8 @@ def post_stop_hook(spawner): # Defaults to an empty set, in which case no user has admin access. c.Authenticator.admin_users = admin = set([]) +c.NotebookApp.allow_remote_access = True + pwd = os.path.dirname(__file__) with open(os.path.join(pwd, 'userlist')) as f: for line in f: From 17294f8c546c14bf5793037e59630032210f8cc5 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 18 Jun 2021 16:08:03 -0400 Subject: [PATCH 058/192] Added addition config to test 403 fix. --- jupyterhub/jupyterhub_config.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/jupyterhub/jupyterhub_config.py b/jupyterhub/jupyterhub_config.py index 372a435067..4c79532484 100644 --- a/jupyterhub/jupyterhub_config.py +++ b/jupyterhub/jupyterhub_config.py @@ -415,6 +415,8 @@ def post_stop_hook(spawner): # Defaults to an empty set, in which case no user has admin access. c.Authenticator.admin_users = admin = set([]) +c.NotebookApp.allow_origin = "*" +c.NotebookApp.ip = "0.0.0.0" c.NotebookApp.allow_remote_access = True pwd = os.path.dirname(__file__) From 0a1632ac0153c174229521b7377d80101209e9cc Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 18 Jun 2021 16:40:17 -0400 Subject: [PATCH 059/192] Moved new config lines to the jupyter notebook config file. --- jupyter_notebook_config.py | 4 ++++ jupyterhub/jupyterhub_config.py | 4 ---- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/jupyter_notebook_config.py b/jupyter_notebook_config.py index 66b8ea4bad..a3517f56f1 100644 --- a/jupyter_notebook_config.py +++ b/jupyter_notebook_config.py @@ -53,6 +53,10 @@ ## The default URL to redirect to from `/` c.NotebookApp.default_url = '/stochss/home' +# c.NotebookApp.allow_origin = "*" +# c.NotebookApp.ip = "0.0.0.0" +c.NotebookApp.allow_remote_access = True + #------------------------------------------------------------------------------ # KernelManager(ConnectionFileMixin) configuration #------------------------------------------------------------------------------ diff --git a/jupyterhub/jupyterhub_config.py b/jupyterhub/jupyterhub_config.py index 4c79532484..64c02e7605 100644 --- a/jupyterhub/jupyterhub_config.py +++ b/jupyterhub/jupyterhub_config.py @@ -415,10 +415,6 @@ def post_stop_hook(spawner): # Defaults to an empty set, in which case no user has admin access. c.Authenticator.admin_users = admin = set([]) -c.NotebookApp.allow_origin = "*" -c.NotebookApp.ip = "0.0.0.0" -c.NotebookApp.allow_remote_access = True - pwd = os.path.dirname(__file__) with open(os.path.join(pwd, 'userlist')) as f: for line in f: From e4937837319be565ab4bcd814274f26daefadfbf Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Mon, 21 Jun 2021 08:21:38 -0400 Subject: [PATCH 060/192] Refactored the jupyter notebook config to test fix for model presentations. --- jupyter_notebook_config.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/jupyter_notebook_config.py b/jupyter_notebook_config.py index a3517f56f1..a05cc36f84 100644 --- a/jupyter_notebook_config.py +++ b/jupyter_notebook_config.py @@ -53,8 +53,8 @@ ## The default URL to redirect to from `/` c.NotebookApp.default_url = '/stochss/home' -# c.NotebookApp.allow_origin = "*" -# c.NotebookApp.ip = "0.0.0.0" +c.NotebookApp.allow_origin = "*" +c.NotebookApp.ip = "0.0.0.0" c.NotebookApp.allow_remote_access = True #------------------------------------------------------------------------------ From a6935dca4f5f968dd20b68992597eb6e4c99dd90 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Mon, 21 Jun 2021 09:17:18 -0400 Subject: [PATCH 061/192] Set logger for debug. --- jupyterhub/model_presentation.py | 1 + 1 file changed, 1 insertion(+) diff --git a/jupyterhub/model_presentation.py b/jupyterhub/model_presentation.py index a8e52ea197..262f366ae8 100644 --- a/jupyterhub/model_presentation.py +++ b/jupyterhub/model_presentation.py @@ -51,6 +51,7 @@ async def get(self): Attributes ---------- ''' + log.setLevel(logging.DEBUG) owner = self.get_query_argument(name="owner") log.debug("Container id of the owner: %s", owner) file = self.get_query_argument(name="file") From bd31c26c8272878cad3e1868c89a789941935b76 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Mon, 21 Jun 2021 15:36:55 -0400 Subject: [PATCH 062/192] Removed the added config lines for permissions fix attempt. --- jupyter_notebook_config.py | 4 ---- 1 file changed, 4 deletions(-) diff --git a/jupyter_notebook_config.py b/jupyter_notebook_config.py index a05cc36f84..66b8ea4bad 100644 --- a/jupyter_notebook_config.py +++ b/jupyter_notebook_config.py @@ -53,10 +53,6 @@ ## The default URL to redirect to from `/` c.NotebookApp.default_url = '/stochss/home' -c.NotebookApp.allow_origin = "*" -c.NotebookApp.ip = "0.0.0.0" -c.NotebookApp.allow_remote_access = True - #------------------------------------------------------------------------------ # KernelManager(ConnectionFileMixin) configuration #------------------------------------------------------------------------------ From 0fbdb2f28ff983e7cba1bcd050103af0f588bd26 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Mon, 21 Jun 2021 15:38:42 -0400 Subject: [PATCH 063/192] Removed the web.authenticate decorators. --- jupyterhub/model_presentation.py | 3 --- 1 file changed, 3 deletions(-) diff --git a/jupyterhub/model_presentation.py b/jupyterhub/model_presentation.py index 262f366ae8..d32b800ffa 100644 --- a/jupyterhub/model_presentation.py +++ b/jupyterhub/model_presentation.py @@ -24,7 +24,6 @@ import tempfile import docker -from tornado import web from notebook.base.handlers import APIHandler # APIHandler documentation: # https://github.com/jupyter/notebook/blob/master/notebook/base/handlers.py#L583 @@ -43,7 +42,6 @@ class JsonFileAPIHandler(APIHandler): Base Handler for getting model presentations from user containers. ################################################################################################ ''' - @web.authenticated async def get(self): ''' Load the model presentation from User's presentations directory. @@ -77,7 +75,6 @@ class DownModelPresentationAPIHandler(APIHandler): Base Handler for downloading model presentations from user containers. ################################################################################################ ''' - @web.authenticated async def get(self, owner, file): ''' Download the model presentation from User's presentations directory. From 4337e606d608aa94a86b59240c601c0040d61fca Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Mon, 21 Jun 2021 15:41:23 -0400 Subject: [PATCH 064/192] Updated the species viewer to use the species editor in read only mode. --- client/pages/model-presentation.js | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/client/pages/model-presentation.js b/client/pages/model-presentation.js index 02dd4f2806..198c758bd7 100644 --- a/client/pages/model-presentation.js +++ b/client/pages/model-presentation.js @@ -28,8 +28,8 @@ let Model = require('../models/model'); let PageView = require('./base'); let Rules = require('../views/rules-viewer'); let Events = require('../views/events-viewer'); -let Species = require('../views/species-viewer'); -let Reactions = require('../views/reactions-viewer'); +let Species = require('../views/species-editor'); +let Reactions = require('../views/reactions-editor'); let Parameters = require('../views/parameters-editor'); let SBMLComponents = require('../views/sbml-component-editor'); //templates @@ -85,7 +85,8 @@ let ModelPresentationPage = PageView.extend({ }, renderReactionsContainer: function () { let reactions = new Reactions({ - collection: this.model.reactions + collection: this.model.reactions, + readOnly: true }); app.registerRenderSubview(this, reactions, "model-reactions"); }, @@ -104,7 +105,8 @@ let ModelPresentationPage = PageView.extend({ }, renderSpeciesContainer: function () { let species = new Species({ - collection: this.model.species + collection: this.model.species, + readOnly: true }); app.registerRenderSubview(this, species, "model-species"); } From 394e8deeee524a3c84fd906d78e77cbd680e751f Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Mon, 21 Jun 2021 16:20:43 -0400 Subject: [PATCH 065/192] Added allow remote access notebook app flag the attempt premissions fix when the container is rebuilt. --- jupyter_notebook_config.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/jupyter_notebook_config.py b/jupyter_notebook_config.py index 66b8ea4bad..5d9fd3da1d 100644 --- a/jupyter_notebook_config.py +++ b/jupyter_notebook_config.py @@ -53,6 +53,8 @@ ## The default URL to redirect to from `/` c.NotebookApp.default_url = '/stochss/home' +c.NotebookApp.allow_remote_access = True + #------------------------------------------------------------------------------ # KernelManager(ConnectionFileMixin) configuration #------------------------------------------------------------------------------ From 5eca22c617a2b22a067e9de92af7dfe1f526ca98 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Tue, 22 Jun 2021 13:55:29 -0400 Subject: [PATCH 066/192] Set the GillesPy2 version to 1.6.1. --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 64cdace781..f6ce0cc0de 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==1.6.0 +gillespy2==1.6.1 sciope==0.4 pygmsh==5.0.2 meshio==2.3.10 From 7f6c4bd02faa69033daa1f71cda60c05abe05679 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Thu, 24 Jun 2021 08:57:45 -0400 Subject: [PATCH 067/192] Cleaned up reaction template for notebooks. --- stochss/handlers/util/stochss_notebook.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/stochss/handlers/util/stochss_notebook.py b/stochss/handlers/util/stochss_notebook.py index 41840f149e..5cf4937aa5 100644 --- a/stochss/handlers/util/stochss_notebook.py +++ b/stochss/handlers/util/stochss_notebook.py @@ -572,7 +572,7 @@ def __create_reaction_strings(self, model, pad): if reac['reactionType'] == 'custom-propensity': reac_str += f'propensity_function="{reac["propensity"]}")' else: - reac_str += f'rate=self.listOfParameters["{reac["rate"]["name"]}"])' + reac_str += f'rate="{reac["rate"]["name"]}")' if not self.s_model['is_spatial']: reac_str += ")" reactions.append(reac_str) From 07fa6600ff136a3d8f0606eb49c173bfb146c372 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Tue, 29 Jun 2021 09:03:17 -0400 Subject: [PATCH 068/192] Switched the APIHandler to BaseHandler. --- jupyterhub/model_presentation.py | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/jupyterhub/model_presentation.py b/jupyterhub/model_presentation.py index d32b800ffa..8c17278105 100644 --- a/jupyterhub/model_presentation.py +++ b/jupyterhub/model_presentation.py @@ -24,11 +24,7 @@ import tempfile import docker -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 jupyterhub.handlers.base import BaseHandler from presentation_error import StochSSAPIError, report_error @@ -36,7 +32,7 @@ # pylint: disable=abstract-method # pylint: disable=too-few-public-methods -class JsonFileAPIHandler(APIHandler): +class JsonFileAPIHandler(BaseHandler): ''' ################################################################################################ Base Handler for getting model presentations from user containers. @@ -69,7 +65,7 @@ async def get(self): self.finish() -class DownModelPresentationAPIHandler(APIHandler): +class DownModelPresentationAPIHandler(BaseHandler): ''' ################################################################################################ Base Handler for downloading model presentations from user containers. From 4aedd04264e7789b4ec893a980e3d4f916fda614 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Tue, 29 Jun 2021 10:39:55 -0400 Subject: [PATCH 069/192] Added missing print logs function. --- jupyterhub/presentation_base.py | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/jupyterhub/presentation_base.py b/jupyterhub/presentation_base.py index bf201c867a..605dbec65f 100644 --- a/jupyterhub/presentation_base.py +++ b/jupyterhub/presentation_base.py @@ -55,3 +55,19 @@ def get_name(self, path=None): if "." not in name: return name return '.'.join(name.split('.')[:-1]) + + + def print_logs(self, log): + ''' + Display all internal logs to the console + + Attributes + ---------- + log : obj + Logging object + ''' + displays = {"debug":log.debug, "info":log.info, "warning":log.warning, + "error":log.error, "critical":log.critical} + for entry in self.logs: + log_display = displays[entry["level"]] + log_display(entry["message"]) From e75ea574a5e90036c50385e827f43d7e4feffbf8 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Tue, 29 Jun 2021 10:57:23 -0400 Subject: [PATCH 070/192] Fixed the model presentation page. --- client/pages/model-presentation.js | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/client/pages/model-presentation.js b/client/pages/model-presentation.js index 198c758bd7..d94542905e 100644 --- a/client/pages/model-presentation.js +++ b/client/pages/model-presentation.js @@ -26,8 +26,8 @@ let app = require('../app'); let Model = require('../models/model'); //views let PageView = require('./base'); -let Rules = require('../views/rules-viewer'); -let Events = require('../views/events-viewer'); +let Rules = require('../views/rules-editor'); +let Events = require('../views/events-editor'); let Species = require('../views/species-editor'); let Reactions = require('../views/reactions-editor'); let Parameters = require('../views/parameters-editor'); @@ -72,7 +72,8 @@ let ModelPresentationPage = PageView.extend({ }, renderEventsContainer: function () { let events = new Events({ - collection: this.model.eventsCollection + collection: this.model.eventsCollection, + readOnly: true }); app.registerRenderSubview(this, events, "model-events"); }, @@ -93,6 +94,7 @@ let ModelPresentationPage = PageView.extend({ renderRulesContainer: function () { let rules = new Rules({ collection: this.model.rules + readOnly: true }); app.registerRenderSubview(this, rules, "model-rules"); }, From 377235f47cc906101e2d0c373a557faf456459b2 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Tue, 29 Jun 2021 13:04:35 -0400 Subject: [PATCH 071/192] Added the StochSSBase as the base class for StochSSModel and StochSSSpatialModel. Cleaned up the StochSSBase class. --- jupyterhub/model_presentation.py | 7 +++++-- jupyterhub/presentation_base.py | 20 +------------------- 2 files changed, 6 insertions(+), 21 deletions(-) diff --git a/jupyterhub/model_presentation.py b/jupyterhub/model_presentation.py index 8c17278105..8f825d752b 100644 --- a/jupyterhub/model_presentation.py +++ b/jupyterhub/model_presentation.py @@ -26,6 +26,7 @@ import docker from jupyterhub.handlers.base import BaseHandler +from presentation_base import StochSSBase from presentation_error import StochSSAPIError, report_error log = logging.getLogger('stochss') @@ -122,7 +123,7 @@ def get_presentation_from_user(owner, file): return json.load(mdl_file) -class StochSSModel(): +class StochSSModel(StochSSBase): ''' ################################################################################################ StochSS model object @@ -138,6 +139,7 @@ def __init__(self, model): model : dict Existing model data ''' + super().__init__() self.model = model @@ -228,7 +230,7 @@ def load(self): return self.model -class StochSSSpatialModel(): +class StochSSSpatialModel(StochSSBase): ''' ################################################################################################ StochSS spatial model object @@ -244,6 +246,7 @@ def __init__(self, model): model : dict Existing model data ''' + super().__init__() self.model = model diff --git a/jupyterhub/presentation_base.py b/jupyterhub/presentation_base.py index 605dbec65f..0ccb395525 100644 --- a/jupyterhub/presentation_base.py +++ b/jupyterhub/presentation_base.py @@ -26,7 +26,7 @@ class StochSSBase(): ''' user_dir = os.path.expanduser("~") # returns the path to the users home directory - def __init__(self, path): + def __init__(self, path=None): ''' Intitialize a file object @@ -39,24 +39,6 @@ def __init__(self, path): self.logs = [] - def get_name(self, path=None): - ''' - Get the name from the file object's path or provided path - - Attributes - ---------- - path : str - Path to a file object - ''' - name = self.path if path is None else path - if name.endswith("/"): - name = name[:-1] - name = name.split('/').pop() - if "." not in name: - return name - return '.'.join(name.split('.')[:-1]) - - def print_logs(self, log): ''' Display all internal logs to the console From 4c964f91821296e781a9d33b8155b2d09458f320 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Tue, 29 Jun 2021 13:06:10 -0400 Subject: [PATCH 072/192] Updated the copyright for the presentation files. --- client/pages/job-presentation.js | 2 +- client/pages/model-presentation.js | 2 +- jupyterhub/handlers.py | 2 +- jupyterhub/model_presentation.py | 2 +- jupyterhub/presentation_base.py | 2 +- jupyterhub/presentation_error.py | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/client/pages/job-presentation.js b/client/pages/job-presentation.js index b38c7c7fa6..fe34aeb5f6 100644 --- a/client/pages/job-presentation.js +++ b/client/pages/job-presentation.js @@ -1,6 +1,6 @@ /* StochSS is a platform for simulating biochemical systems -Copyright (C) 2019-2020 StochSS developers. +Copyright (C) 2019-2021 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 diff --git a/client/pages/model-presentation.js b/client/pages/model-presentation.js index d94542905e..49d2222435 100644 --- a/client/pages/model-presentation.js +++ b/client/pages/model-presentation.js @@ -1,6 +1,6 @@ /* StochSS is a platform for simulating biochemical systems -Copyright (C) 2019-2020 StochSS developers. +Copyright (C) 2019-2021 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 diff --git a/jupyterhub/handlers.py b/jupyterhub/handlers.py index b98c406d1d..46ba1b5cd9 100644 --- a/jupyterhub/handlers.py +++ b/jupyterhub/handlers.py @@ -1,6 +1,6 @@ ''' StochSS is a platform for simulating biochemical systems -Copyright (C) 2019-2020 StochSS developers. +Copyright (C) 2019-2021 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 diff --git a/jupyterhub/model_presentation.py b/jupyterhub/model_presentation.py index 8f825d752b..f442893769 100644 --- a/jupyterhub/model_presentation.py +++ b/jupyterhub/model_presentation.py @@ -1,6 +1,6 @@ ''' StochSS is a platform for simulating biochemical systems -Copyright (C) 2019-2020 StochSS developers. +Copyright (C) 2019-2021 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 diff --git a/jupyterhub/presentation_base.py b/jupyterhub/presentation_base.py index 0ccb395525..430d5a8d90 100644 --- a/jupyterhub/presentation_base.py +++ b/jupyterhub/presentation_base.py @@ -1,6 +1,6 @@ ''' StochSS is a platform for simulating biochemical systems -Copyright (C) 2019-2020 StochSS developers. +Copyright (C) 2019-2021 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 diff --git a/jupyterhub/presentation_error.py b/jupyterhub/presentation_error.py index ead4cbb8ef..79cfe04e07 100644 --- a/jupyterhub/presentation_error.py +++ b/jupyterhub/presentation_error.py @@ -1,6 +1,6 @@ ''' StochSS is a platform for simulating biochemical systems -Copyright (C) 2019-2020 StochSS developers. +Copyright (C) 2019-2021 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 From 219dbf9de38752034db115e551a39e09c171e42d Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Tue, 29 Jun 2021 14:37:35 -0400 Subject: [PATCH 073/192] Fixed bug in the reder subviews function. --- client/pages/model-presentation.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/client/pages/model-presentation.js b/client/pages/model-presentation.js index 49d2222435..b31c7a2230 100644 --- a/client/pages/model-presentation.js +++ b/client/pages/model-presentation.js @@ -62,7 +62,7 @@ let ModelPresentationPage = PageView.extend({ this.open = "open.stochss.org?open=" + this.model.directory; }, renderSubviews: function () { - PageView.prototype.render.apply(this, options); + PageView.prototype.render.apply(this, arguments); this.renderSpeciesContainer(); this.renderParametersContainer(); this.renderReactionsContainer(); From b87da41ad44db9f95928e2527c96579485988074 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Wed, 30 Jun 2021 11:21:17 -0400 Subject: [PATCH 074/192] Set the gillespy2 version to 1.6.2. Fixed compID for species in the cylinder demo. --- public_models/3D_Cylinder/3D_cylinder.smdl | 2 +- requirements.txt | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/public_models/3D_Cylinder/3D_cylinder.smdl b/public_models/3D_Cylinder/3D_cylinder.smdl index 3eb1226d2e..87f03f038a 100644 --- a/public_models/3D_Cylinder/3D_cylinder.smdl +++ b/public_models/3D_Cylinder/3D_cylinder.smdl @@ -1 +1 @@ -{"annotation":"SpatialPy 3D Cylinder Demo Model","defaultID":9,"defaultMode":"discrete","domain":{"boundary_condition":{"reflect_x":true,"reflect_y":true,"reflect_z":true},"c_0":10,"gravity":[0, 0, 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A","types":[2]},{"annotation":"","compID":7,"massaction":true,"name":"r2","products":[{"ratio":1,"specie":{"annotation":"","compID":2,"diffusionCoeff":0.1,"isSwitchTol":true,"mode":"discrete","name":"B","switchMin":100,"switchTol":0.03,"types":[1,3],"value":0}}],"propensity":"","rate":{"compID":5,"expression":197.70475491603773,"name":"k_creat2"},"reactants":[],"reactionType":"creation","summary":"\\emptyset \\rightarrow B","types":[3]},{"annotation":"","compID":8,"massaction":true,"name":"r3","products":[],"propensity":"","rate":{"compID":3,"expression":1,"name":"k_react"},"reactants":[{"ratio":1,"specie":{"annotation":"","compID":1,"diffusionCoeff":0.1,"isSwitchTol":true,"mode":"discrete","name":"A","switchMin":100,"switchTol":0.03,"types":[1,2],"value":0}},{"ratio":1,"specie":{"annotation":"","compID":2,"diffusionCoeff":0.1,"isSwitchTol":true,"mode":"discrete","name":"B","switchMin":100,"switchTol":0.03,"types":[1,3],"value":0}}],"reactionType":"custom-massaction","summary":"A + B \\rightarrow \\emptyset","types":[1,2,3]}],"rules":[],"species":[{"annotation":"","compID":1,"diffusionCoeff":0.1,"isSwitchTol":true,"mode":"discrete","name":"A","switchMin":100,"switchTol":0.03,"types":[1,2],"value":0,"diffusionConst":0.1},{"annotation":"","compID":2,"diffusionCoeff":0.1,"isSwitchTol":true,"mode":"discrete","name":"B","switchMin":100,"switchTol":0.03,"types":[1,3],"value":0,"diffusionConst":0.1}],"volume":1,"name":"cylinder_demo3d"} \ No newline at end of file diff --git a/requirements.txt b/requirements.txt index f6ce0cc0de..630c67b797 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==1.6.1 +gillespy2==1.6.2 sciope==0.4 pygmsh==5.0.2 meshio==2.3.10 From b6a7479dd95b4e3ba79b1c47eda207144389aa2a Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Wed, 30 Jun 2021 15:43:43 -0400 Subject: [PATCH 075/192] Added styling to the model header and buttons. Fixed the open link. Added a download button. --- client/pages/model-presentation.js | 4 +++- client/styles/styles.css | 5 +++++ client/templates/pages/modelPresentation.pug | 10 ++++++++-- 3 files changed, 16 insertions(+), 3 deletions(-) diff --git a/client/pages/model-presentation.js b/client/pages/model-presentation.js index b31c7a2230..590a224072 100644 --- a/client/pages/model-presentation.js +++ b/client/pages/model-presentation.js @@ -59,7 +59,9 @@ let ModelPresentationPage = PageView.extend({ self.renderSubviews(); } }); - this.open = "open.stochss.org?open=" + this.model.directory; + let downloadStart = "https://live.stochss.org/stochss/download_presentation"; + this.downloadLink = path.join(downloadStart, owner, file); + this.openLink = "open.stochss.org?open=" + this.downloadLink; }, renderSubviews: function () { PageView.prototype.render.apply(this, arguments); diff --git a/client/styles/styles.css b/client/styles/styles.css index 64935dff14..00885b0518 100644 --- a/client/styles/styles.css +++ b/client/styles/styles.css @@ -706,3 +706,8 @@ span.checkbox { .card-header { background-color: rgba(0, 0, 0, 0.1); } + +.presentation-header { + margin-top: 32px; + padding: 20px 16px; +} diff --git a/client/templates/pages/modelPresentation.pug b/client/templates/pages/modelPresentation.pug index 0edbe87293..774e81a650 100644 --- a/client/templates/pages/modelPresentation.pug +++ b/client/templates/pages/modelPresentation.pug @@ -2,7 +2,9 @@ section.page div#model-presentation.container - h2=this.model.name + div.presentation-header + + h1=this.model.name div(data-hook="model-species") @@ -18,4 +20,8 @@ section.page div.card.card-body="System Volume: "+this.model.volume - a.btn.btn-outline-secondary.box-shadow.text-break(href=this.open role="button") Open in StochSS + div.mt-3 + + a.btn.btn-outline-secondary.box-shadow.text-break(href=this.openLink role="button") Open in StochSS + + a.btn.btn-outline-secondary.box-shadow.text-break(href=this.downloadLink role="button") Download (.mdl) From 1ceeebd4bf9df01959f559092f2c6bb67fea82e4 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Wed, 30 Jun 2021 15:47:34 -0400 Subject: [PATCH 076/192] Fixed bold tags. --- client/templates/pages/modelPresentation.pug | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/client/templates/pages/modelPresentation.pug b/client/templates/pages/modelPresentation.pug index 774e81a650..f6181fd808 100644 --- a/client/templates/pages/modelPresentation.pug +++ b/client/templates/pages/modelPresentation.pug @@ -4,7 +4,7 @@ section.page div.presentation-header - h1=this.model.name + h1="" + this.model.name + "" div(data-hook="model-species") From 27c83c40140b0873c1fa8933373a540e6286270e Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Wed, 30 Jun 2021 17:05:23 -0400 Subject: [PATCH 077/192] Fixed bug that preventing the sbml components from rendering. Fixed model header. --- client/pages/model-presentation.js | 2 +- client/templates/pages/modelPresentation.pug | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/client/pages/model-presentation.js b/client/pages/model-presentation.js index 590a224072..c67df65ffa 100644 --- a/client/pages/model-presentation.js +++ b/client/pages/model-presentation.js @@ -101,7 +101,7 @@ let ModelPresentationPage = PageView.extend({ app.registerRenderSubview(this, rules, "model-rules"); }, renderSBMLComponents: function () { - let sbmlComponents = new SBMLComponentsView({ + let sbmlComponents = new SBMLComponents({ functionDefinitions: this.model.functionDefinitions, viewMode: true }); diff --git a/client/templates/pages/modelPresentation.pug b/client/templates/pages/modelPresentation.pug index f6181fd808..f21036e7dd 100644 --- a/client/templates/pages/modelPresentation.pug +++ b/client/templates/pages/modelPresentation.pug @@ -4,7 +4,7 @@ section.page div.presentation-header - h1="" + this.model.name + "" + h1 "" + this.model.name + "" div(data-hook="model-species") From 938041c7a2500befad7b1972e25fa76d2dcb93a6 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Thu, 1 Jul 2021 11:30:39 -0400 Subject: [PATCH 078/192] Added gillespy2 dependency tests to the unit test suite. --- stochss/tests/run_tests.py | 2 + stochss/tests/test_gillespy2.py | 162 ++++++++++++++++++++++++++++++++ 2 files changed, 164 insertions(+) create mode 100644 stochss/tests/test_gillespy2.py diff --git a/stochss/tests/run_tests.py b/stochss/tests/run_tests.py index b7d5d6d5f7..896b1a3be4 100755 --- a/stochss/tests/run_tests.py +++ b/stochss/tests/run_tests.py @@ -37,10 +37,12 @@ import test_model_template import test_settings_template import test_stochss_base + import test_gillespy2 modules = [ test_model_template, test_settings_template, + test_gillespy2, test_stochss_base ] diff --git a/stochss/tests/test_gillespy2.py b/stochss/tests/test_gillespy2.py new file mode 100644 index 0000000000..636f356ff7 --- /dev/null +++ b/stochss/tests/test_gillespy2.py @@ -0,0 +1,162 @@ +''' +StochSS is a platform for simulating biochemical systems +Copyright (C) 2019-2021 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 unittest + +from gillespy2 import GillesPySolver + +from stochss.handlers import StochSSModel + +os.chdir('/stochss') + +class TestModelTemplate(unittest.TestCase): + ''' + ################################################################################################ + Unit tests for GillesPy2 dependency. + ################################################################################################ + ''' + def setUp(self): + ''' Create a list of common example paths for each test. ''' + self.model_paths = ["Brusselator/Brusselator.mdl", + "Degradation/Degradation.mdl", + "Dimerization/Dimerization.mdl", + "Lotkavolterra_Oscillator/Lotkavolterra_Oscillator.mdl", + "Michaelis_Menten/Michaelis_Menten.mdl", + "Opioid/Opioid.mdl", + "Schlogl/Schlogl.mdl", + "Toggle_Switch/Toggle_Switch.mdl", + "Vilar_Oscillator/Vilar_Oscillator.mdl" + ] + + ################################################################################################ + # Unit tests for GillesPy2 dependency check_cpp_support. + ################################################################################################ + + def test_check_cpp_support(self): + ''' Check if the check cpp support functions works in StochSS. ''' + from gillespy2.solvers.utilities.cpp_support_test import check_cpp_support + + self.assertIsInstance(check_cpp_support(), bool) + + ################################################################################################ + # Unit tests for GillesPy2 dependency get_best_solver. + ################################################################################################ + + def test_get_best_solver(self): + ''' Check if the get best solver function works in StochSS. ''' + test_model = StochSSModel(path=os.path.join("Examples", self.model_paths[0])).convert_to_gillespy2() + test_solver = test_model.get_best_solver() + self.assertIsInstance(test_solver(), GillesPySolver) + + ################################################################################################ + # Unit tests for GillesPy2 dependency get_best_solver_algo. + ################################################################################################ + + def test_get_best_solver_algo(self): + ''' Check if the get best solver algo function works in StochSS. ''' + test_algos = ["ODE", "SSA", "Tau-Leaping"] + test_model = StochSSModel(path=os.path.join("Examples", self.model_paths[0])).convert_to_gillespy2() + for test_algo in test_algos: + with self.subTest(test_algo=test_algo): + test_solver = test_model.get_best_solver_algo(algorithm=test_algo) + self.assertIsInstance(test_solver(), GillesPySolver) + + ################################################################################################ + # Unit tests for GillesPy2 dependency solvers. + ################################################################################################ + + def test_ode_solver(self): + ''' Check if the test_models run with the ODESolver. ''' + from gillespy2 import ODESolver + + self.model_paths.append("Oregonator/Oregonator.mdl") + for model_path in self.model_paths: + with self.subTest(model=model_path.split('/').pop()): + test_model = StochSSModel(path=os.path.join("Examples", model_path)).convert_to_gillespy2() + test_model.run(solver=ODESolver) + + + def test_ode_c_solver(self): + ''' Check if the test_models run with the ODECSolver. ''' + from gillespy2 import ODECSolver + + self.model_paths.append("Oregonator/Oregonator.mdl") + for model_path in self.model_paths: + with self.subTest(model=model_path.split('/').pop()): + test_model = StochSSModel(path=os.path.join("Examples", model_path)).convert_to_gillespy2() + test_solver = ODECSolver(model=test_model) + test_model.run(solver=test_solver) + + + def test_numpy_ssa_solver(self): + ''' Check if the test_models run with the NumPySSASolver. ''' + from gillespy2 import NumPySSASolver + + self.model_paths.append("Tyson_Oscillator/Tyson_Oscillator.mdl") + for model_path in self.model_paths: + with self.subTest(model=model_path.split('/').pop()): + test_model = StochSSModel(path=os.path.join("Examples", model_path)).convert_to_gillespy2() + test_model.run(solver=NumPySSASolver) + + + def test_ssa_c_solver(self): + ''' Check if the test_models run with the SSACSolver. ''' + from gillespy2 import SSACSolver + + self.model_paths.append("Tyson_Oscillator/Tyson_Oscillator.mdl") + for model_path in self.model_paths: + with self.subTest(model=model_path.split('/').pop()): + test_model = StochSSModel(path=os.path.join("Examples", model_path)).convert_to_gillespy2() + test_solver = SSACSolver(model=test_model) + test_model.run(solver=test_solver) + + + def test_tau_leaping_solver(self): + ''' Check if the test_models run with the TauLeapingSolver. ''' + from gillespy2 import TauLeapingSolver + + self.model_paths.append("Tyson_Oscillator/Tyson_Oscillator.mdl") + for model_path in self.model_paths: + with self.subTest(model=model_path.split('/').pop()): + test_model = StochSSModel(path=os.path.join("Examples", model_path)).convert_to_gillespy2() + test_model.run(solver=TauLeapingSolver) + + + def test_tau_leaping_c_solver(self): + ''' Check if the test_models run with the TauLeapingCSolver. ''' + from gillespy2 import TauLeapingCSolver + + self.model_paths.append("Tyson_Oscillator/Tyson_Oscillator.mdl") + for model_path in self.model_paths: + with self.subTest(model=model_path.split('/').pop()): + test_model = StochSSModel(path=os.path.join("Examples", model_path)).convert_to_gillespy2() + test_solver = TauLeapingCSolver(model=test_model) + test_model.run(solver=test_solver) + + + def test_tau_hybrid_solver(self): + ''' Check if the test_models run with the TauHybridSolver. ''' + from gillespy2 import TauHybridSolver + + self.model_paths.append("Oregonator/Oregonator.mdl") + self.model_paths.append("Tyson_Oscillator/Tyson_Oscillator.mdl") + for model_path in self.model_paths: + with self.subTest(model=model_path.split('/').pop()): + test_model = StochSSModel(path=os.path.join("Examples", model_path)).convert_to_gillespy2() + test_model.run(solver=TauHybridSolver) From f1a09b1e0c6fa506f6b5a738731b5aecbdc8cbca Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Thu, 1 Jul 2021 12:44:51 -0400 Subject: [PATCH 079/192] Moved the models being tested for the gillespy2 dependency test to an example models file. --- stochss/tests/example_models.py | 352 ++++++++++++++++++++++++++++++++ 1 file changed, 352 insertions(+) create mode 100644 stochss/tests/example_models.py diff --git a/stochss/tests/example_models.py b/stochss/tests/example_models.py new file mode 100644 index 0000000000..17c415ac7c --- /dev/null +++ b/stochss/tests/example_models.py @@ -0,0 +1,352 @@ +''' +StochSS is a platform for simulating biochemical systems +Copyright (C) 2019-2021 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 numpy as np + +from gillespy2.core import ( + Model, + Species, + Reaction, + Parameter +) + +# pylint: disable=line-too-long +# pylint: disable=missing-class-docstring +# pylint: disable=too-few-public-methods +class Brusselator(Model): + def __init__(self): + Model.__init__(self, name="Brusselator") + self.volume = 1000 + + # Parameters + self.add_parameter(Parameter(name="rate1", expression="5000")) + self.add_parameter(Parameter(name="rate2", expression="50")) + self.add_parameter(Parameter(name="rate3", expression="5e-05")) + self.add_parameter(Parameter(name="rate4", expression="5")) + + # Variables + self.add_species(Species(name="A", initial_value=100000, mode="discrete")) + self.add_species(Species(name="B", initial_value=100000, mode="discrete")) + self.add_species(Species(name="C", initial_value=0, mode="discrete")) + self.add_species(Species(name="D", initial_value=0, mode="discrete")) + self.add_species(Species(name="X", initial_value=2000, mode="discrete")) + self.add_species(Species(name="Y", initial_value=1000, mode="discrete")) + + # Reactions + self.add_reaction(Reaction(name="reaction1", reactants={'A': 1}, products={'X': 1, 'A': 1}, propensity_function="rate1")) + self.add_reaction(Reaction(name="reaction2", reactants={'B': 1, 'X': 1}, products={'Y': 1, 'C': 1, 'B': 1}, propensity_function="rate2*X")) + self.add_reaction(Reaction(name="reaction3", reactants={'X': 2, 'Y': 1}, products={'X': 3}, propensity_function="rate3*Y*X*(X-1)/2")) + self.add_reaction(Reaction(name="reaction4", reactants={'X': 1}, products={'D': 1}, propensity_function="rate4*X")) + + # Timespan + self.timespan(np.arange(0, 30, 0.01)) + + +class Degradation(Model): + def __init__(self): + Model.__init__(self, name="Degradation") + self.volume = 1 + + # Parameters + self.add_parameter(Parameter(name="decayrate", expression="0.05")) + + # Variables + self.add_species(Species(name="protein", initial_value=50, mode="discrete")) + + # Reactions + self.add_reaction(Reaction(name="reaction", reactants={'protein': 1}, products={}, rate=self.listOfParameters["decayrate"])) + + # Timespan + self.timespan(np.arange(0, 100, 1)) + + +class Dimerization(Model): + def __init__(self): + Model.__init__(self, name="Dimerization") + self.volume = 1 + + # Parameters + self.add_parameter(Parameter(name="k_c", expression="0.005")) + self.add_parameter(Parameter(name="k_d", expression="0.08")) + + # Variables + self.add_species(Species(name="Monomer", initial_value=30, mode="discrete")) + self.add_species(Species(name="Dimer", initial_value=0, mode="discrete")) + + # Reactions + self.add_reaction(Reaction(name="r_creation", reactants={'Monomer': 2}, products={'Dimer': 1}, rate=self.listOfParameters["k_c"])) + self.add_reaction(Reaction(name="r_dissociation", reactants={'Dimer': 1}, products={'Monomer': 2}, rate=self.listOfParameters["k_d"])) + + # Timespan + self.timespan(np.arange(0, 100, 1)) + + +class LotkavolterraOscillator(Model): + def __init__(self): + Model.__init__(self, name="Lotkavolterra_Oscillator") + self.volume = 1 + + # Parameters + self.add_parameter(Parameter(name="k1", expression="0.004")) + self.add_parameter(Parameter(name="k2", expression="0.5")) + self.add_parameter(Parameter(name="k3", expression="0.0045")) + + # Variables + self.add_species(Species(name="R", initial_value=0.0095, mode="continuous")) + self.add_species(Species(name="W", initial_value=0.008, mode="continuous")) + + # Reactions + self.add_reaction(Reaction(name="r1", reactants={'R': 1}, products={'R': 2}, rate=self.listOfParameters["k1"])) + self.add_reaction(Reaction(name="r2", reactants={'R': 1, 'W': 1}, products={'W': 2}, rate=self.listOfParameters["k2"])) + self.add_reaction(Reaction(name="r3", reactants={'W': 1}, products={}, rate=self.listOfParameters["k3"])) + + # Timespan + self.timespan(np.arange(0, 9000, 1)) + + +class MichaelisMenten(Model): + def __init__(self): + Model.__init__(self, name="Michaelis_Menten") + self.volume = 1 + + # Parameters + self.add_parameter(Parameter(name="rate1", expression="0.0017")) + self.add_parameter(Parameter(name="rate2", expression="0.5")) + self.add_parameter(Parameter(name="rate3", expression="0.1")) + + # Variables + self.add_species(Species(name="A", initial_value=301, mode="discrete")) + self.add_species(Species(name="B", initial_value=120, mode="discrete")) + self.add_species(Species(name="C", initial_value=0, mode="discrete")) + self.add_species(Species(name="D", initial_value=0, mode="discrete")) + + # Reactions + self.add_reaction(Reaction(name="r1", reactants={'A': 1, 'B': 1}, products={'C': 1}, rate=self.listOfParameters["rate1"])) + self.add_reaction(Reaction(name="r2", reactants={'C': 1}, products={'A': 1, 'B': 1}, rate=self.listOfParameters["rate2"])) + self.add_reaction(Reaction(name="r3", reactants={'C': 1}, products={'B': 1, 'D': 1}, rate=self.listOfParameters["rate3"])) + + # Timespan + self.timespan(np.arange(0, 100, 1)) + + +class Opioid(Model): + def __init__(self): + Model.__init__(self, name="Opioid") + self.volume = 1 + + # Parameters + self.add_parameter(Parameter(name="alpha", expression="0.15")) + self.add_parameter(Parameter(name="epsilon", expression="0.8")) + self.add_parameter(Parameter(name="beta_p", expression="0.00266")) + self.add_parameter(Parameter(name="beta_a", expression="0.00094")) + self.add_parameter(Parameter(name="gamma", expression="0.00744")) + self.add_parameter(Parameter(name="zeta", expression="0.2")) + self.add_parameter(Parameter(name="delta", expression="0.1")) + self.add_parameter(Parameter(name="sigma", expression="0.9")) + self.add_parameter(Parameter(name="mu", expression="0.00729")) + self.add_parameter(Parameter(name="mu_prime", expression="0.01159")) + + # Variables + self.add_species(Species(name="Susceptible", initial_value=200, mode="discrete")) + self.add_species(Species(name="Prescribed_User", initial_value=0, mode="discrete")) + self.add_species(Species(name="Addicted", initial_value=0, mode="discrete")) + self.add_species(Species(name="Rehab", initial_value=0, mode="discrete")) + self.add_species(Species(name="Natural_Deaths", initial_value=0, mode="discrete")) + self.add_species(Species(name="Addicted_Deaths", initial_value=0, mode="discrete")) + + # Reactions + self.add_reaction(Reaction(name="SP", reactants={'Susceptible': 1}, products={'Prescribed_User': 1}, rate=self.listOfParameters["alpha"])) + self.add_reaction(Reaction(name="SA_a", reactants={'Susceptible': 1}, products={'Addicted': 1}, rate=self.listOfParameters["beta_a"])) + self.add_reaction(Reaction(name="SA_p", reactants={'Susceptible': 1}, products={'Addicted': 1}, rate=self.listOfParameters["beta_p"])) + self.add_reaction(Reaction(name="PA", reactants={'Prescribed_User': 1}, products={'Addicted': 1}, rate=self.listOfParameters["gamma"])) + self.add_reaction(Reaction(name="PS", reactants={'Prescribed_User': 1}, products={'Susceptible': 1}, rate=self.listOfParameters["epsilon"])) + self.add_reaction(Reaction(name="AR", reactants={'Addicted': 1}, products={'Rehab': 1}, rate=self.listOfParameters["zeta"])) + self.add_reaction(Reaction(name="RA", reactants={'Rehab': 1}, products={'Addicted': 1}, rate=self.listOfParameters["delta"])) + self.add_reaction(Reaction(name="RS", reactants={'Rehab': 1}, products={'Susceptible': 1}, rate=self.listOfParameters["sigma"])) + self.add_reaction(Reaction(name="mu_S", reactants={'Susceptible': 1}, products={'Susceptible': 1, 'Natural_Deaths': 1}, rate=self.listOfParameters["mu"])) + self.add_reaction(Reaction(name="mu_P", reactants={'Prescribed_User': 1}, products={'Susceptible': 1, 'Natural_Deaths': 1}, rate=self.listOfParameters["mu"])) + self.add_reaction(Reaction(name="mu_R", reactants={'Rehab': 1}, products={'Susceptible': 1, 'Natural_Deaths': 1}, rate=self.listOfParameters["mu"])) + self.add_reaction(Reaction(name="mu_prime_A", reactants={'Addicted': 1}, products={'Susceptible': 1, 'Addicted_Deaths': 1}, rate=self.listOfParameters["mu_prime"])) + + # Timespan + self.timespan(np.arange(0, 200, 1)) + + +class Schlogl(Model): + def __init__(self): + Model.__init__(self, name="Schlogl") + self.volume = 1 + + # Parameters + self.add_parameter(Parameter(name="k1", expression="1")) + self.add_parameter(Parameter(name="k2", expression="1")) + + # Variables + self.add_species(Species(name="s1", initial_value=300, mode="discrete")) + self.add_species(Species(name="s2", initial_value=300, mode="discrete")) + self.add_species(Species(name="s3", initial_value=300, mode="discrete")) + self.add_species(Species(name="s4", initial_value=300, mode="discrete")) + + # Reactions + self.add_reaction(Reaction(name="r1", reactants={'s1': 1, 's4': 1}, products={'s4': 2}, rate=self.listOfParameters["k1"])) + self.add_reaction(Reaction(name="r2", reactants={'s2': 1, 's4': 1}, products={'s3': 1}, rate=self.listOfParameters["k2"])) + + # Timespan + self.timespan(np.arange(0, 100000, 1000)) + + +class ToggleSwitch(Model): + def __init__(self): + Model.__init__(self, name="Toggle_Switch") + self.volume = 1 + + # Parameters + self.add_parameter(Parameter(name="alpha1", expression="10")) + self.add_parameter(Parameter(name="alpha2", expression="10")) + self.add_parameter(Parameter(name="beta", expression="2")) + self.add_parameter(Parameter(name="gamma", expression="2")) + self.add_parameter(Parameter(name="mu", expression="1")) + + # Variables + self.add_species(Species(name="A", initial_value=2, mode="discrete")) + self.add_species(Species(name="B", initial_value=2, mode="discrete")) + + # Reactions + self.add_reaction(Reaction(name="cu", reactants={}, products={'A': 1}, propensity_function="alpha1/(1+pow(B, beta))")) + self.add_reaction(Reaction(name="cv", reactants={}, products={'B': 1}, propensity_function="alpha2/(1+pow(A, gamma))")) + self.add_reaction(Reaction(name="du", reactants={'A': 1}, products={}, rate=self.listOfParameters["mu"])) + self.add_reaction(Reaction(name="dv", reactants={'B': 1}, products={}, rate=self.listOfParameters["mu"])) + + # Timespan + self.timespan(np.arange(0, 250, 1)) + + +class VilarOscillator(Model): + def __init__(self): + Model.__init__(self, name="Vilar_Oscillator") + self.volume = 1 + + # Parameters + self.add_parameter(Parameter(name="alpha_a", expression="50")) + self.add_parameter(Parameter(name="alpha_a_prime", expression="500")) + self.add_parameter(Parameter(name="alpha_r", expression="0.01")) + self.add_parameter(Parameter(name="alpha_r_prime", expression="50")) + self.add_parameter(Parameter(name="beta_a", expression="50")) + self.add_parameter(Parameter(name="beta_r", expression="5")) + self.add_parameter(Parameter(name="delta_ma", expression="10")) + self.add_parameter(Parameter(name="delta_mr", expression="0.5")) + self.add_parameter(Parameter(name="delta_a", expression="1")) + self.add_parameter(Parameter(name="delta_r", expression="0.2")) + self.add_parameter(Parameter(name="gamma_a", expression="1")) + self.add_parameter(Parameter(name="gamma_r", expression="1")) + self.add_parameter(Parameter(name="gamma_c", expression="2")) + self.add_parameter(Parameter(name="theta_a", expression="50")) + self.add_parameter(Parameter(name="theta_r", expression="100")) + + # Variables + self.add_species(Species(name="Da", initial_value=1, mode="discrete")) + self.add_species(Species(name="Da_prime", initial_value=0, mode="discrete")) + self.add_species(Species(name="Ma", initial_value=0, mode="discrete")) + self.add_species(Species(name="Dr", initial_value=1, mode="discrete")) + self.add_species(Species(name="Dr_prime", initial_value=0, mode="discrete")) + self.add_species(Species(name="Mr", initial_value=0, mode="discrete")) + self.add_species(Species(name="C", initial_value=10, mode="discrete")) + self.add_species(Species(name="A", initial_value=10, mode="discrete")) + self.add_species(Species(name="R", initial_value=10, mode="discrete")) + + # Reactions + self.add_reaction(Reaction(name="r1", reactants={'Da_prime': 1}, products={'Da': 1}, rate=self.listOfParameters["theta_a"])) + self.add_reaction(Reaction(name="r2", reactants={'Da': 1, 'A': 1}, products={'Da_prime': 1}, rate=self.listOfParameters["gamma_a"])) + self.add_reaction(Reaction(name="r3", reactants={'Dr_prime': 1}, products={'Dr': 1}, rate=self.listOfParameters["theta_r"])) + self.add_reaction(Reaction(name="r4", reactants={'Dr': 1, 'A': 1}, products={'Dr_prime': 1}, rate=self.listOfParameters["gamma_r"])) + self.add_reaction(Reaction(name="r5", reactants={'Da_prime': 1}, products={'Da_prime': 1, 'Ma': 1}, rate=self.listOfParameters["alpha_a_prime"])) + self.add_reaction(Reaction(name="r6", reactants={'Da': 1}, products={'Da': 1, 'Ma': 1}, rate=self.listOfParameters["alpha_a"])) + self.add_reaction(Reaction(name="r7", reactants={'Ma': 1}, products={}, rate=self.listOfParameters["delta_ma"])) + self.add_reaction(Reaction(name="r8", reactants={'Ma': 1}, products={'A': 1, 'Ma': 1}, rate=self.listOfParameters["beta_a"])) + self.add_reaction(Reaction(name="r9", reactants={'Da_prime': 1}, products={'Da_prime': 1, 'A': 1}, rate=self.listOfParameters["theta_a"])) + self.add_reaction(Reaction(name="r10", reactants={'Dr_prime': 1}, products={'Dr_prime': 1, 'A': 1}, rate=self.listOfParameters["theta_a"])) + self.add_reaction(Reaction(name="r11", reactants={'A': 1}, products={}, rate=self.listOfParameters["gamma_c"])) + self.add_reaction(Reaction(name="r12", reactants={'A': 1, 'R': 1}, products={'C': 1}, rate=self.listOfParameters["gamma_c"])) + self.add_reaction(Reaction(name="r13", reactants={'Dr_prime': 1}, products={'Dr_prime': 1, 'Mr': 1}, rate=self.listOfParameters["alpha_r_prime"])) + self.add_reaction(Reaction(name="r14", reactants={'Dr': 1}, products={'Dr': 1, 'Mr': 1}, rate=self.listOfParameters["alpha_r"])) + self.add_reaction(Reaction(name="r15", reactants={'Mr': 1}, products={}, rate=self.listOfParameters["delta_mr"])) + self.add_reaction(Reaction(name="r16", reactants={'Mr': 1}, products={'Mr': 1, 'R': 1}, rate=self.listOfParameters["beta_r"])) + self.add_reaction(Reaction(name="r17", reactants={'R': 1}, products={}, rate=self.listOfParameters["delta_r"])) + self.add_reaction(Reaction(name="r18", reactants={'C': 1}, products={'R': 1}, rate=self.listOfParameters["delta_a"])) + + # Timespan + self.timespan(np.arange(0, 200, 1)) + + +class Oregonator(Model): + def __init__(self): + Model.__init__(self, name="Oregonator") + self.volume = 1 + + # Parameters + self.add_parameter(Parameter(name="k1", expression="2")) + self.add_parameter(Parameter(name="k2", expression="0.1")) + self.add_parameter(Parameter(name="k3", expression="104")) + self.add_parameter(Parameter(name="k4", expression="4e-07")) + self.add_parameter(Parameter(name="k5", expression="26")) + + # Variables + self.add_species(Species(name="F", initial_value=2, mode="continuous")) + self.add_species(Species(name="A", initial_value=250, mode="continuous")) + self.add_species(Species(name="B", initial_value=500, mode="continuous")) + self.add_species(Species(name="C", initial_value=1000, mode="continuous")) + self.add_species(Species(name="P", initial_value=0, mode="continuous")) + + # Reactions + self.add_reaction(Reaction(name="reaction1", reactants={'B': 1, 'F': 1}, products={'A': 1, 'F': 1}, rate=self.listOfParameters["k1"])) + self.add_reaction(Reaction(name="reaction2", reactants={'A': 1, 'B': 1}, products={'P': 1}, rate=self.listOfParameters["k2"])) + self.add_reaction(Reaction(name="reaction3", reactants={'A': 1, 'F': 1}, products={'A': 2, 'C': 1, 'F': 1}, rate=self.listOfParameters["k3"])) + self.add_reaction(Reaction(name="reaction4", reactants={'A': 2}, products={'P': 1}, rate=self.listOfParameters["k4"])) + self.add_reaction(Reaction(name="reaction5", reactants={'C': 1, 'F': 1}, products={'B': 1, 'F': 1}, rate=self.listOfParameters["k5"])) + + # Timespan + self.timespan(np.arange(0, 5, 0.1)) + + +class TysonOscillator(Model): + def __init__(self): + Model.__init__(self, name="Tyson_Oscillator") + self.volume = 300 + + # Parameters + self.add_parameter(Parameter(name="P", expression="2")) + self.add_parameter(Parameter(name="kt", expression="20")) + self.add_parameter(Parameter(name="kd", expression="1")) + self.add_parameter(Parameter(name="a0", expression="0.005")) + self.add_parameter(Parameter(name="a1", expression="0.05")) + self.add_parameter(Parameter(name="a2", expression="0.1")) + self.add_parameter(Parameter(name="kdx", expression="1")) + + # Variables + self.add_species(Species(name="X", initial_value=197, mode="discrete")) + self.add_species(Species(name="Y", initial_value=255, mode="discrete")) + + # Reactions + self.add_reaction(Reaction(name="rxn1", reactants={}, products={'X': 1}, propensity_function="vol*1/(1+(Y*Y/((vol*vol))))")) + self.add_reaction(Reaction(name="rxn2", reactants={'X': 1}, products={}, rate=self.listOfParameters["kdx"])) + self.add_reaction(Reaction(name="rxn3", reactants={'X': 1}, products={'X': 1, 'Y': 1}, rate=self.listOfParameters["kt"])) + self.add_reaction(Reaction(name="rxn4", reactants={'Y': 1}, products={}, rate=self.listOfParameters["kd"])) + self.add_reaction(Reaction(name="rxn5", reactants={'Y': 1}, products={}, propensity_function="Y/(a0 + a1*(Y/vol)+a2*Y*Y/(vol*vol))")) + + # Timespan + self.timespan(np.arange(0, 100, 1)) From 3169bfb2a2e937e7117f621efec74193634ddaac Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Thu, 1 Jul 2021 12:45:47 -0400 Subject: [PATCH 080/192] Refactored the test to use the models in the new location. --- stochss/tests/test_gillespy2.py | 171 ++++++++++++++++---------------- 1 file changed, 88 insertions(+), 83 deletions(-) diff --git a/stochss/tests/test_gillespy2.py b/stochss/tests/test_gillespy2.py index 636f356ff7..b16fbfa94a 100644 --- a/stochss/tests/test_gillespy2.py +++ b/stochss/tests/test_gillespy2.py @@ -21,142 +21,147 @@ from gillespy2 import GillesPySolver -from stochss.handlers import StochSSModel +from example_models import ( + Brusselator, + Degradation, + Dimerization, + LotkavolterraOscillator, + MichaelisMenten, + Opioid, + Schlogl, + ToggleSwitch, + VilarOscillator, + Oregonator, + TysonOscillator +) os.chdir('/stochss') -class TestModelTemplate(unittest.TestCase): +# pylint: disable=import-outside-toplevel +class TestGillesPy2Dependency(unittest.TestCase): ''' ################################################################################################ Unit tests for GillesPy2 dependency. ################################################################################################ ''' def setUp(self): - ''' Create a list of common example paths for each test. ''' - self.model_paths = ["Brusselator/Brusselator.mdl", - "Degradation/Degradation.mdl", - "Dimerization/Dimerization.mdl", - "Lotkavolterra_Oscillator/Lotkavolterra_Oscillator.mdl", - "Michaelis_Menten/Michaelis_Menten.mdl", - "Opioid/Opioid.mdl", - "Schlogl/Schlogl.mdl", - "Toggle_Switch/Toggle_Switch.mdl", - "Vilar_Oscillator/Vilar_Oscillator.mdl" - ] - - ################################################################################################ + ''' Create a list of common example paths for each test. ''' + self.test_models = [Brusselator, Degradation, Dimerization, LotkavolterraOscillator, + MichaelisMenten, Opioid, Schlogl, ToggleSwitch, VilarOscillator] + + ################################################################################################ # Unit tests for GillesPy2 dependency check_cpp_support. ################################################################################################ def test_check_cpp_support(self): - ''' Check if the check cpp support functions works in StochSS. ''' - from gillespy2.solvers.utilities.cpp_support_test import check_cpp_support + ''' Check if the check cpp support functions works in StochSS. ''' + from gillespy2.solvers.utilities.cpp_support_test import check_cpp_support - self.assertIsInstance(check_cpp_support(), bool) + self.assertIsInstance(check_cpp_support(), bool) ################################################################################################ # Unit tests for GillesPy2 dependency get_best_solver. ################################################################################################ def test_get_best_solver(self): - ''' Check if the get best solver function works in StochSS. ''' - test_model = StochSSModel(path=os.path.join("Examples", self.model_paths[0])).convert_to_gillespy2() - test_solver = test_model.get_best_solver() - self.assertIsInstance(test_solver(), GillesPySolver) + ''' Check if the get best solver function works in StochSS. ''' + test_model = self.test_models[0]() + test_solver = test_model.get_best_solver() + self.assertIsInstance(test_solver(), GillesPySolver) ################################################################################################ # Unit tests for GillesPy2 dependency get_best_solver_algo. ################################################################################################ def test_get_best_solver_algo(self): - ''' Check if the get best solver algo function works in StochSS. ''' - test_algos = ["ODE", "SSA", "Tau-Leaping"] - test_model = StochSSModel(path=os.path.join("Examples", self.model_paths[0])).convert_to_gillespy2() - for test_algo in test_algos: - with self.subTest(test_algo=test_algo): - test_solver = test_model.get_best_solver_algo(algorithm=test_algo) - self.assertIsInstance(test_solver(), GillesPySolver) + ''' Check if the get best solver algo function works in StochSS. ''' + test_algos = ["ODE", "SSA", "Tau-Leaping"] + test_model = self.test_models[0]() + for test_algo in test_algos: + with self.subTest(test_algo=test_algo): + test_solver = test_model.get_best_solver_algo(algorithm=test_algo) + self.assertIsInstance(test_solver(), GillesPySolver) ################################################################################################ # Unit tests for GillesPy2 dependency solvers. ################################################################################################ def test_ode_solver(self): - ''' Check if the test_models run with the ODESolver. ''' - from gillespy2 import ODESolver + ''' Check if the test_models run with the ODESolver. ''' + from gillespy2 import ODESolver - self.model_paths.append("Oregonator/Oregonator.mdl") - for model_path in self.model_paths: - with self.subTest(model=model_path.split('/').pop()): - test_model = StochSSModel(path=os.path.join("Examples", model_path)).convert_to_gillespy2() - test_model.run(solver=ODESolver) + self.test_models.append(Oregonator) + for model in self.test_models: + test_model = model() + with self.subTest(model=test_model.name): + test_model.run(solver=ODESolver) def test_ode_c_solver(self): - ''' Check if the test_models run with the ODECSolver. ''' - from gillespy2 import ODECSolver + ''' Check if the test_models run with the ODECSolver. ''' + from gillespy2 import ODECSolver - self.model_paths.append("Oregonator/Oregonator.mdl") - for model_path in self.model_paths: - with self.subTest(model=model_path.split('/').pop()): - test_model = StochSSModel(path=os.path.join("Examples", model_path)).convert_to_gillespy2() - test_solver = ODECSolver(model=test_model) - test_model.run(solver=test_solver) + self.test_models.append(Oregonator) + for model in self.test_models: + test_model = model() + with self.subTest(model=test_model.name): + test_solver = ODECSolver(model=test_model) + test_model.run(solver=test_solver) def test_numpy_ssa_solver(self): - ''' Check if the test_models run with the NumPySSASolver. ''' - from gillespy2 import NumPySSASolver + ''' Check if the test_models run with the NumPySSASolver. ''' + from gillespy2 import NumPySSASolver - self.model_paths.append("Tyson_Oscillator/Tyson_Oscillator.mdl") - for model_path in self.model_paths: - with self.subTest(model=model_path.split('/').pop()): - test_model = StochSSModel(path=os.path.join("Examples", model_path)).convert_to_gillespy2() - test_model.run(solver=NumPySSASolver) + self.test_models.append(TysonOscillator) + for model in self.test_models: + test_model = model() + with self.subTest(model=test_model.name): + test_model.run(solver=NumPySSASolver) def test_ssa_c_solver(self): - ''' Check if the test_models run with the SSACSolver. ''' - from gillespy2 import SSACSolver + ''' Check if the test_models run with the SSACSolver. ''' + from gillespy2 import SSACSolver - self.model_paths.append("Tyson_Oscillator/Tyson_Oscillator.mdl") - for model_path in self.model_paths: - with self.subTest(model=model_path.split('/').pop()): - test_model = StochSSModel(path=os.path.join("Examples", model_path)).convert_to_gillespy2() - test_solver = SSACSolver(model=test_model) - test_model.run(solver=test_solver) + self.test_models.append(TysonOscillator) + for model in self.test_models: + test_model = model() + with self.subTest(model=test_model.name): + test_solver = SSACSolver(model=test_model) + test_model.run(solver=test_solver) def test_tau_leaping_solver(self): - ''' Check if the test_models run with the TauLeapingSolver. ''' - from gillespy2 import TauLeapingSolver + ''' Check if the test_models run with the TauLeapingSolver. ''' + from gillespy2 import TauLeapingSolver - self.model_paths.append("Tyson_Oscillator/Tyson_Oscillator.mdl") - for model_path in self.model_paths: - with self.subTest(model=model_path.split('/').pop()): - test_model = StochSSModel(path=os.path.join("Examples", model_path)).convert_to_gillespy2() - test_model.run(solver=TauLeapingSolver) + self.test_models.append(TysonOscillator) + for model in self.test_models: + test_model = model() + with self.subTest(model=test_model.name): + test_model.run(solver=TauLeapingSolver) def test_tau_leaping_c_solver(self): - ''' Check if the test_models run with the TauLeapingCSolver. ''' - from gillespy2 import TauLeapingCSolver + ''' Check if the test_models run with the TauLeapingCSolver. ''' + from gillespy2 import TauLeapingCSolver - self.model_paths.append("Tyson_Oscillator/Tyson_Oscillator.mdl") - for model_path in self.model_paths: - with self.subTest(model=model_path.split('/').pop()): - test_model = StochSSModel(path=os.path.join("Examples", model_path)).convert_to_gillespy2() - test_solver = TauLeapingCSolver(model=test_model) - test_model.run(solver=test_solver) + self.test_models.append(TysonOscillator) + for model in self.test_models: + test_model = model() + with self.subTest(model=test_model.name): + test_solver = TauLeapingCSolver(model=test_model) + test_model.run(solver=test_solver) def test_tau_hybrid_solver(self): - ''' Check if the test_models run with the TauHybridSolver. ''' - from gillespy2 import TauHybridSolver - - self.model_paths.append("Oregonator/Oregonator.mdl") - self.model_paths.append("Tyson_Oscillator/Tyson_Oscillator.mdl") - for model_path in self.model_paths: - with self.subTest(model=model_path.split('/').pop()): - test_model = StochSSModel(path=os.path.join("Examples", model_path)).convert_to_gillespy2() - test_model.run(solver=TauHybridSolver) + ''' Check if the test_models run with the TauHybridSolver. ''' + from gillespy2 import TauHybridSolver + + self.test_models.append(Oregonator) + self.test_models.append(TysonOscillator) + for model in self.test_models: + test_model = model() + with self.subTest(model=test_model.name): + test_model.run(solver=TauHybridSolver) From 306c27baee0095c338cb44f70c51187cd15e2070 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Thu, 1 Jul 2021 12:46:53 -0400 Subject: [PATCH 081/192] Added pylint decorators to ignore warnings for tests. --- stochss/tests/test_stochss_base.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/stochss/tests/test_stochss_base.py b/stochss/tests/test_stochss_base.py index 81c5c979d3..11e2f1f920 100644 --- a/stochss/tests/test_stochss_base.py +++ b/stochss/tests/test_stochss_base.py @@ -33,6 +33,8 @@ os.chdir('/stochss') +# pylint: disable=too-many-public-methods +# pylint: disable=line-too-long class TestStochSSBaseObject(unittest.TestCase): ''' ################################################################################################ From a92eabb07a490093363d83a303e9d21e8af69e12 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Thu, 1 Jul 2021 14:55:26 -0400 Subject: [PATCH 082/192] Added model view file. Moved the model mode section out of the model editor page and into the model view file. Added edit/view tabs for model mode. Implemneted read only mode for the model view. Removed the tooltips for the model editor and added the text to the model mode section. --- client/pages/model-editor.js | 58 +++----------- client/templates/includes/modelView.pug | 50 ++++++++++++ client/templates/pages/modelEditor.pug | 20 +---- client/tooltips.js | 7 -- client/views/model-view.js | 101 ++++++++++++++++++++++++ 5 files changed, 164 insertions(+), 72 deletions(-) create mode 100644 client/templates/includes/modelView.pug create mode 100644 client/views/model-view.js diff --git a/client/pages/model-editor.js b/client/pages/model-editor.js index dea04098a6..fc55624a5a 100644 --- a/client/pages/model-editor.js +++ b/client/pages/model-editor.js @@ -26,6 +26,7 @@ var tests = require('../views/tests'); let Tooltips = require("../tooltips"); //views var PageView = require('../pages/base'); +let ModelView = require('../views/model-view'); var InputView = require('../views/input'); var DomainViewer = require('../views/domain-viewer'); var SpeciesEditorView = require('../views/species-editor'); @@ -51,9 +52,6 @@ import initPage from './page.js'; let ModelEditor = PageView.extend({ template: template, events: { - 'change [data-hook=all-continuous]' : 'setDefaultMode', - 'change [data-hook=all-discrete]' : 'setDefaultMode', - 'change [data-hook=advanced]' : 'setDefaultMode', 'click [data-hook=edit-model-help]' : function () { let modal = $(modals.operationInfoModalHtml('model-editor')).modal(); }, @@ -67,7 +65,6 @@ let ModelEditor = PageView.extend({ }, initialize: function (attrs, options) { PageView.prototype.initialize.apply(this, arguments); - this.tooltips = Tooltips.modelEditor var self = this; let urlParams = new URLSearchParams(window.location.search) var directory = urlParams.get('path'); @@ -220,12 +217,6 @@ let ModelEditor = PageView.extend({ } }, renderSubviews: function () { - if(this.model.defaultMode === "" && !this.model.is_spatial){ - this.getInitialDefaultMode(); - }else{ - let dataHooks = {'continuous':'all-continuous', 'discrete':'all-discrete', 'dynamic':'advanced'} - $(this.queryByHook(dataHooks[this.model.defaultMode])).prop('checked', true) - } this.modelSettings = new TimespanSettingsView({ parent: this, model: this.model.modelSettings, @@ -240,7 +231,6 @@ let ModelEditor = PageView.extend({ app.registerRenderSubview(this, this.modelStateButtons, 'model-state-buttons-container'); if(this.model.is_spatial) { $(this.queryByHook("system-volume-container")).css("display", "none"); - $(this.queryByHook("advaced-model-mode")).css("display", "none"); $(this.queryByHook("spatial-beta-message")).css("display", "block"); this.renderDomainViewer(); this.renderInitialConditions(); @@ -427,25 +417,6 @@ let ModelEditor = PageView.extend({ let pngButton = $('div[data-hook=preview-plot-container] a[data-title*="Download plot as a png"]')[0] pngButton.click() }, - getInitialDefaultMode: function () { - var self = this; - if(document.querySelector('#defaultModeModal')) { - document.querySelector('#defaultModeModal').remove(); - } - let modal = $(modals.renderDefaultModeModalHtml()).modal(); - let continuous = document.querySelector('#defaultModeModal .concentration-btn'); - let discrete = document.querySelector('#defaultModeModal .population-btn'); - let dynamic = document.querySelector('#defaultModeModal .hybrid-btn'); - continuous.addEventListener('click', function (e) { - self.setInitialDefaultMode(modal, "continuous"); - }); - discrete.addEventListener('click', function (e) { - self.setInitialDefaultMode(modal, "discrete"); - }); - dynamic.addEventListener('click', function (e) { - self.setInitialDefaultMode(modal, "dynamic"); - }); - }, setAllSpeciesModes: function (prevMode) { let self = this; this.model.species.forEach(function (specie) { @@ -459,22 +430,6 @@ let ModelEditor = PageView.extend({ this.speciesEditor.renderViewSpeciesView(); } }, - setDefaultMode: function (e) { - let prevMode = this.model.defaultMode; - this.model.defaultMode = e.target.dataset.name; - this.speciesEditor.defaultMode = e.target.dataset.name; - this.setAllSpeciesModes(prevMode); - this.toggleVolumeContainer(); - }, - setInitialDefaultMode: function (modal, mode) { - var dataHooks = {'continuous':'all-continuous', 'discrete':'all-discrete', 'dynamic':'advanced'}; - modal.modal('hide'); - $(this.queryByHook(dataHooks[mode])).prop('checked', true); - this.model.defaultMode = mode; - this.speciesEditor.defaultMode = mode; - this.setAllSpeciesModes(); - this.toggleVolumeContainer(); - }, toggleVolumeContainer: function () { if(!this.model.is_spatial) { if(this.model.defaultMode === "continuous") { @@ -486,6 +441,17 @@ let ModelEditor = PageView.extend({ }, updateVolumeViewer: function (e) { $(this.queryByHook("view-volume")).html("Volume: " + this.model.volume) + }, + subviews: { + modelView: { + waitFor: 'model.defaultMode', + hook: 'model-view-container', + prepareView: function (el) { + return new ModelView({ + model: this.model + }); + } + } } }); diff --git a/client/templates/includes/modelView.pug b/client/templates/includes/modelView.pug new file mode 100644 index 0000000000..35c5f8446b --- /dev/null +++ b/client/templates/includes/modelView.pug @@ -0,0 +1,50 @@ +div#model-view + + div.card + + div.card-header.pb-0 + + h3.inline.mr-3 Model Mode + + div.inline.mr-3 + + ul.nav.nav-tabs.card-header-tabs(id="model-mode-tabs") + + li.nav-item + + a.nav-link.tab.active(data-hook="model-mode-edit-tab" data-toggle="tab" href="#edit-model-mode") Edit + + li.nav-item + + a.nav-link.tab(data-hook="model-mode-view-tab" data-toggle="tab" href="#view-model-mode") View + + div.card-body + + p.mb-0 + | Concentration - Variables will only be represented using continuous (floating point) values.
+ | Population - Variables will only be represented using discrete (integer count) values.
+ if !this.model.is_spatial + | Hybrid Concentration/Population - Allows a variables to be represented using continuous and/or discrete values. + + div.tab-content(id="model-mode-section" data-hook="model-mode-section") + + div.tab-pane.active(id="edit-model-mode" data-hook="edit-model-mode") + + hr + + div.row + div.col-sm-4 + input.mr-2(type="radio" name="default-mode" data-hook="all-continuous" data-name="continuous") + span Concentration + div.col-sm-4 + input.mr-2(type="radio" name="default-mode" data-hook="all-discrete" data-name="discrete") + span Population + div.col-sm-4(data-hook="advanced-model-mode") + input.mr-2(type="radio" name="default-mode" data-hook="advanced" data-name="dynamic") + span Hybrid Concentration/Population + + div.tab-pane(id="view-model-mode" data-hook="view-model-mode") + + hr + + div="Model Mode: " + this.modelMode diff --git a/client/templates/pages/modelEditor.pug b/client/templates/pages/modelEditor.pug index 1c1d3cc683..a01526aff0 100644 --- a/client/templates/pages/modelEditor.pug +++ b/client/templates/pages/modelEditor.pug @@ -26,25 +26,7 @@ section.page ol.breadcrumb li.breadcrumb-item.active(aria-current="page")=this.model.name - div.card - - div.card-header.pb-0 - - h3.inline Model Mode - - div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.modelMode) - - div.card-body - div.row - div.col-sm-4 - input.mr-2(type="radio" name="default-mode" data-hook="all-continuous" data-name="continuous") - span Concentration - div.col-sm-4 - input.mr-2(type="radio" name="default-mode" data-hook="all-discrete" data-name="discrete") - span Population - div.col-sm-4(data-hook="advaced-model-mode") - input.mr-2(type="radio" name="default-mode" data-hook="advanced" data-name="dynamic") - span Hybrid Concentration/Population + div(data-hook="model-view-container") div(data-hook="domain-viewer-container") diff --git a/client/tooltips.js b/client/tooltips.js index 56fc32971c..5a5f014956 100644 --- a/client/tooltips.js +++ b/client/tooltips.js @@ -17,13 +17,6 @@ along with this program. If not, see . */ module.exports = { - modelEditor: { - modelMode: "Concentration - Variables will only be represented using continuous (floating point) values.
Population - Variables will only be represented "+ - "using discrete (integer count) values.
Hybrid Concentration/Population - Allows a variables to be represented using continuous and/or discrete values.", - - spatialModelMode: "Concentration - Variables will only be represented using continuous (floating point) values.
Population - Variables will only be represented "+ - "using discrete (integer count) values." - }, speciesEditor: { name: "Unique identifier for Variable. Cannot share a name with other model components.", diff --git a/client/views/model-view.js b/client/views/model-view.js new file mode 100644 index 0000000000..dc9782badd --- /dev/null +++ b/client/views/model-view.js @@ -0,0 +1,101 @@ +/* +StochSS is a platform for simulating biochemical systems +Copyright (C) 2019-2021 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 modals = require('../modals'); +//views +let View = require('ampersand-view'); +//templates +let template = require('../templates/includes/modelView.pug'); + +module.exports = View.extend({ + template: template, + events: { + 'change [data-hook=all-continuous]' : 'setDefaultMode', + 'change [data-hook=all-discrete]' : 'setDefaultMode', + 'change [data-hook=advanced]' : 'setDefaultMode' + }, + initialize: function(attrs, options) { + View.prototype.initialize.apply(this, arguments); + this.readOnly = attrs.readOnly ? attrs.readOnly : false; + let modeMap = {continuous: "Concentration", discrete: "Population", dynamic: "Hybrid Concentration/Population"}; + this.modelMode = modeMap[this.model.defaultMode] + }, + render: function(attrs, options) { + View.prototype.render.apply(this, arguments); + if(this.readOnly) { + this.setReadOnlyMode("model-mode"); + }else { + if(this.model.defaultMode === "" && !this.model.is_spatial){ + this.getInitialDefaultMode(); + }else { + let dataHooks = {'continuous':'all-continuous', 'discrete':'all-discrete', 'dynamic':'advanced'}; + $(this.queryByHook(dataHooks[this.model.defaultMode])).prop('checked', true); + if(this.model.is_spatial) { + $(this.queryByHook("advanced-model-mode")).css("display", "none"); + } + } + } + }, + getInitialDefaultMode: function () { + let self = this; + if(document.querySelector('#defaultModeModal')) { + document.querySelector('#defaultModeModal').remove(); + } + let modal = $(modals.renderDefaultModeModalHtml()).modal(); + let continuous = document.querySelector('#defaultModeModal .concentration-btn'); + let discrete = document.querySelector('#defaultModeModal .population-btn'); + let dynamic = document.querySelector('#defaultModeModal .hybrid-btn'); + continuous.addEventListener('click', function (e) { + self.setInitialDefaultMode(modal, "continuous"); + }); + discrete.addEventListener('click', function (e) { + self.setInitialDefaultMode(modal, "discrete"); + }); + dynamic.addEventListener('click', function (e) { + self.setInitialDefaultMode(modal, "dynamic"); + }); + }, + setDefaultMode: function (e) { + let prevMode = this.model.defaultMode; + this.model.defaultMode = e.target.dataset.name; + this.parent.speciesEditor.defaultMode = e.target.dataset.name; + this.parent.setAllSpeciesModes(prevMode); + this.parent.toggleVolumeContainer(); + }, + setInitialDefaultMode: function (modal, mode) { + var dataHooks = {'continuous':'all-continuous', 'discrete':'all-discrete', 'dynamic':'advanced'}; + modal.modal('hide'); + $(this.queryByHook(dataHooks[mode])).prop('checked', true); + this.model.defaultMode = mode; + this.parent.speciesEditor.defaultMode = mode; + this.parent.setAllSpeciesModes(); + this.parent.toggleVolumeContainer(); + }, + setReadOnlyMode: function (component) { + $(this.queryByHook(component + '-edit-tab')).addClass("disabled"); + $(".nav .disabled>a").on("click", function(e) { + e.preventDefault(); + return false; + }); + $(this.queryByHook(component + '-view-tab')).tab('show'); + $(this.queryByHook('edit-' + component)).removeClass('active'); + $(this.queryByHook('view-' + component)).addClass('active'); + } +}); \ No newline at end of file From c8dbd3cc7ca5ab08c595f3b6f9d1975c0ceab6d8 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Thu, 1 Jul 2021 15:32:56 -0400 Subject: [PATCH 083/192] Moved the domain render function and container into the model view. --- client/pages/model-editor.js | 51 +++++-------------------- client/templates/includes/modelView.pug | 2 + client/templates/pages/modelEditor.pug | 2 - client/views/model-view.js | 38 ++++++++++++++++++ 4 files changed, 49 insertions(+), 44 deletions(-) diff --git a/client/pages/model-editor.js b/client/pages/model-editor.js index fc55624a5a..ac474f04ba 100644 --- a/client/pages/model-editor.js +++ b/client/pages/model-editor.js @@ -28,7 +28,6 @@ let Tooltips = require("../tooltips"); var PageView = require('../pages/base'); let ModelView = require('../views/model-view'); var InputView = require('../views/input'); -var DomainViewer = require('../views/domain-viewer'); var SpeciesEditorView = require('../views/species-editor'); var InitialConditionsEditorView = require('../views/initial-conditions-editor'); var ParametersEditorView = require('../views/parameters-editor'); @@ -88,6 +87,7 @@ let ModelEditor = PageView.extend({ app.getXHR(this.model.url(), { success: function (err, response, body) { self.model.set(body) + self.modelLoaded = true if(directory.includes('.proj')) { self.queryByHook("project-breadcrumb-links").style.display = "block" self.queryByHook("model-name-header").style.display = "none" @@ -210,13 +210,20 @@ let ModelEditor = PageView.extend({ }else{ $(this.queryByHook("me-select-particle")).css("display", "block") this.typeQuickViewer = this.renderCollection( - this.domainViewer.model.types, + this.modelView.domainViewer.model.types, QuickviewDomainTypes, this.queryByHook("me-types-quick-view") ); } }, + renderModelView: function () { + this.modelView = new ModelView({ + model: this.model + }); + app.registerRenderSubview(this, this.modelView, "model-view-container") + }, renderSubviews: function () { + this.renderModelView() this.modelSettings = new TimespanSettingsView({ parent: this, model: this.model.modelSettings, @@ -232,7 +239,6 @@ let ModelEditor = PageView.extend({ if(this.model.is_spatial) { $(this.queryByHook("system-volume-container")).css("display", "none"); $(this.queryByHook("spatial-beta-message")).css("display", "block"); - this.renderDomainViewer(); this.renderInitialConditions(); this.renderBoundaryConditionsView(); $(this.queryByHook("toggle-preview-domain")).css("display", "inline-block"); @@ -268,34 +274,6 @@ let ModelEditor = PageView.extend({ }); app.registerRenderSubview(this, this.boundaryConditionsView, "boundary-conditions-container"); }, - renderDomainViewer: function(domainPath=null) { - if(this.domainViewer) { - this.domainViewer.remove() - } - if(domainPath && domainPath !== "viewing") { - let self = this; - let queryStr = "?path=" + this.model.directory + "&domain_path=" + domainPath - let endpoint = path.join(app.getApiPath(), "spatial-model/load-domain") + queryStr - 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({ - parent: this, - model: this.model.domain, - domainPath: domainPath - }); - app.registerRenderSubview(this, this.domainViewer, 'domain-viewer-container'); - } - }, renderSpeciesView: function () { if(this.speciesEditor) { this.speciesEditor.remove() @@ -441,17 +419,6 @@ let ModelEditor = PageView.extend({ }, updateVolumeViewer: function (e) { $(this.queryByHook("view-volume")).html("Volume: " + this.model.volume) - }, - subviews: { - modelView: { - waitFor: 'model.defaultMode', - hook: 'model-view-container', - prepareView: function (el) { - return new ModelView({ - model: this.model - }); - } - } } }); diff --git a/client/templates/includes/modelView.pug b/client/templates/includes/modelView.pug index 35c5f8446b..5890f5086b 100644 --- a/client/templates/includes/modelView.pug +++ b/client/templates/includes/modelView.pug @@ -48,3 +48,5 @@ div#model-view hr div="Model Mode: " + this.modelMode + + div(data-hook="domain-viewer-container") diff --git a/client/templates/pages/modelEditor.pug b/client/templates/pages/modelEditor.pug index a01526aff0..ec0c4fc37e 100644 --- a/client/templates/pages/modelEditor.pug +++ b/client/templates/pages/modelEditor.pug @@ -28,8 +28,6 @@ section.page div(data-hook="model-view-container") - div(data-hook="domain-viewer-container") - div(data-hook="species-editor-container") div(data-hook="initial-conditions-editor-container") diff --git a/client/views/model-view.js b/client/views/model-view.js index dc9782badd..a4f0d7685a 100644 --- a/client/views/model-view.js +++ b/client/views/model-view.js @@ -17,10 +17,15 @@ along with this program. If not, see . */ let $ = require('jquery'); +let path = require('path'); //support files +let app = require('../app'); let modals = require('../modals'); +//models +let Domain = require('../models/domain'); //views let View = require('ampersand-view'); +let DomainViewer = require('../views/domain-viewer'); //templates let template = require('../templates/includes/modelView.pug'); @@ -52,6 +57,9 @@ module.exports = View.extend({ } } } + if(this.model.is_spatial) { + this.renderDomainViewer(); + } }, getInitialDefaultMode: function () { let self = this; @@ -72,6 +80,36 @@ module.exports = View.extend({ self.setInitialDefaultMode(modal, "dynamic"); }); }, + renderDomainViewer: function(domainPath=null) { + if(this.domainViewer) { + this.domainViewer.remove(); + } + if(domainPath && domainPath !== "viewing") { + let self = this; + let queryStr = "?path=" + this.model.directory + "&domain_path=" + domainPath; + let endpoint = path.join(app.getApiPath(), "spatial-model/load-domain") + queryStr; + app.getXHR(endpoint, { + always: function (err, response, body) { + let domain = new Domain(body.domain); + self.domainViewer = new DomainViewer({ + parent: self, + model: domain, + domainPath: domainPath, + readOnly: self.readOnly + }); + app.registerRenderSubview(self, self.domainViewer, 'domain-viewer-container'); + } + }); + }else{ + this.domainViewer = new DomainViewer({ + parent: this, + model: this.model.domain, + domainPath: domainPath, + readOnly: this.readOnly + }); + app.registerRenderSubview(this, this.domainViewer, 'domain-viewer-container'); + } + }, setDefaultMode: function (e) { let prevMode = this.model.defaultMode; this.model.defaultMode = e.target.dataset.name; From acef52b46467ccf0a2ac73752d363575e7a13653 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Thu, 1 Jul 2021 15:45:32 -0400 Subject: [PATCH 084/192] Refactored the domain plot and particle function to use the domain viewer in its new location. --- client/views/domain-viewer.js | 8 ++++---- client/views/model-state-buttons.js | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/client/views/domain-viewer.js b/client/views/domain-viewer.js index 2ff51bcc60..2a439109c6 100644 --- a/client/views/domain-viewer.js +++ b/client/views/domain-viewer.js @@ -84,7 +84,7 @@ module.exports = View.extend({ this.toggleDomainError(); } this.renderTypesViewer(); - this.parent.renderParticleViewer(null); + this.parent.parent.renderParticleViewer(null); let endpoint = path.join(app.getApiPath(), "spatial-model/domain-plot") + queryStr; app.getXHR(endpoint, { always: function (err, response, body) { @@ -119,7 +119,7 @@ module.exports = View.extend({ }, reloadDomain: function (domainPath) { if(this.domainPath !== domainPath || domainPath === "viewing") { - var el = this.parent.queryByHook("domain-plot-container"); + var el = this.parent.parent.queryByHook("domain-plot-container"); el.removeListener('plotly_click', this.selectParticle); Plotly.purge(el); this.plot = null; @@ -193,14 +193,14 @@ module.exports = View.extend({ }, displayDomain: function () { let self = this; - var domainPreview = this.parent.queryByHook("domain-plot-container"); + var domainPreview = this.parent.parent.queryByHook("domain-plot-container"); Plotly.newPlot(domainPreview, this.plot); domainPreview.on('plotly_click', _.bind(this.selectParticle, this)); }, selectParticle: function (data) { let point = data.points[0]; let particle = this.model.particles.get(point.id, "particle_id"); - this.parent.renderParticleViewer(particle); + this.parent.parent.renderParticleViewer(particle); }, editDomain: function (e) { var queryStr = "?path=" + this.parent.model.directory; diff --git a/client/views/model-state-buttons.js b/client/views/model-state-buttons.js index 82f4e40412..72050697cd 100644 --- a/client/views/model-state-buttons.js +++ b/client/views/model-state-buttons.js @@ -304,7 +304,7 @@ module.exports = View.extend({ openDomainSection: function () { let domainSection = $(this.parent.parametersEditor.queryByHook("parameters-list-container")) if(!domainSection.hasClass("show")) { - let domainCollapseBtn = $(this.parent.domainViewer.queryByHook("collapse")) + let domainCollapseBtn = $(this.parent.modelView.domainViewer.queryByHook("collapse")) domainCollapseBtn.click() domainCollapseBtn.html('-') } From d097895551d86929c010b7aa081162b7a47c70bb Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Thu, 1 Jul 2021 16:24:30 -0400 Subject: [PATCH 085/192] Moved the render species function and species container to the model view. Renamed the specie view and template files with names that better fit their function. Refactored the open container function in the model state buttons file to reference the species view in its new location. --- client/pages/model-editor.js | 26 -------------- client/templates/includes/modelView.pug | 2 ++ ...eciesEditor.pug => spatialSpeciesView.pug} | 0 .../{speciesEditor.pug => speciesView.pug} | 0 client/templates/pages/modelEditor.pug | 2 -- client/views/model-state-buttons.js | 4 +-- client/views/model-view.js | 34 ++++++++++++++++--- .../{species-editor.js => species-view.js} | 4 +-- 8 files changed, 36 insertions(+), 36 deletions(-) rename client/templates/includes/{spatialSpeciesEditor.pug => spatialSpeciesView.pug} (100%) rename client/templates/includes/{speciesEditor.pug => speciesView.pug} (100%) rename client/views/{species-editor.js => species-view.js} (98%) diff --git a/client/pages/model-editor.js b/client/pages/model-editor.js index ac474f04ba..f90af7ba2a 100644 --- a/client/pages/model-editor.js +++ b/client/pages/model-editor.js @@ -28,7 +28,6 @@ let Tooltips = require("../tooltips"); var PageView = require('../pages/base'); let ModelView = require('../views/model-view'); var InputView = require('../views/input'); -var SpeciesEditorView = require('../views/species-editor'); var InitialConditionsEditorView = require('../views/initial-conditions-editor'); var ParametersEditorView = require('../views/parameters-editor'); var ParticleViewer = require('../views/view-particle'); @@ -231,7 +230,6 @@ let ModelEditor = PageView.extend({ this.modelStateButtons = new ModelStateButtonsView({ model: this.model }); - this.renderSpeciesView(); this.renderParametersView(); this.renderReactionsView(); app.registerRenderSubview(this, this.modelSettings, 'model-settings-container'); @@ -274,17 +272,6 @@ let ModelEditor = PageView.extend({ }); app.registerRenderSubview(this, this.boundaryConditionsView, "boundary-conditions-container"); }, - renderSpeciesView: function () { - if(this.speciesEditor) { - this.speciesEditor.remove() - } - this.speciesEditor = new SpeciesEditorView({ - collection: this.model.species, - spatial: this.model.is_spatial, - defaultMode: this.model.defaultMode - }); - app.registerRenderSubview(this, this.speciesEditor, 'species-editor-container'); - }, renderInitialConditions: function () { if(this.initialConditionsEditor) { this.initialConditionsEditor.remove(); @@ -395,19 +382,6 @@ let ModelEditor = PageView.extend({ let pngButton = $('div[data-hook=preview-plot-container] a[data-title*="Download plot as a png"]')[0] pngButton.click() }, - setAllSpeciesModes: function (prevMode) { - let self = this; - this.model.species.forEach(function (specie) { - specie.mode = self.model.defaultMode; - self.model.species.trigger('update-species', specie.compID, specie, false, true); - }); - let switchToDynamic = (!Boolean(prevMode) || prevMode !== "dynamic") && this.model.defaultMode === "dynamic"; - let switchFromDynamic = Boolean(prevMode) && prevMode === "dynamic" && this.model.defaultMode !== "dynamic"; - if(switchToDynamic || switchFromDynamic) { - this.speciesEditor.renderEditSpeciesView(); - this.speciesEditor.renderViewSpeciesView(); - } - }, toggleVolumeContainer: function () { if(!this.model.is_spatial) { if(this.model.defaultMode === "continuous") { diff --git a/client/templates/includes/modelView.pug b/client/templates/includes/modelView.pug index 5890f5086b..4c863c4d18 100644 --- a/client/templates/includes/modelView.pug +++ b/client/templates/includes/modelView.pug @@ -50,3 +50,5 @@ div#model-view div="Model Mode: " + this.modelMode div(data-hook="domain-viewer-container") + + div(data-hook="species-view-container") diff --git a/client/templates/includes/spatialSpeciesEditor.pug b/client/templates/includes/spatialSpeciesView.pug similarity index 100% rename from client/templates/includes/spatialSpeciesEditor.pug rename to client/templates/includes/spatialSpeciesView.pug diff --git a/client/templates/includes/speciesEditor.pug b/client/templates/includes/speciesView.pug similarity index 100% rename from client/templates/includes/speciesEditor.pug rename to client/templates/includes/speciesView.pug diff --git a/client/templates/pages/modelEditor.pug b/client/templates/pages/modelEditor.pug index ec0c4fc37e..ae8fc5f2bb 100644 --- a/client/templates/pages/modelEditor.pug +++ b/client/templates/pages/modelEditor.pug @@ -27,8 +27,6 @@ section.page li.breadcrumb-item.active(aria-current="page")=this.model.name div(data-hook="model-view-container") - - div(data-hook="species-editor-container") div(data-hook="initial-conditions-editor-container") diff --git a/client/views/model-state-buttons.js b/client/views/model-state-buttons.js index 72050697cd..f4ed08e0f5 100644 --- a/client/views/model-state-buttons.js +++ b/client/views/model-state-buttons.js @@ -294,9 +294,9 @@ module.exports = View.extend({ } }, openSpeciesSection: function () { - let specSection = $(this.parent.speciesEditor.queryByHook("species-list-container")) + let specSection = $(this.parent.modelView.speciesView.queryByHook("species-list-container")) if(!specSection.hasClass("show")) { - let specCollapseBtn = $(this.parent.speciesEditor.queryByHook("collapse")) + let specCollapseBtn = $(this.parent.modelView.speciesView.queryByHook("collapse")) specCollapseBtn.click() specCollapseBtn.html('-') } diff --git a/client/views/model-view.js b/client/views/model-view.js index a4f0d7685a..2b3e845262 100644 --- a/client/views/model-view.js +++ b/client/views/model-view.js @@ -25,6 +25,7 @@ let modals = require('../modals'); let Domain = require('../models/domain'); //views let View = require('ampersand-view'); +let SpeciesView = require('../views/species-view'); let DomainViewer = require('../views/domain-viewer'); //templates let template = require('../templates/includes/modelView.pug'); @@ -110,11 +111,24 @@ module.exports = View.extend({ app.registerRenderSubview(this, this.domainViewer, 'domain-viewer-container'); } }, + setAllSpeciesModes: function (prevMode) { + let self = this; + this.model.species.forEach(function (specie) { + specie.mode = self.model.defaultMode; + self.model.species.trigger('update-species', specie.compID, specie, false, true); + }); + let switchToDynamic = (!Boolean(prevMode) || prevMode !== "dynamic") && this.model.defaultMode === "dynamic"; + let switchFromDynamic = Boolean(prevMode) && prevMode === "dynamic" && this.model.defaultMode !== "dynamic"; + if(switchToDynamic || switchFromDynamic) { + this.speciesView.renderEditSpeciesView(); + this.speciesView.renderViewSpeciesView(); + } + }, setDefaultMode: function (e) { let prevMode = this.model.defaultMode; this.model.defaultMode = e.target.dataset.name; - this.parent.speciesEditor.defaultMode = e.target.dataset.name; - this.parent.setAllSpeciesModes(prevMode); + this.speciesView.defaultMode = e.target.dataset.name; + this.setAllSpeciesModes(prevMode); this.parent.toggleVolumeContainer(); }, setInitialDefaultMode: function (modal, mode) { @@ -122,8 +136,8 @@ module.exports = View.extend({ modal.modal('hide'); $(this.queryByHook(dataHooks[mode])).prop('checked', true); this.model.defaultMode = mode; - this.parent.speciesEditor.defaultMode = mode; - this.parent.setAllSpeciesModes(); + this.speciesView.defaultMode = mode; + this.setAllSpeciesModes(); this.parent.toggleVolumeContainer(); }, setReadOnlyMode: function (component) { @@ -135,5 +149,17 @@ module.exports = View.extend({ $(this.queryByHook(component + '-view-tab')).tab('show'); $(this.queryByHook('edit-' + component)).removeClass('active'); $(this.queryByHook('view-' + component)).addClass('active'); + }, + subviews: { + speciesView: { + hook: "species-view-container", + prepareView: function (el) { + return new SpeciesView({ + collection: this.model.species, + spatial: this.model.is_spatial, + defaultMode: this.model.defaultMode + }); + } + } } }); \ No newline at end of file diff --git a/client/views/species-editor.js b/client/views/species-view.js similarity index 98% rename from client/views/species-editor.js rename to client/views/species-view.js index 9ac3ae456e..c6a4dbc4b5 100644 --- a/client/views/species-editor.js +++ b/client/views/species-view.js @@ -24,8 +24,8 @@ let Tooltips = require('../tooltips'); let View = require('ampersand-view'); let SpecieView = require('./edit-species'); //templates -let speciesTemplate = require('../templates/includes/speciesEditor.pug'); -let spatialSpeciesTemplate = require('../templates/includes/spatialSpeciesEditor.pug'); +let speciesTemplate = require('../templates/includes/speciesView.pug'); +let spatialSpeciesTemplate = require('../templates/includes/spatialSpeciesView.pug'); module.exports = View.extend({ events: { From a1bd97cab920e80f088053894b84fd99c0faa07c Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Thu, 1 Jul 2021 16:42:38 -0400 Subject: [PATCH 086/192] Moved the tooltip jquery function to app.js as tooltipSetup and created a documentSetup function. --- client/app.js | 17 ++++++++++++++++- 1 file changed, 16 insertions(+), 1 deletion(-) diff --git a/client/app.js b/client/app.js index e809e61721..c5d3b297a3 100644 --- a/client/app.js +++ b/client/app.js @@ -193,6 +193,19 @@ let newWorkflow = (parent, mdlPath, isSpatial, type) => { }); } +tooltipSetup = () => { + $(function () { + $('[data-toggle="tooltip"]').tooltip(); + $('[data-toggle="tooltip"]').click(function () { + $('[data-toggle="tooltip"]').tooltip("hide"); + }); + }); +} + +documentSetup = () => { + documentSetup(); +} + module.exports = { routePrefix: routePrefix, getApiPath: getApiPath, @@ -202,7 +215,9 @@ module.exports = { changeCollapseButtonText: changeCollapseButtonText, newWorkflow: newWorkflow, getXHR: getXHR, - postXHR: postXHR + postXHR: postXHR, + tooltipSetup: tooltipSetup, + documentSetup: documentSetup }; From 3651e96c93aafcdd953ab36b94ec86bdcc930631 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Thu, 1 Jul 2021 16:43:10 -0400 Subject: [PATCH 087/192] Cleaned up the species view file. --- client/views/species-view.js | 44 +++++++++++------------------------- 1 file changed, 13 insertions(+), 31 deletions(-) diff --git a/client/views/species-view.js b/client/views/species-view.js index c6a4dbc4b5..28d76cc8af 100644 --- a/client/views/species-view.js +++ b/client/views/species-view.js @@ -34,12 +34,12 @@ module.exports = View.extend({ }, initialize: function (attrs, options) { View.prototype.initialize.apply(this, arguments); - this.spatial = attrs.spatial + this.spatial = attrs.spatial; this.readOnly = attrs.readOnly ? attrs.readOnly : false; this.template = this.spatial ? spatialSpeciesTemplate : speciesTemplate; this.tooltips = Tooltips.speciesEditor; this.defaultMode = attrs.defaultMode; - let self = this + let self = this; this.collection.on('update-species', function (compID, specie, isNameUpdate, isDefaultMode) { self.collection.parent.reactions.forEach(function (reaction) { reaction.reactants.forEach(function (reactant) { @@ -103,19 +103,13 @@ module.exports = View.extend({ var types = this.parent.model.domain.types.map(function (type) { return type.typeID; }); - types.shift() + types.shift(); }else{ - var types = [] + var types = []; } this.collection.addSpecie(types); - this.toggleSpeciesCollectionError() - $(function () { - $('[data-toggle="tooltip"]').tooltip(); - $('[data-toggle="tooltip"]').click(function () { - $('[data-toggle="tooltip"]').tooltip("hide"); - - }); - }); + this.toggleSpeciesCollectionError(); + app.tooltipSetup(); }, changeCollapseButtonText: function (e) { app.changeCollapseButtonText(this, e); @@ -139,13 +133,7 @@ module.exports = View.extend({ SpecieView, this.queryByHook('edit-specie-list') ); - $(function () { - $('[data-toggle="tooltip"]').tooltip(); - $('[data-toggle="tooltip"]').click(function () { - $('[data-toggle="tooltip"]').tooltip("hide"); - - }); - }); + app.tooltipSetup(); }, renderViewSpeciesView: function () { if(this.viewSpeciesView){ @@ -169,23 +157,17 @@ module.exports = View.extend({ this.queryByHook('view-specie-list'), options ); - $(function () { - $('[data-toggle="tooltip"]').tooltip(); - $('[data-toggle="tooltip"]').click(function () { - $('[data-toggle="tooltip"]').tooltip("hide"); - - }); - }); + app.tooltipSetup(); }, toggleSpeciesCollectionError: function () { if(this.spatial) {return}; - let errorMsg = $(this.queryByHook('species-collection-error')) + let errorMsg = $(this.queryByHook('species-collection-error')); if(this.collection.length <= 0) { - errorMsg.addClass('component-invalid') - errorMsg.removeClass('component-valid') + errorMsg.addClass('component-invalid'); + errorMsg.removeClass('component-valid'); }else{ - errorMsg.addClass('component-valid') - errorMsg.removeClass('component-invalid') + errorMsg.addClass('component-valid'); + errorMsg.removeClass('component-invalid'); } } }); From a41c37e8c1cb3855b4afc6d852c9646332be40f1 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Thu, 1 Jul 2021 16:51:13 -0400 Subject: [PATCH 088/192] Renamed the specie view with a name that better fits its function. --- .../views/{edit-species.js => specie-view.js} | 30 +++++++++---------- client/views/species-view.js | 2 +- 2 files changed, 16 insertions(+), 16 deletions(-) rename client/views/{edit-species.js => specie-view.js} (95%) diff --git a/client/views/edit-species.js b/client/views/specie-view.js similarity index 95% rename from client/views/edit-species.js rename to client/views/specie-view.js index 39a7e6f744..be1d092944 100644 --- a/client/views/edit-species.js +++ b/client/views/specie-view.js @@ -196,38 +196,38 @@ module.exports = View.extend({ if(this.viewMode || this.parent.spatial) {return} // Update validation requirements and re-run tests for inputSwitchTol. // This removes error reporting not using switching tolerance - let shouldValidateTol = this.model.mode === "dynamic" && this.model.isSwitchTol + let shouldValidateTol = this.model.mode === "dynamic" && this.model.isSwitchTol; this.inputSwitchTol.required = shouldValidateTol; - this.inputSwitchTol.tests = shouldValidateTol ? tests.valueTests : [] - this.inputSwitchTol.runTests() + this.inputSwitchTol.tests = shouldValidateTol ? tests.valueTests : []; + this.inputSwitchTol.runTests(); // Update validation requirements and re-run tests for inputSwitchMin. // This removes error reporting when not using minimum value for switching. - let shouldValidateMin = this.model.mode === "dynamic" && !this.model.isSwitchTol + let shouldValidateMin = this.model.mode === "dynamic" && !this.model.isSwitchTol; this.inputSwitchMin.required = shouldValidateMin; - this.inputSwitchMin.tests = shouldValidateMin ? tests.valueTests : [] - this.inputSwitchMin.runTests() + this.inputSwitchMin.tests = shouldValidateMin ? tests.valueTests : []; + this.inputSwitchMin.runTests(); // Add/Remove 'input-invalid' class from inputSwitchTol and inputSwitchMin based on whether // the user is using switching tolerance or minimum value for switching - let tolInput = $(this.queryByHook('switching-tolerance')).find('input')[0] - let minInput = $(this.queryByHook('switching-threshold')).find('input')[0] + let tolInput = $(this.queryByHook('switching-tolerance')).find('input')[0]; + let minInput = $(this.queryByHook('switching-threshold')).find('input')[0]; if(this.model.mode !== "dynamic") { - $(tolInput).removeClass('input-invalid') - $(minInput).removeClass('input-invalid') + $(tolInput).removeClass('input-invalid'); + $(minInput).removeClass('input-invalid'); }else if(this.model.isSwitchTol){ - $(minInput).removeClass('input-invalid') + $(minInput).removeClass('input-invalid'); if(this.model.switchTol === "" || isNaN(this.model.switchTol)){ - $(tolInput).addClass('input-invalid') + $(tolInput).addClass('input-invalid'); } }else{ - $(tolInput).removeClass('input-invalid') + $(tolInput).removeClass('input-invalid'); if(this.model.switchMin === "" || isNaN(this.model.switchMin)){ - $(minInput).addClass('input-invalid') + $(minInput).addClass('input-invalid'); } } }, updateValid: function (e) {}, updateViewer: function () { - this.parent.renderViewSpeciesView() + this.parent.renderViewSpeciesView(); }, subviews: { inputName: { diff --git a/client/views/species-view.js b/client/views/species-view.js index 28d76cc8af..d5a5942337 100644 --- a/client/views/species-view.js +++ b/client/views/species-view.js @@ -22,7 +22,7 @@ let app = require('../app'); let Tooltips = require('../tooltips'); //views let View = require('ampersand-view'); -let SpecieView = require('./edit-species'); +let SpecieView = require('./specie-view'); //templates let speciesTemplate = require('../templates/includes/speciesView.pug'); let spatialSpeciesTemplate = require('../templates/includes/spatialSpeciesView.pug'); From 22bcbdaae34521d8ab345962f5683d7646c6656c Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Thu, 1 Jul 2021 16:54:36 -0400 Subject: [PATCH 089/192] Tweaked the styling for the collapse button to allow the tabs to meet the card boby. --- client/styles/styles.css | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/client/styles/styles.css b/client/styles/styles.css index 64935dff14..ccafa8ec60 100644 --- a/client/styles/styles.css +++ b/client/styles/styles.css @@ -339,10 +339,9 @@ input[type="file"]::-ms-browse { .btn-outline-collapse { color: #000; - padding: 0px 10px; + padding: 0px 10px 6px 10px; font-size: 20px; vertical-align: middle; - margin-bottom: 0.75rem; } .btn-outline-collapse:hover { From 48bdbf5123ee25007d5365257311686f0dd32d64 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 2 Jul 2021 08:33:42 -0400 Subject: [PATCH 090/192] Renamed the initial conditions view and template files with names that better fix their functions. --- client/pages/model-editor.js | 1 - ...nsEditor.pug => initialConditionsView.pug} | 0 .../includes/initialConditionsViewer.pug | 28 ---------- client/templates/includes/modelView.pug | 2 + client/templates/pages/modelEditor.pug | 2 - ...condition.js => initial-condition-view.js} | 0 ...s-editor.js => initial-conditions-view.js} | 4 +- client/views/initial-conditions-viewer.js | 54 ------------------- client/views/model-view.js | 1 + 9 files changed, 5 insertions(+), 87 deletions(-) rename client/templates/includes/{initialConditionsEditor.pug => initialConditionsView.pug} (100%) delete mode 100644 client/templates/includes/initialConditionsViewer.pug rename client/views/{edit-initial-condition.js => initial-condition-view.js} (100%) rename client/views/{initial-conditions-editor.js => initial-conditions-view.js} (96%) delete mode 100644 client/views/initial-conditions-viewer.js diff --git a/client/pages/model-editor.js b/client/pages/model-editor.js index f90af7ba2a..ea58c83e16 100644 --- a/client/pages/model-editor.js +++ b/client/pages/model-editor.js @@ -28,7 +28,6 @@ let Tooltips = require("../tooltips"); var PageView = require('../pages/base'); let ModelView = require('../views/model-view'); var InputView = require('../views/input'); -var InitialConditionsEditorView = require('../views/initial-conditions-editor'); var ParametersEditorView = require('../views/parameters-editor'); var ParticleViewer = require('../views/view-particle'); var ReactionsEditorView = require('../views/reactions-editor'); diff --git a/client/templates/includes/initialConditionsEditor.pug b/client/templates/includes/initialConditionsView.pug similarity index 100% rename from client/templates/includes/initialConditionsEditor.pug rename to client/templates/includes/initialConditionsView.pug diff --git a/client/templates/includes/initialConditionsViewer.pug b/client/templates/includes/initialConditionsViewer.pug deleted file mode 100644 index deb22b01b6..0000000000 --- a/client/templates/includes/initialConditionsViewer.pug +++ /dev/null @@ -1,28 +0,0 @@ -div#initial-conditions.card.card-body - - div - - h3.inline Initial Conditions - - button.btn.btn-outline-collapse(data-toggle="collapse" data-target="#initial-condition" data-hook="initial-condition-button") - - - div.collapse.show(id="initial-condition" data-hook="initial-conditions") - - table.table - - thead - - tr - - th(scope="col") Type - - th(scope="col") Variable - - th(scope="col") Count - - th(scope="col") Details - - tbody(data-hook="initial-conditions-collection") - - if this.collection.parent.for === "edit" - button.btn.btn-outline-primary.box-shadow(data-hook="edit-species") Edit Variables \ No newline at end of file diff --git a/client/templates/includes/modelView.pug b/client/templates/includes/modelView.pug index 4c863c4d18..e79a39ad6a 100644 --- a/client/templates/includes/modelView.pug +++ b/client/templates/includes/modelView.pug @@ -52,3 +52,5 @@ div#model-view div(data-hook="domain-viewer-container") div(data-hook="species-view-container") + + div(data-hook="initial-conditions-editor-container") diff --git a/client/templates/pages/modelEditor.pug b/client/templates/pages/modelEditor.pug index ae8fc5f2bb..78645ae1ef 100644 --- a/client/templates/pages/modelEditor.pug +++ b/client/templates/pages/modelEditor.pug @@ -28,8 +28,6 @@ section.page div(data-hook="model-view-container") - div(data-hook="initial-conditions-editor-container") - div(data-hook="parameters-editor-container") div(data-hook="reactions-editor-container") diff --git a/client/views/edit-initial-condition.js b/client/views/initial-condition-view.js similarity index 100% rename from client/views/edit-initial-condition.js rename to client/views/initial-condition-view.js diff --git a/client/views/initial-conditions-editor.js b/client/views/initial-conditions-view.js similarity index 96% rename from client/views/initial-conditions-editor.js rename to client/views/initial-conditions-view.js index 54a9c1d4f2..ecde95f9cf 100644 --- a/client/views/initial-conditions-editor.js +++ b/client/views/initial-conditions-view.js @@ -22,9 +22,9 @@ let app = require('../app'); let Tooltips = require('../tooltips'); //views var View = require('ampersand-view'); -var EditInitialCondition = require('./edit-initial-condition'); +var EditInitialCondition = require('./initial-condition-view'); //templates -var template = require('../templates/includes/initialConditionsEditor.pug'); +var template = require('../templates/includes/initialConditionsView.pug'); module.exports = View.extend({ template: template, diff --git a/client/views/initial-conditions-viewer.js b/client/views/initial-conditions-viewer.js deleted file mode 100644 index 66bfc3e51f..0000000000 --- a/client/views/initial-conditions-viewer.js +++ /dev/null @@ -1,54 +0,0 @@ -/* -StochSS is a platform for simulating biochemical systems -Copyright (C) 2019-2021 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 -let app = require('../app'); -//views -var View = require('ampersand-view'); -var ViewInitialCondition = require('./view-initial-condition'); -//templates -var template = require('../templates/includes/initialConditionsViewer.pug'); - -module.exports = View.extend({ - template: template, - events: { - 'click [data-hook=initial-condition-button]' : 'changeCollapseButtonText', - 'click [data-hook=edit-species]' : '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, ViewInitialCondition, this.queryByHook('initial-conditions-collection')) - $(document).ready(function () { - $('[data-toggle="tooltip"]').tooltip(); - $('[data-toggle="tooltip"]').click(function () { - $('[data-toggle="tooltip"]').tooltip("hide"); - }); - }); - }, - switchToEditMode: function (e) { - this.parent.renderInitialConditions("edit", true); - }, - changeCollapseButtonText: function (e) { - app.changeCollapseButtonText(this, e); - }, -}); \ No newline at end of file diff --git a/client/views/model-view.js b/client/views/model-view.js index 2b3e845262..9342fa81b1 100644 --- a/client/views/model-view.js +++ b/client/views/model-view.js @@ -27,6 +27,7 @@ let Domain = require('../models/domain'); let View = require('ampersand-view'); let SpeciesView = require('../views/species-view'); let DomainViewer = require('../views/domain-viewer'); +let InitialConditionsEditorView = require('../views/initial-conditions-view'); //templates let template = require('../templates/includes/modelView.pug'); From 98eb16f2334e85c6f1d67ead42569e12a698e62f Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 2 Jul 2021 09:09:33 -0400 Subject: [PATCH 091/192] Moved the initial conditions render function and container into the model view. --- client/pages/model-editor.js | 10 ---------- client/templates/includes/modelView.pug | 2 +- client/views/model-view.js | 15 +++++++++++++-- 3 files changed, 14 insertions(+), 13 deletions(-) diff --git a/client/pages/model-editor.js b/client/pages/model-editor.js index ea58c83e16..b16583643c 100644 --- a/client/pages/model-editor.js +++ b/client/pages/model-editor.js @@ -236,7 +236,6 @@ let ModelEditor = PageView.extend({ if(this.model.is_spatial) { $(this.queryByHook("system-volume-container")).css("display", "none"); $(this.queryByHook("spatial-beta-message")).css("display", "block"); - this.renderInitialConditions(); this.renderBoundaryConditionsView(); $(this.queryByHook("toggle-preview-domain")).css("display", "inline-block"); this.openDomainPlot(); @@ -271,15 +270,6 @@ let ModelEditor = PageView.extend({ }); app.registerRenderSubview(this, this.boundaryConditionsView, "boundary-conditions-container"); }, - renderInitialConditions: function () { - if(this.initialConditionsEditor) { - this.initialConditionsEditor.remove(); - } - this.initialConditionsEditor = new InitialConditionsEditorView({ - collection: this.model.initialConditions, - }); - app.registerRenderSubview(this, this.initialConditionsEditor, 'initial-conditions-editor-container'); - }, renderParametersView: function () { if(this.parametersEditor) { this.parametersEditor.remove() diff --git a/client/templates/includes/modelView.pug b/client/templates/includes/modelView.pug index e79a39ad6a..3f4c18100c 100644 --- a/client/templates/includes/modelView.pug +++ b/client/templates/includes/modelView.pug @@ -53,4 +53,4 @@ div#model-view div(data-hook="species-view-container") - div(data-hook="initial-conditions-editor-container") + div(data-hook="initial-conditions-view-container") diff --git a/client/views/model-view.js b/client/views/model-view.js index 9342fa81b1..4e646cf106 100644 --- a/client/views/model-view.js +++ b/client/views/model-view.js @@ -27,7 +27,7 @@ let Domain = require('../models/domain'); let View = require('ampersand-view'); let SpeciesView = require('../views/species-view'); let DomainViewer = require('../views/domain-viewer'); -let InitialConditionsEditorView = require('../views/initial-conditions-view'); +let InitialConditionsView = require('../views/initial-conditions-view'); //templates let template = require('../templates/includes/modelView.pug'); @@ -158,7 +158,18 @@ module.exports = View.extend({ return new SpeciesView({ collection: this.model.species, spatial: this.model.is_spatial, - defaultMode: this.model.defaultMode + defaultMode: this.model.defaultMode, + readOnly: this.readOnly + }); + } + }, + initialConditionsView: { + waitFor: "model.is_spatial", + hook: "initial-conditions-view-container", + prepareView: function (el) { + return new InitialConditionsView({ + collection: this.model.initialConditions, + readOnly: this.readOnly }); } } From ec2ddae54a0d73b6da31bba54e80fefe78aa8bc8 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 2 Jul 2021 09:23:27 -0400 Subject: [PATCH 092/192] Added model input focus and model remove events to the document setup function. Cleaned up the initial condition view files. --- client/app.js | 8 +++++- client/views/initial-condition-view.js | 35 +++++++++++-------------- client/views/initial-conditions-view.js | 30 +++++++-------------- 3 files changed, 32 insertions(+), 41 deletions(-) diff --git a/client/app.js b/client/app.js index c5d3b297a3..957b326f06 100644 --- a/client/app.js +++ b/client/app.js @@ -203,7 +203,13 @@ tooltipSetup = () => { } documentSetup = () => { - documentSetup(); + tooltipSetup(); + $(document).on('shown.bs.modal', function (e) { + $('[autofocus]', e.target).focus(); + }); + $(document).on('hide.bs.modal', '.modal', function (e) { + e.target.remove() + }); } module.exports = { diff --git a/client/views/initial-condition-view.js b/client/views/initial-condition-view.js index 80b9489814..0d1fa6c3d3 100644 --- a/client/views/initial-condition-view.js +++ b/client/views/initial-condition-view.js @@ -20,13 +20,13 @@ let $ = require('jquery'); let _ = require('underscore'); //support files let app = require('../app'); -var tests = require('./tests'); +let tests = require('./tests'); let modals = require('../modals'); //views -var View = require('ampersand-view'); -var InputView = require('./input'); -var SelectView = require('ampersand-select-view'); -var TypesView = require('./component-types'); +let InputView = require('./input'); +let View = require('ampersand-view'); +let TypesView = require('./component-types'); +let SelectView = require('ampersand-select-view'); //templates let editTemplate = require('../templates/includes/editInitialCondition.pug'); let viewTemplate = require('../templates/includes/viewInitialCondition.pug'); @@ -47,31 +47,26 @@ module.exports = View.extend({ this.types = []; this.model.types.forEach(function (index) { let type = self.model.collection.parent.domain.types.get(index, "typeID"); - self.types.push(type.name) + self.types.push(type.name); }); } }, render: function () { this.template = this.viewMode ? viewTemplate : editTemplate; View.prototype.render.apply(this, arguments); + app.documentSetup(); if(!this.viewMode) { this.model.on('change', _.bind(this.updateViewer, this)); } - $(document).on('shown.bs.modal', function (e) { - $('[autofocus]', e.target).focus(); - }); - $(document).on('hide.bs.modal', '.modal', function (e) { - e.target.remove() - }); if(!this.model.annotation){ - $(this.queryByHook('edit-annotation-btn')).text('Add') + $(this.queryByHook('edit-annotation-btn')).text('Add'); } this.toggleDetailsView(); }, editAnnotation: function () { - var self = this; - var name = this.model.name; - var annotation = this.model.annotation; + let self = this; + let name = this.model.name; + let annotation = this.model.annotation; if(document.querySelector('#initialConditionAnnotationModal')) { document.querySelector('#initialConditionAnnotationModal').remove(); } @@ -115,11 +110,11 @@ module.exports = View.extend({ }, toggleDetailsView: function () { if(this.model.icType === "Place") { - $(this.queryByHook("scatter-details")).css("display", "none") - $(this.queryByHook("place-details")).css("display", "block") + $(this.queryByHook("scatter-details")).css("display", "none"); + $(this.queryByHook("place-details")).css("display", "block"); }else { - $(this.queryByHook("place-details")).css("display", "none") - $(this.queryByHook("scatter-details")).css("display", "block") + $(this.queryByHook("place-details")).css("display", "none"); + $(this.queryByHook("scatter-details")).css("display", "block"); } }, update: function () {}, diff --git a/client/views/initial-conditions-view.js b/client/views/initial-conditions-view.js index ecde95f9cf..caa473fc9a 100644 --- a/client/views/initial-conditions-view.js +++ b/client/views/initial-conditions-view.js @@ -16,15 +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'); //support files let app = require('../app'); let Tooltips = require('../tooltips'); //views -var View = require('ampersand-view'); -var EditInitialCondition = require('./initial-condition-view'); +let View = require('ampersand-view'); +let InitialConditionView = require('./initial-condition-view'); //templates -var template = require('../templates/includes/initialConditionsView.pug'); +let template = require('../templates/includes/initialConditionsView.pug'); module.exports = View.extend({ template: template, @@ -73,23 +73,18 @@ module.exports = View.extend({ }, renderEditInitialConditionsView: function () { if(this.editInitialConditionView) { - this.editInitialConditionView.remove() + this.editInitialConditionView.remove(); } this.editInitialConditionView = this.renderCollection( this.collection, - EditInitialCondition, + InitialConditionView, this.queryByHook('edit-initial-conditions-collection') ); - $(function () { - $('[data-toggle="tooltip"]').tooltip(); - $('[data-toggle="tooltip"]').click(function () { - $('[data-toggle="tooltip"]').tooltip("hide"); - }); - }); + app.tooltipSetup(); }, renderViewInitialConditionsView: function () { if(this.viewInitialConditionView) { - this.viewInitialConditionView.remove() + this.viewInitialConditionView.remove(); } this.containsMdlWithAnn = this.collection.filter(function (model) {return model.annotation}).length > 0; if(!this.containsMdlWithAnn) { @@ -100,16 +95,11 @@ module.exports = View.extend({ let options = {viewOptions: {viewMode: true}}; this.viewInitialConditionView = this.renderCollection( this.collection, - EditInitialCondition, + InitialConditionView, this.queryByHook('view-initial-conditions-collection'), options ); - $(function () { - $('[data-toggle="tooltip"]').tooltip(); - $('[data-toggle="tooltip"]').click(function () { - $('[data-toggle="tooltip"]').tooltip("hide"); - }); - }); + app.tooltipSetup(); }, update: function () {}, updateValid: function () {} From 824919c658280e39dadf4852d9eef4b397814e92 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 2 Jul 2021 09:37:42 -0400 Subject: [PATCH 093/192] Renamed the parameter view and template file to better fit their function. --- client/pages/model-editor.js | 2 +- .../includes/{parametersEditor.pug => parametersView.pug} | 0 client/views/{edit-parameter.js => parameter-view.js} | 0 client/views/{parameters-editor.js => parameters-view.js} | 4 ++-- 4 files changed, 3 insertions(+), 3 deletions(-) rename client/templates/includes/{parametersEditor.pug => parametersView.pug} (100%) rename client/views/{edit-parameter.js => parameter-view.js} (100%) rename client/views/{parameters-editor.js => parameters-view.js} (97%) diff --git a/client/pages/model-editor.js b/client/pages/model-editor.js index b16583643c..27fe9c20e2 100644 --- a/client/pages/model-editor.js +++ b/client/pages/model-editor.js @@ -28,7 +28,7 @@ let Tooltips = require("../tooltips"); var PageView = require('../pages/base'); let ModelView = require('../views/model-view'); var InputView = require('../views/input'); -var ParametersEditorView = require('../views/parameters-editor'); +var ParametersEditorView = require('../views/parameters-view'); var ParticleViewer = require('../views/view-particle'); var ReactionsEditorView = require('../views/reactions-editor'); var EventsEditorView = require('../views/events-editor'); diff --git a/client/templates/includes/parametersEditor.pug b/client/templates/includes/parametersView.pug similarity index 100% rename from client/templates/includes/parametersEditor.pug rename to client/templates/includes/parametersView.pug diff --git a/client/views/edit-parameter.js b/client/views/parameter-view.js similarity index 100% rename from client/views/edit-parameter.js rename to client/views/parameter-view.js diff --git a/client/views/parameters-editor.js b/client/views/parameters-view.js similarity index 97% rename from client/views/parameters-editor.js rename to client/views/parameters-view.js index d7623c1a93..fdbd72de8a 100644 --- a/client/views/parameters-editor.js +++ b/client/views/parameters-view.js @@ -22,9 +22,9 @@ let app = require('../app'); var Tooltips = require('../tooltips'); //views var View = require('ampersand-view'); -var EditParameterView = require('./edit-parameter'); +var EditParameterView = require('./parameter-view'); //templates -var template = require('../templates/includes/parametersEditor.pug'); +var template = require('../templates/includes/parametersView.pug'); module.exports = View.extend({ template: template, From 6159700d38e74a33f3e324573a25641dac29ab3c Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 2 Jul 2021 10:32:24 -0400 Subject: [PATCH 094/192] Moved the parameters render function and container to the model view page. --- client/pages/model-editor.js | 9 --------- client/templates/includes/modelView.pug | 2 ++ client/templates/pages/modelEditor.pug | 2 -- client/views/model-state-buttons.js | 6 +++--- client/views/model-view.js | 12 +++++++++++- 5 files changed, 16 insertions(+), 15 deletions(-) diff --git a/client/pages/model-editor.js b/client/pages/model-editor.js index 27fe9c20e2..57ca622d76 100644 --- a/client/pages/model-editor.js +++ b/client/pages/model-editor.js @@ -28,7 +28,6 @@ let Tooltips = require("../tooltips"); var PageView = require('../pages/base'); let ModelView = require('../views/model-view'); var InputView = require('../views/input'); -var ParametersEditorView = require('../views/parameters-view'); var ParticleViewer = require('../views/view-particle'); var ReactionsEditorView = require('../views/reactions-editor'); var EventsEditorView = require('../views/events-editor'); @@ -229,7 +228,6 @@ let ModelEditor = PageView.extend({ this.modelStateButtons = new ModelStateButtonsView({ model: this.model }); - this.renderParametersView(); this.renderReactionsView(); app.registerRenderSubview(this, this.modelSettings, 'model-settings-container'); app.registerRenderSubview(this, this.modelStateButtons, 'model-state-buttons-container'); @@ -270,13 +268,6 @@ let ModelEditor = PageView.extend({ }); app.registerRenderSubview(this, this.boundaryConditionsView, "boundary-conditions-container"); }, - renderParametersView: function () { - if(this.parametersEditor) { - this.parametersEditor.remove() - } - this.parametersEditor = new ParametersEditorView({collection: this.model.parameters}); - app.registerRenderSubview(this, this.parametersEditor, 'parameters-editor-container'); - }, renderReactionsView: function () { if(this.reactionsEditor) { this.reactionsEditor.remove() diff --git a/client/templates/includes/modelView.pug b/client/templates/includes/modelView.pug index 3f4c18100c..2fb6e91f6e 100644 --- a/client/templates/includes/modelView.pug +++ b/client/templates/includes/modelView.pug @@ -54,3 +54,5 @@ div#model-view div(data-hook="species-view-container") div(data-hook="initial-conditions-view-container") + + div(data-hook="parameters-view-container") diff --git a/client/templates/pages/modelEditor.pug b/client/templates/pages/modelEditor.pug index 78645ae1ef..f9761adc9c 100644 --- a/client/templates/pages/modelEditor.pug +++ b/client/templates/pages/modelEditor.pug @@ -28,8 +28,6 @@ section.page div(data-hook="model-view-container") - div(data-hook="parameters-editor-container") - div(data-hook="reactions-editor-container") div.card(data-hook="model-editor-advanced-container") diff --git a/client/views/model-state-buttons.js b/client/views/model-state-buttons.js index f4ed08e0f5..6f777bd399 100644 --- a/client/views/model-state-buttons.js +++ b/client/views/model-state-buttons.js @@ -302,7 +302,7 @@ module.exports = View.extend({ } }, openDomainSection: function () { - let domainSection = $(this.parent.parametersEditor.queryByHook("parameters-list-container")) + let domainSection = $(this.parent.modelView.domainViewer.queryByHook("domain-container")) if(!domainSection.hasClass("show")) { let domainCollapseBtn = $(this.parent.modelView.domainViewer.queryByHook("collapse")) domainCollapseBtn.click() @@ -310,9 +310,9 @@ module.exports = View.extend({ } }, openParametersSection: function () { - let paramSection = $(this.parent.parametersEditor.queryByHook("parameters-list-container")) + let paramSection = $(this.parent.modelView.parametersView.queryByHook("parameters-list-container")) if(!paramSection.hasClass("show")) { - let paramCollapseBtn = $(this.parent.parametersEditor.queryByHook("collapse")) + let paramCollapseBtn = $(this.parent.modelView.parametersView.queryByHook("collapse")) paramCollapseBtn.click() paramCollapseBtn.html('-') } diff --git a/client/views/model-view.js b/client/views/model-view.js index 4e646cf106..d20e5149f8 100644 --- a/client/views/model-view.js +++ b/client/views/model-view.js @@ -27,6 +27,7 @@ let Domain = require('../models/domain'); let View = require('ampersand-view'); let SpeciesView = require('../views/species-view'); let DomainViewer = require('../views/domain-viewer'); +let ParametersView = require('../views/parameters-view'); let InitialConditionsView = require('../views/initial-conditions-view'); //templates let template = require('../templates/includes/modelView.pug'); @@ -40,7 +41,7 @@ module.exports = View.extend({ }, initialize: function(attrs, options) { View.prototype.initialize.apply(this, arguments); - this.readOnly = attrs.readOnly ? attrs.readOnly : false; + this.readOnly = attrs.readOnly ? attrs.readOnly : true; let modeMap = {continuous: "Concentration", discrete: "Population", dynamic: "Hybrid Concentration/Population"}; this.modelMode = modeMap[this.model.defaultMode] }, @@ -172,6 +173,15 @@ module.exports = View.extend({ readOnly: this.readOnly }); } + }, + parametersView: { + hook: "parameters-view-container", + prepareView: function (el) { + return new ParametersView({ + collection: this.model.parameters, + readOnly: this.readOnly + }); + } } } }); \ No newline at end of file From e5def824bd15cd83d2ec6d2e617d63aad7d57636 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 2 Jul 2021 10:42:38 -0400 Subject: [PATCH 095/192] Cleaned up the parameter view files. --- client/views/parameter-view.js | 67 ++++++++++++++------------------- client/views/parameters-view.js | 42 +++++++-------------- 2 files changed, 43 insertions(+), 66 deletions(-) diff --git a/client/views/parameter-view.js b/client/views/parameter-view.js index bc2bec13e9..ff80b985a3 100644 --- a/client/views/parameter-view.js +++ b/client/views/parameter-view.js @@ -16,16 +16,16 @@ 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 _ = require('underscore'); //support files -var tests = require('./tests'); -var modals = require('../modals') +let tests = require('./tests'); +let modals = require('../modals') //views -var View = require('ampersand-view'); -var InputView = require('./input'); +let InputView = require('./input'); +let View = require('ampersand-view'); //templates -var editTemplate = require('../templates/includes/editParameter.pug'); +let editTemplate = require('../templates/includes/editParameter.pug'); let viewTemplate = require('../templates/includes/viewParameters.pug'); module.exports = View.extend({ @@ -33,43 +33,30 @@ module.exports = View.extend({ 'model.inUse': { hook: 'remove', type: 'booleanAttribute', - name: 'disabled', - }, + name: 'disabled' + } }, events: { 'click [data-hook=edit-annotation-btn]' : 'editAnnotation', 'click [data-hook=remove]' : 'removeParameter', - 'change [data-hook=input-name-container]' : 'setParameterName', + 'change [data-hook=input-name-container]' : 'setParameterName' }, initialize: function (attrs, options) { View.prototype.initialize.apply(this, arguments); - this.previousName = this.model.name + 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); + app.documentSetup(); if(!this.viewMode){ - this.model.on('change', _.bind(this.updateViewer, this)) + this.model.on('change', _.bind(this.updateViewer, this)); } - $(document).on('shown.bs.modal', function (e) { - $('[autofocus]', e.target).focus(); - }); - $(document).on('hide.bs.modal', '.modal', function (e) { - e.target.remove() - }); if(!this.model.annotation){ - $(this.queryByHook('edit-annotation-btn')).text('Add') + $(this.queryByHook('edit-annotation-btn')).text('Add'); } }, - update: function () { - }, - updateValid: function () { - }, - removeParameter: function () { - this.remove(); - this.collection.removeParameter(this.model); - }, editAnnotation: function () { var self = this; var name = this.model.name; @@ -92,18 +79,24 @@ module.exports = View.extend({ modal.modal('hide'); }); }, + removeParameter: function () { + this.remove(); + this.collection.removeParameter(this.model); + }, setParameterName: function (e) { if(!e.target.value.trim()) { - this.model.name = this.previousName - this.parent.renderEditParameter() + this.model.name = this.previousName; + this.parent.renderEditParameter(); }else{ this.previousName = this.model.name this.model.collection.trigger('update-parameters', this.model.compID, this.model); - this.model.collection.trigger('remove') + this.model.collection.trigger('remove'); } }, + update: function () {}, + updateValid: function () {}, updateViewer: function () { - this.parent.renderViewParameter() + this.parent.renderViewParameter(); }, subviews: { inputName: { @@ -113,13 +106,12 @@ module.exports = View.extend({ parent: this, required: true, name: 'name', - label: '', tests: tests.nameTests, modelKey: 'name', valueType: 'string', - value: this.model.name, + value: this.model.name }); - }, + } }, inputValue: { hook: 'input-value-container', @@ -128,13 +120,12 @@ module.exports = View.extend({ parent: this, required: true, name: 'expression', - label: '', tests: tests.valueTests, modelKey: 'expression', valueType: 'number', - value: this.model.expression, + value: this.model.expression }); - }, - }, - }, + } + } + } }); \ No newline at end of file diff --git a/client/views/parameters-view.js b/client/views/parameters-view.js index fdbd72de8a..ff33549c0a 100644 --- a/client/views/parameters-view.js +++ b/client/views/parameters-view.js @@ -16,15 +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'); //support files let app = require('../app'); -var Tooltips = require('../tooltips'); +let Tooltips = require('../tooltips'); //views -var View = require('ampersand-view'); -var EditParameterView = require('./parameter-view'); +let View = require('ampersand-view'); +let EditParameterView = require('./parameter-view'); //templates -var template = require('../templates/includes/parametersView.pug'); +let template = require('../templates/includes/parametersView.pug'); module.exports = View.extend({ template: template, @@ -33,10 +33,10 @@ module.exports = View.extend({ '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.tooltips = Tooltips.parametersEditor; + let self = this; this.collection.on('update-parameters', function (compID, parameter) { self.collection.parent.reactions.map(function (reaction) { if(reaction.rate && reaction.rate.compID === compID){ @@ -76,9 +76,12 @@ module.exports = View.extend({ } this.renderViewParameter(); }, - update: function () { + addParameter: function () { + this.collection.addParameter(); + app.tooltipSetup(); }, - updateValid: function () { + changeCollapseButtonText: function (e) { + app.changeCollapseButtonText(this, e); }, renderEditParameter: function () { if(this.editParameterView){ @@ -89,12 +92,6 @@ module.exports = View.extend({ EditParameterView, this.queryByHook('edit-parameter-list') ); - $(function () { - $('[data-toggle="tooltip"]').tooltip(); - $('[data-toggle="tooltip"]').click(function () { - $('[data-toggle="tooltip"]').tooltip("hide"); - }); - }); }, renderViewParameter: function () { if(this.viewParameterView) { @@ -114,17 +111,6 @@ module.exports = View.extend({ options ); }, - addParameter: function () { - this.collection.addParameter(); - $(document).ready(function () { - $('[data-toggle="tooltip"]').tooltip(); - $('[data-toggle="tooltip"]').click(function () { - $('[data-toggle="tooltip"]').tooltip("hide"); - - }); - }); - }, - changeCollapseButtonText: function (e) { - app.changeCollapseButtonText(this, e); - }, + update: function () {}, + updateValid: function () {} }); \ No newline at end of file From ec54ec6a43fc9d816a26bc361bc2d45ed85ba691 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 2 Jul 2021 10:44:41 -0400 Subject: [PATCH 096/192] Added missing app require statement. --- client/views/model-view.js | 2 +- client/views/parameter-view.js | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/client/views/model-view.js b/client/views/model-view.js index d20e5149f8..944eaced21 100644 --- a/client/views/model-view.js +++ b/client/views/model-view.js @@ -41,7 +41,7 @@ module.exports = View.extend({ }, initialize: function(attrs, options) { View.prototype.initialize.apply(this, arguments); - this.readOnly = attrs.readOnly ? attrs.readOnly : true; + this.readOnly = attrs.readOnly ? attrs.readOnly : false; let modeMap = {continuous: "Concentration", discrete: "Population", dynamic: "Hybrid Concentration/Population"}; this.modelMode = modeMap[this.model.defaultMode] }, diff --git a/client/views/parameter-view.js b/client/views/parameter-view.js index ff80b985a3..61c8159643 100644 --- a/client/views/parameter-view.js +++ b/client/views/parameter-view.js @@ -19,6 +19,7 @@ along with this program. If not, see . let $ = require('jquery'); let _ = require('underscore'); //support files +let app = require('../app'); let tests = require('./tests'); let modals = require('../modals') //views From 7fda3397fb6b4c642382e07ed646dae4bc3b5407 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 2 Jul 2021 12:37:33 -0400 Subject: [PATCH 097/192] Renamed the reaction view and template files to names that better fit their functions. --- client/pages/model-editor.js | 2 +- .../includes/{reactionsEditor.pug => reactionsView.pug} | 0 client/views/{reactions-editor.js => reactions-view.js} | 2 +- 3 files changed, 2 insertions(+), 2 deletions(-) rename client/templates/includes/{reactionsEditor.pug => reactionsView.pug} (100%) rename client/views/{reactions-editor.js => reactions-view.js} (99%) diff --git a/client/pages/model-editor.js b/client/pages/model-editor.js index 57ca622d76..82e8c92dd8 100644 --- a/client/pages/model-editor.js +++ b/client/pages/model-editor.js @@ -29,7 +29,7 @@ var PageView = require('../pages/base'); let ModelView = require('../views/model-view'); var InputView = require('../views/input'); var ParticleViewer = require('../views/view-particle'); -var ReactionsEditorView = require('../views/reactions-editor'); +var ReactionsEditorView = require('../views/reactions-view'); var EventsEditorView = require('../views/events-editor'); var RulesEditorView = require('../views/rules-editor'); var SBMLComponentView = require('../views/sbml-component-editor'); diff --git a/client/templates/includes/reactionsEditor.pug b/client/templates/includes/reactionsView.pug similarity index 100% rename from client/templates/includes/reactionsEditor.pug rename to client/templates/includes/reactionsView.pug diff --git a/client/views/reactions-editor.js b/client/views/reactions-view.js similarity index 99% rename from client/views/reactions-editor.js rename to client/views/reactions-view.js index e6539a856e..22b6567d9c 100644 --- a/client/views/reactions-editor.js +++ b/client/views/reactions-view.js @@ -31,7 +31,7 @@ var View = require('ampersand-view'); var ReactionListingView = require('./reaction-listing'); var ReactionDetailsView = require('./reaction-details'); //templates -var template = require('../templates/includes/reactionsEditor.pug'); +var template = require('../templates/includes/reactionsView.pug'); module.exports = View.extend({ template: template, From a6ef9d3f454b4431d0ab8ac7c6cac4be7e8c11af Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 2 Jul 2021 13:04:53 -0400 Subject: [PATCH 098/192] Moved the reactions render function and container to the model view. --- client/pages/model-editor.js | 78 ------------------------ client/templates/includes/modelView.pug | 2 + client/templates/pages/modelEditor.pug | 2 - client/views/model-state-buttons.js | 4 +- client/views/model-view.js | 80 +++++++++++++++++++++++++ client/views/species-view.js | 2 +- 6 files changed, 85 insertions(+), 83 deletions(-) diff --git a/client/pages/model-editor.js b/client/pages/model-editor.js index 82e8c92dd8..32f95bba06 100644 --- a/client/pages/model-editor.js +++ b/client/pages/model-editor.js @@ -29,7 +29,6 @@ var PageView = require('../pages/base'); let ModelView = require('../views/model-view'); var InputView = require('../views/input'); var ParticleViewer = require('../views/view-particle'); -var ReactionsEditorView = require('../views/reactions-view'); var EventsEditorView = require('../views/events-editor'); var RulesEditorView = require('../views/rules-editor'); var SBMLComponentView = require('../views/sbml-component-editor'); @@ -93,18 +92,6 @@ let ModelEditor = PageView.extend({ self.model.updateValid() } }) - this.model.reactions.on("change", function (reactions) { - this.updateSpeciesInUse(); - this.updateParametersInUse(); - }, this); - this.model.eventsCollection.on("add change remove", function (){ - this.updateSpeciesInUse(); - this.updateParametersInUse(); - }, this); - this.model.rules.on("add change remove", function() { - this.updateSpeciesInUse(); - this.updateParametersInUse(); - }, this); window.addEventListener("pageshow", function (event) { var navType = window.performance.navigation.type if(navType === 2){ @@ -134,63 +121,6 @@ let ModelEditor = PageView.extend({ window.location.href = endpoint }, this)) }, - updateSpeciesInUse: function () { - var species = this.model.species; - var reactions = this.model.reactions; - var events = this.model.eventsCollection; - var rules = this.model.rules; - species.forEach(function (specie) { specie.inUse = false; }); - var updateInUseForReaction = function (stoichSpecie) { - _.where(species.models, { compID: stoichSpecie.specie.compID }) - .forEach(function (specie) { - specie.inUse = true; - }); - } - var updateInUseForOther = function (specie) { - _.where(species.models, { compID: specie.compID }) - .forEach(function (specie) { - specie.inUse = true; - }); - } - reactions.forEach(function (reaction) { - reaction.products.forEach(updateInUseForReaction); - reaction.reactants.forEach(updateInUseForReaction); - }); - events.forEach(function (event) { - event.eventAssignments.forEach(function (assignment) { - updateInUseForOther(assignment.variable) - }); - }); - rules.forEach(function (rule) { - updateInUseForOther(rule.variable); - }); - }, - updateParametersInUse: function () { - var parameters = this.model.parameters; - var reactions = this.model.reactions; - var events = this.model.eventsCollection; - var rules = this.model.rules; - parameters.forEach(function (param) { param.inUse = false; }); - var updateInUse = function (param) { - _.where(parameters.models, { compID: param.compID }) - .forEach(function (param) { - param.inUse = true; - }); - } - reactions.forEach(function (reaction) { - if(reaction.reactionType !== "custom-propensity"){ - updateInUse(reaction.rate); - } - }); - events.forEach(function (event) { - event.eventAssignments.forEach(function (assignment) { - updateInUse(assignment.variable) - }); - }); - rules.forEach(function (rule) { - updateInUse(rule.variable); - }); - }, renderParticleViewer: function (particle=null) { if(this.particleViewer) { this.particleViewer.remove(); @@ -228,7 +158,6 @@ let ModelEditor = PageView.extend({ this.modelStateButtons = new ModelStateButtonsView({ model: this.model }); - this.renderReactionsView(); app.registerRenderSubview(this, this.modelSettings, 'model-settings-container'); app.registerRenderSubview(this, this.modelStateButtons, 'model-state-buttons-container'); if(this.model.is_spatial) { @@ -268,13 +197,6 @@ let ModelEditor = PageView.extend({ }); app.registerRenderSubview(this, this.boundaryConditionsView, "boundary-conditions-container"); }, - renderReactionsView: function () { - if(this.reactionsEditor) { - this.reactionsEditor.remove() - } - this.reactionsEditor = new ReactionsEditorView({collection: this.model.reactions}); - app.registerRenderSubview(this, this.reactionsEditor, 'reactions-editor-container'); - }, renderEventsView: function () { if(this.eventsEditor){ this.eventsEditor.remove(); diff --git a/client/templates/includes/modelView.pug b/client/templates/includes/modelView.pug index 2fb6e91f6e..580a89a61b 100644 --- a/client/templates/includes/modelView.pug +++ b/client/templates/includes/modelView.pug @@ -56,3 +56,5 @@ div#model-view div(data-hook="initial-conditions-view-container") div(data-hook="parameters-view-container") + + div(data-hook="reactions-view-container") diff --git a/client/templates/pages/modelEditor.pug b/client/templates/pages/modelEditor.pug index f9761adc9c..64fc1812f8 100644 --- a/client/templates/pages/modelEditor.pug +++ b/client/templates/pages/modelEditor.pug @@ -28,8 +28,6 @@ section.page div(data-hook="model-view-container") - div(data-hook="reactions-editor-container") - div.card(data-hook="model-editor-advanced-container") div.card-header.pb-0 diff --git a/client/views/model-state-buttons.js b/client/views/model-state-buttons.js index 6f777bd399..1cb6bb9883 100644 --- a/client/views/model-state-buttons.js +++ b/client/views/model-state-buttons.js @@ -319,9 +319,9 @@ module.exports = View.extend({ }, openReactionsSection: function (isCollection = false) { let error = this.model.error - let reacSection = $(this.parent.reactionsEditor.queryByHook("reactions-list-container")) + let reacSection = $(this.parent.modelView.reactionsEditor.queryByHook("reactions-list-container")) if(!reacSection.hasClass("show")) { - let reacCollapseBtn = $(this.parent.reactionsEditor.queryByHook("collapse")) + let reacCollapseBtn = $(this.parent.modelView.reactionsEditor.queryByHook("collapse")) reacCollapseBtn.click() reacCollapseBtn.html('-') } diff --git a/client/views/model-view.js b/client/views/model-view.js index 944eaced21..6f7efc5f4f 100644 --- a/client/views/model-view.js +++ b/client/views/model-view.js @@ -18,6 +18,7 @@ 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'); @@ -27,6 +28,7 @@ let Domain = require('../models/domain'); let View = require('ampersand-view'); let SpeciesView = require('../views/species-view'); let DomainViewer = require('../views/domain-viewer'); +let ReactionsView = require('../views/reactions-view'); let ParametersView = require('../views/parameters-view'); let InitialConditionsView = require('../views/initial-conditions-view'); //templates @@ -59,6 +61,18 @@ module.exports = View.extend({ $(this.queryByHook("advanced-model-mode")).css("display", "none"); } } + this.model.reactions.on("change", function (reactions) { + this.updateSpeciesInUse(); + this.updateParametersInUse(); + }, this); + this.model.eventsCollection.on("add change remove", function (){ + this.updateSpeciesInUse(); + this.updateParametersInUse(); + }, this); + this.model.rules.on("add change remove", function() { + this.updateSpeciesInUse(); + this.updateParametersInUse(); + }, this); } if(this.model.is_spatial) { this.renderDomainViewer(); @@ -152,6 +166,63 @@ module.exports = View.extend({ $(this.queryByHook('edit-' + component)).removeClass('active'); $(this.queryByHook('view-' + component)).addClass('active'); }, + updateParametersInUse: function () { + var parameters = this.model.parameters; + var reactions = this.model.reactions; + var events = this.model.eventsCollection; + var rules = this.model.rules; + parameters.forEach(function (param) { param.inUse = false; }); + var updateInUse = function (param) { + _.where(parameters.models, { compID: param.compID }) + .forEach(function (param) { + param.inUse = true; + }); + } + reactions.forEach(function (reaction) { + if(reaction.reactionType !== "custom-propensity"){ + updateInUse(reaction.rate); + } + }); + events.forEach(function (event) { + event.eventAssignments.forEach(function (assignment) { + updateInUse(assignment.variable) + }); + }); + rules.forEach(function (rule) { + updateInUse(rule.variable); + }); + }, + updateSpeciesInUse: function () { + var species = this.model.species; + var reactions = this.model.reactions; + var events = this.model.eventsCollection; + var rules = this.model.rules; + species.forEach(function (specie) { specie.inUse = false; }); + var updateInUseForReaction = function (stoichSpecie) { + _.where(species.models, { compID: stoichSpecie.specie.compID }) + .forEach(function (specie) { + specie.inUse = true; + }); + } + var updateInUseForOther = function (specie) { + _.where(species.models, { compID: specie.compID }) + .forEach(function (specie) { + specie.inUse = true; + }); + } + reactions.forEach(function (reaction) { + reaction.products.forEach(updateInUseForReaction); + reaction.reactants.forEach(updateInUseForReaction); + }); + events.forEach(function (event) { + event.eventAssignments.forEach(function (assignment) { + updateInUseForOther(assignment.variable) + }); + }); + rules.forEach(function (rule) { + updateInUseForOther(rule.variable); + }); + }, subviews: { speciesView: { hook: "species-view-container", @@ -182,6 +253,15 @@ module.exports = View.extend({ readOnly: this.readOnly }); } + }, + reactionsView: { + hook: "reactions-view-container", + prepareView: function (el) { + return new ReactionsView({ + collection: this.model.reactions, + readOnly: this.readOnly + }); + } } } }); \ No newline at end of file diff --git a/client/views/species-view.js b/client/views/species-view.js index d5a5942337..6d79742329 100644 --- a/client/views/species-view.js +++ b/client/views/species-view.js @@ -55,7 +55,7 @@ module.exports = View.extend({ if(isNameUpdate) { reaction.buildSummary(); if(reaction.selected) { - self.parent.reactionsEditor.setDetailsView(reaction); + self.parent.reactionsView.setDetailsView(reaction); } }else if(!isDefaultMode || specie.compID === self.collection.models[self.collection.length-1].compID){ reaction.checkModes(); From c7aa65962ba9c9afc841314a2dde859f6c2ad974 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 2 Jul 2021 14:35:33 -0400 Subject: [PATCH 099/192] Cleaned up the reaction view files. --- client/views/reactant-product.js | 72 +++++----- client/views/reaction-details.js | 228 ++++++++++++++----------------- client/views/reaction-listing.js | 65 ++++----- client/views/reaction-types.js | 6 +- client/views/reactions-view.js | 219 ++++++++++++++--------------- 5 files changed, 273 insertions(+), 317 deletions(-) diff --git a/client/views/reactant-product.js b/client/views/reactant-product.js index 8a982bcc03..e2866f4e9f 100644 --- a/client/views/reactant-product.js +++ b/client/views/reactant-product.js @@ -16,16 +16,16 @@ 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'); //models -var StoichSpecie = require('../models/stoich-specie'); +let StoichSpecie = require('../models/stoich-specie'); //views -var View = require('ampersand-view'); -var SelectView = require('ampersand-select-view'); -var EditStoichSpecieView = require('./edit-stoich-specie'); -var EditCustomStoichSpecieView = require('./edit-custom-stoich-specie'); +let View = require('ampersand-view'); +let SelectView = require('ampersand-select-view'); +let EditStoichSpecieView = require('./edit-stoich-specie'); +let EditCustomStoichSpecieView = require('./edit-custom-stoich-specie'); //templates -var template = require('../templates/includes/reactantProduct.pug'); +let template = require('../templates/includes/reactantProduct.pug'); module.exports = View.extend({ template: template, @@ -43,37 +43,41 @@ module.exports = View.extend({ this.fieldTitle = args.fieldTitle; }, render: function () { - var self = this; View.prototype.render.apply(this, arguments); - var args = { + let args = { viewOptions: { name: 'stoich-specie', - label: '', required: true, textAttribute: 'name', eagerValidate: true, - // Set idAttribute to name. Models may not be saved yet so id is unreliable (so is cid). - // Use name since it *should be* unique. idAttribute: 'name', - options: self.species + options: this.species } }; - var type = self.reactionType; - var StoichSpeciesView = (type.startsWith('custom')) ? EditCustomStoichSpecieView : EditStoichSpecieView - self.renderCollection( - self.collection, + let type = this.reactionType; + let StoichSpeciesView = (type.startsWith('custom')) ? EditCustomStoichSpecieView : EditStoichSpecieView; + this.renderCollection( + this.collection, StoichSpeciesView, - self.queryByHook('reactants-editor'), + this.queryByHook('reactants-editor'), args ); if(this.reactionType.startsWith('custom')) { - $(this.queryByHook('collapse')).collapse() + $(this.queryByHook('collapse')).collapse(); } this.toggleAddSpecieButton(); if(this.fieldTitle === "Reactants"){ - $(this.queryByHook('field-title-tooltip')).prop('title', this.parent.parent.tooltips.reactant) + $(this.queryByHook('field-title-tooltip')).prop('title', this.parent.parent.tooltips.reactant); }else{ - $(this.queryByHook('field-title-tooltip')).prop('title', this.parent.parent.tooltips.product) + $(this.queryByHook('field-title-tooltip')).prop('title', this.parent.parent.tooltips.product); + } + }, + addSelectedSpecie: function () { + var specieName = this.specieName ? this.specieName : 'Pick a variable'; + if(this.validateAddSpecie()) { + this.collection.addStoichSpecie(specieName); + this.toggleAddSpecieButton(); + this.collection.parent.trigger('change-reaction'); } }, selectSpecie: function (e) { @@ -85,14 +89,6 @@ module.exports = View.extend({ } this.toggleAddSpecieButton(); }, - addSelectedSpecie: function () { - var specieName = this.specieName ? this.specieName : 'Pick a variable'; - if(this.validateAddSpecie()) { - this.collection.addStoichSpecie(specieName); - this.toggleAddSpecieButton(); - this.collection.parent.trigger('change-reaction') - } - }, toggleAddSpecieButton: function () { if(!this.validateAddSpecie()){ $(this.queryByHook('add-selected-specie')).prop('disabled', true); @@ -103,13 +99,10 @@ module.exports = View.extend({ }, validateAddSpecie: function () { if(this.hasSelectedSpecie){ - if(!this.collection.length) return true; - if(this.collection.length < 2 && this.collection.at(0).ratio < 2) - return true; - if(this.reactionType !== 'custom-massaction') - return true; - if(!this.isReactants) - return true; + if(!this.collection.length) { return true; } + if(this.collection.length < 2 && this.collection.at(0).ratio < 2) { return true; } + if(this.reactionType !== 'custom-massaction') { return true; } + if(!this.isReactants) { return true; } return false; } return false; @@ -120,17 +113,14 @@ module.exports = View.extend({ prepareView: function (el) { return new SelectView({ name: 'stoich-specie', - label: '', required: false, textAttribute: 'name', eagerValidate: false, - // Set idAttribute to name. Models may not be saved yet so id is unreliable (so is cid). - // Use name since it *should be* unique. idAttribute: 'name', options: this.species, - unselectedText: this.unselectedText, + unselectedText: this.unselectedText }); } } - }, + } }); \ No newline at end of file diff --git a/client/views/reaction-details.js b/client/views/reaction-details.js index 00f27574a7..042a3d768d 100644 --- a/client/views/reaction-details.js +++ b/client/views/reaction-details.js @@ -16,23 +16,22 @@ 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 katex = require('katex'); +let $ = require('jquery'); +let katex = require('katex'); +let _ = require('underscore'); //support files let app = require('../app'); -//config -var ReactionTypes = require('../reaction-types'); +let ReactionTypes = require('../reaction-types'); //models -var StoichSpecie = require('../models/stoich-specie'); +let StoichSpecie = require('../models/stoich-specie'); //views -var View = require('ampersand-view'); -var SelectView = require('ampersand-select-view'); -var InputView = require('./input'); -var ReactionTypesView = require('./reaction-types'); -var ReactantProductView = require('./reactant-product'); +let InputView = require('./input'); +let View = require('ampersand-view'); +let SelectView = require('ampersand-select-view'); +let ReactionTypesView = require('./reaction-types'); +let ReactantProductView = require('./reactant-product'); //templates -var template = require('../templates/includes/reactionDetails.pug'); +let template = require('../templates/includes/reactionDetails.pug'); module.exports = View.extend({ template: template, @@ -53,68 +52,51 @@ module.exports = View.extend({ 'model.hasConflict': { type: function (el, value, previousValue) { if(value) { - $(this.queryByHook('conflicting-modes-message')).collapse('show') + $(this.queryByHook('conflicting-modes-message')).collapse('show'); }else{ - $(this.queryByHook('conflicting-modes-message')).collapse('hide') + $(this.queryByHook('conflicting-modes-message')).collapse('hide'); } }, - hook: 'conflicting-modes-message', - }, + hook: 'conflicting-modes-message' + } }, events: { 'change [data-hook=select-rate-parameter]' : 'selectRateParam', - 'change [data-hook=select-reaction-type]' : 'selectReactionType', + 'change [data-hook=select-reaction-type]' : 'selectReactionType' }, initialize: function (attrs, options) { View.prototype.initialize.apply(this, arguments); - var self = this; + let self = this; this.model.on("change:reaction_type", function (model) { self.updateStoichSpeciesForReactionType(model.reactionType); }); }, render: function () { View.prototype.render.apply(this, arguments); - var self = this; - var reactantsView = new ReactantProductView({ - collection: this.model.reactants, - species: this.model.collection.parent.species, - reactionType: this.model.reactionType, - fieldTitle: 'Reactants', - isReactants: true - }); - var productsView = new ReactantProductView({ - collection: this.model.products, - species: this.model.collection.parent.species, - reactionType: this.model.reactionType, - fieldTitle: 'Products', - isReactants: false - }); - this.renderReactionTypesSelectView() + let self = this; + this.renderReactionTypesSelectView(); if(this.model.reactionType === 'custom-propensity'){ - var propensityView = new InputView({ + let propensityView = new InputView({ parent: this, required: true, name: 'rate', - label: '', - tests:'', modelKey:'propensity', valueType: 'string', value: this.model.propensity, placeholder: "--No Expression Entered--" }); - app.registerRenderSubview(this, propensityView, 'select-rate-parameter') - $(this.queryByHook('rate-parameter-label')).text('Propensity:') + 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{ // make sure the reaction has a rate and that rate exists in the parameters collection let paramIDs = this.model.collection.parent.parameters.map(function (param) { - return param.compID + return param.compID; }); if(!this.model.rate.compID || !paramIDs.includes(this.model.rate.compID)) { - this.model.rate = this.model.collection.getDefaultRate() + this.model.rate = this.model.collection.getDefaultRate(); } - var rateParameterView = new SelectView({ - label: '', + let rateParameterView = new SelectView({ name: 'rate', required: true, idAttribute: 'cid', @@ -123,135 +105,135 @@ module.exports = View.extend({ options: this.model.collection.parent.parameters, // For new reactions (with no rate.name) just use the first parameter in the Parameters collection // 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), + value: this.model.rate.name ? this.getRateFromParameters(this.model.rate.name) : this.model.collection.parent.parameters.at(0) }); app.registerRenderSubview(this, rateParameterView, 'select-rate-parameter'); - $(this.queryByHook('rate-parameter-label')).text('Rate Parameter:') + $(this.queryByHook('rate-parameter-label')).text('Rate Parameter:'); $(this.queryByHook('rate-parameter-tooltip')).prop('title', this.parent.tooltips.rate); } + let reactantsView = new ReactantProductView({ + collection: this.model.reactants, + species: this.model.collection.parent.species, + reactionType: this.model.reactionType, + fieldTitle: 'Reactants', + isReactants: true + }); + app.registerRenderSubview(this, reactantsView, 'reactants-editor'); + let productsView = new ReactantProductView({ + collection: this.model.products, + species: this.model.collection.parent.species, + reactionType: this.model.reactionType, + fieldTitle: 'Products', + isReactants: false + }); + app.registerRenderSubview(this, productsView, 'products-editor'); if(this.model.collection.parent.is_spatial) { - var typesView = new ReactionTypesView({ + let typesView = new ReactionTypesView({ model: this.model, parent: this }); app.registerRenderSubview(this, typesView, 'domain-types-editor'); } - app.registerRenderSubview(this, reactantsView, 'reactants-editor'); - app.registerRenderSubview(this, productsView, 'products-editor'); this.totalRatio = this.getTotalReactantRatio(); - $(document).ready(function () { - $('[data-toggle="tooltip"]').tooltip(); - $('[data-toggle="tooltip"]').click(function () { - $('[data-toggle="tooltip"]').tooltip("hide"); - - }); - }); + app.tooltipSetup(); this.toggleCustomReactionError(); }, - update: function () { + getArrayOfDefaultStoichSpecies: function (arr) { + return arr.map(function (params) { + let stoichSpecie = new StoichSpecie(params); + stoichSpecie.specie = this.parent.getDefaultSpecie(); + return stoichSpecie; + }, this); + }, + getRateFromParameters: function (name) { + // Seems like model.rate is not actually part of the Parameters collection + // Get the Parameter from Parameters that matches model.rate + // TODO this is some garbagio, get model.rate into Parameters collection...? + if (!name) { name = this.model.rate.name }; + let rate = this.model.collection.parent.parameters.filter(function (param) { + return param.name === name; + })[0]; + return rate; + }, + getReactionTypeLabels: function () { + return _.map(ReactionTypes, function (val, key) { return val.label; }); }, - updateValid: function () { + getTotalReactantRatio: function () { + return this.model.reactants.length; + }, + renderReactionTypes: function () { + if(this.model.collection.parent.parameters.length < 1){ return }; + let options = { + displayMode: true, + output: 'html' + } + katex.render(ReactionTypes['creation'].label, this.queryByHook('select-reaction-type').firstChild.children[1]['0'], options); + katex.render(ReactionTypes['destruction'].label, this.queryByHook('select-reaction-type').firstChild.children[1]['1'], options); + katex.render(ReactionTypes['change'].label, this.queryByHook('select-reaction-type').firstChild.children[1]['2'], options); + katex.render(ReactionTypes['dimerization'].label, this.queryByHook('select-reaction-type').firstChild.children[1]['3'], options); + katex.render(ReactionTypes['merge'].label, this.queryByHook('select-reaction-type').firstChild.children[1]['4'], options); + katex.render(ReactionTypes['split'].label, this.queryByHook('select-reaction-type').firstChild.children[1]['5'], options); + katex.render(ReactionTypes['four'].label, this.queryByHook('select-reaction-type').firstChild.children[1]['6'], options); }, renderReactionTypesSelectView: function () { if(this.reactionTypesSelectView) { - this.reactionTypesSelectView.remove() + this.reactionTypesSelectView.remove(); } - - var options = []; if(this.model.collection.parent.parameters.length <= 0){ - options = ["Custom propensity"]; + var options = ["Custom propensity"]; } else{ - options = this.getReactionTypeLabels(); + var options = this.getReactionTypeLabels(); } - this.reactionTypesSelectView = new SelectView({ label: 'Reaction Type:', name: 'reaction-type', required: true, idAttribute: 'cid', options: options, - value: ReactionTypes[this.model.reactionType].label, + value: ReactionTypes[this.model.reactionType].label }); - app.registerRenderSubview(this, this.reactionTypesSelectView, 'select-reaction-type'); this.renderReactionTypes(); }, selectRateParam: function (e) { if(this.model.reactionType !== 'custom-propensity') { - var val = e.target.selectedOptions.item(0).text; - var param = this.getRateFromParameters(val); + let val = e.target.selectedOptions.item(0).text; + let param = this.getRateFromParameters(val); this.model.rate = param || this.model.rate; this.model.trigger("change"); this.model.collection.trigger("change"); } }, - getRateFromParameters: function (name) { - // Seems like model.rate is not actually part of the Parameters collection - // Get the Parameter from Parameters that matches model.rate - // TODO this is some garbagio, get model.rate into Parameters collection...? - if (!name) { name = this.model.rate.name } - var rate = this.model.collection.parent.parameters.filter(function (param) { - return param.name === name; - })[0]; - return rate - }, selectReactionType: function (e) { - var label = e.target.selectedOptions.item(0).value; - var type = _.findKey(ReactionTypes, function (o) { return o.label === label; }); + let label = e.target.selectedOptions.item(0).value; + let type = _.findKey(ReactionTypes, function (o) { return o.label === label; }); this.model.reactionType = type; - this.model.summary = label + this.model.summary = label; this.updateStoichSpeciesForReactionType(type); this.model.collection.trigger("change"); - this.model.trigger('change-reaction') + this.model.trigger('change-reaction'); this.render(); }, - updateStoichSpeciesForReactionType: function (type) { - var args = this.parent.getStoichArgsForReactionType(type); - var newReactants = this.getArrayOfDefaultStoichSpecies(args.reactants); - var newProducts = this.getArrayOfDefaultStoichSpecies(args.products); - this.model.reactants.reset(newReactants); - this.model.products.reset(newProducts); - if(type !== 'custom-propensity') - this.model.rate = this.model.collection.getDefaultRate(); - }, - getArrayOfDefaultStoichSpecies: function (arr) { - return arr.map(function (params) { - var stoichSpecie = new StoichSpecie(params); - stoichSpecie.specie = this.parent.getDefaultSpecie(); - return stoichSpecie; - }, this); - }, - getReactionTypeLabels: function () { - return _.map(ReactionTypes, function (val, key) { return val.label; }) - }, - getTotalReactantRatio: function () { - return this.model.reactants.length; - }, toggleCustomReactionError: function () { - let errorMsg = $(this.queryByHook("custom-reaction-error")) + let errorMsg = $(this.queryByHook("custom-reaction-error")); if(this.model.reactants.length <= 0 && this.model.products.length <= 0) { - errorMsg.addClass('component-invalid') - errorMsg.removeClass('component-valid') + errorMsg.addClass('component-invalid'); + errorMsg.removeClass('component-valid'); }else{ - errorMsg.addClass('component-valid') - errorMsg.removeClass('component-invalid') + errorMsg.addClass('component-valid'); + errorMsg.removeClass('component-invalid'); } }, - renderReactionTypes: function () { - if(this.model.collection.parent.parameters.length < 1){ - return - } - var options = { - displayMode: true, - output: 'html' - } - katex.render(ReactionTypes['creation'].label, this.queryByHook('select-reaction-type').firstChild.children[1]['0'], options); - katex.render(ReactionTypes['destruction'].label, this.queryByHook('select-reaction-type').firstChild.children[1]['1'], options); - katex.render(ReactionTypes['change'].label, this.queryByHook('select-reaction-type').firstChild.children[1]['2'], options); - katex.render(ReactionTypes['dimerization'].label, this.queryByHook('select-reaction-type').firstChild.children[1]['3'], options); - katex.render(ReactionTypes['merge'].label, this.queryByHook('select-reaction-type').firstChild.children[1]['4'], options); - katex.render(ReactionTypes['split'].label, this.queryByHook('select-reaction-type').firstChild.children[1]['5'], options); - katex.render(ReactionTypes['four'].label, this.queryByHook('select-reaction-type').firstChild.children[1]['6'], options); + update: function () {}, + updateStoichSpeciesForReactionType: function (type) { + let args = this.parent.getStoichArgsForReactionType(type); + let newReactants = this.getArrayOfDefaultStoichSpecies(args.reactants); + let newProducts = this.getArrayOfDefaultStoichSpecies(args.products); + this.model.reactants.reset(newReactants); + this.model.products.reset(newProducts); + if(type !== 'custom-propensity') + this.model.rate = this.model.collection.getDefaultRate(); }, + updateValid: function () {} }); \ No newline at end of file diff --git a/client/views/reaction-listing.js b/client/views/reaction-listing.js index 2503be8ee3..c59aaea928 100644 --- a/client/views/reaction-listing.js +++ b/client/views/reaction-listing.js @@ -16,18 +16,19 @@ You should have received a copy of the GNU General Public License along with this program. If not, see . */ -var $ = require('jquery'); -var katex = require('katex'); +let $ = require('jquery'); +let katex = require('katex'); let _ = require('underscore'); //support files -var tests = require('./tests'); -var modals = require('../modals'); +let app = require('../app'); +let tests = require('./tests'); +let modals = require('../modals'); //views -var View = require('ampersand-view'); -var InputView = require('./input'); +let InputView = require('./input'); +let View = require('ampersand-view'); //templates -var editTemplate = require('../templates/includes/reactionListing.pug'); let viewTemplate = require('../templates/includes/viewReactions.pug'); +let editTemplate = require('../templates/includes/reactionListing.pug'); module.exports = View.extend({ bindings: { @@ -40,10 +41,10 @@ module.exports = View.extend({ katex.render(this.model.summary, this.queryByHook('summary'), { displayMode: true, output: 'html', - maxSize: 5, + maxSize: 5 }); }, - hook: 'summary', + hook: 'summary' }, 'model.selected' : { type: function (el, value, previousValue) { @@ -67,7 +68,7 @@ module.exports = View.extend({ if(this.model.types) { this.model.types.forEach(function (index) { let type = self.model.collection.parent.domain.types.get(index, "typeID"); - self.types.push(type.name) + self.types.push(type.name); }); } }else{ @@ -77,34 +78,18 @@ module.exports = View.extend({ render: function () { this.template = this.viewMode ? viewTemplate : editTemplate; View.prototype.render.apply(this, arguments); - $(document).on('shown.bs.modal', function (e) { - $('[autofocus]', e.target).focus(); - }); - $(document).on('hide.bs.modal', '.modal', function (e) { - e.target.remove() - }); + app.documentSetup(); if(!this.model.annotation){ - $(this.queryByHook('edit-annotation-btn')).text('Add') + $(this.queryByHook('edit-annotation-btn')).text('Add'); } }, - update: function () { - }, - updateValid: function () { - }, - selectReaction: function (e) { - this.model.collection.trigger("select", this.model); - }, - removeReaction: function (e) { - this.collection.removeReaction(this.model); - this.parent.collection.trigger("change"); - }, editAnnotation: function () { - var self = this; - var name = this.model.name; - var annotation = this.model.annotation; if(document.querySelector('#reactionAnnotationModal')) { document.querySelector('#reactionAnnotationModal').remove(); } + let self = this; + let name = this.model.name; + let annotation = this.model.annotation; let modal = $(modals.annotationModalHtml("reaction", name, annotation)).modal(); let okBtn = document.querySelector('#reactionAnnotationModal .ok-model-btn'); let input = document.querySelector('#reactionAnnotationModal #reactionAnnotationInput'); @@ -120,6 +105,15 @@ module.exports = View.extend({ modal.modal('hide'); }); }, + removeReaction: function (e) { + this.collection.removeReaction(this.model); + this.parent.collection.trigger("change"); + }, + selectReaction: function (e) { + this.model.collection.trigger("select", this.model); + }, + update: function () {}, + updateValid: function () {}, updateViewer: function () { this.parent.renderViewReactionView(); }, @@ -131,13 +125,12 @@ module.exports = View.extend({ parent: this, required: true, name: 'name', - label: '', tests: tests.nameTests, modelKey: 'name', valueType: 'string', - value: this.model.name, + value: this.model.name }); - }, - }, - }, + } + } + } }); \ No newline at end of file diff --git a/client/views/reaction-types.js b/client/views/reaction-types.js index e57eddcc06..a744e809ad 100644 --- a/client/views/reaction-types.js +++ b/client/views/reaction-types.js @@ -17,10 +17,10 @@ along with this program. If not, see . */ //views -var View = require('ampersand-view'); -var TypesView = require('./component-types'); +let View = require('ampersand-view'); +let TypesView = require('./component-types'); //templates -var template = require('../templates/includes/reactionTypes.pug'); +let template = require('../templates/includes/reactionTypes.pug'); module.exports = View.extend({ template: template, diff --git a/client/views/reactions-view.js b/client/views/reactions-view.js index 22b6567d9c..141b2fd6bc 100644 --- a/client/views/reactions-view.js +++ b/client/views/reactions-view.js @@ -16,22 +16,22 @@ You should have received a copy of the GNU General Public License along with this program. If not, see . */ -var ViewSwitcher = require('ampersand-view-switcher'); -var katex = require('katex'); -var _ = require('underscore'); -var $ = require('jquery'); +let $ = require('jquery'); +let katex = require('katex'); +let _ = require('underscore'); //support files let app = require('../app'); -var ReactionTypes = require('../reaction-types'); -var Tooltips = require('../tooltips'); +let Tooltips = require('../tooltips'); +let ReactionTypes = require('../reaction-types'); //models -var StoichSpeciesCollection = require('../models/stoich-species'); +let StoichSpeciesCollection = require('../models/stoich-species'); //views -var View = require('ampersand-view'); -var ReactionListingView = require('./reaction-listing'); -var ReactionDetailsView = require('./reaction-details'); +let View = require('ampersand-view'); +let ViewSwitcher = require('ampersand-view-switcher'); +let ReactionListingView = require('./reaction-listing'); +let ReactionDetailsView = require('./reaction-details'); //templates -var template = require('../templates/includes/reactionsView.pug'); +let template = require('../templates/includes/reactionsView.pug'); module.exports = View.extend({ template: template, @@ -49,7 +49,7 @@ module.exports = View.extend({ }, initialize: function (attrs, options) { View.prototype.initialize.apply(this, arguments); - this.tooltips = Tooltips.reactionsEditor + this.tooltips = Tooltips.reactionsEditor; this.readOnly = attrs.readOnly ? attrs.readOnly : false; if(!this.readOnly) { this.collection.on("select", function (reaction) { @@ -59,23 +59,24 @@ module.exports = View.extend({ this.collection.on("remove", function (reaction) { // Select the last reaction by default // But only if there are other reactions other than the one we're removing - if (reaction.detailsView) + if (reaction.detailsView){ reaction.detailsView.remove(); + } this.collection.removeReaction(reaction); if (this.collection.length) { - var selected = this.collection.at(this.collection.length-1); + let selected = this.collection.at(this.collection.length-1); this.collection.trigger("select", selected); } }, this); this.collection.parent.species.on('add remove', this.toggleAddReactionButton, this); this.collection.parent.parameters.on('add remove', this.toggleReactionTypes, this); - this.collection.parent.on('change', this.toggleProcessError, this) + this.collection.parent.on('change', this.toggleProcessError, this); } }, render: function () { View.prototype.render.apply(this, arguments); if(this.readOnly) { - this.renderViewReactionView() + this.renderViewReactionView(); $(this.queryByHook('reactions-edit-tab')).addClass("disabled"); $(".nav .disabled>a").on("click", function(e) { e.preventDefault(); @@ -86,10 +87,6 @@ module.exports = View.extend({ $(this.queryByHook('view-reactions')).addClass('active'); }else{ this.renderReactionListingViews(); - this.detailsContainer = this.queryByHook('reaction-details-container'); - this.detailsViewSwitcher = new ViewSwitcher({ - el: this.detailsContainer, - }); if (this.collection.length) { this.setSelectedReaction(this.collection.at(0)); this.collection.trigger("select", this.selectedReaction); @@ -98,8 +95,7 @@ module.exports = View.extend({ this.toggleAddReactionButton(); if(this.collection.parent.parameters.length > 0){ $(this.queryByHook('add-reaction-partial')).prop('hidden', true); - } - else{ + }else { $(this.queryByHook('add-reaction-full')).prop('hidden', true); } this.renderReactionTypes(); @@ -107,17 +103,47 @@ module.exports = View.extend({ displayMode: false, output: 'html', }); - this.toggleProcessError() + this.toggleProcessError(); $(this.queryByHook('massaction-message')).prop('hidden', this.collection.parent.parameters.length > 0); } }, - update: function () { + changeCollapseButtonText: function (e) { + app.changeCollapseButtonText(this, e); }, - updateValid: function () { + getAnnotation: function (type) { + return ReactionTypes[type].label; }, - renderReactionListingViews: function () { - this.renderEditReactionListingView(); - this.renderViewReactionView(); + getDefaultSpecie: function () { + return this.collection.parent.species.models[0]; + }, + getStoichArgsForReactionType: function(type) { + return ReactionTypes[type]; + }, + handleAddReactionClick: function (e) { + let reactionType = e.delegateTarget.dataset.hook; + let stoichArgs = this.getStoichArgsForReactionType(reactionType); + if(this.parent.model.domain.types) { + var types = this.parent.model.domain.types.map(function (type) { + return type.typeID; + }); + types.shift(); + }else{ + var types = []; + } + let reaction = this.collection.addReaction(reactionType, stoichArgs, types); + reaction.detailsView = this.newDetailsView(reaction); + this.collection.trigger("select", reaction); + app.tooltipSetup(); + }, + newDetailsView: function (reaction) { + let detailsView = new ReactionDetailsView({ model: reaction }); + detailsView.parent = this; + return detailsView; + }, + openReactionsContainer: function () { + $(this.queryByHook('reactions-list-container')).collapse('show'); + let collapseBtn = $(this.queryByHook('collapse')); + collapseBtn.trigger('click'); }, renderEditReactionListingView: function () { if(this.editReactionListingView){ @@ -126,7 +152,7 @@ module.exports = View.extend({ if(this.collection.parent.parameters.length <= 0) { for(var i = 0; i < this.collection.length; i++) { if(this.collection.models[i].reactionType !== "custom-propensity"){ - this.collection.models[i].reactionType = "custom-propensity" + this.collection.models[i].reactionType = "custom-propensity"; } } } @@ -135,12 +161,24 @@ module.exports = View.extend({ ReactionListingView, this.queryByHook('edit-reaction-list') ); - $(document).ready(function () { - $('[data-toggle="tooltip"]').tooltip(); - $('[data-toggle="tooltip"]').click(function () { - $('[data-toggle="tooltip"]').tooltip("hide"); - }); - }); + app.tooltipSetup(); + }, + renderReactionListingViews: function () { + this.renderEditReactionListingView(); + this.renderViewReactionView(); + }, + renderReactionTypes: function () { + let options = { + displayMode: false, + output: 'html' + } + katex.render(ReactionTypes['creation'].label, this.queryByHook('creation-lb1'), options); + katex.render(ReactionTypes['destruction'].label, this.queryByHook('destruction-lb1'), options); + katex.render(ReactionTypes['change'].label, this.queryByHook('change-lb1'), options); + katex.render(ReactionTypes['dimerization'].label, this.queryByHook('dimerization-lb1'), options); + katex.render(ReactionTypes['merge'].label, this.queryByHook('merge-lb1'), options); + katex.render(ReactionTypes['split'].label, this.queryByHook('split-lb1'), options); + katex.render(ReactionTypes['four'].label, this.queryByHook('four-lb1'), options); }, renderViewReactionView: function () { if(this.viewReactionListingView){ @@ -163,10 +201,31 @@ module.exports = View.extend({ options ); }, + setDetailsView: function (reaction) { + reaction.detailsView = this.newDetailsView(reaction); + this.detailsViewSwitcher.set(reaction.detailsView); + }, + setSelectedReaction: function (reaction) { + this.collection.each(function (m) { m.selected = false; }); + reaction.selected = true; + this.selectedReaction = reaction; + }, toggleAddReactionButton: function () { $(this.queryByHook('add-reaction-full')).prop('disabled', (this.collection.parent.species.length <= 0)); $(this.queryByHook('add-reaction-partial')).prop('disabled', (this.collection.parent.species.length <= 0)); }, + toggleProcessError: function () { + let model = this.collection.parent; + if(model.is_spatial) {return}; + let errorMsg = $(this.queryByHook('process-component-error')); + if(this.collection.length <= 0 && model.eventsCollection.length <= 0 && model.rules.length <= 0) { + errorMsg.addClass('component-invalid'); + errorMsg.removeClass('component-valid'); + }else{ + errorMsg.addClass('component-valid'); + errorMsg.removeClass('component-invalid'); + } + }, toggleReactionTypes: function (e, prev, curr) { if(curr && curr.add && this.collection.parent.parameters.length === 1){ $(this.queryByHook('massaction-message')).prop('hidden', true); @@ -178,87 +237,19 @@ module.exports = View.extend({ $(this.queryByHook('add-reaction-partial')).prop('hidden', false); } if(this.selectedReaction){ - this.selectedReaction.detailsView.renderReactionTypesSelectView() - } - }, - setSelectedReaction: function (reaction) { - this.collection.each(function (m) { m.selected = false; }); - reaction.selected = true; - this.selectedReaction = reaction; - }, - setDetailsView: function (reaction) { - reaction.detailsView = this.newDetailsView(reaction); - this.detailsViewSwitcher.set(reaction.detailsView); - }, - handleAddReactionClick: function (e) { - var reactionType = e.delegateTarget.dataset.hook; - var stoichArgs = this.getStoichArgsForReactionType(reactionType); - if(this.parent.model.domain.types) { - var types = this.parent.model.domain.types.map(function (type) { - return type.typeID; - }); - types.shift() - }else{ - var types = [] + this.selectedReaction.detailsView.renderReactionTypesSelectView(); } - var reaction = this.collection.addReaction(reactionType, stoichArgs, types); - reaction.detailsView = this.newDetailsView(reaction); - this.collection.trigger("select", reaction); - $(document).ready(function () { - $('[data-toggle="tooltip"]').tooltip(); - $('[data-toggle="tooltip"]').click(function () { - $('[data-toggle="tooltip"]').tooltip("hide"); - - }); - }); }, - getStoichArgsForReactionType: function(type) { - var args = ReactionTypes[type]; - return args; - }, - newDetailsView: function (reaction) { - var detailsView = new ReactionDetailsView({ model: reaction }); - detailsView.parent = this; - return detailsView - }, - openReactionsContainer: function () { - $(this.queryByHook('reactions-list-container')).collapse('show'); - let collapseBtn = $(this.queryByHook('collapse')) - collapseBtn.trigger('click') - }, - changeCollapseButtonText: function (e) { - app.changeCollapseButtonText(this, e); - }, - getDefaultSpecie: function () { - var value = this.collection.parent.species.models[0]; - return value; - }, - getAnnotation: function (type) { - return ReactionTypes[type].label - }, - toggleProcessError: function () { - let model = this.collection.parent - if(model.is_spatial) {return}; - let errorMsg = $(this.queryByHook('process-component-error')) - if(this.collection.length <= 0 && model.eventsCollection.length <= 0 && model.rules.length <= 0) { - errorMsg.addClass('component-invalid') - errorMsg.removeClass('component-valid') - }else{ - errorMsg.addClass('component-valid') - errorMsg.removeClass('component-invalid') - } - }, - renderReactionTypes: function () { - var options = { - displayMode: false, - output: 'html', + update: function () {}, + updateValid: function () {}, + subviews: { + detailsViewSwitcher: { + hook: "reaction-details-container", + prepareView: function (el) { + return new ViewSwitcher({ + el: el + }); + } } - katex.render(ReactionTypes['creation'].label, this.queryByHook('creation-lb1'), options); - katex.render(ReactionTypes['destruction'].label, this.queryByHook('destruction-lb1'), options); - katex.render(ReactionTypes['change'].label, this.queryByHook('change-lb1'), options); - katex.render(ReactionTypes['dimerization'].label, this.queryByHook('dimerization-lb1'), options); - katex.render(ReactionTypes['merge'].label, this.queryByHook('merge-lb1'), options); - katex.render(ReactionTypes['split'].label, this.queryByHook('split-lb1'), options); - katex.render(ReactionTypes['four'].label, this.queryByHook('four-lb1'), options); } }); \ No newline at end of file From ca6bf0c3f0adcc2fac725fd9e736b47d36e49a03 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 2 Jul 2021 14:44:40 -0400 Subject: [PATCH 100/192] Moved the advanced section to the model view. --- client/pages/model-editor.js | 1 - client/templates/includes/modelView.pug | 12 +++++ client/templates/pages/modelEditor.pug | 60 ++++++++++--------------- client/views/model-view.js | 6 ++- 4 files changed, 41 insertions(+), 38 deletions(-) diff --git a/client/pages/model-editor.js b/client/pages/model-editor.js index 32f95bba06..81a146a3cb 100644 --- a/client/pages/model-editor.js +++ b/client/pages/model-editor.js @@ -51,7 +51,6 @@ let ModelEditor = PageView.extend({ let modal = $(modals.operationInfoModalHtml('model-editor')).modal(); }, 'change [data-hook=edit-volume]' : 'updateVolumeViewer', - 'click [data-hook=collapse-me-advanced-section]' : 'changeCollapseButtonText', 'click [data-hook=project-breadcrumb-link]' : 'handleProjectBreadcrumbClick', 'click [data-hook=toggle-preview-plot]' : 'togglePreviewPlot', 'click [data-hook=toggle-preview-domain]' : 'toggleDomainPlot', diff --git a/client/templates/includes/modelView.pug b/client/templates/includes/modelView.pug index 580a89a61b..31cb0b88f6 100644 --- a/client/templates/includes/modelView.pug +++ b/client/templates/includes/modelView.pug @@ -58,3 +58,15 @@ div#model-view div(data-hook="parameters-view-container") div(data-hook="reactions-view-container") + + div.card(data-hook="model-view-advanced-container") + + div.card-header.pb-0 + + h3.inline Advanced + + button.btn.btn-outline-collapse(data-toggle="collapse" data-target="#mv-advanced-section" data-hook="collapse-mv-advanced-section") + + + div.collapse(id="mv-advanced-section" data-hook="mv-advanced-section") + + div.card-body diff --git a/client/templates/pages/modelEditor.pug b/client/templates/pages/modelEditor.pug index 64fc1812f8..725a80065a 100644 --- a/client/templates/pages/modelEditor.pug +++ b/client/templates/pages/modelEditor.pug @@ -28,64 +28,52 @@ section.page div(data-hook="model-view-container") - div.card(data-hook="model-editor-advanced-container") + div(data-hook="events-editor-container") - div.card-header.pb-0 - - h3.inline Advanced - - button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#me-advanced-section", data-hook="collapse-me-advanced-section") + - - div.collapse(id="me-advanced-section", data-hook="me-advanced-section") + div(data-hook="rules-editor-container") - div.card-body + div(data-hook="boundary-conditions-container") - div(data-hook="events-editor-container") + div(data-hook="sbml-component-container") - div(data-hook="rules-editor-container") + div.card.collapse.show(data-hook="system-volume-container") - div(data-hook="boundary-conditions-container") - - div(data-hook="sbml-component-container") - - div.card.collapse.show(data-hook="system-volume-container") + div.card-header.pb-0 - div.card-header.pb-0 + h3.inline.mr-3 System Volume - h3.inline.mr-3 System Volume + div.inline.mr-3 - div.inline.mr-3 + ul.nav.nav-tabs.card-header-tabs(id="volume-tabs") - ul.nav.nav-tabs.card-header-tabs(id="volume-tabs") + li.nav-item - li.nav-item + a.nav-link.tab.active(data-hook="volume-edit-tab" data-toggle="tab" href="#edit-system-volume") Edit - a.nav-link.tab.active(data-hook="volume-edit-tab" data-toggle="tab" href="#edit-system-volume") Edit + li.nav-item - li.nav-item + a.nav-link.tab(data-hook="volume-view-tab" data-toggle="tab" href="#view-system-volume") View - a.nav-link.tab(data-hook="volume-view-tab" data-toggle="tab" href="#view-system-volume") View + button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-system-volume", data-hook="collapse-system-volume") + - button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-system-volume", data-hook="collapse-system-volume") + + div.card-body - div.card-body - - p.mb-0 - | System volume affects custom propensities or stochastic reactions with two reactants. The volume sets the implicit parameter 'vol' which can be used in custom propensity functions. A single well-mixed volume is assumed. Compartments are not currently supported. In most cases this should not be changed. please review your model requirements carefully before changing this property. + p.mb-0 + | System volume affects custom propensities or stochastic reactions with two reactants. The volume sets the implicit parameter 'vol' which can be used in custom propensity functions. A single well-mixed volume is assumed. Compartments are not currently supported. In most cases this should not be changed. please review your model requirements carefully before changing this property. - div.collapse.tab-content(id="collapse-system-volume" data-hook="system-volume-section") + div.collapse.tab-content(id="collapse-system-volume" data-hook="system-volume-section") - div.tab-pane.active(id="edit-system-volume" data-hook="edit-system-volume") + div.tab-pane.active(id="edit-system-volume" data-hook="edit-system-volume") - hr + hr - div(data-hook="edit-volume") + div(data-hook="edit-volume") - div.tab-pane(id="view-system-volume" data-hook="view-system-volume") + div.tab-pane(id="view-system-volume" data-hook="view-system-volume") - hr + hr - div(data-hook="view-volume") + div(data-hook="view-volume") div(data-hook="model-settings-container") diff --git a/client/views/model-view.js b/client/views/model-view.js index 6f7efc5f4f..c11ffd4cfd 100644 --- a/client/views/model-view.js +++ b/client/views/model-view.js @@ -39,7 +39,8 @@ module.exports = View.extend({ events: { 'change [data-hook=all-continuous]' : 'setDefaultMode', 'change [data-hook=all-discrete]' : 'setDefaultMode', - 'change [data-hook=advanced]' : 'setDefaultMode' + 'change [data-hook=advanced]' : 'setDefaultMode', + 'click [data-hook=collapse-mv-advanced-section]' : 'changeCollapseButtonText' }, initialize: function(attrs, options) { View.prototype.initialize.apply(this, arguments); @@ -78,6 +79,9 @@ module.exports = View.extend({ this.renderDomainViewer(); } }, + changeCollapseButtonText: function (e) { + app.changeCollapseButtonText(this, e); + }, getInitialDefaultMode: function () { let self = this; if(document.querySelector('#defaultModeModal')) { From 331810bad8a133008040ebddb4c1009868d9c93c Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 2 Jul 2021 15:19:06 -0400 Subject: [PATCH 101/192] Renamed the events view and template functions to names that better fit their function. --- client/pages/model-editor.js | 3 +-- .../templates/includes/{eventsEditor.pug => eventsView.pug} | 0 client/views/{events-editor.js => events-view.js} | 2 +- client/views/model-state-buttons.js | 4 ++-- 4 files changed, 4 insertions(+), 5 deletions(-) rename client/templates/includes/{eventsEditor.pug => eventsView.pug} (100%) rename client/views/{events-editor.js => events-view.js} (98%) diff --git a/client/pages/model-editor.js b/client/pages/model-editor.js index 81a146a3cb..899fa1781a 100644 --- a/client/pages/model-editor.js +++ b/client/pages/model-editor.js @@ -29,7 +29,7 @@ var PageView = require('../pages/base'); let ModelView = require('../views/model-view'); var InputView = require('../views/input'); var ParticleViewer = require('../views/view-particle'); -var EventsEditorView = require('../views/events-editor'); +var EventsEditorView = require('../views/events-view'); var RulesEditorView = require('../views/rules-editor'); var SBMLComponentView = require('../views/sbml-component-editor'); var TimespanSettingsView = require('../views/timespan-settings'); @@ -82,7 +82,6 @@ let ModelEditor = PageView.extend({ app.getXHR(this.model.url(), { success: function (err, response, body) { self.model.set(body) - self.modelLoaded = true if(directory.includes('.proj')) { self.queryByHook("project-breadcrumb-links").style.display = "block" self.queryByHook("model-name-header").style.display = "none" diff --git a/client/templates/includes/eventsEditor.pug b/client/templates/includes/eventsView.pug similarity index 100% rename from client/templates/includes/eventsEditor.pug rename to client/templates/includes/eventsView.pug diff --git a/client/views/events-editor.js b/client/views/events-view.js similarity index 98% rename from client/views/events-editor.js rename to client/views/events-view.js index ff6b3b34f8..bbfbd80d8a 100644 --- a/client/views/events-editor.js +++ b/client/views/events-view.js @@ -26,7 +26,7 @@ var View = require('ampersand-view'); var EventListings = require('./event-listings'); var EventDetails = require('./event-details'); //templates -var template = require('../templates/includes/eventsEditor.pug'); +var template = require('../templates/includes/eventsView.pug'); module.exports = View.extend({ template: template, diff --git a/client/views/model-state-buttons.js b/client/views/model-state-buttons.js index 1cb6bb9883..e64ca30b8b 100644 --- a/client/views/model-state-buttons.js +++ b/client/views/model-state-buttons.js @@ -334,9 +334,9 @@ module.exports = View.extend({ }, openEventsSection: function () { let error = this.model.error - let advSection = $(this.parent.queryByHook("me-advanced-section")) + let advSection = $(this.parent.modelView.queryByHook("mv-advanced-section")) if(!advSection.hasClass("show")) { - let advCollapseBtn = $(this.parent.queryByHook("collapse-me-advanced-section")) + let advCollapseBtn = $(this.parent.modelView.queryByHook("collapse-mv-advanced-section")) advCollapseBtn.click() advCollapseBtn.html('-') } From 60e9d7d3a04438e6487fc36c8e15154f96ce6307 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 2 Jul 2021 15:50:02 -0400 Subject: [PATCH 102/192] Added the derived property not_spatial to help with spatial model view rendering. --- client/models/model.js | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/client/models/model.js b/client/models/model.js index 9799e6e4f2..a31cf685db 100644 --- a/client/models/model.js +++ b/client/models/model.js @@ -84,6 +84,12 @@ module.exports = Model.extend({ let queryStr = "?path=" + this.directory; return path.join(app.getBasePath(), "stochss/models/edit") + queryStr; } + }, + not_spatial: { + deps: ["collection"], + fn: function () { + return !this.is_spatial + } } }, initialize: function (attrs, options){ From 6a05dc660fa5679464463f1b2598790e7a4d7420 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 2 Jul 2021 15:50:52 -0400 Subject: [PATCH 103/192] Moved the event render function and container to the model view. --- client/pages/model-editor.js | 9 --------- client/templates/includes/modelView.pug | 2 ++ client/views/events-view.js | 5 ----- client/views/model-state-buttons.js | 4 ++-- client/views/model-view.js | 11 +++++++++++ 5 files changed, 15 insertions(+), 16 deletions(-) diff --git a/client/pages/model-editor.js b/client/pages/model-editor.js index 899fa1781a..4cc2bc5022 100644 --- a/client/pages/model-editor.js +++ b/client/pages/model-editor.js @@ -29,7 +29,6 @@ var PageView = require('../pages/base'); let ModelView = require('../views/model-view'); var InputView = require('../views/input'); var ParticleViewer = require('../views/view-particle'); -var EventsEditorView = require('../views/events-view'); var RulesEditorView = require('../views/rules-editor'); var SBMLComponentView = require('../views/sbml-component-editor'); var TimespanSettingsView = require('../views/timespan-settings'); @@ -165,7 +164,6 @@ let ModelEditor = PageView.extend({ $(this.queryByHook("toggle-preview-domain")).css("display", "inline-block"); this.openDomainPlot(); }else { - this.renderEventsView(); this.renderRulesView(); if(this.model.functionDefinitions.length) { var sbmlComponentView = new SBMLComponentView({ @@ -195,13 +193,6 @@ let ModelEditor = PageView.extend({ }); app.registerRenderSubview(this, this.boundaryConditionsView, "boundary-conditions-container"); }, - renderEventsView: function () { - if(this.eventsEditor){ - this.eventsEditor.remove(); - } - this.eventsEditor = new EventsEditorView({collection: this.model.eventsCollection}); - app.registerRenderSubview(this, this.eventsEditor, 'events-editor-container'); - }, renderRulesView: function () { if(this.rulesEditor){ this.rulesEditor.remove(); diff --git a/client/templates/includes/modelView.pug b/client/templates/includes/modelView.pug index 31cb0b88f6..27fd1e491f 100644 --- a/client/templates/includes/modelView.pug +++ b/client/templates/includes/modelView.pug @@ -70,3 +70,5 @@ div#model-view div.collapse(id="mv-advanced-section" data-hook="mv-advanced-section") div.card-body + + div(data-hook="events-view-container") diff --git a/client/views/events-view.js b/client/views/events-view.js index bbfbd80d8a..ce8acb782f 100644 --- a/client/views/events-view.js +++ b/client/views/events-view.js @@ -32,7 +32,6 @@ module.exports = View.extend({ template: template, events: { 'click [data-hook=add-event]' : 'addEvent', - 'click [data-hook=save-events]' : 'switchToViewMode', 'click [data-hook=collapse]' : 'changeCollapseButtonText', }, initialize: function (attrs, options) { @@ -165,10 +164,6 @@ module.exports = View.extend({ detailsView.parent = this; return detailsView }, - switchToViewMode: function (e) { - this.parent.modelStateButtons.clickSaveHandler(e); - this.parent.renderEventsView(mode="view"); - }, changeCollapseButtonText: function (e) { app.changeCollapseButtonText(this, e); }, diff --git a/client/views/model-state-buttons.js b/client/views/model-state-buttons.js index e64ca30b8b..3c63084322 100644 --- a/client/views/model-state-buttons.js +++ b/client/views/model-state-buttons.js @@ -340,9 +340,9 @@ module.exports = View.extend({ advCollapseBtn.click() advCollapseBtn.html('-') } - let evtSection = $(this.eventsEditor.queryByHook("events")) + let evtSection = $(this.parent.modelView.eventsEditor.queryByHook("events")) if(!evtSection.hasClass("show")) { - let evtCollapseBtn = $(this.parent.eventsEditor.queryByHook("collapse")) + let evtCollapseBtn = $(this.parent.modelView.eventsEditor.queryByHook("collapse")) evtCollapseBtn.click() evtCollapseBtn.html('-') } diff --git a/client/views/model-view.js b/client/views/model-view.js index c11ffd4cfd..7c77995c6f 100644 --- a/client/views/model-view.js +++ b/client/views/model-view.js @@ -26,6 +26,7 @@ let modals = require('../modals'); let Domain = require('../models/domain'); //views let View = require('ampersand-view'); +let EventsView = require('../views/events-view'); let SpeciesView = require('../views/species-view'); let DomainViewer = require('../views/domain-viewer'); let ReactionsView = require('../views/reactions-view'); @@ -266,6 +267,16 @@ module.exports = View.extend({ readOnly: this.readOnly }); } + }, + eventsView: { + waitFor: "model.not_spatial", + hook: "events-view-container", + prepareView: function (el) { + return new EventsView({ + collection: this.model.eventsCollection, + readOnly: this.readOnly + }); + } } } }); \ No newline at end of file From 0e6811efa6aa90d40464caa0d98ca4bfe50da6f8 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 2 Jul 2021 15:52:47 -0400 Subject: [PATCH 104/192] Fixed the open functions for reactions and events. --- client/views/model-state-buttons.js | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/client/views/model-state-buttons.js b/client/views/model-state-buttons.js index 3c63084322..d87f63e2b5 100644 --- a/client/views/model-state-buttons.js +++ b/client/views/model-state-buttons.js @@ -319,9 +319,9 @@ module.exports = View.extend({ }, openReactionsSection: function (isCollection = false) { let error = this.model.error - let reacSection = $(this.parent.modelView.reactionsEditor.queryByHook("reactions-list-container")) + let reacSection = $(this.parent.modelView.reactionsView.queryByHook("reactions-list-container")) if(!reacSection.hasClass("show")) { - let reacCollapseBtn = $(this.parent.modelView.reactionsEditor.queryByHook("collapse")) + let reacCollapseBtn = $(this.parent.modelView.reactionsView.queryByHook("collapse")) reacCollapseBtn.click() reacCollapseBtn.html('-') } @@ -340,9 +340,9 @@ module.exports = View.extend({ advCollapseBtn.click() advCollapseBtn.html('-') } - let evtSection = $(this.parent.modelView.eventsEditor.queryByHook("events")) + let evtSection = $(this.parent.modelView.eventsView.queryByHook("events")) if(!evtSection.hasClass("show")) { - let evtCollapseBtn = $(this.parent.modelView.eventsEditor.queryByHook("collapse")) + let evtCollapseBtn = $(this.parent.modelView.eventsView.queryByHook("collapse")) evtCollapseBtn.click() evtCollapseBtn.html('-') } From d61632df95909f9fa90a31c814331995c744b9bc Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 2 Jul 2021 17:00:31 -0400 Subject: [PATCH 105/192] Cleaned up event view files. --- ...ntsEditor.pug => eventAssignmentsView.pug} | 0 ...assignment.js => event-assignment-view.js} | 42 ++++--- ...ts-editor.js => event-assignments-view.js} | 4 +- client/views/event-details.js | 70 ++++++------ client/views/event-listings.js | 72 ++++++------ client/views/events-view.js | 103 ++++++++---------- 6 files changed, 127 insertions(+), 164 deletions(-) rename client/templates/includes/{eventAssignmentsEditor.pug => eventAssignmentsView.pug} (100%) rename client/views/{edit-event-assignment.js => event-assignment-view.js} (79%) rename client/views/{event-assignments-editor.js => event-assignments-view.js} (95%) diff --git a/client/templates/includes/eventAssignmentsEditor.pug b/client/templates/includes/eventAssignmentsView.pug similarity index 100% rename from client/templates/includes/eventAssignmentsEditor.pug rename to client/templates/includes/eventAssignmentsView.pug diff --git a/client/views/edit-event-assignment.js b/client/views/event-assignment-view.js similarity index 79% rename from client/views/edit-event-assignment.js rename to client/views/event-assignment-view.js index 8bb53ad728..5fb865389b 100644 --- a/client/views/edit-event-assignment.js +++ b/client/views/event-assignment-view.js @@ -16,16 +16,16 @@ 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 let app = require('../app'); //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'); //templates -var editTemplate = require('../templates/includes/editEventAssignment.pug'); -var viewTemplate = require('../templates/includes/viewEventAssignment.pug'); +let editTemplate = require('../templates/includes/editEventAssignment.pug'); +let viewTemplate = require('../templates/includes/viewEventAssignment.pug'); module.exports = View.extend({ events: { @@ -41,28 +41,24 @@ module.exports = View.extend({ this.template = this.viewMode ? viewTemplate : editTemplate; View.prototype.render.apply(this, arguments); }, - update: function () { - }, - updateValid: function () { - }, - removeAssignment: function () { - this.remove(); - this.collection.removeEventAssignment(this.model) - this.collection.parent.collection.trigger('change') - }, getOptions: function () { var species = this.model.collection.parent.collection.parent.species; var parameters = this.model.collection.parent.collection.parent.parameters; var specs = species.map(function (specie) { - return [specie.compID, specie.name] + return [specie.compID, specie.name]; }); var params = parameters.map(function (parameter) { - return [parameter.compID, parameter.name] + return [parameter.compID, parameter.name]; }); - let options = [{groupName: "Variables", options: specs}, - {groupName: "Parameters", options: params}] + let options = [{groupName: Boolean(specs) ? "Variables" : "Variables (empty)", options: specs}, + {groupName: Boolean(params) ? "Parameters" : "Parameters (empty)", options: params}]; return options; }, + removeAssignment: function () { + this.remove(); + this.collection.removeEventAssignment(this.model); + this.collection.parent.collection.trigger('change'); + }, selectAssignmentVariable: function (e) { var species = this.model.collection.parent.collection.parent.species; var parameters = this.model.collection.parent.collection.parent.parameters; @@ -83,6 +79,8 @@ module.exports = View.extend({ this.updateViewer(); this.model.collection.parent.collection.trigger('change'); }, + update: function () {}, + updateValid: function () {}, updateViewer: function () { this.model.collection.parent.trigger('change'); }, @@ -97,9 +95,9 @@ module.exports = View.extend({ placeholder: "---No Expression Entered---", modelKey: 'expression', valueType: 'string', - value: this.model.expression, + value: this.model.expression }); - }, + } }, variableSelectView: { hook: 'event-assignment-variable', @@ -110,7 +108,7 @@ module.exports = View.extend({ required: true, idAttributes: 'cid', groupOptions: options, - value: this.model.variable.compID, + value: this.model.variable.compID }); } } diff --git a/client/views/event-assignments-editor.js b/client/views/event-assignments-view.js similarity index 95% rename from client/views/event-assignments-editor.js rename to client/views/event-assignments-view.js index 3640c137e9..ab53de27a3 100644 --- a/client/views/event-assignments-editor.js +++ b/client/views/event-assignments-view.js @@ -21,9 +21,9 @@ let $ = require('jquery'); let app = require('../app'); //views var View = require('ampersand-view'); -var EditEventAssignment = require('./edit-event-assignment'); +var EditEventAssignment = require('./event-assignment-view'); //templates -var template = require('../templates/includes/eventAssignmentsEditor.pug'); +var template = require('../templates/includes/eventAssignmentsView.pug'); module.exports = View.extend({ template: template, diff --git a/client/views/event-details.js b/client/views/event-details.js index a4cf72f6c9..8aabc4823e 100644 --- a/client/views/event-details.js +++ b/client/views/event-details.js @@ -16,16 +16,16 @@ 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 let app = require('../app'); -var tests = require('./tests'); +let tests = require('./tests'); //views -var View = require('ampersand-view'); -var InputView = require('./input'); -var EventAssignment = require('./event-assignments-editor'); +let InputView = require('./input'); +let View = require('ampersand-view'); +let EventAssignment = require('./event-assignments-view'); //templates -var template = require('../templates/includes/eventDetails.pug'); +let template = require('../templates/includes/eventDetails.pug'); module.exports = View.extend({ template: template, @@ -33,12 +33,12 @@ module.exports = View.extend({ 'model.initialValue': { hook: 'event-trigger-init-value', type: 'booleanAttribute', - name: 'checked', + name: 'checked' }, 'model.persistent': { hook: 'event-trigger-persistent', type: 'booleanAttribute', - name: 'checked', + name: 'checked' }, }, events: { @@ -46,7 +46,7 @@ module.exports = View.extend({ 'change [data-hook=event-trigger-persistent]' : 'setTriggerPersistent', 'change [data-hook=edit-trigger-time]' : 'setUseValuesFromTriggerTime', 'change [data-hook=edit-assignment-time]' : 'setUseValuesFromTriggerTime', - 'click [data-hook=advanced-event-button]' : 'changeCollapseButtonText', + 'click [data-hook=advanced-event-button]' : 'changeCollapseButtonText' }, initialize: function (attrs, options) { View.prototype.initialize.apply(this, arguments); @@ -55,25 +55,25 @@ module.exports = View.extend({ View.prototype.render.apply(this, arguments); this.renderEventAssignments(); if(this.model.useValuesFromTriggerTime){ - $(this.queryByHook('edit-trigger-time')).prop('checked', true) + $(this.queryByHook('edit-trigger-time')).prop('checked', true); }else{ - $(this.queryByHook('edit-assignment-time')).prop('checked', true) + $(this.queryByHook('edit-assignment-time')).prop('checked', true); } - $(function () { - $('[data-toggle="tooltip"]').tooltip(); - $('[data-toggle="tooltip"]').click(function () { - $('[data-toggle="tooltip"]').tooltip("hide"); - - }); - }); + app.tooltipSetup(); }, - update: function () { + changeCollapseButtonText: function (e) { + app.changeCollapseButtonText(this, e); }, - updateValid: function () { + openAdvancedSection: function () { + if(this.model.advanced_error && !$(this.queryByHook("advanced-event-section")).hasClass('show')) { + let advCollapseBtn = $(this.queryByHook("advanced-event-button")); + advCollapseBtn.click(); + advCollapseBtn.html('-'); + } }, renderEventAssignments: function () { if(this.eventAssignmentsView){ - this.eventAssignmentsView.remove() + this.eventAssignmentsView.remove(); } this.eventAssignmentsView = new EventAssignment({ collection: this.model.eventAssignments, @@ -81,13 +81,6 @@ module.exports = View.extend({ }); app.registerRenderSubview(this, this.eventAssignmentsView, 'event-assignments'); }, - openAdvancedSection: function () { - if(this.model.advanced_error && !$(this.queryByHook("advanced-event-section")).hasClass('show')) { - let advCollapseBtn = $(this.queryByHook("advanced-event-button")) - advCollapseBtn.click() - advCollapseBtn.html('-') - } - }, setTriggerInitialValue: function (e) { this.model.initialValue = e.target.checked; }, @@ -97,9 +90,8 @@ module.exports = View.extend({ setUseValuesFromTriggerTime: function (e) { this.model.useValuesFromTriggerTime = e.target.dataset.name === "trigger"; }, - changeCollapseButtonText: function (e) { - app.changeCollapseButtonText(this, e); - }, + update: function () {}, + updateValid: function () {}, subviews: { inputDelay: { hook: 'event-delay', @@ -111,9 +103,9 @@ module.exports = View.extend({ placeholder: '---No Expression Entered---', modelKey: 'delay', valueType: 'string', - value: this.model.delay, + value: this.model.delay }); - }, + } }, inputPriority: { hook: 'event-priority', @@ -124,9 +116,9 @@ module.exports = View.extend({ name: 'priority', modelKey: 'priority', valueType: 'string', - value: this.model.priority, + value: this.model.priority }); - }, + } }, inputTriggerExpression: { hook: 'event-trigger-expression', @@ -138,9 +130,9 @@ module.exports = View.extend({ placeholder: '---No Expression Entered---', modelKey: 'triggerExpression', valueType: 'string', - value: this.model.triggerExpression, + value: this.model.triggerExpression }); - }, - }, - }, + } + } + } }); \ No newline at end of file diff --git a/client/views/event-listings.js b/client/views/event-listings.js index 0a7c7866fe..f0885a7c3c 100644 --- a/client/views/event-listings.js +++ b/client/views/event-listings.js @@ -16,19 +16,19 @@ 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 _ = require('underscore'); //support files let app = require('../app'); -var tests = require('./tests'); -var modals = require('../modals'); +let tests = require('./tests'); +let modals = require('../modals'); //views -var View = require('ampersand-view'); -var InputView = require('./input'); -var EventAssignment = require('./event-assignments-editor'); +let InputView = require('./input'); +let View = require('ampersand-view'); +let EventAssignment = require('./event-assignments-view'); //templates -var editTemplate = require('../templates/includes/eventListings.pug'); let viewTemplate = require('../templates/includes/viewEvents.pug'); +let editTemplate = require('../templates/includes/eventListings.pug'); module.exports = View.extend({ bindings: { @@ -41,18 +41,18 @@ module.exports = View.extend({ 'model.initialValue': { hook: 'event-trigger-init-value', type: 'booleanAttribute', - name: 'checked', + name: 'checked' }, 'model.persistent': { hook: 'event-trigger-persistent', type: 'booleanAttribute', - name: 'checked', + name: 'checked' } }, events: { 'click [data-hook=select]' : 'selectEvent', 'click [data-hook=edit-annotation-btn]' : 'editAnnotation', - 'click [data-hook=remove]' : 'removeEvent', + 'click [data-hook=remove]' : 'removeEvent' }, initialize: function (attrs, options) { View.prototype.initialize.apply(this, arguments); @@ -66,17 +66,11 @@ module.exports = View.extend({ render: function () { this.template = this.viewMode ? viewTemplate : editTemplate; View.prototype.render.apply(this, arguments); - $(document).on('shown.bs.modal', function (e) { - $('[autofocus]', e.target).focus(); - }); - $(document).on('hide.bs.modal', '.modal', function (e) { - e.target.remove() - }); + app.documentSetup(); if(!this.model.annotation){ $(this.queryByHook('edit-annotation-btn')).text('Add'); } if(this.viewMode) { - this.renderViewEventAssignments(); if(this.model.useValuesFromTriggerTime) { $(this.queryByHook("view-trigger-time")).prop('checked', true); }else{ @@ -84,20 +78,13 @@ module.exports = View.extend({ } } }, - update: function () { - }, - updateValid: function () { - }, - selectEvent: function (e) { - this.model.collection.trigger("select", this.model); - }, editAnnotation: function () { - var self = this; - var name = this.model.name; - var annotation = this.model.annotation; if(document.querySelector('#eventAnnotationModal')) { document.querySelector('#eventAnnotationModal').remove(); } + let self = this; + let name = this.model.name; + let annotation = this.model.annotation; let modal = $(modals.annotationModalHtml("event", name, annotation)).modal(); let okBtn = document.querySelector('#eventAnnotationModal .ok-model-btn'); let input = document.querySelector('#eventAnnotationModal #eventAnnotationInput'); @@ -117,17 +104,11 @@ module.exports = View.extend({ this.remove(); this.collection.removeEvent(this.model); }, - renderViewEventAssignments: function () { - if(this.viewEventAssignmentsView){ - this.viewEventAssignmentsView.remove() - } - this.viewEventAssignmentsView = new EventAssignment({ - collection: this.model.eventAssignments, - tooltips: this.parent.tooltips, - readOnly: true - }); - app.registerRenderSubview(this, this.viewEventAssignmentsView, 'assignment-viewer'); + selectEvent: function (e) { + this.model.collection.trigger("select", this.model); }, + update: function () {}, + updateValid: function () {}, updateViewer: function () { this.parent.renderViewEventListingView(); }, @@ -139,13 +120,22 @@ module.exports = View.extend({ parent: this, required: true, name: 'name', - label: '', tests: tests.nameTests, modelKey: 'name', valueType: 'string', - value: this.model.name, + value: this.model.name }); - }, + } }, - }, + viewEventAssignmentsView: { + hook: "assignment-viewer", + prepareView: function (el) { + return new EventAssignment({ + collection: this.model.eventAssignments, + tooltips: this.parent.tooltips, + readOnly: true + }); + } + } + } }); \ No newline at end of file diff --git a/client/views/events-view.js b/client/views/events-view.js index ce8acb782f..a3af64889e 100644 --- a/client/views/events-view.js +++ b/client/views/events-view.js @@ -16,28 +16,28 @@ You should have received a copy of the GNU General Public License along with this program. If not, see . */ -var ViewSwitcher = require('ampersand-view-switcher'); -var $ = require('jquery'); +let $ = require('jquery'); //support files let app = require('../app'); -var Tooltips = require("../tooltips"); +let Tooltips = require("../tooltips"); //views -var View = require('ampersand-view'); -var EventListings = require('./event-listings'); -var EventDetails = require('./event-details'); +let View = require('ampersand-view'); +let EventDetails = require('./event-details'); +let EventListings = require('./event-listings'); +let ViewSwitcher = require('ampersand-view-switcher'); //templates -var template = require('../templates/includes/eventsView.pug'); +let template = require('../templates/includes/eventsView.pug'); module.exports = View.extend({ template: template, events: { 'click [data-hook=add-event]' : 'addEvent', - 'click [data-hook=collapse]' : 'changeCollapseButtonText', + 'click [data-hook=collapse]' : 'changeCollapseButtonText' }, initialize: function (attrs, options) { View.prototype.initialize.apply(this, arguments); this.readOnly = attrs.readOnly ? attrs.readOnly : false; - this.tooltips = Tooltips.eventsEditor + this.tooltips = Tooltips.eventsEditor; if(!this.readOnly) { this.collection.on("select", function (event) { this.setSelectedEvent(event); @@ -46,11 +46,12 @@ module.exports = View.extend({ this.collection.on("remove", function (event) { // Select the last event by default // But only if there are other events other than the one we're removing - if (event.detailsView) + if (event.detailsView){ event.detailsView.remove(); + } this.collection.removeEvent(event); if (this.collection.length) { - var selected = this.collection.at(this.collection.length-1); + let selected = this.collection.at(this.collection.length-1); this.collection.trigger("select", selected); } }, this); @@ -73,19 +74,29 @@ module.exports = View.extend({ this.renderEditEventListingsView(); this.detailsContainer = this.queryByHook('event-details-container'); this.detailsViewSwitcher = new ViewSwitcher({ - el: this.detailsContainer, + el: this.detailsContainer }); if(this.collection.length) { this.setSelectedEvent(this.collection.at(0)); this.collection.trigger("select", this.selectedEvent); } - this.toggleAddEventButton() + this.toggleAddEventButton(); } this.renderViewEventListingView(); }, - update: function () { + addEvent: function () { + let event = this.collection.addEvent(); + event.detailsView = this.newDetailsView(event); + this.collection.trigger("select", event); + app.tooltipSetup(); }, - updateValid: function () { + changeCollapseButtonText: function (e) { + app.changeCollapseButtonText(this, e); + }, + newDetailsView: function (event) { + let detailsView = new EventDetails({ model: event }); + detailsView.parent = this; + return detailsView; }, renderEditEventListingsView: function () { if(this.editEventListingsView){ @@ -96,12 +107,7 @@ module.exports = View.extend({ EventListings, this.queryByHook('edit-event-listing-container') ); - $(document).ready(function () { - $('[data-toggle="tooltip"]').tooltip(); - $('[data-toggle="tooltip"]').click(function () { - $('[data-toggle="tooltip"]').tooltip("hide"); - }); - }); + app.tooltipSetup(); }, renderViewEventListingView: function () { if(this.viewEventListingsView) { @@ -120,51 +126,28 @@ module.exports = View.extend({ this.queryByHook('view-event-listing-container'), options ); - $(document).ready(function () { - $('[data-toggle="tooltip"]').tooltip(); - $('[data-toggle="tooltip"]').click(function () { - $('[data-toggle="tooltip"]').tooltip("hide"); - }); - }); + app.tooltipSetup(); }, - toggleAddEventButton: function () { - this.collection.map(function (event) { - if(event.detailsView && event.selected){ - event.detailsView.renderEventAssignments(); - } - }) - var numSpecies = this.collection.parent.species.length; - var numParameters = this.collection.parent.parameters.length; - var disabled = numSpecies <= 0 && numParameters <= 0 - $(this.queryByHook('add-event')).prop('disabled', disabled); + setDetailsView: function (event) { + event.detailsView = event.detailsView || this.newDetailsView(event); + this.detailsViewSwitcher.set(event.detailsView); }, setSelectedEvent: function (event) { this.collection.each(function (m) { m.selected = false; }); event.selected = true; this.selectedEvent = event; }, - setDetailsView: function (event) { - event.detailsView = event.detailsView || this.newDetailsView(event); - this.detailsViewSwitcher.set(event.detailsView); - }, - addEvent: function () { - var event = this.collection.addEvent(); - event.detailsView = this.newDetailsView(event); - this.collection.trigger("select", event); - $(document).ready(function () { - $('[data-toggle="tooltip"]').tooltip(); - $('[data-toggle="tooltip"]').click(function () { - $('[data-toggle="tooltip"]').tooltip("hide"); - - }); + toggleAddEventButton: function () { + this.collection.map(function (event) { + if(event.detailsView && event.selected){ + event.detailsView.renderEventAssignments(); + } }); + let numSpecies = this.collection.parent.species.length; + let numParameters = this.collection.parent.parameters.length; + let disabled = numSpecies <= 0 && numParameters <= 0; + $(this.queryByHook('add-event')).prop('disabled', disabled); }, - newDetailsView: function (event) { - var detailsView = new EventDetails({ model: event }); - detailsView.parent = this; - return detailsView - }, - changeCollapseButtonText: function (e) { - app.changeCollapseButtonText(this, e); - }, -}) \ No newline at end of file + update: function () {}, + updateValid: function () {} +}); \ No newline at end of file From f90288b6c8cefe5167c04cccc8c4cd92e83fe549 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Tue, 6 Jul 2021 08:47:01 -0400 Subject: [PATCH 106/192] Added the excapism dependency to allow consistent and proper encoding of user names for stable docker container lookups. --- requirements.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/requirements.txt b/requirements.txt index eb3d418969..e27b864c4c 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,6 +1,7 @@ python-libsbml==5.18.0 python-libsedml==2.0.9 python-libcombine==0.2.7 +escapism==1.0.1 gillespy2==1.5.11 sciope==0.4 pygmsh==5.0.2 From d939420cea808c8177428697bdcee4d111d916e0 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Tue, 6 Jul 2021 08:50:43 -0400 Subject: [PATCH 107/192] Refactored the presentation links to use the user name instead of the container id as the owner for more stable container lookups. --- jupyterhub/model_presentation.py | 5 +++-- stochss/handlers/util/stochss_model.py | 6 +++++- 2 files changed, 8 insertions(+), 3 deletions(-) diff --git a/jupyterhub/model_presentation.py b/jupyterhub/model_presentation.py index f442893769..ecccc25d52 100644 --- a/jupyterhub/model_presentation.py +++ b/jupyterhub/model_presentation.py @@ -24,11 +24,12 @@ import tempfile import docker -from jupyterhub.handlers.base import BaseHandler from presentation_base import StochSSBase from presentation_error import StochSSAPIError, report_error +from jupyterhub.handlers.base import BaseHandler + log = logging.getLogger('stochss') # pylint: disable=abstract-method @@ -106,7 +107,7 @@ def get_presentation_from_user(owner, file): ''' client = docker.from_env() containers = client.containers.list() - user_container = list(filter(lambda container: container.id.startswith(owner), + user_container = list(filter(lambda container: container.name == f"jupyter-{owner}", containers))[0] user_model_path = f'/home/jovyan/.presentations/{file}' tar_mdl = tempfile.TemporaryFile() diff --git a/stochss/handlers/util/stochss_model.py b/stochss/handlers/util/stochss_model.py index 999157034d..444d22c007 100644 --- a/stochss/handlers/util/stochss_model.py +++ b/stochss/handlers/util/stochss_model.py @@ -19,11 +19,13 @@ import os import ast import json +import string import hashlib import tempfile import traceback import numpy +from escapism import escape from gillespy2.sbml.SBMLexport import export from gillespy2 import Model, Species, Parameter, Reaction, Event, EventTrigger, EventAssignment, \ RateRule, AssignmentRule, FunctionDefinition @@ -474,7 +476,9 @@ def publish_presentation(self): os.mkdir(present_dir) try: self.load() - hostname = os.uname()[1] + safe_chars = set(string.ascii_letters + string.digits) + hostname = escape(os.environ.get('JUPYTER_USER'), + safe_chars=safe_chars, escape_char="-").lower() model = json.dumps(self.model, sort_keys=True) # replace with gillespy2.Model.to_json file = f"{hashlib.md5(model.encode('utf-8')).hexdigest()}.mdl" From 53d87d7df7648d397eeaffcf2f64209cfe134d98 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Tue, 6 Jul 2021 10:42:36 -0400 Subject: [PATCH 108/192] Fixed issue with escape function. --- stochss/handlers/util/stochss_model.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/stochss/handlers/util/stochss_model.py b/stochss/handlers/util/stochss_model.py index 444d22c007..501870cab1 100644 --- a/stochss/handlers/util/stochss_model.py +++ b/stochss/handlers/util/stochss_model.py @@ -477,8 +477,7 @@ def publish_presentation(self): try: self.load() safe_chars = set(string.ascii_letters + string.digits) - hostname = escape(os.environ.get('JUPYTER_USER'), - safe_chars=safe_chars, escape_char="-").lower() + hostname = escape(os.environ.get('JUPYTER_USER'), safe=safe_chars).lower() model = json.dumps(self.model, sort_keys=True) # replace with gillespy2.Model.to_json file = f"{hashlib.md5(model.encode('utf-8')).hexdigest()}.mdl" From eb441fc8e0be279ba71d78a07d3ae727e0ca441e Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Tue, 6 Jul 2021 10:45:35 -0400 Subject: [PATCH 109/192] Testing jupyterhub nbviewer service. --- jupyterhub/jupyterhub_config.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/jupyterhub/jupyterhub_config.py b/jupyterhub/jupyterhub_config.py index 64c02e7605..b1046bd58f 100644 --- a/jupyterhub/jupyterhub_config.py +++ b/jupyterhub/jupyterhub_config.py @@ -134,6 +134,11 @@ 'name': 'cull-idle', 'admin': True, 'command': [sys.executable, '/srv/jupyterhub/cull_idle_servers.py', '--timeout=28800'], + }, + { + 'name': 'nbviewer', + 'url': 'http://127.0.0.1:9000', + 'command': ['python', '-m', 'nbviewer'] } ] From 6b36fc33be823c5b7df74387ea308cf9b941df4a Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Tue, 6 Jul 2021 11:23:51 -0400 Subject: [PATCH 110/192] Exposed port 9000. --- jupyterhub/docker-compose.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/jupyterhub/docker-compose.yml b/jupyterhub/docker-compose.yml index ef5468f473..c4105ee86a 100644 --- a/jupyterhub/docker-compose.yml +++ b/jupyterhub/docker-compose.yml @@ -33,6 +33,7 @@ services: - "${PWD}:/srv/jupyterhub" ports: - "8000:8000" + - "9000:9000" links: - hub-db environment: From 7c1569b90b65a7028188ff1f278bcc42151f46f0 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Tue, 6 Jul 2021 11:55:05 -0400 Subject: [PATCH 111/192] Added nbviewer to jupyterhub requirements. --- jupyterhub/Dockerfile.jupyterhub | 1 + jupyterhub/docker-compose.yml | 1 - 2 files changed, 1 insertion(+), 1 deletion(-) diff --git a/jupyterhub/Dockerfile.jupyterhub b/jupyterhub/Dockerfile.jupyterhub index 38df4d10b2..eed510b44b 100644 --- a/jupyterhub/Dockerfile.jupyterhub +++ b/jupyterhub/Dockerfile.jupyterhub @@ -40,6 +40,7 @@ RUN python3 -m pip install --no-cache-dir \ oauthenticator==0.11.* \ dockerspawner==0.11.* \ psycopg2==2.7.* \ + nbviewer==1.0.1 \ notebook COPY static/* /usr/local/share/jupyterhub/static/ diff --git a/jupyterhub/docker-compose.yml b/jupyterhub/docker-compose.yml index c4105ee86a..ef5468f473 100644 --- a/jupyterhub/docker-compose.yml +++ b/jupyterhub/docker-compose.yml @@ -33,7 +33,6 @@ services: - "${PWD}:/srv/jupyterhub" ports: - "8000:8000" - - "9000:9000" links: - hub-db environment: From 6fe12eff45125296d8cbd8d7e9f27b845ae8a0e6 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Tue, 6 Jul 2021 12:24:32 -0400 Subject: [PATCH 112/192] Exposed port 9000 take 2. --- jupyterhub/docker-compose.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/jupyterhub/docker-compose.yml b/jupyterhub/docker-compose.yml index ef5468f473..c4105ee86a 100644 --- a/jupyterhub/docker-compose.yml +++ b/jupyterhub/docker-compose.yml @@ -33,6 +33,7 @@ services: - "${PWD}:/srv/jupyterhub" ports: - "8000:8000" + - "9000:9000" links: - hub-db environment: From e8223c3ad15d3f5cde98933f426af67a5e0ba3a1 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Tue, 6 Jul 2021 14:47:16 -0400 Subject: [PATCH 113/192] Added escape char argument to the escape function to fix none type error. --- stochss/handlers/util/stochss_model.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/stochss/handlers/util/stochss_model.py b/stochss/handlers/util/stochss_model.py index 501870cab1..ba2825ddf5 100644 --- a/stochss/handlers/util/stochss_model.py +++ b/stochss/handlers/util/stochss_model.py @@ -477,7 +477,8 @@ def publish_presentation(self): try: self.load() safe_chars = set(string.ascii_letters + string.digits) - hostname = escape(os.environ.get('JUPYTER_USER'), safe=safe_chars).lower() + hostname = escape(os.environ.get('JUPYTER_USER'), + safe=safe_chars, escape_char="_").lower() model = json.dumps(self.model, sort_keys=True) # replace with gillespy2.Model.to_json file = f"{hashlib.md5(model.encode('utf-8')).hexdigest()}.mdl" From c5e71f4ef5f2f5ea82251054773309a613ea0e8d Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Tue, 6 Jul 2021 14:50:29 -0400 Subject: [PATCH 114/192] Fixed environment variable name. --- stochss/handlers/util/stochss_model.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/stochss/handlers/util/stochss_model.py b/stochss/handlers/util/stochss_model.py index ba2825ddf5..b1d6b975cc 100644 --- a/stochss/handlers/util/stochss_model.py +++ b/stochss/handlers/util/stochss_model.py @@ -477,7 +477,7 @@ def publish_presentation(self): try: self.load() safe_chars = set(string.ascii_letters + string.digits) - hostname = escape(os.environ.get('JUPYTER_USER'), + hostname = escape(os.environ.get('JUPYTERHUB_USER'), safe=safe_chars, escape_char="_").lower() model = json.dumps(self.model, sort_keys=True) # replace with gillespy2.Model.to_json From 44321cd150608248679cb6927672879a1ef522bf Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Tue, 6 Jul 2021 14:53:43 -0400 Subject: [PATCH 115/192] Added service script for notebook presentations. --- jupyterhub/jupyterhub_config.py | 3 +- jupyterhub/notebook_presentation.py | 80 +++++++++++++++++++++++++++++ 2 files changed, 82 insertions(+), 1 deletion(-) create mode 100644 jupyterhub/notebook_presentation.py diff --git a/jupyterhub/jupyterhub_config.py b/jupyterhub/jupyterhub_config.py index b1046bd58f..6ea8fcc943 100644 --- a/jupyterhub/jupyterhub_config.py +++ b/jupyterhub/jupyterhub_config.py @@ -137,8 +137,9 @@ }, { 'name': 'nbviewer', + 'admin': True, 'url': 'http://127.0.0.1:9000', - 'command': ['python', '-m', 'nbviewer'] + 'command': [sys.executable, '/srv/jupyterhub/notbook_presentation.py'] } ] diff --git a/jupyterhub/notebook_presentation.py b/jupyterhub/notebook_presentation.py new file mode 100644 index 0000000000..d260902e5f --- /dev/null +++ b/jupyterhub/notebook_presentation.py @@ -0,0 +1,80 @@ +#!/usr/bin/env python3 + +''' +StochSS is a platform for simulating biochemical systems +Copyright (C) 2019-2021 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 tarfile +import tempfile +import nbformat + +from nbviewer.render import render_notebook +from nbconvert.exporters import HTMLExporter + +import docker + +def convert_notebook_to_html(notebook): + ''' + Convert the notebook object into html. + + Attributes + ---------- + notebook : NotebookNode + Notebook read in using nbformat + ''' + nb_format = {"exporter": HTMLExporter} + html, config = render_notebook(format=nb_format, nb=nb) + return html + + +def get_presentation_from_user(owner, file, as_dict=False): + ''' + Get the model presentation from the users container + + Attributes + ---------- + owner : str + Hostname of the user container + file : str + Name of the model presentation file + ''' + client = docker.from_env() + containers = client.containers.list() + user_container = list(filter(lambda container: container.name == f"jupyter-{owner}", + containers))[0] + user_nb_path = f'/home/jovyan/.presentations/{file}' + tar_nb = tempfile.TemporaryFile() + bits, _ = user_container.get_archive(user_nb_path) + for chunk in bits: + tar_nb.write(chunk) + tar_nb.seek(0) + tar_file = tarfile.TarFile(fileobj=tar_nb) + tmp_dir = tempfile.TemporaryDirectory() + tar_file.extractall(tmp_dir.name) + tar_nb.close() + nb_path = os.path.join(tmp_dir.name, file) + with open(nb_path, "r") as nb_file: + if as_dict: + return json.load(nb_file) + return nbformat.read(nb_file, as_version=4) + + +if __main__ == "__name__": + nb = get_presentation_from_user() + return convert_notebook_to_html(notebook=nb) From 197f214f8b38e62aeeb8c3679b9b4c9021b40df7 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Tue, 6 Jul 2021 15:40:17 -0400 Subject: [PATCH 116/192] Fixed model presentation header. --- client/templates/pages/modelPresentation.pug | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/client/templates/pages/modelPresentation.pug b/client/templates/pages/modelPresentation.pug index f21036e7dd..7fe07e5ed2 100644 --- a/client/templates/pages/modelPresentation.pug +++ b/client/templates/pages/modelPresentation.pug @@ -4,7 +4,7 @@ section.page div.presentation-header - h1 "" + this.model.name + "" + h1 this.model.name div(data-hook="model-species") From 897a67420782a379a1c76fba9402f96d572af395 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Tue, 6 Jul 2021 15:41:13 -0400 Subject: [PATCH 117/192] Removed the lower function from the hostname generation line. --- stochss/handlers/util/stochss_model.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/stochss/handlers/util/stochss_model.py b/stochss/handlers/util/stochss_model.py index b1d6b975cc..959afaa78d 100644 --- a/stochss/handlers/util/stochss_model.py +++ b/stochss/handlers/util/stochss_model.py @@ -477,8 +477,7 @@ def publish_presentation(self): try: self.load() safe_chars = set(string.ascii_letters + string.digits) - hostname = escape(os.environ.get('JUPYTERHUB_USER'), - safe=safe_chars, escape_char="_").lower() + hostname = escape(os.environ.get('JUPYTERHUB_USER'), safe=safe_chars) model = json.dumps(self.model, sort_keys=True) # replace with gillespy2.Model.to_json file = f"{hashlib.md5(model.encode('utf-8')).hexdigest()}.mdl" From 99d261d4034a7c2d02b160f20c50de119f03bc7f Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Tue, 6 Jul 2021 15:48:40 -0400 Subject: [PATCH 118/192] Removed the main function and added an api handler to load the notebook in html format. --- jupyterhub/notebook_presentation.py | 34 +++++++++++++++++++++++------ 1 file changed, 27 insertions(+), 7 deletions(-) diff --git a/jupyterhub/notebook_presentation.py b/jupyterhub/notebook_presentation.py index d260902e5f..e5bdb18b8f 100644 --- a/jupyterhub/notebook_presentation.py +++ b/jupyterhub/notebook_presentation.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python3 - ''' StochSS is a platform for simulating biochemical systems Copyright (C) 2019-2021 StochSS developers. @@ -29,6 +27,33 @@ import docker +from jupyterhub.handlers.base import BaseHandler + +# pylint: disable=abstract-method +# pylint: disable=too-few-public-methods +class NotebookAPIHandler(BaseHandler): + ''' + ################################################################################################ + Base Handler for getting notebook presentations from user containers. + ################################################################################################ + ''' + async def get(self): + ''' + Load the notebook presentation from User's presentations directory. + + Attributes + ---------- + ''' + owner = self.get_query_argument(name="owner") + log.debug("Container id of the owner: %s", owner) + file = self.get_query_argument(name="file") + log.debug("Name to the file: %s", file) + notebook = get_presentation_from_user(owner=owner, file=file) + html = convert_notebook_to_html(notebook=notebook) + self.write(html) + self.finish() + + def convert_notebook_to_html(notebook): ''' Convert the notebook object into html. @@ -73,8 +98,3 @@ def get_presentation_from_user(owner, file, as_dict=False): if as_dict: return json.load(nb_file) return nbformat.read(nb_file, as_version=4) - - -if __main__ == "__name__": - nb = get_presentation_from_user() - return convert_notebook_to_html(notebook=nb) From 5edba39d31dcb13001f34e8b53cf07648195be00 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Tue, 6 Jul 2021 15:49:37 -0400 Subject: [PATCH 119/192] Removed port 9000 from the list of exposed ports. --- jupyterhub/docker-compose.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/jupyterhub/docker-compose.yml b/jupyterhub/docker-compose.yml index c4105ee86a..ef5468f473 100644 --- a/jupyterhub/docker-compose.yml +++ b/jupyterhub/docker-compose.yml @@ -33,7 +33,6 @@ services: - "${PWD}:/srv/jupyterhub" ports: - "8000:8000" - - "9000:9000" links: - hub-db environment: From 625603fdccd3531a95c331032cd1606a31135c5b Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Tue, 6 Jul 2021 16:11:27 -0400 Subject: [PATCH 120/192] Removed the nbviewer service and added routes to load the notebook presentation page and notebook presentation. --- jupyterhub/jupyterhub_config.py | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/jupyterhub/jupyterhub_config.py b/jupyterhub/jupyterhub_config.py index 6ea8fcc943..28b1422d04 100644 --- a/jupyterhub/jupyterhub_config.py +++ b/jupyterhub/jupyterhub_config.py @@ -84,7 +84,9 @@ (r"/stochss\/?", HomeHandler), (r"/stochss/present-job\/?", JobPresentationHandler), (r"/stochss/present-model\/?", ModelPresentationHandler), + (r"/stochss/present-notebook\/?", NotebookPresentationHandler), (r"/stochss/api/file/json-data\/?", JsonFileAPIHandler), + (r"/stochss/api/notebook/load\/?", NotebookAPIHandler), (r"/stochss/presentation-download/(\w+)/(.+)\/?", DownModelPresentationAPIHandler) ] @@ -134,12 +136,6 @@ 'name': 'cull-idle', 'admin': True, 'command': [sys.executable, '/srv/jupyterhub/cull_idle_servers.py', '--timeout=28800'], - }, - { - 'name': 'nbviewer', - 'admin': True, - 'url': 'http://127.0.0.1:9000', - 'command': [sys.executable, '/srv/jupyterhub/notbook_presentation.py'] } ] From 06aad850a0b5bf107bfd5271da1a7455deb3238b Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Tue, 6 Jul 2021 16:15:17 -0400 Subject: [PATCH 121/192] Added the notebook presentation page to the jupyterhub container. --- client/pages/model-presentation.js | 2 +- client/pages/notebook-presentation.js | 54 +++++++++++++++++++ .../templates/pages/notebookPresentation.pug | 11 ++++ jupyterhub/handlers.py | 17 ++++++ webpack.hub.config.js | 10 +++- 5 files changed, 92 insertions(+), 2 deletions(-) create mode 100644 client/pages/notebook-presentation.js create mode 100644 client/templates/pages/notebookPresentation.pug diff --git a/client/pages/model-presentation.js b/client/pages/model-presentation.js index c67df65ffa..4916a533d7 100644 --- a/client/pages/model-presentation.js +++ b/client/pages/model-presentation.js @@ -44,7 +44,7 @@ let ModelPresentationPage = PageView.extend({ initialize: function (attrs, options) { PageView.prototype.initialize.apply(this, arguments); let urlParams = new URLSearchParams(window.location.search); - let owner = urlParams.get("owner") + let owner = urlParams.get("owner"); let file = urlParams.get("file"); this.model = new Model({ directory: file, diff --git a/client/pages/notebook-presentation.js b/client/pages/notebook-presentation.js new file mode 100644 index 0000000000..4a4189959b --- /dev/null +++ b/client/pages/notebook-presentation.js @@ -0,0 +1,54 @@ +/* +StochSS is a platform for simulating biochemical systems +Copyright (C) 2019-2021 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'); +let domReady = require('domready'); +let bootstrap = require('bootstrap'); +//views +let PageView = require('./base'); +//templates +let template = require('../templates/pages/notebookPresentation.pug'); + +import bootstrapStyles from '../styles/bootstrap.css'; +import styles from '../styles/styles.css'; +import fontawesomeStyles from '@fortawesome/fontawesome-free/css/svg-with-js.min.css' + +let NotebookPresentationPage = PageView.extend({ + template: template, + initialize: function (attrs, options) { + PageView.prototype.initialize.apply(this, arguments); + let urlParams = new URLSearchParams(window.location.search); + let owner = urlParams.get("owner"); + let file = urlParams.get("file"); + let queryStr = "?owner=" + owner + "&file=" + file; + this.loadLink = "https://live.stochss.org/stochss/api/notebook/load" + queryStr; + let downloadStart = "https://live.stochss.org/stochss/download_presentation"; + this.downloadLink = path.join(downloadStart, owner, file); + this.openLink = "open.stochss.org?open=" + this.downloadLink; + }, + render: function (attrs, options) { + PageView.prototype.render.apply(this, arguments); + } +}); + +domReady(() => { + let p = new ModelPresentationPage({ + el: document.body + }); + p.render(); +}); diff --git a/client/templates/pages/notebookPresentation.pug b/client/templates/pages/notebookPresentation.pug new file mode 100644 index 0000000000..902c0c35cc --- /dev/null +++ b/client/templates/pages/notebookPresentation.pug @@ -0,0 +1,11 @@ +section.page + + div#notebook-presentation.container + + div.presentation-header + + h1 this.name + + div + + iframe(src=this.loadLink) diff --git a/jupyterhub/handlers.py b/jupyterhub/handlers.py index 46ba1b5cd9..d891ed670f 100644 --- a/jupyterhub/handlers.py +++ b/jupyterhub/handlers.py @@ -69,3 +69,20 @@ async def get(self): ''' html = self.render_template("stochss-model-presentation.html") self.finish(html) + + +class NotebookPresentationHandler(BaseHandler): + ''' + ################################################################################################ + Handler for rendering jupyterhub notebook presentation page. + ################################################################################################ + ''' + async def get(self): + ''' + Render the jupyterhub notebook presentation page. + + Attributes + ---------- + ''' + html = self.render_template("stochss-notebook-presentation.html") + self.finish(html) diff --git a/webpack.hub.config.js b/webpack.hub.config.js index 658b62b9ff..72bacecc99 100644 --- a/webpack.hub.config.js +++ b/webpack.hub.config.js @@ -6,7 +6,8 @@ module.exports = { entry: { home: './client/pages/home.js', jobPresentation: './client/pages/job-presentation.js', - modelPresentation: './client/pages/model-presentation.js' + modelPresentation: './client/pages/model-presentation.js', + notebookPresentation: '.client/pages/notebook-presentation.js' }, output: { filename: 'stochss-[name].bundle.js', @@ -34,6 +35,13 @@ module.exports = { template: 'jupyterhub/home_template.pug', name: 'modelPresentation', inject: false + }), + new HtmlWebpackPlugin({ + title: 'StochSS | Notebook Presentation', + filename: '../templates/stochss-notebook-presentation.html', + template: 'jupyterhub/home_template.pug', + name: 'notebookPresentation', + inject: false }) ], module: { From 115df275a9984984c6faefc56b465313ba528452 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Tue, 6 Jul 2021 16:33:39 -0400 Subject: [PATCH 122/192] Fixed pathing issue with the notebook template. --- webpack.hub.config.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/webpack.hub.config.js b/webpack.hub.config.js index 72bacecc99..62330fdbe3 100644 --- a/webpack.hub.config.js +++ b/webpack.hub.config.js @@ -7,7 +7,7 @@ module.exports = { home: './client/pages/home.js', jobPresentation: './client/pages/job-presentation.js', modelPresentation: './client/pages/model-presentation.js', - notebookPresentation: '.client/pages/notebook-presentation.js' + notebookPresentation: './client/pages/notebook-presentation.js' }, output: { filename: 'stochss-[name].bundle.js', From 3291c2fa650651d0f0c1c3ebd5326505dc1ba034 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Tue, 6 Jul 2021 16:34:39 -0400 Subject: [PATCH 123/192] Switch all generated paths for presentations from live to staging. --- client/pages/model-presentation.js | 2 +- client/pages/notebook-presentation.js | 4 ++-- stochss/handlers/util/stochss_model.py | 6 +++--- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/client/pages/model-presentation.js b/client/pages/model-presentation.js index 4916a533d7..64ba808e22 100644 --- a/client/pages/model-presentation.js +++ b/client/pages/model-presentation.js @@ -59,7 +59,7 @@ let ModelPresentationPage = PageView.extend({ self.renderSubviews(); } }); - let downloadStart = "https://live.stochss.org/stochss/download_presentation"; + let downloadStart = "https://staging.stochss.org/stochss/download_presentation"; this.downloadLink = path.join(downloadStart, owner, file); this.openLink = "open.stochss.org?open=" + this.downloadLink; }, diff --git a/client/pages/notebook-presentation.js b/client/pages/notebook-presentation.js index 4a4189959b..7c0138a169 100644 --- a/client/pages/notebook-presentation.js +++ b/client/pages/notebook-presentation.js @@ -36,8 +36,8 @@ let NotebookPresentationPage = PageView.extend({ let owner = urlParams.get("owner"); let file = urlParams.get("file"); let queryStr = "?owner=" + owner + "&file=" + file; - this.loadLink = "https://live.stochss.org/stochss/api/notebook/load" + queryStr; - let downloadStart = "https://live.stochss.org/stochss/download_presentation"; + this.loadLink = "https://staging.stochss.org/stochss/api/notebook/load" + queryStr; + let downloadStart = "https://staging.stochss.org/stochss/download_presentation"; this.downloadLink = path.join(downloadStart, owner, file); this.openLink = "open.stochss.org?open=" + this.downloadLink; }, diff --git a/stochss/handlers/util/stochss_model.py b/stochss/handlers/util/stochss_model.py index 959afaa78d..f0044bd1dc 100644 --- a/stochss/handlers/util/stochss_model.py +++ b/stochss/handlers/util/stochss_model.py @@ -486,10 +486,10 @@ def publish_presentation(self): message = "A presentation with this name already exists" raise StochSSFileExistsError(message) query_str = f"?owner={hostname}&file={file}" - present_link = f"https://live.stochss.org/stochss/present-model{query_str}" - download_link = os.path.join("https://live.stochss.org/stochss/download_presentation", + present_link = f"https://staging.stochss.org/stochss/present-model{query_str}" + download_link = os.path.join("https://staging.stochss.org/stochss/download_presentation", hostname, file) - open_link = f"https://live.stochss.org?open={download_link}" + open_link = f"https://staging.stochss.org?open={download_link}" links = {"presentation": present_link, "download": download_link, "open": open_link} data = {"path": dst, "new":True, "model":self.model} return links, data From 5e372e29614258d3425a1f4598f61e8f42474ae4 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Tue, 6 Jul 2021 16:52:09 -0400 Subject: [PATCH 124/192] Added NotebookAPIHandler import. --- jupyterhub/jupyterhub_config.py | 1 + 1 file changed, 1 insertion(+) diff --git a/jupyterhub/jupyterhub_config.py b/jupyterhub/jupyterhub_config.py index 28b1422d04..cd6e1708bf 100644 --- a/jupyterhub/jupyterhub_config.py +++ b/jupyterhub/jupyterhub_config.py @@ -29,6 +29,7 @@ from handlers import * # API Handlers from model_presentation import JsonFileAPIHandler, DownModelPresentationAPIHandler +from notebook_presentation import NotebookAPIHandler ## Class for authenticating users. # From 7ba99ea137803ee3e0991beb45f71a07d268fdbb Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Tue, 6 Jul 2021 17:16:00 -0400 Subject: [PATCH 125/192] Fixed page render function for notebook presentations. --- client/pages/notebook-presentation.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/client/pages/notebook-presentation.js b/client/pages/notebook-presentation.js index 7c0138a169..0b83cf09bd 100644 --- a/client/pages/notebook-presentation.js +++ b/client/pages/notebook-presentation.js @@ -47,7 +47,7 @@ let NotebookPresentationPage = PageView.extend({ }); domReady(() => { - let p = new ModelPresentationPage({ + let p = new NotebookPresentationPage({ el: document.body }); p.render(); From 0a7959c67a9d7abb0eeb7d5831f0fc314912bdf7 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Wed, 7 Jul 2021 10:24:59 -0400 Subject: [PATCH 126/192] Fixed log error. --- jupyterhub/notebook_presentation.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/jupyterhub/notebook_presentation.py b/jupyterhub/notebook_presentation.py index e5bdb18b8f..98d43c0713 100644 --- a/jupyterhub/notebook_presentation.py +++ b/jupyterhub/notebook_presentation.py @@ -19,6 +19,7 @@ import os import json import tarfile +import logging import tempfile import nbformat @@ -29,6 +30,8 @@ from jupyterhub.handlers.base import BaseHandler +log = logging.getLogger('stochss') + # pylint: disable=abstract-method # pylint: disable=too-few-public-methods class NotebookAPIHandler(BaseHandler): From 64cf20be69fa302608ad92494aa976185e41a1e3 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Wed, 7 Jul 2021 10:26:22 -0400 Subject: [PATCH 127/192] Fixed page header. Added spacing between the buttons at the bottom of the page. --- client/templates/pages/modelPresentation.pug | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/client/templates/pages/modelPresentation.pug b/client/templates/pages/modelPresentation.pug index 7fe07e5ed2..a142db5e60 100644 --- a/client/templates/pages/modelPresentation.pug +++ b/client/templates/pages/modelPresentation.pug @@ -4,7 +4,7 @@ section.page div.presentation-header - h1 this.model.name + h1=this.model.name div(data-hook="model-species") @@ -22,6 +22,6 @@ section.page div.mt-3 - a.btn.btn-outline-secondary.box-shadow.text-break(href=this.openLink role="button") Open in StochSS + a.btn.btn-outline-secondary.box-shadow.text-break.mr-3(href=this.openLink role="button") Open in StochSS a.btn.btn-outline-secondary.box-shadow.text-break(href=this.downloadLink role="button") Download (.mdl) From b2a255f450c46b8aa231fc68ecc1d4953bc0153d Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Wed, 7 Jul 2021 10:30:09 -0400 Subject: [PATCH 128/192] Added missing name property for notebook presentations. --- client/pages/notebook-presentation.js | 1 + 1 file changed, 1 insertion(+) diff --git a/client/pages/notebook-presentation.js b/client/pages/notebook-presentation.js index 0b83cf09bd..655e7c0ee9 100644 --- a/client/pages/notebook-presentation.js +++ b/client/pages/notebook-presentation.js @@ -35,6 +35,7 @@ let NotebookPresentationPage = PageView.extend({ let urlParams = new URLSearchParams(window.location.search); let owner = urlParams.get("owner"); let file = urlParams.get("file"); + this.name = file.split('/').pop().split('.ipynb')[0] let queryStr = "?owner=" + owner + "&file=" + file; this.loadLink = "https://staging.stochss.org/stochss/api/notebook/load" + queryStr; let downloadStart = "https://staging.stochss.org/stochss/download_presentation"; From c1d60f253c1a601793d4967ce740fad465b3a557 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Wed, 7 Jul 2021 10:31:11 -0400 Subject: [PATCH 129/192] Added size attributed to the iframe. Removed the border from the iframe. Fixed page header. --- client/templates/pages/notebookPresentation.pug | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/client/templates/pages/notebookPresentation.pug b/client/templates/pages/notebookPresentation.pug index 902c0c35cc..3969619af8 100644 --- a/client/templates/pages/notebookPresentation.pug +++ b/client/templates/pages/notebookPresentation.pug @@ -4,8 +4,8 @@ section.page div.presentation-header - h1 this.name + h1 this.name div - iframe(src=this.loadLink) + iframe(src=this.loadLink width="100%" height="800" frameborder="0") From a63237be318d144d9cb422cdda8f3fb74d11449e Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Wed, 7 Jul 2021 10:55:02 -0400 Subject: [PATCH 130/192] Fixed notebook render function args issue and notebook header issue. --- client/templates/pages/notebookPresentation.pug | 2 +- jupyterhub/notebook_presentation.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/client/templates/pages/notebookPresentation.pug b/client/templates/pages/notebookPresentation.pug index 3969619af8..588d25b20e 100644 --- a/client/templates/pages/notebookPresentation.pug +++ b/client/templates/pages/notebookPresentation.pug @@ -4,7 +4,7 @@ section.page div.presentation-header - h1 this.name + h1=this.name div diff --git a/jupyterhub/notebook_presentation.py b/jupyterhub/notebook_presentation.py index 98d43c0713..f1b7593f98 100644 --- a/jupyterhub/notebook_presentation.py +++ b/jupyterhub/notebook_presentation.py @@ -67,7 +67,7 @@ def convert_notebook_to_html(notebook): Notebook read in using nbformat ''' nb_format = {"exporter": HTMLExporter} - html, config = render_notebook(format=nb_format, nb=nb) + html, config = render_notebook(format=nb_format, nb=notebook) return html From 93902b4b24a2f5389c4dd585a597278255439c39 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Wed, 7 Jul 2021 13:24:36 -0400 Subject: [PATCH 131/192] Added styling for notebook presentations. --- client/styles/styles.css | 5 +++++ client/templates/pages/notebookPresentation.pug | 4 ++-- 2 files changed, 7 insertions(+), 2 deletions(-) diff --git a/client/styles/styles.css b/client/styles/styles.css index 00885b0518..42bdce8a44 100644 --- a/client/styles/styles.css +++ b/client/styles/styles.css @@ -711,3 +711,8 @@ span.checkbox { margin-top: 32px; padding: 20px 16px; } + +.iframe-container { + max-height: 100% !important; + display: grid; +} diff --git a/client/templates/pages/notebookPresentation.pug b/client/templates/pages/notebookPresentation.pug index 588d25b20e..2e500b5423 100644 --- a/client/templates/pages/notebookPresentation.pug +++ b/client/templates/pages/notebookPresentation.pug @@ -6,6 +6,6 @@ section.page h1=this.name - div + div.iframe-container - iframe(src=this.loadLink width="100%" height="800" frameborder="0") + iframe(src=this.loadLink width="100%" height="100%" frameborder="0") From 708569302e0edba8c1f2a173f729716a5ea1635d Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Wed, 7 Jul 2021 14:00:42 -0400 Subject: [PATCH 132/192] Tweaked css for the iframe. --- client/templates/pages/notebookPresentation.pug | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/client/templates/pages/notebookPresentation.pug b/client/templates/pages/notebookPresentation.pug index 2e500b5423..204b7c3528 100644 --- a/client/templates/pages/notebookPresentation.pug +++ b/client/templates/pages/notebookPresentation.pug @@ -1,4 +1,4 @@ -section.page +section.page.pb-0 div#notebook-presentation.container @@ -6,6 +6,12 @@ section.page h1=this.name - div.iframe-container + div.iframe-container.card.card-body - iframe(src=this.loadLink width="100%" height="100%" frameborder="0") + iframe(src=this.loadLink width="100%" height="90%" frameborder="0") + + div.mt-3 + + a.btn.btn-outline-secondary.box-shadow.text-break.mr-3(href=this.openLink role="button") Open in StochSS + + a.btn.btn-outline-secondary.box-shadow.text-break(href=this.downloadLink role="button") Download (.ipynb) From 5e455867c27d709ddbfa18c0faa290cb7797035a Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Wed, 7 Jul 2021 14:47:07 -0400 Subject: [PATCH 133/192] Final css tweak. --- client/templates/pages/notebookPresentation.pug | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/client/templates/pages/notebookPresentation.pug b/client/templates/pages/notebookPresentation.pug index 204b7c3528..58231d16fc 100644 --- a/client/templates/pages/notebookPresentation.pug +++ b/client/templates/pages/notebookPresentation.pug @@ -1,4 +1,4 @@ -section.page.pb-0 +section.page div#notebook-presentation.container From 25e5929837cfa377f956762a41ae35bb255e59e5 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Wed, 7 Jul 2021 14:48:39 -0400 Subject: [PATCH 134/192] Added download handler for notebook presentations. Refactored the get presentation function to handler a presentation dict of the notebook. --- jupyterhub/notebook_presentation.py | 28 ++++++++++++++++++++++++++-- 1 file changed, 26 insertions(+), 2 deletions(-) diff --git a/jupyterhub/notebook_presentation.py b/jupyterhub/notebook_presentation.py index f1b7593f98..1e719c82c2 100644 --- a/jupyterhub/notebook_presentation.py +++ b/jupyterhub/notebook_presentation.py @@ -57,6 +57,29 @@ async def get(self): self.finish() +class DownNotebookPresentationAPIHandler(BaseHandler): + ''' + ################################################################################################ + Base Handler for downloading notebook presentations from user containers. + ################################################################################################ + ''' + async def get(self, owner, file): + ''' + Download the notebook presentation from User's presentations directory. + + Attributes + ---------- + ''' + log.debug("Container id of the owner: %s", owner) + log.debug("Name to the file: %s", file) + self.set_header('Content-Type', 'application/json') + nb_presentation = get_presentation_from_user(owner=owner, file=file, as_dict=True) + self.set_header('Content-Disposition', f'attachment; filename="{nb_presentation['file']}"') + log.debug("Contents of the json file: %s", nb_presentation['notebook']) + self.write(nb_presentation['notebook']) + self.finish() + + def convert_notebook_to_html(notebook): ''' Convert the notebook object into html. @@ -98,6 +121,7 @@ def get_presentation_from_user(owner, file, as_dict=False): tar_nb.close() nb_path = os.path.join(tmp_dir.name, file) with open(nb_path, "r") as nb_file: + nb_presentation = json.load(nb_file) if as_dict: - return json.load(nb_file) - return nbformat.read(nb_file, as_version=4) + return nb_presentation + return nbformat.reads(json.dumps(nb_presentation['notebook']), as_version=4) From f36fdb353dc17ccdb48786d5180cab95dc300fd6 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Wed, 7 Jul 2021 15:13:01 -0400 Subject: [PATCH 135/192] Modified the download link to be unique to notebook presentations. --- client/pages/notebook-presentation.js | 2 +- client/templates/pages/notebookPresentation.pug | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/client/pages/notebook-presentation.js b/client/pages/notebook-presentation.js index 655e7c0ee9..f31a45d52c 100644 --- a/client/pages/notebook-presentation.js +++ b/client/pages/notebook-presentation.js @@ -38,7 +38,7 @@ let NotebookPresentationPage = PageView.extend({ this.name = file.split('/').pop().split('.ipynb')[0] let queryStr = "?owner=" + owner + "&file=" + file; this.loadLink = "https://staging.stochss.org/stochss/api/notebook/load" + queryStr; - let downloadStart = "https://staging.stochss.org/stochss/download_presentation"; + let downloadStart = "https://staging.stochss.org/stochss/notebook/download_presentation"; this.downloadLink = path.join(downloadStart, owner, file); this.openLink = "open.stochss.org?open=" + this.downloadLink; }, diff --git a/client/templates/pages/notebookPresentation.pug b/client/templates/pages/notebookPresentation.pug index 58231d16fc..95e25dd6ca 100644 --- a/client/templates/pages/notebookPresentation.pug +++ b/client/templates/pages/notebookPresentation.pug @@ -8,7 +8,7 @@ section.page div.iframe-container.card.card-body - iframe(src=this.loadLink width="100%" height="90%" frameborder="0") + iframe(src=this.loadLink width="100%" height="100%" frameborder="0") div.mt-3 From 72bdd0d56acfce2159f77941e7c27c4142b4617b Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Wed, 7 Jul 2021 15:15:55 -0400 Subject: [PATCH 136/192] Added the download route for notebook presentations. --- jupyterhub/jupyterhub_config.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/jupyterhub/jupyterhub_config.py b/jupyterhub/jupyterhub_config.py index cd6e1708bf..a2395320da 100644 --- a/jupyterhub/jupyterhub_config.py +++ b/jupyterhub/jupyterhub_config.py @@ -29,7 +29,7 @@ from handlers import * # API Handlers from model_presentation import JsonFileAPIHandler, DownModelPresentationAPIHandler -from notebook_presentation import NotebookAPIHandler +from notebook_presentation import NotebookAPIHandler, DownNotebookPresentationAPIHandler ## Class for authenticating users. # @@ -87,8 +87,9 @@ (r"/stochss/present-model\/?", ModelPresentationHandler), (r"/stochss/present-notebook\/?", NotebookPresentationHandler), (r"/stochss/api/file/json-data\/?", JsonFileAPIHandler), + (r"/stochss/presentation-download/(\w+)/(.+)\/?", DownModelPresentationAPIHandler), (r"/stochss/api/notebook/load\/?", NotebookAPIHandler), - (r"/stochss/presentation-download/(\w+)/(.+)\/?", DownModelPresentationAPIHandler) + (r"/stochss/notebook/presentation-download/(\w+)/(.+)\/?", DownNotebookPresentationAPIHandler) ] ## Paths to search for jinja templates, before using the default templates. From 2b03960c0c5ad35c1435bbf458d404a1a9b4df43 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Thu, 8 Jul 2021 11:14:28 -0400 Subject: [PATCH 137/192] Created executable script to read presentation files. --- .../util/scripts/read_presentation.py | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100755 stochss/handlers/util/scripts/read_presentation.py diff --git a/stochss/handlers/util/scripts/read_presentation.py b/stochss/handlers/util/scripts/read_presentation.py new file mode 100755 index 0000000000..7888a3227f --- /dev/null +++ b/stochss/handlers/util/scripts/read_presentation.py @@ -0,0 +1,45 @@ +#!/usr/bin/env python3 + +''' +StochSS is a platform for simulating biochemical systems +Copyright (C) 2019-2021 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 argparse + +def get_parsed_args(): + ''' + Initializes an argpaser to document this script and returns a dict of + the arguments that were passed to the script from the command line. + + Attributes + ---------- + ''' + description = "Run a preview of a model. Prints the results of the first trajectory after 5s." + parser = argparse.ArgumentParser(description=description) + parser.add_argument('file', help="Name of the presentation file.") + parser.add_argument('-b', '--binary', help="Indicates a binary file.", action="store_true") + return parser.parse_args() + + +if __name__ == "__main__": + args = get_parsed_args() + mode = "rb" if args.binary else "r" + path = os.path.join(os.path.expanduser("~"), '.presentations', args.file) + with open(path, mode) as presentation_file: + contents = presentation_file.read() + print(contents) From 31a8e324f1e646e1dacd99f03cb72e0a98a8d0e1 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Thu, 8 Jul 2021 11:57:48 -0400 Subject: [PATCH 138/192] Fixed the download handler for notebook presentations. --- jupyterhub/notebook_presentation.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/jupyterhub/notebook_presentation.py b/jupyterhub/notebook_presentation.py index 1e719c82c2..30639eb11d 100644 --- a/jupyterhub/notebook_presentation.py +++ b/jupyterhub/notebook_presentation.py @@ -74,7 +74,7 @@ async def get(self, owner, file): log.debug("Name to the file: %s", file) self.set_header('Content-Type', 'application/json') nb_presentation = get_presentation_from_user(owner=owner, file=file, as_dict=True) - self.set_header('Content-Disposition', f'attachment; filename="{nb_presentation['file']}"') + self.set_header('Content-Disposition', f'attachment; filename="{nb_presentation["file"]}"') log.debug("Contents of the json file: %s", nb_presentation['notebook']) self.write(nb_presentation['notebook']) self.finish() From 0c7ccdeddd18e6786b1106d0f467cf8c03d83e16 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Thu, 8 Jul 2021 16:32:38 -0400 Subject: [PATCH 139/192] Generalized the function for work for any presentation type. Refactored the function to handler the use case where the users container was stopped. --- jupyterhub/model_presentation.py | 70 +++++++++++------------------ jupyterhub/notebook_presentation.py | 63 ++++++++------------------ jupyterhub/presentation_base.py | 53 ++++++++++++++++++++++ 3 files changed, 98 insertions(+), 88 deletions(-) diff --git a/jupyterhub/model_presentation.py b/jupyterhub/model_presentation.py index ecccc25d52..2467333363 100644 --- a/jupyterhub/model_presentation.py +++ b/jupyterhub/model_presentation.py @@ -16,16 +16,11 @@ along with this program. If not, see . ''' -import os import ast import json import logging -import tarfile -import tempfile -import docker - -from presentation_base import StochSSBase +from presentation_base import StochSSBase, get_presentation_from_user from presentation_error import StochSSAPIError, report_error from jupyterhub.handlers.base import BaseHandler @@ -47,20 +42,15 @@ async def get(self): Attributes ---------- ''' - log.setLevel(logging.DEBUG) owner = self.get_query_argument(name="owner") log.debug("Container id of the owner: %s", owner) file = self.get_query_argument(name="file") log.debug("Name to the file: %s", file) self.set_header('Content-Type', 'application/json') - file_objs = {"mdl":StochSSModel, "smdl":StochSSSpatialModel} - ext = file.split(".").pop() try: - model = get_presentation_from_user(owner=owner, file=file) - file_obj = file_objs[ext](model=model) - model = file_obj.load() + model = get_presentation_from_user(owner=owner, file=file, kwargs={"file": file}, + process_func=process_model_presentation) log.debug("Contents of the json file: %s", model) - file_obj.print_logs(log) self.write(model) except StochSSAPIError as load_err: report_error(self, log, load_err) @@ -83,45 +73,39 @@ async def get(self, owner, file): log.debug("Container id of the owner: %s", owner) log.debug("Name to the file: %s", file) self.set_header('Content-Type', 'application/json') - try: - model = get_presentation_from_user(owner=owner, file=file) - ext = file.split(".").pop() - self.set_header('Content-Disposition', f'attachment; filename="{model["name"]}.{ext}"') - log.debug("Contents of the json file: %s", model) - self.write(model) - except StochSSAPIError as load_err: - report_error(self, log, load_err) + model = get_presentation_from_user(owner=owner, file=file, + kwargs={"for_download": True}, + process_func=process_model_presentation) + ext = file.split(".").pop() + self.set_header('Content-Disposition', f'attachment; filename="{model["name"]}.{ext}"') + log.debug("Contents of the json file: %s", model) + self.write(model) self.finish() -def get_presentation_from_user(owner, file): +def process_model_presentation(path, file=None, for_download=False): ''' - Get the model presentation from the users container + Get the model presentation data from the file. Attributes ---------- - owner : str - Hostname of the user container + path : str + Path to the model presentation file. file : str - Name of the model presentation file + Name of the presentation file. + for_download : bool + Whether or not the model presentation is being downloaded. ''' - client = docker.from_env() - containers = client.containers.list() - user_container = list(filter(lambda container: container.name == f"jupyter-{owner}", - containers))[0] - user_model_path = f'/home/jovyan/.presentations/{file}' - tar_mdl = tempfile.TemporaryFile() - bits, _ = user_container.get_archive(user_model_path) - for chunk in bits: - tar_mdl.write(chunk) - tar_mdl.seek(0) - tar_file = tarfile.TarFile(fileobj=tar_mdl) - tmp_dir = tempfile.TemporaryDirectory() - tar_file.extractall(tmp_dir.name) - tar_mdl.close() - mdl_path = os.path.join(tmp_dir.name, file) - with open(mdl_path, "r") as mdl_file: - return json.load(mdl_file) + with open(path, "r") as mdl_file: + model = json.load(mdl_file) + if for_download: + return model + file_objs = {"mdl":StochSSModel, "smdl":StochSSSpatialModel} + ext = file.split(".").pop() + file_obj = file_objs[ext](model=model) + model_pres = file_obj.load() + file_obj.print_logs(log) + return model_pres class StochSSModel(StochSSBase): diff --git a/jupyterhub/notebook_presentation.py b/jupyterhub/notebook_presentation.py index 30639eb11d..ac0903b246 100644 --- a/jupyterhub/notebook_presentation.py +++ b/jupyterhub/notebook_presentation.py @@ -16,17 +16,14 @@ along with this program. If not, see . ''' -import os import json -import tarfile import logging -import tempfile import nbformat from nbviewer.render import render_notebook from nbconvert.exporters import HTMLExporter -import docker +from presentation_base import get_presentation_from_user from jupyterhub.handlers.base import BaseHandler @@ -51,8 +48,8 @@ async def get(self): log.debug("Container id of the owner: %s", owner) file = self.get_query_argument(name="file") log.debug("Name to the file: %s", file) - notebook = get_presentation_from_user(owner=owner, file=file) - html = convert_notebook_to_html(notebook=notebook) + html = get_presentation_from_user(owner=owner, file=file, + process_func=process_notebook_presentation) self.write(html) self.finish() @@ -73,55 +70,31 @@ async def get(self, owner, file): log.debug("Container id of the owner: %s", owner) log.debug("Name to the file: %s", file) self.set_header('Content-Type', 'application/json') - nb_presentation = get_presentation_from_user(owner=owner, file=file, as_dict=True) + nb_presentation = get_presentation_from_user(owner=owner, file=file, + kwargs={"as_dict": True}, + process_func=process_notebook_presentation) self.set_header('Content-Disposition', f'attachment; filename="{nb_presentation["file"]}"') log.debug("Contents of the json file: %s", nb_presentation['notebook']) self.write(nb_presentation['notebook']) self.finish() -def convert_notebook_to_html(notebook): +def process_notebook_presentation(path, as_dict=False): ''' - Convert the notebook object into html. + Get the notebook presentation data from the file. Attributes ---------- - notebook : NotebookNode - Notebook read in using nbformat + path : str + Path to the notebook presentation file + as_dict : bool + Whether or not to return the data as a dictionary ''' + with open(path, "r") as nb_file: + nb_presentation = json.load(nb_file) + if as_dict: + return nb_presentation + notebook = nbformat.reads(json.dumps(nb_presentation['notebook']), as_version=4) nb_format = {"exporter": HTMLExporter} - html, config = render_notebook(format=nb_format, nb=notebook) + html, _ = render_notebook(format=nb_format, nb=notebook) return html - - -def get_presentation_from_user(owner, file, as_dict=False): - ''' - Get the model presentation from the users container - - Attributes - ---------- - owner : str - Hostname of the user container - file : str - Name of the model presentation file - ''' - client = docker.from_env() - containers = client.containers.list() - user_container = list(filter(lambda container: container.name == f"jupyter-{owner}", - containers))[0] - user_nb_path = f'/home/jovyan/.presentations/{file}' - tar_nb = tempfile.TemporaryFile() - bits, _ = user_container.get_archive(user_nb_path) - for chunk in bits: - tar_nb.write(chunk) - tar_nb.seek(0) - tar_file = tarfile.TarFile(fileobj=tar_nb) - tmp_dir = tempfile.TemporaryDirectory() - tar_file.extractall(tmp_dir.name) - tar_nb.close() - nb_path = os.path.join(tmp_dir.name, file) - with open(nb_path, "r") as nb_file: - nb_presentation = json.load(nb_file) - if as_dict: - return nb_presentation - return nbformat.reads(json.dumps(nb_presentation['notebook']), as_version=4) diff --git a/jupyterhub/presentation_base.py b/jupyterhub/presentation_base.py index 430d5a8d90..3388087d39 100644 --- a/jupyterhub/presentation_base.py +++ b/jupyterhub/presentation_base.py @@ -17,6 +17,59 @@ ''' import os +import tarfile +import tempfile + +import docker + + +def get_presentation_from_user(owner, file, process_func, kwargs=None): + ''' + Get the model presentation from the users container + + Attributes + ---------- + owner : str + Hostname of the user container + file : str + Name of the model presentation file + process_func : function + Function used to process the presentation file + kwargs : dict + Args to be passed to the process function + ''' + client = docker.from_env() + containers = client.containers.list() + try: + user_container = list(filter(lambda container: container.name == f"jupyter-{owner}", + containers))[0] + except IndexError: + volumes = client.volumes.list() + user_volume = list(filter(lambda volume: volume.name == f"jupyterhub-user-{owner}", + volumes))[0] + volume_mnts = {user_volume.name: {"bind": "/user_volume", "mode": "ro"}, + "/stochss/jupyterhub": {"bind": "/mnt/cache", "mode": "rw"}} + command = ['cp', os.path.join('/user_volume/.presentations', file), + '/mnt/cache/presentation_cache/'] + client.containers.run('stochss-lab', command, volumes=volume_mnts) + file_path = os.path.join('/srv/jupyterhub/presentation_cache', file) + else: + user_file_path = os.path.join('/home/jovyan/.presentations', file) + tar_pres = tempfile.TemporaryFile() + bits, _ = user_container.get_archive(user_file_path) + for chunk in bits: + tar_pres.write(chunk) + tar_pres.seek(0) + tar_file = tarfile.TarFile(fileobj=tar_pres) + tmp_dir = tempfile.TemporaryDirectory() + tar_file.extractall(tmp_dir.name) + tar_pres.close() + file_path = os.path.join(tmp_dir.name, file) + finally: + if kwargs is None: + kwargs = {} + return process_func(file_path, **kwargs) + class StochSSBase(): ''' From 2d9a12841a14091805caf2d430b27c00e9bcb712 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Thu, 8 Jul 2021 16:33:46 -0400 Subject: [PATCH 140/192] Removed the read presentation script. --- .../util/scripts/read_presentation.py | 45 ------------------- 1 file changed, 45 deletions(-) delete mode 100755 stochss/handlers/util/scripts/read_presentation.py diff --git a/stochss/handlers/util/scripts/read_presentation.py b/stochss/handlers/util/scripts/read_presentation.py deleted file mode 100755 index 7888a3227f..0000000000 --- a/stochss/handlers/util/scripts/read_presentation.py +++ /dev/null @@ -1,45 +0,0 @@ -#!/usr/bin/env python3 - -''' -StochSS is a platform for simulating biochemical systems -Copyright (C) 2019-2021 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 argparse - -def get_parsed_args(): - ''' - Initializes an argpaser to document this script and returns a dict of - the arguments that were passed to the script from the command line. - - Attributes - ---------- - ''' - description = "Run a preview of a model. Prints the results of the first trajectory after 5s." - parser = argparse.ArgumentParser(description=description) - parser.add_argument('file', help="Name of the presentation file.") - parser.add_argument('-b', '--binary', help="Indicates a binary file.", action="store_true") - return parser.parse_args() - - -if __name__ == "__main__": - args = get_parsed_args() - mode = "rb" if args.binary else "r" - path = os.path.join(os.path.expanduser("~"), '.presentations', args.file) - with open(path, mode) as presentation_file: - contents = presentation_file.read() - print(contents) From 5c752bf07b7783e84ff0451898e6a6dc49d62867 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Thu, 8 Jul 2021 17:22:45 -0400 Subject: [PATCH 141/192] Added function to publish notebook presentations. --- stochss/handlers/util/stochss_notebook.py | 34 ++++++++++++++++++++++- 1 file changed, 33 insertions(+), 1 deletion(-) diff --git a/stochss/handlers/util/stochss_notebook.py b/stochss/handlers/util/stochss_notebook.py index ee84eaf346..5503406a51 100644 --- a/stochss/handlers/util/stochss_notebook.py +++ b/stochss/handlers/util/stochss_notebook.py @@ -16,16 +16,20 @@ along with this program. If not, see . ''' +import os import json import string +import hashlib import traceback import nbformat +from escapism import escape from nbformat import v4 as nbf from gillespy2.solvers.utilities.cpp_support_test import check_cpp_support from .stochss_base import StochSSBase -from .stochss_errors import StochSSFileNotFoundError, StochSSModelFormatError +from .stochss_errors import StochSSFileNotFoundError, StochSSModelFormatError, \ + StochSSPermissionsError, StochSSFileExistsError class StochSSNotebook(StochSSBase): ''' @@ -1021,6 +1025,34 @@ def load(self): message = f"Could not find the notebook file: {str(err)}" raise StochSSFileNotFoundError(message, traceback.format_exc()) from err + def publish_presentation(self): + '''Publish a notebook presentation''' + present_dir = os.path.join(self.user_dir, ".presentations") + if not os.path.exists(present_dir): + os.mkdir(present_dir) + try: + notebook = self.load() + safe_chars = set(string.ascii_letters + string.digits) + hostname = escape(os.environ.get('JUPYTERHUB_USER'), safe=safe_chars) + nb_str = json.dumps(notebook, sort_keys=True) + file = f"{hashlib.md5(nb_str.encode('utf-8')).hexdigest()}.ipynb" + dst = os.path.join(present_dir, file) + if os.path.exists(dst): + message = "A presentation with this name already exists" + raise StochSSFileExistsError(message) + query_str = f"?owner={hostname}&file={file}" + present_link = f"https://staging.stochss.org/stochss/present-notebook{query_str}" + download_link = os.path.join("https://staging.stochss.org/stochss/notebook/download_presentation", + hostname, file) + open_link = f"https://staging.stochss.org?open={download_link}" + links = {"presentation": present_link, "download": download_link, "open": open_link} + with open(dst, "w") as presentation_file: + json.dump(notebook, presentation_file) + return links + except PermissionError as err: + message = f"You do not have permission to publish this file: {str(err)}" + raise StochSSPermissionsError(message, traceback.format_exc()) from err + def write_notebook_file(self, cells): '''Write the new notebook file to disk From 9f3d4f625ea2f62f9f5f51d70db9af14664fc2e7 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 9 Jul 2021 08:59:04 -0400 Subject: [PATCH 142/192] Pylint updates. Added missing log function for presentation base class. --- jupyter_notebook_config.py | 1 - jupyterhub/jupyterhub_config.py | 61 ++++++++++++++--------- jupyterhub/presentation_base.py | 44 +++++++++++----- stochss/handlers/util/stochss_model.py | 8 +-- stochss/handlers/util/stochss_notebook.py | 18 ++++--- 5 files changed, 83 insertions(+), 49 deletions(-) diff --git a/jupyter_notebook_config.py b/jupyter_notebook_config.py index 5d9fd3da1d..4fc197c473 100644 --- a/jupyter_notebook_config.py +++ b/jupyter_notebook_config.py @@ -184,4 +184,3 @@ ## This class manages the configuration. It's its own singleton class so that we # can share these values across all objects. It also contains some helper methods # to build request arguments out of the various config options. - diff --git a/jupyterhub/jupyterhub_config.py b/jupyterhub/jupyterhub_config.py index a2395320da..7da4a96ffb 100644 --- a/jupyterhub/jupyterhub_config.py +++ b/jupyterhub/jupyterhub_config.py @@ -1,8 +1,8 @@ # Configuration file for jupyterhub. -#------------------------------------------------------------------------------ +#--------------------------------------------------------------------------------------------------- # Application(SingletonConfigurable) configuration -#------------------------------------------------------------------------------ +#--------------------------------------------------------------------------------------------------- ## This is an application. @@ -15,21 +15,23 @@ ## Set the log level by value or name. #c.Application.log_level = 30 -#------------------------------------------------------------------------------ +#--------------------------------------------------------------------------------------------------- # JupyterHub(Application) configuration -#------------------------------------------------------------------------------ +#--------------------------------------------------------------------------------------------------- import os import os.path import sys import logging -sys.path.append('/srv/jupyterhub/') +sys.path.append('/srv/jupyterhub/') # pylint: disable=wrong-import-position -# Page handlers -from handlers import * # API Handlers from model_presentation import JsonFileAPIHandler, DownModelPresentationAPIHandler from notebook_presentation import NotebookAPIHandler, DownNotebookPresentationAPIHandler +# Page handlers +from handlers import ( + HomeHandler, JobPresentationHandler, ModelPresentationHandler, NotebookPresentationHandler +) ## Class for authenticating users. # @@ -89,7 +91,8 @@ (r"/stochss/api/file/json-data\/?", JsonFileAPIHandler), (r"/stochss/presentation-download/(\w+)/(.+)\/?", DownModelPresentationAPIHandler), (r"/stochss/api/notebook/load\/?", NotebookAPIHandler), - (r"/stochss/notebook/presentation-download/(\w+)/(.+)\/?", DownNotebookPresentationAPIHandler) + (r"/stochss/notebook/presentation-download/(\w+)/(.+)\/?", + DownNotebookPresentationAPIHandler) ] ## Paths to search for jinja templates, before using the default templates. @@ -137,13 +140,14 @@ { 'name': 'cull-idle', 'admin': True, - 'command': [sys.executable, '/srv/jupyterhub/cull_idle_servers.py', '--timeout=28800'], + 'command': [sys.executable, '/srv/jupyterhub/cull_idle_servers.py', + '--timeout=28800'], } ] -#------------------------------------------------------------------------------ +#--------------------------------------------------------------------------------------------------- # Dockerspawner configuration -#------------------------------------------------------------------------------ +#--------------------------------------------------------------------------------------------------- c.DockerSpawner.image = os.environ['DOCKER_STOCHSS_IMAGE'] # JupyterHub requires a single-user instance of the Notebook server, so we @@ -151,8 +155,8 @@ # jupyter/docker-stacks *-notebook images as the Docker run command when # spawning containers. Optionally, you can override the Docker run command # using the DOCKER_SPAWN_CMD environment variable. -spawn_cmd = "start-singleuser.sh" -c.DockerSpawner.extra_create_kwargs.update({ 'command': spawn_cmd }) +SPAWN_CMD = "start-singleuser.sh" +c.DockerSpawner.extra_create_kwargs.update({ 'command': SPAWN_CMD }) # Connect containers to this Docker network network_name = os.environ['DOCKER_NETWORK_NAME'] c.DockerSpawner.use_internal_ip = True @@ -180,9 +184,9 @@ # For debugging arguments passed to spawned containers c.DockerSpawner.debug = True -#------------------------------------------------------------------------------ +#--------------------------------------------------------------------------------------------------- # Spawner(LoggingConfigurable) configuration -#------------------------------------------------------------------------------ +#--------------------------------------------------------------------------------------------------- def get_user_cpu_count_or_fail(): ''' @@ -193,12 +197,15 @@ def get_user_cpu_count_or_fail(): log.info("RESERVED_CPUS environment variable is set to %s", reserve_count) # Round up to an even number of reserved cpus if reserve_count % 2 > 0: - log.warning("Increasing reserved cpu count by one so it's an even number. This helps allocate logical cpus to users more easily.") + message = "Increasing reserved cpu count by one so it's an even number." + message += " This helps allocate logical cpus to users more easily." + log.warning(message) reserve_count += 1 total_cpus = os.cpu_count() log.info("Total cpu count as reported by os.count: %s", total_cpus) if reserve_count >= total_cpus: - e_message = "RESERVED_CPUS environment cannot be greater than or equal to the number of cpus returned by os.cpu_count()" + e_message = "RESERVED_CPUS environment cannot be greater than or equal to the number of" + e_message += " cpus returned by os.cpu_count()" log.error(e_message) raise ValueError(e_message) user_cpu_count = total_cpus - reserve_count @@ -268,7 +275,9 @@ def pre_spawn_hook(spawner): avail_cpus = palloc[div:] # If <= 4 cpus available then use 1 cpu for each user instead of 2 if not avail_cpus: - log.warning("The host system only has 4 logical cpus, so we'll only reserve one logical cpu per user container, instead of the normal 2") + message = "The host system only has 4 logical cpus, so we'll only reserve" + message += " one logical cpu per user container, instead of the normal 2" + log.warning(message) avail_cpus = palloc least_used_cpu = min(avail_cpus) cpu1_index = avail_cpus.index(least_used_cpu) @@ -299,7 +308,9 @@ def post_stop_hook(spawner): palloc[int(cpu2_index)] -= 1 log.warning('Reserved CPUs: %s', reserved) log.warning('Number of user containers using each logical core: %s', palloc) - except: + except Exception as err: + message = "Exception thrown due to cpuset_cpus not being set (power user)" + log.error("%s\n%s", message, err) # Exception thrown due to cpuset_cpus not being set (power user) pass @@ -312,9 +323,11 @@ def post_stop_hook(spawner): # # Example uses: # -# - You can set `notebook_dir` to `/` and `default_url` to `/tree/home/{username}` to allow people to -# navigate the whole filesystem from their notebook server, but still start in their home directory. -# - Start with `/notebooks` instead of `/tree` if `default_url` points to a notebook instead of a directory. +# - You can set `notebook_dir` to `/` and `default_url` to `/tree/home/{username}` to allow people +# to navigate the whole filesystem from their notebook server, but still start in their home +# directory. +# - Start with `/notebooks` instead of `/tree` if `default_url` points to a notebook instead of a +# directory. # - You can set this to `/lab` to have JupyterLab start by default, rather than Jupyter Notebook. c.Spawner.default_url = '/stochss/models' @@ -399,9 +412,9 @@ def post_stop_hook(spawner): # for it to be enforced. c.Spawner.mem_guarantee = '2G' -#------------------------------------------------------------------------------ +#--------------------------------------------------------------------------------------------------- # Authenticator(LoggingConfigurable) configuration -#------------------------------------------------------------------------------ +#--------------------------------------------------------------------------------------------------- ## Base class for implementing an authentication provider for JupyterHub diff --git a/jupyterhub/presentation_base.py b/jupyterhub/presentation_base.py index 3388087d39..421a9ed4b4 100644 --- a/jupyterhub/presentation_base.py +++ b/jupyterhub/presentation_base.py @@ -23,6 +23,19 @@ import docker +def __get_presentation_from_volume(client, owner, file): + volumes = client.volumes.list() + user_volume = list(filter(lambda volume: volume.name == f"jupyterhub-user-{owner}", + volumes))[0] + volume_mnts = {user_volume.name: {"bind": "/user_volume", "mode": "ro"}, + "/stochss/jupyterhub": {"bind": "/mnt/cache", "mode": "rw"}} + command = ['cp', os.path.join('/user_volume/.presentations', file), + '/mnt/cache/presentation_cache/'] + client.containers.run('stochss-lab', command, volumes=volume_mnts) + file_path = os.path.join('/srv/jupyterhub/presentation_cache', file) + return file_path + + def get_presentation_from_user(owner, file, process_func, kwargs=None): ''' Get the model presentation from the users container @@ -44,15 +57,7 @@ def get_presentation_from_user(owner, file, process_func, kwargs=None): user_container = list(filter(lambda container: container.name == f"jupyter-{owner}", containers))[0] except IndexError: - volumes = client.volumes.list() - user_volume = list(filter(lambda volume: volume.name == f"jupyterhub-user-{owner}", - volumes))[0] - volume_mnts = {user_volume.name: {"bind": "/user_volume", "mode": "ro"}, - "/stochss/jupyterhub": {"bind": "/mnt/cache", "mode": "rw"}} - command = ['cp', os.path.join('/user_volume/.presentations', file), - '/mnt/cache/presentation_cache/'] - client.containers.run('stochss-lab', command, volumes=volume_mnts) - file_path = os.path.join('/srv/jupyterhub/presentation_cache', file) + file_path = __get_presentation_from_volume(client, owner, file) else: user_file_path = os.path.join('/home/jovyan/.presentations', file) tar_pres = tempfile.TemporaryFile() @@ -65,10 +70,9 @@ def get_presentation_from_user(owner, file, process_func, kwargs=None): tar_file.extractall(tmp_dir.name) tar_pres.close() file_path = os.path.join(tmp_dir.name, file) - finally: - if kwargs is None: - kwargs = {} - return process_func(file_path, **kwargs) + if kwargs is None: + kwargs = {} + return process_func(file_path, **kwargs) class StochSSBase(): @@ -92,6 +96,20 @@ def __init__(self, path=None): self.logs = [] + 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 print_logs(self, log): ''' Display all internal logs to the console diff --git a/stochss/handlers/util/stochss_model.py b/stochss/handlers/util/stochss_model.py index f0044bd1dc..cc562540cc 100644 --- a/stochss/handlers/util/stochss_model.py +++ b/stochss/handlers/util/stochss_model.py @@ -487,10 +487,10 @@ def publish_presentation(self): raise StochSSFileExistsError(message) query_str = f"?owner={hostname}&file={file}" present_link = f"https://staging.stochss.org/stochss/present-model{query_str}" - download_link = os.path.join("https://staging.stochss.org/stochss/download_presentation", - hostname, file) - open_link = f"https://staging.stochss.org?open={download_link}" - links = {"presentation": present_link, "download": download_link, "open": open_link} + downloadlink = os.path.join("https://staging.stochss.org/stochss/download_presentation", + hostname, file) + open_link = f"https://staging.stochss.org?open={downloadlink}" + links = {"presentation": present_link, "download": downloadlink, "open": open_link} data = {"path": dst, "new":True, "model":self.model} return links, data except PermissionError as err: diff --git a/stochss/handlers/util/stochss_notebook.py b/stochss/handlers/util/stochss_notebook.py index 5503406a51..8e76400c73 100644 --- a/stochss/handlers/util/stochss_notebook.py +++ b/stochss/handlers/util/stochss_notebook.py @@ -870,6 +870,15 @@ def __get_gillespy2_solver_name(self): 'ODE': self.model.get_best_solver_algo("ODE").name} return algorithm_map[self.settings['simulationSettings']['algorithm']] + @classmethod + def __get_presentation_links(cls, hostname, file): + query_str = f"?owner={hostname}&file={file}" + present_link = f"https://staging.stochss.org/stochss/present-notebook{query_str}" + dl_link_base = "https://staging.stochss.org/stochss/notebook/download_presentation" + download_link = os.path.join(dl_link_base, hostname, file) + open_link = f"https://staging.stochss.org?open={download_link}" + return {"presentation": present_link, "download": download_link, "open": open_link} + def create_1dps_notebook(self): '''Create a 1D parameter sweep jupiter notebook for a StochSS model/workflow @@ -942,7 +951,7 @@ def create_ses_notebook(self): species = self.s_model['species'][0]['name'] plot_str = f"results.plot_species('{species}', animated=True, width=None, height=None)" else: - plot_str = f"results.plot_property('type', animated=True, width=None, height=None)" + plot_str = "results.plot_property('type', animated=True, width=None, height=None)" cells = self.__create_common_cells() if 'boundaryConditions' in self.s_model.keys(): bc_cells = self.__create_boundary_condition_cells() @@ -1040,12 +1049,7 @@ def publish_presentation(self): if os.path.exists(dst): message = "A presentation with this name already exists" raise StochSSFileExistsError(message) - query_str = f"?owner={hostname}&file={file}" - present_link = f"https://staging.stochss.org/stochss/present-notebook{query_str}" - download_link = os.path.join("https://staging.stochss.org/stochss/notebook/download_presentation", - hostname, file) - open_link = f"https://staging.stochss.org?open={download_link}" - links = {"presentation": present_link, "download": download_link, "open": open_link} + links = self.__get_presentation_links(hostname, file) with open(dst, "w") as presentation_file: json.dump(notebook, presentation_file) return links From 78cfcd861d56fe7d24d11869362e7dec5d07e1af Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 9 Jul 2021 09:14:38 -0400 Subject: [PATCH 143/192] Added the api handler and route for publishing notebook presentations. --- stochss/handlers/__init__.py | 1 + stochss/handlers/file_browser.py | 31 +++++++++++++++++++++++++++++++ 2 files changed, 32 insertions(+) diff --git a/stochss/handlers/__init__.py b/stochss/handlers/__init__.py index 6e1e8be756..de707d4ddb 100644 --- a/stochss/handlers/__init__.py +++ b/stochss/handlers/__init__.py @@ -66,6 +66,7 @@ def get_page_handlers(route_start): (r"/stochss/api/file/json-data\/?", JsonFileAPIHandler), (r"/stochss/api/file/duplicate\/?", DuplicateModelHandler), (r"/stochss/api/file/unzip\/?", UnzipFileAPIHandler), + (r"/stochss/api/notebook/presentation\/?", NotebookPresentationAPIHandler), (r"/stochss/api/directory/duplicate\/?", DuplicateDirectoryHandler), (r"/stochss/api/directory/create\/?", CreateDirectoryHandler), (r"/stochss/api/spatial/to-model\/?", ConvertToModelAPIHandler), diff --git a/stochss/handlers/file_browser.py b/stochss/handlers/file_browser.py index 2afb26ca41..5d1b7f4ffd 100644 --- a/stochss/handlers/file_browser.py +++ b/stochss/handlers/file_browser.py @@ -730,3 +730,34 @@ async def get(self): except StochSSAPIError as err: report_error(self, log, err) self.finish() + + +class NotebookPresentationAPIHandler(APIHandler): + ''' + ################################################################################################ + Handler publishing notebook presentations. + ################################################################################################ + ''' + @web.authenticated + async def get(self): + ''' + Publish a notebook presentation. + + Attributes + ---------- + ''' + self.set_header('Content-Type', 'application/json') + path = self.get_query_argument(name="path") + log.debug("Path to the file: %s", path) + try: + notebook = StochSSNotebook(path=path) + log.info("Publishing the %s presentation", notebook.get_name()) + links = notebook.publish_presentation() + resp = {"message": f"Successfully published the {notebook.get_name()} presentation", + "links": links} + log.info(resp['message']) + log.debug("Response Message: %s", resp) + self.write(resp) + except StochSSAPIError as err: + report_error(self, log, err) + self.finish() From 48a46b69ad843db66e268b6025695e95396f0ed3 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 9 Jul 2021 09:55:58 -0400 Subject: [PATCH 144/192] Added context menu option to notebooks for publishing presentations. --- client/pages/file-browser.js | 35 ++++++++++++++++++++++++++++++- client/views/file-browser-view.js | 35 ++++++++++++++++++++++++++++++- 2 files changed, 68 insertions(+), 2 deletions(-) diff --git a/client/pages/file-browser.js b/client/pages/file-browser.js index 080cc866dd..bb488e43ca 100644 --- a/client/pages/file-browser.js +++ b/client/pages/file-browser.js @@ -898,6 +898,22 @@ let FileBrowser = PageView.extend({ }); }); }, + publishNotebookPresentation: function (o) { + let queryStr = "?path=" + o.original._path; + let endpoint = path.join(app.getApiPath(), "notebook/presentation") + queryStr; + app.getXHR(endpoint, { + success: function (err, response, body) { + let title = body.message; + let linkHeaders = ["Presentation Link", "Download Link", "Open Link"]; + let links = body.links; + let name = o.original._path.split('/').pop().split('.ipynb')[0]; + $(modals.presentationLinks(title, name, linkHeaders, links)).modal(); + }, + error: function (err, response, body) { + $(modals.newProjectModelErrorHtml(body.Reason, body.Message)).modal(); + } + }); + }, setupJstree: function () { var self = this; $.jstree.defaults.contextmenu.items = (o, cb) => { @@ -1314,6 +1330,17 @@ let FileBrowser = PageView.extend({ } } } + let notebook = { + "publishPresentation" : { + "label" : "Publish Presentation", + "_disabled" : false, + "separator_before" : false, + "separator_after" : false, + "action" : function (data) { + self.publishNotebookPresentation(o); + } + } + } if (o.type === 'root'){ return folder } @@ -1341,7 +1368,13 @@ let FileBrowser = PageView.extend({ if (o.text.endsWith(".zip")) { return $.extend(open, extractAll, common) } - if (o.type === 'notebook' || o.type === "other") { + if (o.type === 'notebook') { + if(app.getBasePath() === "/") { + return $.extend(open, common) + } + return $.extend(open, notebook, common) + } + if (o.type === 'other') { return $.extend(open, common) } if (o.type === 'sbml-model') { diff --git a/client/views/file-browser-view.js b/client/views/file-browser-view.js index b60f2bf2b9..ab054333ef 100644 --- a/client/views/file-browser-view.js +++ b/client/views/file-browser-view.js @@ -942,6 +942,22 @@ module.exports = View.extend({ } }); }, + publishNotebookPresentation: function (o) { + let queryStr = "?path=" + o.original._path; + let endpoint = path.join(app.getApiPath(), "notebook/presentation") + queryStr; + app.getXHR(endpoint, { + success: function (err, response, body) { + let title = body.message; + let linkHeaders = ["Presentation Link", "Download Link", "Open Link"]; + let links = body.links; + let name = o.original._path.split('/').pop().split('.ipynb')[0]; + $(modals.presentationLinks(title, name, linkHeaders, links)).modal(); + }, + error: function (err, response, body) { + $(modals.newProjectModelErrorHtml(body.Reason, body.Message)).modal(); + } + }); + }, setupJstree: function () { var self = this; $.jstree.defaults.contextmenu.items = (o, cb) => { @@ -1373,6 +1389,17 @@ module.exports = View.extend({ } } } + let notebook = { + "publishPresentation" : { + "label" : "Publish Presentation", + "_disabled" : false, + "separator_before" : false, + "separator_after" : false, + "action" : function (data) { + self.publishNotebookPresentation(o); + } + } + } if (o.type === 'root'){ return $.extend(refresh, project, commonFolder, downloadWCombine, {"Rename": common.Rename}) } @@ -1400,7 +1427,13 @@ module.exports = View.extend({ if (o.text.endsWith(".zip")) { return $.extend(open, extractAll, download, common) } - if (o.type === 'notebook' || o.type === "other") { + if (o.type === 'notebook') { + if(app.getBasePath() === "/") { + return $.extend(open, download, common) + } + return $.extend(open, notebook, download, common) + } + if (o.type === 'other') { return $.extend(open, download, common) } if (o.type === 'sbml-model') { From b4081bec82b469f670d65bb624c5c97aba821d2c Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 9 Jul 2021 11:41:34 -0400 Subject: [PATCH 145/192] Fixed issue with notebook presentation files. --- stochss/handlers/util/stochss_notebook.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/stochss/handlers/util/stochss_notebook.py b/stochss/handlers/util/stochss_notebook.py index 8e76400c73..e4fd63bc89 100644 --- a/stochss/handlers/util/stochss_notebook.py +++ b/stochss/handlers/util/stochss_notebook.py @@ -1040,10 +1040,10 @@ def publish_presentation(self): if not os.path.exists(present_dir): os.mkdir(present_dir) try: - notebook = self.load() + notebook_pres = {"notebook": self.load(), "file": self.get_file()} safe_chars = set(string.ascii_letters + string.digits) hostname = escape(os.environ.get('JUPYTERHUB_USER'), safe=safe_chars) - nb_str = json.dumps(notebook, sort_keys=True) + nb_str = json.dumps(notebook_pres['notebook'], sort_keys=True) file = f"{hashlib.md5(nb_str.encode('utf-8')).hexdigest()}.ipynb" dst = os.path.join(present_dir, file) if os.path.exists(dst): @@ -1051,7 +1051,7 @@ def publish_presentation(self): raise StochSSFileExistsError(message) links = self.__get_presentation_links(hostname, file) with open(dst, "w") as presentation_file: - json.dump(notebook, presentation_file) + json.dump(notebook_pres, presentation_file) return links except PermissionError as err: message = f"You do not have permission to publish this file: {str(err)}" From 9bd32c8c8446b4c2f6807f6f662898283e7e1ac7 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 9 Jul 2021 11:42:45 -0400 Subject: [PATCH 146/192] Re-implemented the registation button that exposes the registation form. --- client/templates/pages/home.pug | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/client/templates/pages/home.pug b/client/templates/pages/home.pug index 8b73387efb..f155b025dc 100644 --- a/client/templates/pages/home.pug +++ b/client/templates/pages/home.pug @@ -40,10 +40,10 @@ section.page p.home-p | StochSS is open-source software. To obtain continued funding for sustained development, we must show that StochSS is making an impact in the scientific community. For this, we need to know who is using the software, and a bit about what they are using it for. Please consider registering StochSS to show your support. - div.collapse(data-hook="registration-link") + div.collapse.show(data-hook="registration-link") button.btn.btn-primary.box-shadow(data-hook="registration-link-button" style="margin: 1.5rem;") Register Stochss - div.collapse.show(data-hook="registration-form" id="registration-form") + div.collapse(data-hook="registration-form" id="registration-form") iframe(src="https://docs.google.com/forms/d/12tAH4f8CJ-3F-lK44Q9uQHFio_mGoK0oY829q5lD7i4/viewform?embedded=true" width="100%" height="800" frameborder="0") From 8d0d0788a0830eee670b5942b5201d08a6e837a5 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 9 Jul 2021 11:43:57 -0400 Subject: [PATCH 147/192] Added header row to presentation pages. Refactored the notebook presentation page to manually set the notebook html and get the file name. --- client/pages/notebook-presentation.js | 13 +++-- client/templates/pages/modelPresentation.pug | 54 ++++++++++++++----- .../templates/pages/notebookPresentation.pug | 44 ++++++++++++--- 3 files changed, 87 insertions(+), 24 deletions(-) diff --git a/client/pages/notebook-presentation.js b/client/pages/notebook-presentation.js index f31a45d52c..a7d9a5bf64 100644 --- a/client/pages/notebook-presentation.js +++ b/client/pages/notebook-presentation.js @@ -35,15 +35,22 @@ let NotebookPresentationPage = PageView.extend({ let urlParams = new URLSearchParams(window.location.search); let owner = urlParams.get("owner"); let file = urlParams.get("file"); - this.name = file.split('/').pop().split('.ipynb')[0] + let self = this; let queryStr = "?owner=" + owner + "&file=" + file; - this.loadLink = "https://staging.stochss.org/stochss/api/notebook/load" + queryStr; + let endpoint = "api/notebook/load" + queryStr; + app.getXHR(endpoint, { + success: function (err, response, body) { + self.name = body.file.split('/').pop().split('.ipynb')[0]; + self.renderSubviews(body.html); + } + }); let downloadStart = "https://staging.stochss.org/stochss/notebook/download_presentation"; this.downloadLink = path.join(downloadStart, owner, file); this.openLink = "open.stochss.org?open=" + this.downloadLink; }, - render: function (attrs, options) { + renderSubviews: function (html) { PageView.prototype.render.apply(this, arguments); + $("#notebook").contents().find('body').html(html); } }); diff --git a/client/templates/pages/modelPresentation.pug b/client/templates/pages/modelPresentation.pug index a142db5e60..19aa4c42c4 100644 --- a/client/templates/pages/modelPresentation.pug +++ b/client/templates/pages/modelPresentation.pug @@ -1,27 +1,55 @@ section.page - div#model-presentation.container + nav.navbar.navbar-expand-md.p-1.navbar-light.bg-light.fixed-top + a.navbar-brand(href="/hub/spawn") + img(style="height: 38px;margin-left: -1.2em;" src="static/stochss-logo.png") - div.presentation-header + button.navbar-toggler(type="button" data-toggle="collapse" data-target="#navbar" aria-controls="navbarNav" aria-expanded="false" aria-label="Toggle navigation") + span.navbar-toggler-icon - h1=this.model.name + div#navbar.collapse.navbar-collapse.justify-content-end(role="navigation") + ul.navbar-nav.float-right + li.nav-item: a.nav-link(href="http://www.stochss.org", target="_blank") + | About - div(data-hook="model-species") + li.nav-item: a.nav-link(href="https://docs.google.com/forms/d/12tAH4f8CJ-3F-lK44Q9uQHFio_mGoK0oY829q5lD7i4/viewform?embedded=true", target="_blank") + | Register - div(data-hook="model-parameters") + li.nav-item: a.nav-link(href="http://www.stochss.org/documentation", target="_blank") + | Documentation - div(data-hook="model-reactions") + li.nav-item: a.nav-link(href="https://forms.gle/hpGJ1ruxR7wTT43h8" target="_blank") + | Submit Feedback - div(data-hook="model-events") + li.nav-item + div.dropdown + button.dropdown-toggle.nav-item.nav-link.dropbtn Contact + div.dropdown-content + a.nav-link(href="https://gitter.im/StochSS/community#", target="_blank") Community Chat + a.nav-link(href="https://github.com/StochSS/stochss/issues/new", target="_blank") Report Issue - div(data-hook="model-rules") + div#model-presentation.container - div(data-hook="model-sbml-components") + div.presentation-header - div.card.card-body="System Volume: "+this.model.volume + h1=this.model.name - div.mt-3 + div(data-hook="model-species") - a.btn.btn-outline-secondary.box-shadow.text-break.mr-3(href=this.openLink role="button") Open in StochSS + div(data-hook="model-parameters") - a.btn.btn-outline-secondary.box-shadow.text-break(href=this.downloadLink role="button") Download (.mdl) + div(data-hook="model-reactions") + + div(data-hook="model-events") + + div(data-hook="model-rules") + + div(data-hook="model-sbml-components") + + div.card.card-body="System Volume: "+this.model.volume + + div.mt-3 + + a.btn.btn-outline-secondary.box-shadow.text-break.mr-3(href=this.openLink role="button") Open in StochSS + + a.btn.btn-outline-secondary.box-shadow.text-break(href=this.downloadLink role="button") Download (.mdl) diff --git a/client/templates/pages/notebookPresentation.pug b/client/templates/pages/notebookPresentation.pug index 95e25dd6ca..77b87bc6bc 100644 --- a/client/templates/pages/notebookPresentation.pug +++ b/client/templates/pages/notebookPresentation.pug @@ -1,17 +1,45 @@ section.page - div#notebook-presentation.container + nav.navbar.navbar-expand-md.p-1.navbar-light.bg-light.fixed-top + a.navbar-brand(href="/hub/spawn") + img(style="height: 38px;margin-left: -1.2em;" src="static/stochss-logo.png") - div.presentation-header + button.navbar-toggler(type="button" data-toggle="collapse" data-target="#navbar" aria-controls="navbarNav" aria-expanded="false" aria-label="Toggle navigation") + span.navbar-toggler-icon - h1=this.name + div#navbar.collapse.navbar-collapse.justify-content-end(role="navigation") + ul.navbar-nav.float-right + li.nav-item: a.nav-link(href="http://www.stochss.org", target="_blank") + | About - div.iframe-container.card.card-body + li.nav-item: a.nav-link(href="https://docs.google.com/forms/d/12tAH4f8CJ-3F-lK44Q9uQHFio_mGoK0oY829q5lD7i4/viewform?embedded=true", target="_blank") + | Register - iframe(src=this.loadLink width="100%" height="100%" frameborder="0") + li.nav-item: a.nav-link(href="http://www.stochss.org/documentation", target="_blank") + | Documentation - div.mt-3 + li.nav-item: a.nav-link(href="https://forms.gle/hpGJ1ruxR7wTT43h8" target="_blank") + | Submit Feedback - a.btn.btn-outline-secondary.box-shadow.text-break.mr-3(href=this.openLink role="button") Open in StochSS + li.nav-item + div.dropdown + button.dropdown-toggle.nav-item.nav-link.dropbtn Contact + div.dropdown-content + a.nav-link(href="https://gitter.im/StochSS/community#", target="_blank") Community Chat + a.nav-link(href="https://github.com/StochSS/stochss/issues/new", target="_blank") Report Issue - a.btn.btn-outline-secondary.box-shadow.text-break(href=this.downloadLink role="button") Download (.ipynb) + div#notebook-presentation.container + + div.presentation-header + + h1=this.name + + div.iframe-container.card.card-body + + iframe(id="notebook" width="100%" height="100%" frameborder="0") + + div.mt-3 + + a.btn.btn-outline-secondary.box-shadow.text-break.mr-3(href=this.openLink role="button") Open in StochSS + + a.btn.btn-outline-secondary.box-shadow.text-break(href=this.downloadLink role="button") Download (.ipynb) From a7c2fd84b909fefbb75433ac6f80a36d6d8e34b6 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 9 Jul 2021 12:02:09 -0400 Subject: [PATCH 148/192] Added missing dependencies. --- client/pages/notebook-presentation.js | 3 +++ 1 file changed, 3 insertions(+) diff --git a/client/pages/notebook-presentation.js b/client/pages/notebook-presentation.js index a7d9a5bf64..a62421267b 100644 --- a/client/pages/notebook-presentation.js +++ b/client/pages/notebook-presentation.js @@ -16,9 +16,12 @@ 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 domReady = require('domready'); let bootstrap = require('bootstrap'); +//support files +let app = require('../app'); //views let PageView = require('./base'); //templates From d74b3f140406bab168e2e84787bdf0578f87b050 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 9 Jul 2021 12:23:17 -0400 Subject: [PATCH 149/192] Fixed logo paths. --- client/templates/pages/modelPresentation.pug | 2 +- client/templates/pages/notebookPresentation.pug | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/client/templates/pages/modelPresentation.pug b/client/templates/pages/modelPresentation.pug index 19aa4c42c4..8695ee0c76 100644 --- a/client/templates/pages/modelPresentation.pug +++ b/client/templates/pages/modelPresentation.pug @@ -2,7 +2,7 @@ section.page nav.navbar.navbar-expand-md.p-1.navbar-light.bg-light.fixed-top a.navbar-brand(href="/hub/spawn") - img(style="height: 38px;margin-left: -1.2em;" src="static/stochss-logo.png") + img(style="height: 38px;margin-left: -1.2em;" src="/hub/static/stochss-logo.png") button.navbar-toggler(type="button" data-toggle="collapse" data-target="#navbar" aria-controls="navbarNav" aria-expanded="false" aria-label="Toggle navigation") span.navbar-toggler-icon diff --git a/client/templates/pages/notebookPresentation.pug b/client/templates/pages/notebookPresentation.pug index 77b87bc6bc..a83acece2e 100644 --- a/client/templates/pages/notebookPresentation.pug +++ b/client/templates/pages/notebookPresentation.pug @@ -2,7 +2,7 @@ section.page nav.navbar.navbar-expand-md.p-1.navbar-light.bg-light.fixed-top a.navbar-brand(href="/hub/spawn") - img(style="height: 38px;margin-left: -1.2em;" src="static/stochss-logo.png") + img(style="height: 38px;margin-left: -1.2em;" src="/hub/static/stochss-logo.png") button.navbar-toggler(type="button" data-toggle="collapse" data-target="#navbar" aria-controls="navbarNav" aria-expanded="false" aria-label="Toggle navigation") span.navbar-toggler-icon From 70226279b3b69c163032551533ad24d1b23aef22 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 9 Jul 2021 12:24:24 -0400 Subject: [PATCH 150/192] Fixed the load api handler return. --- jupyterhub/notebook_presentation.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/jupyterhub/notebook_presentation.py b/jupyterhub/notebook_presentation.py index ac0903b246..4482b4ed12 100644 --- a/jupyterhub/notebook_presentation.py +++ b/jupyterhub/notebook_presentation.py @@ -44,6 +44,7 @@ async def get(self): Attributes ---------- ''' + self.set_header('Content-Type', 'application/json') owner = self.get_query_argument(name="owner") log.debug("Container id of the owner: %s", owner) file = self.get_query_argument(name="file") @@ -97,4 +98,4 @@ def process_notebook_presentation(path, as_dict=False): notebook = nbformat.reads(json.dumps(nb_presentation['notebook']), as_version=4) nb_format = {"exporter": HTMLExporter} html, _ = render_notebook(format=nb_format, nb=notebook) - return html + return {"file": nb_presentation['file'], "html": html} From 3adf5c8f7eebc56aa0d872ed61b550d4085f072c Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 9 Jul 2021 13:50:45 -0400 Subject: [PATCH 151/192] Attempt #2 to set iframe dynamically. --- client/pages/notebook-presentation.js | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/client/pages/notebook-presentation.js b/client/pages/notebook-presentation.js index a62421267b..33fefc378b 100644 --- a/client/pages/notebook-presentation.js +++ b/client/pages/notebook-presentation.js @@ -53,7 +53,10 @@ let NotebookPresentationPage = PageView.extend({ }, renderSubviews: function (html) { PageView.prototype.render.apply(this, arguments); - $("#notebook").contents().find('body').html(html); + var $frame = $('#notebook'); + var doc = $frame[0].contentWindow.document; + var $body = $('body', doc); + $body.html(html);; } }); From 31e9439b031789780c1ebe26d2ac9cf220d8bbc0 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 9 Jul 2021 13:51:05 -0400 Subject: [PATCH 152/192] Tweaked css. --- client/styles/styles.css | 9 ++++++++- client/templates/pages/home.pug | 4 ++-- 2 files changed, 10 insertions(+), 3 deletions(-) diff --git a/client/styles/styles.css b/client/styles/styles.css index 42bdce8a44..5d8ce3a966 100644 --- a/client/styles/styles.css +++ b/client/styles/styles.css @@ -554,6 +554,13 @@ span.checkbox { border-radius: 1.5rem; } +.register-stochss-btn { + padding: 1.5rem 1.5rem; + font-size: 1.75rem; + line-height: 1; + border-radius: 1.5rem; +} + .user-home-btn { padding: 1rem 1rem; font-size: 1.5rem; @@ -708,7 +715,7 @@ span.checkbox { } .presentation-header { - margin-top: 32px; + margin-top: 64px; padding: 20px 16px; } diff --git a/client/templates/pages/home.pug b/client/templates/pages/home.pug index f155b025dc..2c0cdf24f1 100644 --- a/client/templates/pages/home.pug +++ b/client/templates/pages/home.pug @@ -31,7 +31,7 @@ section.page li Bring Your Own Cloud div.centered - a.try-stochss-btn.btn.btn-primary.box-shadow(href="/hub/spawn" role="button") Click here to login + a.register-stochss-btn.btn.btn-primary.box-shadow(href="/hub/spawn" role="button") Click here to login div#registration-home.container.card.card-body @@ -42,7 +42,7 @@ section.page div.collapse.show(data-hook="registration-link") - button.btn.btn-primary.box-shadow(data-hook="registration-link-button" style="margin: 1.5rem;") Register Stochss + button.try-stochss-btn.btn.btn-primary.box-shadow(data-hook="registration-link-button" style="margin: 1.5rem;") Register Stochss div.collapse(data-hook="registration-form" id="registration-form") From f97a567af7b716b1f026900b97131cd13eab8aa3 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 9 Jul 2021 14:25:05 -0400 Subject: [PATCH 153/192] Attempt #3 to set iframe content dynamically. --- client/pages/notebook-presentation.js | 2 +- client/templates/pages/home.pug | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/client/pages/notebook-presentation.js b/client/pages/notebook-presentation.js index 33fefc378b..3f5c8db55d 100644 --- a/client/pages/notebook-presentation.js +++ b/client/pages/notebook-presentation.js @@ -55,7 +55,7 @@ let NotebookPresentationPage = PageView.extend({ PageView.prototype.render.apply(this, arguments); var $frame = $('#notebook'); var doc = $frame[0].contentWindow.document; - var $body = $('body', doc); + var $body = $('html', doc); $body.html(html);; } }); diff --git a/client/templates/pages/home.pug b/client/templates/pages/home.pug index 2c0cdf24f1..47b87ae585 100644 --- a/client/templates/pages/home.pug +++ b/client/templates/pages/home.pug @@ -31,7 +31,7 @@ section.page li Bring Your Own Cloud div.centered - a.register-stochss-btn.btn.btn-primary.box-shadow(href="/hub/spawn" role="button") Click here to login + a.try-stochss-btn.btn.btn-primary.box-shadow(href="/hub/spawn" role="button") Click here to login div#registration-home.container.card.card-body @@ -42,7 +42,7 @@ section.page div.collapse.show(data-hook="registration-link") - button.try-stochss-btn.btn.btn-primary.box-shadow(data-hook="registration-link-button" style="margin: 1.5rem;") Register Stochss + button.register-stochss-btn.btn.btn-primary.box-shadow(data-hook="registration-link-button" style="margin: 1.5rem;") Register Stochss div.collapse(data-hook="registration-form" id="registration-form") From cf8c9d5fcaaf7b43a91f883194dbd639148725c7 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 9 Jul 2021 14:45:15 -0400 Subject: [PATCH 154/192] Attempt #4 to set iframe content dynamically. --- client/pages/notebook-presentation.js | 21 +++++++++++++++++---- 1 file changed, 17 insertions(+), 4 deletions(-) diff --git a/client/pages/notebook-presentation.js b/client/pages/notebook-presentation.js index 3f5c8db55d..7c0b8b6abd 100644 --- a/client/pages/notebook-presentation.js +++ b/client/pages/notebook-presentation.js @@ -53,10 +53,23 @@ let NotebookPresentationPage = PageView.extend({ }, renderSubviews: function (html) { PageView.prototype.render.apply(this, arguments); - var $frame = $('#notebook'); - var doc = $frame[0].contentWindow.document; - var $body = $('html', doc); - $body.html(html);; + var iframe = document.getElementById('notebook'); + var iframedoc = iframe.document; + if (iframe.contentDocument) { + iframedoc = iframe.contentDocument; + console.log("iframe has contentDocument"); + }else if (iframe.contentWindow) { + iframedoc = iframe.contentWindow.document; + console.log("iframe has contentWindow.document"); + } + if (iframedoc) { + //iframedoc.open(); + iframedoc.write(responseText); + iframedoc.close(); + console.log("iframedoc is not NULL"); + } else { + alert('Cannot inject dynamic contents into iframe.'); + } } }); From 1ac01abbc8711ed9b234af270736b4e91ab86870 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 9 Jul 2021 15:08:02 -0400 Subject: [PATCH 155/192] fixed the write function issue. --- client/pages/notebook-presentation.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/client/pages/notebook-presentation.js b/client/pages/notebook-presentation.js index 7c0b8b6abd..45b9300efb 100644 --- a/client/pages/notebook-presentation.js +++ b/client/pages/notebook-presentation.js @@ -64,7 +64,7 @@ let NotebookPresentationPage = PageView.extend({ } if (iframedoc) { //iframedoc.open(); - iframedoc.write(responseText); + iframedoc.write(html); iframedoc.close(); console.log("iframedoc is not NULL"); } else { From 3b10cc30ee0a5c55d1997a1e673657c5936c33b4 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 9 Jul 2021 15:42:07 -0400 Subject: [PATCH 156/192] Fixed iframe height issue with chrome and firefox browsers. --- client/pages/notebook-presentation.js | 11 +++-------- 1 file changed, 3 insertions(+), 8 deletions(-) diff --git a/client/pages/notebook-presentation.js b/client/pages/notebook-presentation.js index 45b9300efb..27cfc97ed0 100644 --- a/client/pages/notebook-presentation.js +++ b/client/pages/notebook-presentation.js @@ -53,22 +53,17 @@ let NotebookPresentationPage = PageView.extend({ }, renderSubviews: function (html) { PageView.prototype.render.apply(this, arguments); - var iframe = document.getElementById('notebook'); - var iframedoc = iframe.document; + let iframe = document.getElementById('notebook'); + let iframedoc = iframe.document; if (iframe.contentDocument) { iframedoc = iframe.contentDocument; - console.log("iframe has contentDocument"); }else if (iframe.contentWindow) { iframedoc = iframe.contentWindow.document; - console.log("iframe has contentWindow.document"); } if (iframedoc) { - //iframedoc.open(); iframedoc.write(html); iframedoc.close(); - console.log("iframedoc is not NULL"); - } else { - alert('Cannot inject dynamic contents into iframe.'); + iframe.height = iframe.contentWindow.document.body.scrollHeight; } } }); From ba72c4e6ad3c397ca8d30930263cee8e80af2e34 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 9 Jul 2021 16:09:12 -0400 Subject: [PATCH 157/192] Attempt #2 to fix iframe hieght issue with chrome and firefox . --- client/pages/notebook-presentation.js | 2 +- client/styles/styles.css | 5 ----- client/templates/pages/notebookPresentation.pug | 2 +- 3 files changed, 2 insertions(+), 7 deletions(-) diff --git a/client/pages/notebook-presentation.js b/client/pages/notebook-presentation.js index 27cfc97ed0..f44ed6e4f2 100644 --- a/client/pages/notebook-presentation.js +++ b/client/pages/notebook-presentation.js @@ -62,8 +62,8 @@ let NotebookPresentationPage = PageView.extend({ } if (iframedoc) { iframedoc.write(html); + iframe.height = iframedoc.body.scrollHeight; iframedoc.close(); - iframe.height = iframe.contentWindow.document.body.scrollHeight; } } }); diff --git a/client/styles/styles.css b/client/styles/styles.css index 5d8ce3a966..10d2a5bdbe 100644 --- a/client/styles/styles.css +++ b/client/styles/styles.css @@ -718,8 +718,3 @@ span.checkbox { margin-top: 64px; padding: 20px 16px; } - -.iframe-container { - max-height: 100% !important; - display: grid; -} diff --git a/client/templates/pages/notebookPresentation.pug b/client/templates/pages/notebookPresentation.pug index a83acece2e..a3b404b915 100644 --- a/client/templates/pages/notebookPresentation.pug +++ b/client/templates/pages/notebookPresentation.pug @@ -34,7 +34,7 @@ section.page h1=this.name - div.iframe-container.card.card-body + div.card.card-body iframe(id="notebook" width="100%" height="100%" frameborder="0") From 07649687c5b1272650f615d8b08a26ece88fae72 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 9 Jul 2021 16:27:24 -0400 Subject: [PATCH 158/192] Attempt #3 to fixed iframe height for chrome and firefox browsers. --- client/pages/notebook-presentation.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/client/pages/notebook-presentation.js b/client/pages/notebook-presentation.js index f44ed6e4f2..9d6eccae11 100644 --- a/client/pages/notebook-presentation.js +++ b/client/pages/notebook-presentation.js @@ -62,8 +62,8 @@ let NotebookPresentationPage = PageView.extend({ } if (iframedoc) { iframedoc.write(html); - iframe.height = iframedoc.body.scrollHeight; iframedoc.close(); + $("#notebook").height($("#notebook").contents().find('html').height()); } } }); From ba296dea15bacbf8a3b435b3ec951bf458102781 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 9 Jul 2021 17:01:07 -0400 Subject: [PATCH 159/192] Attempt #4 to fix the iframe height issue for chrome and firefox browsers. --- client/pages/notebook-presentation.js | 1 - client/templates/pages/notebookPresentation.pug | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/client/pages/notebook-presentation.js b/client/pages/notebook-presentation.js index 9d6eccae11..0817d71136 100644 --- a/client/pages/notebook-presentation.js +++ b/client/pages/notebook-presentation.js @@ -63,7 +63,6 @@ let NotebookPresentationPage = PageView.extend({ if (iframedoc) { iframedoc.write(html); iframedoc.close(); - $("#notebook").height($("#notebook").contents().find('html').height()); } } }); diff --git a/client/templates/pages/notebookPresentation.pug b/client/templates/pages/notebookPresentation.pug index a3b404b915..ba03a11038 100644 --- a/client/templates/pages/notebookPresentation.pug +++ b/client/templates/pages/notebookPresentation.pug @@ -36,7 +36,7 @@ section.page div.card.card-body - iframe(id="notebook" width="100%" height="100%" frameborder="0") + iframe(id="notebook" width="100%" height="100%" frameborder="0" onload="this.height=this.contentWindow.document.body.scrollHeight;") div.mt-3 From fdd0b6bc829295d68ec88548eb6ec8171d068391 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Thu, 15 Jul 2021 14:27:37 -0400 Subject: [PATCH 160/192] Fixed the issue with duplicate reaction and event containers. --- client/views/reactions-view.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/client/views/reactions-view.js b/client/views/reactions-view.js index 141b2fd6bc..d046bcb016 100644 --- a/client/views/reactions-view.js +++ b/client/views/reactions-view.js @@ -90,8 +90,8 @@ module.exports = View.extend({ if (this.collection.length) { this.setSelectedReaction(this.collection.at(0)); this.collection.trigger("select", this.selectedReaction); + this.collection.trigger("change"); } - this.collection.trigger("change"); this.toggleAddReactionButton(); if(this.collection.parent.parameters.length > 0){ $(this.queryByHook('add-reaction-partial')).prop('hidden', true); From 6a5bf0041dcd804c6ff7c5f2c7f91a28d174cdd3 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Thu, 15 Jul 2021 16:05:16 -0400 Subject: [PATCH 161/192] Renamed rule views and templates with names that better fit their new role. Moved the rules render function and container to the model view. --- client/pages/model-editor.js | 9 --------- client/templates/includes/modelView.pug | 2 ++ .../includes/{ruleEditor.pug => rulesView.pug} | 0 client/templates/pages/modelEditor.pug | 4 ---- client/views/model-state-buttons.js | 4 ++-- client/views/model-view.js | 11 +++++++++++ client/views/parameters-view.js | 2 +- client/views/{edit-rule.js => rule-view.js} | 0 client/views/{rules-editor.js => rules-view.js} | 4 ++-- client/views/species-view.js | 2 +- 10 files changed, 19 insertions(+), 19 deletions(-) rename client/templates/includes/{ruleEditor.pug => rulesView.pug} (100%) rename client/views/{edit-rule.js => rule-view.js} (100%) rename client/views/{rules-editor.js => rules-view.js} (97%) diff --git a/client/pages/model-editor.js b/client/pages/model-editor.js index 4cc2bc5022..e6faee4424 100644 --- a/client/pages/model-editor.js +++ b/client/pages/model-editor.js @@ -29,7 +29,6 @@ var PageView = require('../pages/base'); let ModelView = require('../views/model-view'); var InputView = require('../views/input'); var ParticleViewer = require('../views/view-particle'); -var RulesEditorView = require('../views/rules-editor'); var SBMLComponentView = require('../views/sbml-component-editor'); var TimespanSettingsView = require('../views/timespan-settings'); var ModelStateButtonsView = require('../views/model-state-buttons'); @@ -164,7 +163,6 @@ let ModelEditor = PageView.extend({ $(this.queryByHook("toggle-preview-domain")).css("display", "inline-block"); this.openDomainPlot(); }else { - this.renderRulesView(); if(this.model.functionDefinitions.length) { var sbmlComponentView = new SBMLComponentView({ functionDefinitions: this.model.functionDefinitions @@ -193,13 +191,6 @@ let ModelEditor = PageView.extend({ }); app.registerRenderSubview(this, this.boundaryConditionsView, "boundary-conditions-container"); }, - renderRulesView: function () { - if(this.rulesEditor){ - this.rulesEditor.remove(); - } - this.rulesEditor = new RulesEditorView({collection: this.model.rules}); - app.registerRenderSubview(this, this.rulesEditor, 'rules-editor-container'); - }, renderSystemVolumeView: function () { if(this.systemVolumeView) { this.systemVolumeView.remove() diff --git a/client/templates/includes/modelView.pug b/client/templates/includes/modelView.pug index 27fd1e491f..652ab99f85 100644 --- a/client/templates/includes/modelView.pug +++ b/client/templates/includes/modelView.pug @@ -72,3 +72,5 @@ div#model-view div.card-body div(data-hook="events-view-container") + + div(data-hook="rules-view-container") diff --git a/client/templates/includes/ruleEditor.pug b/client/templates/includes/rulesView.pug similarity index 100% rename from client/templates/includes/ruleEditor.pug rename to client/templates/includes/rulesView.pug diff --git a/client/templates/pages/modelEditor.pug b/client/templates/pages/modelEditor.pug index 725a80065a..34877b823a 100644 --- a/client/templates/pages/modelEditor.pug +++ b/client/templates/pages/modelEditor.pug @@ -28,10 +28,6 @@ section.page div(data-hook="model-view-container") - div(data-hook="events-editor-container") - - div(data-hook="rules-editor-container") - div(data-hook="boundary-conditions-container") div(data-hook="sbml-component-container") diff --git a/client/views/model-state-buttons.js b/client/views/model-state-buttons.js index d87f63e2b5..435ab50fbc 100644 --- a/client/views/model-state-buttons.js +++ b/client/views/model-state-buttons.js @@ -359,9 +359,9 @@ module.exports = View.extend({ advCollapseBtn.click() advCollapseBtn.html('-') } - let ruleSection = $(this.rulesEditor.queryByHook("rules-list-container")) + let ruleSection = $(this.parent.modelView.rulesView.queryByHook("rules-list-container")) if(!ruleSection.hasClass("show")) { - let ruleCollapseBtn = $(this.parent.rulesEditor.queryByHook("collapse")) + let ruleCollapseBtn = $(this.parent.modelView.rulesView.queryByHook("collapse")) ruleCollapseBtn.click() ruleCollapseBtn.html('-') } diff --git a/client/views/model-view.js b/client/views/model-view.js index 7c77995c6f..8b37954ba4 100644 --- a/client/views/model-view.js +++ b/client/views/model-view.js @@ -26,6 +26,7 @@ let modals = require('../modals'); let Domain = require('../models/domain'); //views let View = require('ampersand-view'); +let RulesView = require('../views/rules-view'); let EventsView = require('../views/events-view'); let SpeciesView = require('../views/species-view'); let DomainViewer = require('../views/domain-viewer'); @@ -277,6 +278,16 @@ module.exports = View.extend({ readOnly: this.readOnly }); } + }, + rulesView: { + waitFor: "model.not_spatial", + hook: "rules-view-container", + prepareView: function (el) { + return new RulesView({ + collection: this.model.rules, + readOnly: this.readOnly + }); + } } } }); \ No newline at end of file diff --git a/client/views/parameters-view.js b/client/views/parameters-view.js index ff33549c0a..7e51981fd1 100644 --- a/client/views/parameters-view.js +++ b/client/views/parameters-view.js @@ -57,7 +57,7 @@ module.exports = View.extend({ rule.variable = parameter; } }); - self.parent.renderRulesView(); + self.parent.rulesView.renderEditRules(); }); }, render: function () { diff --git a/client/views/edit-rule.js b/client/views/rule-view.js similarity index 100% rename from client/views/edit-rule.js rename to client/views/rule-view.js diff --git a/client/views/rules-editor.js b/client/views/rules-view.js similarity index 97% rename from client/views/rules-editor.js rename to client/views/rules-view.js index 489a41e770..43d8520c04 100644 --- a/client/views/rules-editor.js +++ b/client/views/rules-view.js @@ -22,9 +22,9 @@ let app = require('../app'); var Tooltips = require('../tooltips'); //views var View = require('ampersand-view'); -var RuleView = require('./edit-rule'); +var RuleView = require('./rule-view'); //templates -var template = require('../templates/includes/ruleEditor.pug'); +var template = require('../templates/includes/rulesView.pug'); module.exports = View.extend({ template: template, diff --git a/client/views/species-view.js b/client/views/species-view.js index 6d79742329..05b659aea0 100644 --- a/client/views/species-view.js +++ b/client/views/species-view.js @@ -77,7 +77,7 @@ module.exports = View.extend({ } }); if(isNameUpdate) { - self.parent.renderRulesView(); + self.parent.rulesView.renderEditRules(); } }); }, From 08dd1a0b4e1f9ae2fb98dd23be88b0d1a13bcf85 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Thu, 15 Jul 2021 16:12:33 -0400 Subject: [PATCH 162/192] Renamed the boundary conditions view and template files with names that better fit their new roles. --- ...{boundaryConditionsEditor.pug => boundaryConditionsView.pug} | 0 ...oundary-conditions-editor.js => boundary-conditions-view.js} | 2 +- 2 files changed, 1 insertion(+), 1 deletion(-) rename client/templates/includes/{boundaryConditionsEditor.pug => boundaryConditionsView.pug} (100%) rename client/views/{boundary-conditions-editor.js => boundary-conditions-view.js} (99%) diff --git a/client/templates/includes/boundaryConditionsEditor.pug b/client/templates/includes/boundaryConditionsView.pug similarity index 100% rename from client/templates/includes/boundaryConditionsEditor.pug rename to client/templates/includes/boundaryConditionsView.pug diff --git a/client/views/boundary-conditions-editor.js b/client/views/boundary-conditions-view.js similarity index 99% rename from client/views/boundary-conditions-editor.js rename to client/views/boundary-conditions-view.js index bfc9607a00..3d4ef14711 100644 --- a/client/views/boundary-conditions-editor.js +++ b/client/views/boundary-conditions-view.js @@ -28,7 +28,7 @@ let View = require('ampersand-view'); let SelectView = require('ampersand-select-view'); let BoundaryConditionView = require('./boundary-condition-view'); //templates -let template = require('../templates/includes/boundaryConditionsEditor.pug'); +let template = require('../templates/includes/boundaryConditionsView.pug'); module.exports = View.extend({ template: template, From 1cae5861bbe165375e73be542afee3b5df958264 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Thu, 15 Jul 2021 16:27:54 -0400 Subject: [PATCH 163/192] Moved the boundary conditions render function and container to the model view file. --- client/pages/model-editor.js | 11 ----------- client/templates/includes/modelView.pug | 2 ++ client/templates/pages/modelEditor.pug | 2 -- client/views/model-view.js | 13 ++++++++++++- 4 files changed, 14 insertions(+), 14 deletions(-) diff --git a/client/pages/model-editor.js b/client/pages/model-editor.js index e6faee4424..191a557aaf 100644 --- a/client/pages/model-editor.js +++ b/client/pages/model-editor.js @@ -33,7 +33,6 @@ var SBMLComponentView = require('../views/sbml-component-editor'); var TimespanSettingsView = require('../views/timespan-settings'); var ModelStateButtonsView = require('../views/model-state-buttons'); var QuickviewDomainTypes = require('../views/quickview-domain-types'); -let BoundaryConditionsView = require('../views/boundary-conditions-editor'); //models var Model = require('../models/model'); var Domain = require('../models/domain'); @@ -159,7 +158,6 @@ let ModelEditor = PageView.extend({ if(this.model.is_spatial) { $(this.queryByHook("system-volume-container")).css("display", "none"); $(this.queryByHook("spatial-beta-message")).css("display", "block"); - this.renderBoundaryConditionsView(); $(this.queryByHook("toggle-preview-domain")).css("display", "inline-block"); this.openDomainPlot(); }else { @@ -182,15 +180,6 @@ let ModelEditor = PageView.extend({ e.target.remove() }); }, - renderBoundaryConditionsView: function() { - if(this.boundaryConditionsView) { - this.boundaryConditionsView.remove(); - } - this.boundaryConditionsView = new BoundaryConditionsView({ - collection: this.model.boundaryConditions - }); - app.registerRenderSubview(this, this.boundaryConditionsView, "boundary-conditions-container"); - }, renderSystemVolumeView: function () { if(this.systemVolumeView) { this.systemVolumeView.remove() diff --git a/client/templates/includes/modelView.pug b/client/templates/includes/modelView.pug index 652ab99f85..2f91c3c5d6 100644 --- a/client/templates/includes/modelView.pug +++ b/client/templates/includes/modelView.pug @@ -74,3 +74,5 @@ div#model-view div(data-hook="events-view-container") div(data-hook="rules-view-container") + + div(data-hook="boundary-conditions-view-container") diff --git a/client/templates/pages/modelEditor.pug b/client/templates/pages/modelEditor.pug index 34877b823a..e31f68253b 100644 --- a/client/templates/pages/modelEditor.pug +++ b/client/templates/pages/modelEditor.pug @@ -28,8 +28,6 @@ section.page div(data-hook="model-view-container") - div(data-hook="boundary-conditions-container") - div(data-hook="sbml-component-container") div.card.collapse.show(data-hook="system-volume-container") diff --git a/client/views/model-view.js b/client/views/model-view.js index 8b37954ba4..424b72d01e 100644 --- a/client/views/model-view.js +++ b/client/views/model-view.js @@ -33,6 +33,7 @@ let DomainViewer = require('../views/domain-viewer'); let ReactionsView = require('../views/reactions-view'); let ParametersView = require('../views/parameters-view'); let InitialConditionsView = require('../views/initial-conditions-view'); +let BoundaryConditionsView = require('../views/boundary-conditions-view'); //templates let template = require('../templates/includes/modelView.pug'); @@ -48,7 +49,7 @@ module.exports = View.extend({ View.prototype.initialize.apply(this, arguments); this.readOnly = attrs.readOnly ? attrs.readOnly : false; let modeMap = {continuous: "Concentration", discrete: "Population", dynamic: "Hybrid Concentration/Population"}; - this.modelMode = modeMap[this.model.defaultMode] + this.modelMode = modeMap[this.model.defaultMode]; }, render: function(attrs, options) { View.prototype.render.apply(this, arguments); @@ -288,6 +289,16 @@ module.exports = View.extend({ readOnly: this.readOnly }); } + }, + boundaryConditionsView: { + waitFor: "model.is_spatial", + hook: "boundary-conditions-view-container", + prepareView: function (el) { + return new BoundaryConditionsView({ + collection: this.model.boundaryConditions, + readOnly: this.readOnly + }); + } } } }); \ No newline at end of file From 3acdadf6ef5a79a96264eeeb9fd44c1f4779b303 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Thu, 15 Jul 2021 16:44:51 -0400 Subject: [PATCH 164/192] Cleaned up rule view files. --- client/app.js | 2 +- client/views/rule-view.js | 72 +++++++++++++++++--------------------- client/views/rules-view.js | 58 +++++++++++------------------- 3 files changed, 53 insertions(+), 79 deletions(-) diff --git a/client/app.js b/client/app.js index 957b326f06..5fd33ed0e3 100644 --- a/client/app.js +++ b/client/app.js @@ -208,7 +208,7 @@ documentSetup = () => { $('[autofocus]', e.target).focus(); }); $(document).on('hide.bs.modal', '.modal', function (e) { - e.target.remove() + e.target.remove(); }); } diff --git a/client/views/rule-view.js b/client/views/rule-view.js index 66e36128b8..8febcb192b 100644 --- a/client/views/rule-view.js +++ b/client/views/rule-view.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 $ = require('jquery'); +let $ = require('jquery'); let _ = require('underscore'); //support files let app = require('../app'); -var tests = require('./tests'); -var modals = require('../modals'); +let tests = require('./tests'); +let modals = require('../modals'); //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'); //templates -var editTemplate = require('../templates/includes/editRule.pug'); +let editTemplate = require('../templates/includes/editRule.pug'); let viewTemplate = require('../templates/includes/viewRules.pug'); module.exports = View.extend({ @@ -35,7 +35,7 @@ module.exports = View.extend({ 'change [data-hook=rule-type]' : 'selectRuleType', 'change [data-hook=rule-variable]' : 'selectRuleVariable', 'click [data-hook=edit-annotation-btn]' : 'editAnnotation', - 'click [data-hook=remove]' : 'removeRule', + 'click [data-hook=remove]' : 'removeRule' }, initialize: function (attrs, options) { View.prototype.initialize.apply(this, arguments); @@ -45,29 +45,20 @@ module.exports = View.extend({ this.template = this.viewMode ? viewTemplate : editTemplate; View.prototype.render.apply(this, arguments); if(!this.viewMode){ - this.model.on('change', _.bind(this.updateViewer, this)) + this.model.on('change', _.bind(this.updateViewer, this)); } - $(document).on('shown.bs.modal', function (e) { - $('[autofocus]', e.target).focus(); - }); - $(document).on('hide.bs.modal', '.modal', function (e) { - e.target.remove() - }); + app.documentSetup(); if(!this.model.annotation){ - $(this.queryByHook('edit-annotation-btn')).text('Add') + $(this.queryByHook('edit-annotation-btn')).text('Add'); } }, - update: function (e) { - }, - updateValid: function () { - }, editAnnotation: function () { - var self = this; - var name = this.model.name; - var annotation = this.model.annotation; if(document.querySelector('#ruleAnnotationModal')) { document.querySelector('#ruleAnnotationModal').remove(); } + let self = this; + let name = this.model.name; + let annotation = this.model.annotation; let modal = $(modals.annotationModalHtml("rule", name, annotation)).modal(); let okBtn = document.querySelector('#ruleAnnotationModal .ok-model-btn'); let input = document.querySelector('#ruleAnnotationModal #ruleAnnotationInput'); @@ -84,26 +75,29 @@ module.exports = View.extend({ }); }, getOptions: function () { - var species = this.model.collection.parent.species; - var parameters = this.model.collection.parent.parameters; - var specs = species.map(function (specie) { + let species = this.model.collection.parent.species; + let parameters = this.model.collection.parent.parameters; + let specs = species.map(function (specie) { return [specie.compID, specie.name]; }); - var params = parameters.map(function (parameter) { + let params = parameters.map(function (parameter) { return [parameter.compID, parameter.name]; }); - let options = [{groupName: "Variables", options: specs}, - {groupName: "Parameters", options: params}]; + let options = [{groupName: Boolean(specs) ? "Variables" : "Variables (empty)", options: specs}, + {groupName: Boolean(params) ? "Parameters" : "Parameters (empty)", options: params}]; return options; }, + removeRule: function () { + this.model.collection.removeRule(this.model); + }, selectRuleType: function (e) { this.model.type = e.target.value; }, selectRuleVariable: function (e) { - var species = this.model.collection.parent.species; - var parameters = this.model.collection.parent.parameters; - var compID = Number(e.target.value); - var ruleVar = species.filter(function (specie) { + let species = this.model.collection.parent.species; + let parameters = this.model.collection.parent.parameters; + let compID = Number(e.target.value); + let ruleVar = species.filter(function (specie) { if(specie.compID === compID) { return specie; } @@ -117,9 +111,8 @@ module.exports = View.extend({ } this.model.variable = ruleVar[0]; }, - removeRule: function () { - this.model.collection.removeRule(this.model); - }, + update: function (e) {}, + updateValid: function () {}, updateViewer: function () { this.parent.renderViewRules(); }, @@ -131,11 +124,10 @@ module.exports = View.extend({ parent: this, required: true, name: 'rule-name', - label: '', tests: tests.nameTests, modelKey: 'name', valueType: 'string', - value: this.model.name, + value: this.model.name }); } }, @@ -148,7 +140,7 @@ module.exports = View.extend({ required: true, idAttributes: 'cid', options: options, - value: this.model.type, + value: this.model.type }); } }, @@ -161,7 +153,7 @@ module.exports = View.extend({ required: true, idAttributes: 'cid', groupOptions: options, - value: this.model.variable.compID, + value: this.model.variable.compID }); } }, diff --git a/client/views/rules-view.js b/client/views/rules-view.js index 43d8520c04..b3f68b6519 100644 --- a/client/views/rules-view.js +++ b/client/views/rules-view.js @@ -16,29 +16,29 @@ 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 let app = require('../app'); -var Tooltips = require('../tooltips'); +let Tooltips = require('../tooltips'); //views -var View = require('ampersand-view'); -var RuleView = require('./rule-view'); +let View = require('ampersand-view'); +let RuleView = require('./rule-view'); //templates -var template = require('../templates/includes/rulesView.pug'); +let template = require('../templates/includes/rulesView.pug'); module.exports = View.extend({ template: template, events: { 'click [data-hook=rate-rule]' : 'addRule', 'click [data-hook=assignment-rule]' : 'addRule', - 'click [data-hook=collapse]' : 'changeCollapseButtonText', + 'click [data-hook=collapse]' : 'changeCollapseButtonText' }, initialize: function (attrs, options) { View.prototype.initialize.apply(this, arguments); this.readOnly = attrs.readOnly ? attrs.readOnly : false; this.collection.parent.species.on('add remove', this.toggleAddRuleButton, this); this.collection.parent.parameters.on('add remove', this.toggleAddRuleButton, this); - this.tooltips = Tooltips.rulesEditor + this.tooltips = Tooltips.rulesEditor; }, render: function () { View.prototype.render.apply(this, arguments); @@ -57,9 +57,13 @@ module.exports = View.extend({ } this.renderViewRules(); }, - update: function () { + addRule: function (e) { + let type = e.target.dataset.name; + this.collection.addRule(type); + app.tooltipSetup(); }, - updateValid: function () { + changeCollapseButtonText: function (e) { + app.changeCollapseButtonText(this, e); }, renderEditRules: function () { if(this.rulesView) { @@ -70,12 +74,7 @@ module.exports = View.extend({ RuleView, this.queryByHook('edit-rule-list-container') ); - $(function () { - $('[data-toggle="tooltip"]').tooltip(); - $('[data-toggle="tooltip"]').click(function () { - $('[data-toggle="tooltip"]').tooltip("hide"); - }); - }); + app.tooltipSetup(); }, renderViewRules: function () { if(this.viewRulesView) { @@ -94,32 +93,15 @@ module.exports = View.extend({ this.queryByHook('view-rules-list-container'), options ); - $(function () { - $('[data-toggle="tooltip"]').tooltip(); - $('[data-toggle="tooltip"]').click(function () { - $('[data-toggle="tooltip"]').tooltip("hide"); - }); - }); + app.tooltipSetup(); }, toggleAddRuleButton: function () { this.renderEditRules(); - var numSpecies = this.collection.parent.species.length; - var numParameters = this.collection.parent.parameters.length; - var disabled = numSpecies <= 0 && numParameters <= 0 + let numSpecies = this.collection.parent.species.length; + let numParameters = this.collection.parent.parameters.length; + let disabled = numSpecies <= 0 && numParameters <= 0; $(this.queryByHook('add-rule')).prop('disabled', disabled); }, - addRule: function (e) { - var type = e.target.dataset.name - this.collection.addRule(type); - $(function () { - $('[data-toggle="tooltip"]').tooltip(); - $('[data-toggle="tooltip"]').click(function () { - $('[data-toggle="tooltip"]').tooltip("hide"); - - }); - }); - }, - changeCollapseButtonText: function (e) { - app.changeCollapseButtonText(this, e); - }, + update: function () {}, + updateValid: function () {} }); \ No newline at end of file From 6f687534c29b872f7401a0f4934fc6dd40c4a0cc Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Thu, 15 Jul 2021 16:54:07 -0400 Subject: [PATCH 165/192] Cleaned up the boundary conditions view files. --- client/views/boundary-condition-view.js | 12 ++---- client/views/boundary-conditions-view.js | 54 +++++++++++------------- 2 files changed, 29 insertions(+), 37 deletions(-) diff --git a/client/views/boundary-condition-view.js b/client/views/boundary-condition-view.js index a91cf1b9fb..43d5f3332d 100644 --- a/client/views/boundary-condition-view.js +++ b/client/views/boundary-condition-view.js @@ -18,6 +18,7 @@ along with this program. If not, see . let $ = require('jquery'); //support files +let app = require('../app'); let modals = require('../modals'); //views let View = require('ampersand-view'); @@ -33,19 +34,14 @@ module.exports = View.extend({ }, initialize: function (attrs, options) { View.prototype.initialize.apply(this, arguments); - this.viewMode = attrs.viewMode ? attrs.viewMode : false + this.viewMode = attrs.viewMode ? attrs.viewMode : false; }, render: function (attrs, options) { this.template = this.viewMode ? viewTemplate : editTemplate; View.prototype.render.apply(this, arguments); - $(document).on('shown.bs.modal', function (e) { - $('[autofocus]', e.target).focus(); - }); - $(document).on('hide.bs.modal', '.modal', function (e) { - e.target.remove() - }); + app.documentSetup(); if(!this.model.annotation){ - $(this.queryByHook('edit-annotation-btn')).text('Add') + $(this.queryByHook('edit-annotation-btn')).text('Add'); } }, editAnnotation: function () { diff --git a/client/views/boundary-conditions-view.js b/client/views/boundary-conditions-view.js index 3d4ef14711..5fc85bbc1e 100644 --- a/client/views/boundary-conditions-view.js +++ b/client/views/boundary-conditions-view.js @@ -78,13 +78,13 @@ module.exports = View.extend({ app.changeCollapseButtonText(this, e); }, handleAddBCClick: function (e) { - let endpoint = path.join(app.getApiPath(), "model/new-bc") + let endpoint = path.join(app.getApiPath(), "model/new-bc"); let self = this; if(this.newBC.property === "v") { - this.newBC.value = this.newBCVector + this.newBC.value = this.newBCVector; } let data = {model_path: this.collection.parent.directory, - kwargs: this.newBC} + kwargs: this.newBC}; app.postXHR(endpoint, data, { success: function (err, response, body) { self.collection.addNewBoundaryCondition(self.newBCName, body.expression); @@ -112,7 +112,7 @@ module.exports = View.extend({ $(this.queryByHook("new-bc-deterministic")).prop("disabled", true); }else{ let species = this.collection.parent.species.filter(function (specie) { - return specie.compID === Number(target) + return specie.compID === Number(target); })[0].name; this.newBC.property = null; this.newBC.species = species; @@ -129,13 +129,13 @@ module.exports = View.extend({ this.newBC[key] = this.validateNewBCCondition(key, value); }else if(key === "value") { if(e.delegateTarget.dataset.hook.endsWith("x")) { - this.newBCVector[0] = value === "" ? 0 : value + this.newBCVector[0] = value === "" ? 0 : value; }else if(e.delegateTarget.dataset.hook.endsWith("y")) { - this.newBCVector[1] = value === "" ? 0 : value + this.newBCVector[1] = value === "" ? 0 : value; }else if(e.delegateTarget.dataset.hook.endsWith("z")) { - this.newBCVector[2] = value === "" ? 0 : value + this.newBCVector[2] = value === "" ? 0 : value; }else{ - this.newBC[key] = value === "" ? null : value + this.newBC[key] = value === "" ? null : value; } } } @@ -150,12 +150,7 @@ module.exports = View.extend({ BoundaryConditionView, this.queryByHook("edit-boundary-conditions-list") ); - $(document).ready(function () { - $('[data-toggle="tooltip"]').tooltip(); - $('[data-toggle="tooltip"]').click(function () { - $('[data-toggle="tooltip"]').tooltip("hide"); - }); - }); + app.tooltipSetup(); }, renderViewBoundaryConditionView: function () { if(this.viewBoundaryConditionView) { @@ -174,6 +169,7 @@ module.exports = View.extend({ this.queryByHook("view-boundary-conditions-list"), options ); + app.tooltipSetup(); }, resetNewBCViews: function () { $(this.queryByHook("new-bc-deterministic")).prop("checked", this.newBC.deterministic); @@ -194,19 +190,19 @@ module.exports = View.extend({ this.newBCName = ""; this.newBC = {"species": null, "property": "v", "value": null, "deterministic": true, "type_id": null, "xmin": null, "ymin": null, "zmin": null, "xmax": null, "ymax": null, "zmax": null}; - this.newBCVector = [0, 0, 0] + this.newBCVector = [0, 0, 0]; this.setConditions = []; }, toggleAddNewBCButton: function () { - let invalidName = this.newBCName === "" - let invalidValue = this.newBC.property === "v" ? this.newBCVector === [0, 0, 0] : this.newBC.value === null + let invalidName = this.newBCName === ""; + let invalidValue = this.newBC.property === "v" ? this.newBCVector === [0, 0, 0] : this.newBC.value === null; let disabled = invalidName || invalidValue || !this.setConditions.length; $(this.queryByHook("add-new-bc")).prop("disabled", disabled); }, update: function (e) {}, validateNewBCCondition: function(key, value) { if((value === 0 && key === "type_id") || value === "") { - value = null + value = null; if(this.setConditions.includes(key)){ let index = this.setConditions.indexOf(key); this.setConditions.splice(index, 1); @@ -233,11 +229,11 @@ module.exports = View.extend({ hook: "new-bc-target", prepareView: function (el) { let species = this.collection.parent.species.map(function (specie) { - return [specie.compID, specie.name] + return [specie.compID, specie.name]; }); - let properties = [["v", "Velocity"], ["nu", "Viscosity"], ["rho", "Density"]] + let properties = [["v", "Velocity"], ["nu", "Viscosity"], ["rho", "Density"]]; let options = [{groupName: "Properties", options: properties}, - {groupName: "Variables", options: species}] + {groupName: Boolean(species) ? "Variables" : "Variables (empty)", options: species}]; return new SelectView({ parent: this, required: false, @@ -256,7 +252,7 @@ module.exports = View.extend({ required: false, name: 'value', tests: tests.valueTests, - valueType: 'number', + valueType: 'number' }); } }, @@ -308,7 +304,7 @@ module.exports = View.extend({ name: 'xmin', tests: tests.valueTests, valueType: 'number', - value: this.newBC.xmin, + value: this.newBC.xmin }); } }, @@ -321,7 +317,7 @@ module.exports = View.extend({ name: 'ymin', tests: tests.valueTests, valueType: 'number', - value: this.newBC.ymin, + value: this.newBC.ymin }); } }, @@ -334,7 +330,7 @@ module.exports = View.extend({ name: 'zmin', tests: tests.valueTests, valueType: 'number', - value: this.newBC.zmin, + value: this.newBC.zmin }); } }, @@ -347,7 +343,7 @@ module.exports = View.extend({ name: 'xmax', tests: tests.valueTests, valueType: 'number', - value: this.newBC.xmax, + value: this.newBC.xmax }); } }, @@ -360,7 +356,7 @@ module.exports = View.extend({ name: 'ymax', tests: tests.valueTests, valueType: 'number', - value: this.newBC.ymax, + value: this.newBC.ymax }); } }, @@ -373,7 +369,7 @@ module.exports = View.extend({ name: 'zmax', tests: tests.valueTests, valueType: 'number', - value: this.newBC.zmax, + value: this.newBC.zmax }); } }, @@ -386,7 +382,7 @@ module.exports = View.extend({ name: 'type', tests: tests.valueTests, valueType: 'number', - value: this.newBC.type_id, + value: this.newBC.type_id }); } } From 177bcd392a348ea1191280ce314d70dd46801fe3 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 16 Jul 2021 10:23:37 -0400 Subject: [PATCH 166/192] Renamed the sbml component and function definition view and template file with names that better fit their new purpose. --- .../{sbmlComponentEditor.pug => sbmlComponentsView.pug} | 0 ...dit-function-definition.js => function-definition-view.js} | 0 .../{sbml-component-editor.js => sbml-components-view.js} | 4 ++-- 3 files changed, 2 insertions(+), 2 deletions(-) rename client/templates/includes/{sbmlComponentEditor.pug => sbmlComponentsView.pug} (100%) rename client/views/{edit-function-definition.js => function-definition-view.js} (100%) rename client/views/{sbml-component-editor.js => sbml-components-view.js} (96%) diff --git a/client/templates/includes/sbmlComponentEditor.pug b/client/templates/includes/sbmlComponentsView.pug similarity index 100% rename from client/templates/includes/sbmlComponentEditor.pug rename to client/templates/includes/sbmlComponentsView.pug diff --git a/client/views/edit-function-definition.js b/client/views/function-definition-view.js similarity index 100% rename from client/views/edit-function-definition.js rename to client/views/function-definition-view.js diff --git a/client/views/sbml-component-editor.js b/client/views/sbml-components-view.js similarity index 96% rename from client/views/sbml-component-editor.js rename to client/views/sbml-components-view.js index 678984682d..bced88ea6e 100644 --- a/client/views/sbml-component-editor.js +++ b/client/views/sbml-components-view.js @@ -22,9 +22,9 @@ let app = require('../app'); var Tooltips = require('../tooltips'); //views var View = require('ampersand-view'); -var EditFunctionDefinition = require('./edit-function-definition'); +var EditFunctionDefinition = require('./function-definition-view'); //templates -var template = require('../templates/includes/sbmlComponentEditor.pug'); +var template = require('../templates/includes/sbmlComponentsView.pug'); module.exports = View.extend({ template: template, From 96005c3665642a53f90c45ffb55ccc5325e28c40 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 16 Jul 2021 14:22:58 -0400 Subject: [PATCH 167/192] Moved the sbml components render function and container to the model view. Fixed the duplicates reactions, events, rules render issue. Fixed the species and parameter in-use issue. . --- client/models/model.js | 6 - client/pages/model-editor.js | 7 - client/templates/includes/modelView.pug | 2 + client/templates/pages/modelEditor.pug | 2 - client/views/model-view.js | 185 ++++++++++++++---------- client/views/reactions-view.js | 2 +- 6 files changed, 114 insertions(+), 90 deletions(-) diff --git a/client/models/model.js b/client/models/model.js index a31cf685db..9799e6e4f2 100644 --- a/client/models/model.js +++ b/client/models/model.js @@ -84,12 +84,6 @@ module.exports = Model.extend({ let queryStr = "?path=" + this.directory; return path.join(app.getBasePath(), "stochss/models/edit") + queryStr; } - }, - not_spatial: { - deps: ["collection"], - fn: function () { - return !this.is_spatial - } } }, initialize: function (attrs, options){ diff --git a/client/pages/model-editor.js b/client/pages/model-editor.js index 191a557aaf..f032a26a89 100644 --- a/client/pages/model-editor.js +++ b/client/pages/model-editor.js @@ -29,7 +29,6 @@ var PageView = require('../pages/base'); let ModelView = require('../views/model-view'); var InputView = require('../views/input'); var ParticleViewer = require('../views/view-particle'); -var SBMLComponentView = require('../views/sbml-component-editor'); var TimespanSettingsView = require('../views/timespan-settings'); var ModelStateButtonsView = require('../views/model-state-buttons'); var QuickviewDomainTypes = require('../views/quickview-domain-types'); @@ -161,12 +160,6 @@ let ModelEditor = PageView.extend({ $(this.queryByHook("toggle-preview-domain")).css("display", "inline-block"); this.openDomainPlot(); }else { - if(this.model.functionDefinitions.length) { - var sbmlComponentView = new SBMLComponentView({ - functionDefinitions: this.model.functionDefinitions - }); - app.registerRenderSubview(this, sbmlComponentView, 'sbml-component-container'); - } this.renderSystemVolumeView(); } this.model.autoSave(); diff --git a/client/templates/includes/modelView.pug b/client/templates/includes/modelView.pug index 2f91c3c5d6..54e5932095 100644 --- a/client/templates/includes/modelView.pug +++ b/client/templates/includes/modelView.pug @@ -76,3 +76,5 @@ div#model-view div(data-hook="rules-view-container") div(data-hook="boundary-conditions-view-container") + + div(data-hook="sbml-components-view-container") diff --git a/client/templates/pages/modelEditor.pug b/client/templates/pages/modelEditor.pug index e31f68253b..a73704d4f0 100644 --- a/client/templates/pages/modelEditor.pug +++ b/client/templates/pages/modelEditor.pug @@ -28,8 +28,6 @@ section.page div(data-hook="model-view-container") - div(data-hook="sbml-component-container") - div.card.collapse.show(data-hook="system-volume-container") div.card-header.pb-0 diff --git a/client/views/model-view.js b/client/views/model-view.js index 424b72d01e..b6177eb2d6 100644 --- a/client/views/model-view.js +++ b/client/views/model-view.js @@ -32,6 +32,7 @@ let SpeciesView = require('../views/species-view'); let DomainViewer = require('../views/domain-viewer'); let ReactionsView = require('../views/reactions-view'); let ParametersView = require('../views/parameters-view'); +let SBMLComponentsView = require('../views/sbml-components-view'); let InitialConditionsView = require('../views/initial-conditions-view'); let BoundaryConditionsView = require('../views/boundary-conditions-view'); //templates @@ -53,6 +54,17 @@ module.exports = View.extend({ }, render: function(attrs, options) { View.prototype.render.apply(this, arguments); + this.updateSpeciesInUse(); + this.updateParametersInUse(); + this.renderDomainViewer(); + this.renderSpeciesView(); + this.renderInitialConditionsView(); + this.renderParametersView(); + this.renderReactionsView(); + this.renderEventsView(); + this.renderRulesView(); + this.renderBoundaryConditionsView(); + this.renderSbmlComponentView(); if(this.readOnly) { this.setReadOnlyMode("model-mode"); }else { @@ -78,9 +90,6 @@ module.exports = View.extend({ this.updateParametersInUse(); }, this); } - if(this.model.is_spatial) { - this.renderDomainViewer(); - } }, changeCollapseButtonText: function (e) { app.changeCollapseButtonText(this, e); @@ -104,7 +113,20 @@ module.exports = View.extend({ self.setInitialDefaultMode(modal, "dynamic"); }); }, + renderBoundaryConditionsView: function () { + if(!this.model.is_spatial) { return } + if(this.boundaryConditionsView) { + this.boundaryConditionsView.remove(); + } + this.boundaryConditionsView = new BoundaryConditionsView({ + collection: this.model.boundaryConditions, + readOnly: this.readOnly + }); + let hook = "boundary-conditions-view-container"; + app.registerRenderSubview(this, this.boundaryConditionsView, hook); + }, renderDomainViewer: function(domainPath=null) { + if(!this.model.is_spatial) { return } if(this.domainViewer) { this.domainViewer.remove(); } @@ -134,6 +156,89 @@ module.exports = View.extend({ app.registerRenderSubview(this, this.domainViewer, 'domain-viewer-container'); } }, + renderEventsView: function () { + if(this.model.is_spatial) { return } + if(this.eventsView) { + this.eventsView.remove(); + } + this.eventsView = new EventsView({ + collection: this.model.eventsCollection, + readOnly: this.readOnly + }); + let hook = "events-view-container"; + app.registerRenderSubview(this, this.eventsView, hook); + }, + renderInitialConditionsView: function () { + if(!this.model.is_spatial) { return } + if(this.initialConditionsView) { + this.initialConditionsView.remove(); + } + this.initialConditionsView = new InitialConditionsView({ + collection: this.model.initialConditions, + readOnly: this.readOnly + }); + let hook = "initial-conditions-view-container"; + app.registerRenderSubview(this, this.initialConditionsView, hook); + }, + renderParametersView: function () { + if(this.parametersView) { + this.parametersView.remove(); + } + this.parametersView = new ParametersView({ + collection: this.model.parameters, + readOnly: this.readOnly + }); + let hook = "parameters-view-container"; + app.registerRenderSubview(this, this.parametersView, hook); + }, + renderReactionsView: function () { + if(this.reactionsView) { + this.reactionsView.remove(); + } + this.reactionsView = new ReactionsView({ + collection: this.model.reactions, + readOnly: this.readOnly + }); + let hook = "reactions-view-container"; + app.registerRenderSubview(this, this.reactionsView, hook); + }, + renderRulesView: function () { + if(this.model.is_spatial) { return } + if(this.rulesView) { + this.rulesView.remove(); + } + this.rulesView = new RulesView({ + collection: this.model.rules, + readOnly: this.readOnly + }); + let hook = "rules-view-container"; + app.registerRenderSubview(this, this.rulesView, hook); + }, + renderSbmlComponentView: function () { + if(this.model.is_spatial || !this.model.functionDefinitions.length) { return } + if(this.sbmlComponentView) { + this.sbmlComponentView.remove(); + } + this.sbmlComponentView = new SBMLComponentsView({ + functionDefinitions: this.model.functionDefinitions, + readOnly: this.readOnly + }); + let hook = "sbml-components-view-container"; + app.registerRenderSubview(this, this.sbmlComponentView, hook); + }, + renderSpeciesView: function () { + if(this.speciesView) { + this.speciesView.remove(); + } + this.speciesView = new SpeciesView({ + collection: this.model.species, + spatial: this.model.is_spatial, + defaultMode: this.model.defaultMode, + readOnly: this.readOnly + }); + let hook = "species-view-container"; + app.registerRenderSubview(this, this.speciesView, hook); + }, setAllSpeciesModes: function (prevMode) { let self = this; this.model.species.forEach(function (specie) { @@ -230,75 +335,7 @@ module.exports = View.extend({ updateInUseForOther(rule.variable); }); }, - subviews: { - speciesView: { - hook: "species-view-container", - prepareView: function (el) { - return new SpeciesView({ - collection: this.model.species, - spatial: this.model.is_spatial, - defaultMode: this.model.defaultMode, - readOnly: this.readOnly - }); - } - }, - initialConditionsView: { - waitFor: "model.is_spatial", - hook: "initial-conditions-view-container", - prepareView: function (el) { - return new InitialConditionsView({ - collection: this.model.initialConditions, - readOnly: this.readOnly - }); - } - }, - parametersView: { - hook: "parameters-view-container", - prepareView: function (el) { - return new ParametersView({ - collection: this.model.parameters, - readOnly: this.readOnly - }); - } - }, - reactionsView: { - hook: "reactions-view-container", - prepareView: function (el) { - return new ReactionsView({ - collection: this.model.reactions, - readOnly: this.readOnly - }); - } - }, - eventsView: { - waitFor: "model.not_spatial", - hook: "events-view-container", - prepareView: function (el) { - return new EventsView({ - collection: this.model.eventsCollection, - readOnly: this.readOnly - }); - } - }, - rulesView: { - waitFor: "model.not_spatial", - hook: "rules-view-container", - prepareView: function (el) { - return new RulesView({ - collection: this.model.rules, - readOnly: this.readOnly - }); - } - }, - boundaryConditionsView: { - waitFor: "model.is_spatial", - hook: "boundary-conditions-view-container", - prepareView: function (el) { - return new BoundaryConditionsView({ - collection: this.model.boundaryConditions, - readOnly: this.readOnly - }); - } - } - } + // subviews: { + + // } }); \ No newline at end of file diff --git a/client/views/reactions-view.js b/client/views/reactions-view.js index d046bcb016..4ecb155570 100644 --- a/client/views/reactions-view.js +++ b/client/views/reactions-view.js @@ -90,7 +90,7 @@ module.exports = View.extend({ if (this.collection.length) { this.setSelectedReaction(this.collection.at(0)); this.collection.trigger("select", this.selectedReaction); - this.collection.trigger("change"); + // this.collection.trigger("change"); } this.toggleAddReactionButton(); if(this.collection.parent.parameters.length > 0){ From 865cff0d5606483e23e1c6b2bcf86e1533ee2a81 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 16 Jul 2021 15:02:12 -0400 Subject: [PATCH 168/192] Moved the system volume function and container to the model view. --- client/pages/model-editor.js | 42 ---------------------- client/templates/includes/modelView.pug | 39 ++++++++++++++++++++ client/templates/pages/modelEditor.pug | 39 -------------------- client/views/model-view.js | 47 ++++++++++++++++++++++--- 4 files changed, 81 insertions(+), 86 deletions(-) diff --git a/client/pages/model-editor.js b/client/pages/model-editor.js index f032a26a89..604b7988c4 100644 --- a/client/pages/model-editor.js +++ b/client/pages/model-editor.js @@ -22,12 +22,10 @@ let path = require('path'); //support files var app = require('../app'); var modals = require('../modals'); -var tests = require('../views/tests'); let Tooltips = require("../tooltips"); //views var PageView = require('../pages/base'); let ModelView = require('../views/model-view'); -var InputView = require('../views/input'); var ParticleViewer = require('../views/view-particle'); var TimespanSettingsView = require('../views/timespan-settings'); var ModelStateButtonsView = require('../views/model-state-buttons'); @@ -46,7 +44,6 @@ let ModelEditor = PageView.extend({ 'click [data-hook=edit-model-help]' : function () { let modal = $(modals.operationInfoModalHtml('model-editor')).modal(); }, - 'change [data-hook=edit-volume]' : 'updateVolumeViewer', 'click [data-hook=project-breadcrumb-link]' : 'handleProjectBreadcrumbClick', 'click [data-hook=toggle-preview-plot]' : 'togglePreviewPlot', 'click [data-hook=toggle-preview-domain]' : 'toggleDomainPlot', @@ -93,10 +90,6 @@ let ModelEditor = PageView.extend({ } }); }, - update: function () { - }, - updateValid: function () { - }, getFileName: function (file) { if(file.endsWith('/')) { file.slice(0, -1) @@ -155,12 +148,9 @@ let ModelEditor = PageView.extend({ app.registerRenderSubview(this, this.modelSettings, 'model-settings-container'); app.registerRenderSubview(this, this.modelStateButtons, 'model-state-buttons-container'); if(this.model.is_spatial) { - $(this.queryByHook("system-volume-container")).css("display", "none"); $(this.queryByHook("spatial-beta-message")).css("display", "block"); $(this.queryByHook("toggle-preview-domain")).css("display", "inline-block"); this.openDomainPlot(); - }else { - this.renderSystemVolumeView(); } this.model.autoSave(); $(function () { @@ -173,26 +163,6 @@ let ModelEditor = PageView.extend({ e.target.remove() }); }, - renderSystemVolumeView: function () { - if(this.systemVolumeView) { - this.systemVolumeView.remove() - } - this.systemVolumeView = new InputView ({ - parent: this, - required: true, - name: 'system-volume', - label: 'Volume: ', - tests: tests.valueTests, - modelKey: 'volume', - valueType: 'number', - value: this.model.volume, - }); - app.registerRenderSubview(this, this.systemVolumeView, 'edit-volume') - if(this.model.defaultMode === "continuous") { - $(this.queryByHook("system-volume-container")).collapse("hide") - } - $(this.queryByHook("view-volume")).html("Volume: " + this.model.volume) - }, changeCollapseButtonText: function (e) { app.changeCollapseButtonText(this, e); }, @@ -245,18 +215,6 @@ let ModelEditor = PageView.extend({ clickDownloadPNGButton: function (e) { let pngButton = $('div[data-hook=preview-plot-container] a[data-title*="Download plot as a png"]')[0] pngButton.click() - }, - toggleVolumeContainer: function () { - if(!this.model.is_spatial) { - if(this.model.defaultMode === "continuous") { - $(this.queryByHook("system-volume-container")).collapse("hide"); - }else{ - $(this.queryByHook("system-volume-container")).collapse("show"); - } - } - }, - updateVolumeViewer: function (e) { - $(this.queryByHook("view-volume")).html("Volume: " + this.model.volume) } }); diff --git a/client/templates/includes/modelView.pug b/client/templates/includes/modelView.pug index 54e5932095..405185cd64 100644 --- a/client/templates/includes/modelView.pug +++ b/client/templates/includes/modelView.pug @@ -78,3 +78,42 @@ div#model-view div(data-hook="boundary-conditions-view-container") div(data-hook="sbml-components-view-container") + + div.card.collapse.show(data-hook="system-volume-container") + + div.card-header.pb-0 + + h3.inline.mr-3 System Volume + + div.inline.mr-3 + + ul.nav.nav-tabs.card-header-tabs(id="volume-tabs") + + li.nav-item + + a.nav-link.tab.active(data-hook="system-volume-edit-tab" data-toggle="tab" href="#edit-system-volume") Edit + + li.nav-item + + a.nav-link.tab(data-hook="system-volume-view-tab" data-toggle="tab" href="#view-system-volume") View + + button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-system-volume", data-hook="collapse-system-volume") + + + div.card-body + + p.mb-0 + | System volume affects custom propensities or stochastic reactions with two reactants. The volume sets the implicit parameter 'vol' which can be used in custom propensity functions. A single well-mixed volume is assumed. Compartments are not currently supported. In most cases this should not be changed. please review your model requirements carefully before changing this property. + + div.collapse.tab-content(id="collapse-system-volume" data-hook="system-volume-section") + + div.tab-pane.active(id="edit-system-volume" data-hook="edit-system-volume") + + hr + + div(data-hook="edit-volume") + + div.tab-pane(id="view-system-volume" data-hook="view-system-volume") + + hr + + div(data-hook="view-volume") diff --git a/client/templates/pages/modelEditor.pug b/client/templates/pages/modelEditor.pug index a73704d4f0..2d30773d17 100644 --- a/client/templates/pages/modelEditor.pug +++ b/client/templates/pages/modelEditor.pug @@ -28,45 +28,6 @@ section.page div(data-hook="model-view-container") - div.card.collapse.show(data-hook="system-volume-container") - - div.card-header.pb-0 - - h3.inline.mr-3 System Volume - - div.inline.mr-3 - - ul.nav.nav-tabs.card-header-tabs(id="volume-tabs") - - li.nav-item - - a.nav-link.tab.active(data-hook="volume-edit-tab" data-toggle="tab" href="#edit-system-volume") Edit - - li.nav-item - - a.nav-link.tab(data-hook="volume-view-tab" data-toggle="tab" href="#view-system-volume") View - - button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-system-volume", data-hook="collapse-system-volume") + - - div.card-body - - p.mb-0 - | System volume affects custom propensities or stochastic reactions with two reactants. The volume sets the implicit parameter 'vol' which can be used in custom propensity functions. A single well-mixed volume is assumed. Compartments are not currently supported. In most cases this should not be changed. please review your model requirements carefully before changing this property. - - div.collapse.tab-content(id="collapse-system-volume" data-hook="system-volume-section") - - div.tab-pane.active(id="edit-system-volume" data-hook="edit-system-volume") - - hr - - div(data-hook="edit-volume") - - div.tab-pane(id="view-system-volume" data-hook="view-system-volume") - - hr - - div(data-hook="view-volume") - div(data-hook="model-settings-container") div(style="height:425px;") diff --git a/client/views/model-view.js b/client/views/model-view.js index b6177eb2d6..88c5a4e947 100644 --- a/client/views/model-view.js +++ b/client/views/model-view.js @@ -22,10 +22,12 @@ let _ = require('underscore'); //support files let app = require('../app'); let modals = require('../modals'); +let tests = require('../views/tests'); //models let Domain = require('../models/domain'); //views let View = require('ampersand-view'); +let InputView = require('../views/input'); let RulesView = require('../views/rules-view'); let EventsView = require('../views/events-view'); let SpeciesView = require('../views/species-view'); @@ -44,6 +46,7 @@ module.exports = View.extend({ 'change [data-hook=all-continuous]' : 'setDefaultMode', 'change [data-hook=all-discrete]' : 'setDefaultMode', 'change [data-hook=advanced]' : 'setDefaultMode', + 'change [data-hook=edit-volume]' : 'updateVolumeViewer', 'click [data-hook=collapse-mv-advanced-section]' : 'changeCollapseButtonText' }, initialize: function(attrs, options) { @@ -65,8 +68,10 @@ module.exports = View.extend({ this.renderRulesView(); this.renderBoundaryConditionsView(); this.renderSbmlComponentView(); + this.renderSystemVolumeView(); if(this.readOnly) { this.setReadOnlyMode("model-mode"); + this.setReadOnlyMode("system-volume") }else { if(this.model.defaultMode === "" && !this.model.is_spatial){ this.getInitialDefaultMode(); @@ -75,6 +80,7 @@ module.exports = View.extend({ $(this.queryByHook(dataHooks[this.model.defaultMode])).prop('checked', true); if(this.model.is_spatial) { $(this.queryByHook("advanced-model-mode")).css("display", "none"); + $(this.queryByHook("system-volume-container")).css("display", "none"); } } this.model.reactions.on("change", function (reactions) { @@ -239,6 +245,26 @@ module.exports = View.extend({ let hook = "species-view-container"; app.registerRenderSubview(this, this.speciesView, hook); }, + renderSystemVolumeView: function () { + if(this.systemVolumeView) { + this.systemVolumeView.remove(); + } + this.systemVolumeView = new InputView ({ + parent: this, + required: true, + name: 'system-volume', + label: 'Volume: ', + tests: tests.valueTests, + modelKey: 'volume', + valueType: 'number', + value: this.model.volume, + }); + app.registerRenderSubview(this, this.systemVolumeView, 'edit-volume'); + if(this.model.defaultMode === "continuous") { + $(this.queryByHook("system-volume-container")).collapse("hide") + } + $(this.queryByHook("view-volume")).html("Volume: " + this.model.volume) + }, setAllSpeciesModes: function (prevMode) { let self = this; this.model.species.forEach(function (specie) { @@ -257,7 +283,7 @@ module.exports = View.extend({ this.model.defaultMode = e.target.dataset.name; this.speciesView.defaultMode = e.target.dataset.name; this.setAllSpeciesModes(prevMode); - this.parent.toggleVolumeContainer(); + this.toggleVolumeContainer(); }, setInitialDefaultMode: function (modal, mode) { var dataHooks = {'continuous':'all-continuous', 'discrete':'all-discrete', 'dynamic':'advanced'}; @@ -266,7 +292,7 @@ module.exports = View.extend({ this.model.defaultMode = mode; this.speciesView.defaultMode = mode; this.setAllSpeciesModes(); - this.parent.toggleVolumeContainer(); + this.toggleVolumeContainer(); }, setReadOnlyMode: function (component) { $(this.queryByHook(component + '-edit-tab')).addClass("disabled"); @@ -278,6 +304,16 @@ module.exports = View.extend({ $(this.queryByHook('edit-' + component)).removeClass('active'); $(this.queryByHook('view-' + component)).addClass('active'); }, + toggleVolumeContainer: function () { + if(!this.model.is_spatial) { + if(this.model.defaultMode === "continuous") { + $(this.queryByHook("system-volume-container")).collapse("hide"); + }else{ + $(this.queryByHook("system-volume-container")).collapse("show"); + } + } + }, + update: function () {}, updateParametersInUse: function () { var parameters = this.model.parameters; var reactions = this.model.reactions; @@ -335,7 +371,8 @@ module.exports = View.extend({ updateInUseForOther(rule.variable); }); }, - // subviews: { - - // } + updateValid: function () {}, + updateVolumeViewer: function (e) { + $(this.queryByHook("view-volume")).html("Volume: " + this.model.volume); + } }); \ No newline at end of file From e0a29913ed01f3ae67f9d4ff6db85b9ba690f06f Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 16 Jul 2021 15:17:10 -0400 Subject: [PATCH 169/192] Cleaned up the sbml componenet and function definition view files. --- client/views/function-definition-view.js | 17 ++++++------- client/views/sbml-components-view.js | 32 ++++++++---------------- 2 files changed, 19 insertions(+), 30 deletions(-) diff --git a/client/views/function-definition-view.js b/client/views/function-definition-view.js index d582b9dba6..ed94e9aab0 100644 --- a/client/views/function-definition-view.js +++ b/client/views/function-definition-view.js @@ -16,19 +16,20 @@ 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 modals = require('../modals'); +let app = require('../app'); +let modals = require('../modals'); //views -var View = require('ampersand-view'); +let View = require('ampersand-view'); //templates -var editTemplate = require('../templates/includes/editFunctionDefinition.pug'); +let editTemplate = require('../templates/includes/editFunctionDefinition.pug'); let viewTemplate = require('../templates/includes/viewFunctionDefinition.pug'); module.exports = View.extend({ events: { 'click [data-hook=remove]' : 'removeFunctionDefinition', - 'click [data-hook=edit-annotation-btn]' : 'editAnnotation', + 'click [data-hook=edit-annotation-btn]' : 'editAnnotation' }, initialize: function (attrs, options) { View.prototype.initialize.apply(this, arguments); @@ -37,9 +38,7 @@ module.exports = View.extend({ render: function () { this.template = this.viewMode ? viewTemplate : editTemplate; View.prototype.render.apply(this, arguments); - $(document).on('hide.bs.modal', '.modal', function (e) { - e.target.remove() - }); + app.documentSetup(); }, editAnnotation: function () { var self = this; @@ -65,5 +64,5 @@ module.exports = View.extend({ }, removeFunctionDefinition: function () { this.model.collection.remove(this.model); - }, + } }); \ No newline at end of file diff --git a/client/views/sbml-components-view.js b/client/views/sbml-components-view.js index bced88ea6e..61fd44d858 100644 --- a/client/views/sbml-components-view.js +++ b/client/views/sbml-components-view.js @@ -16,15 +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'); //support files let app = require('../app'); -var Tooltips = require('../tooltips'); +let Tooltips = require('../tooltips'); //views -var View = require('ampersand-view'); -var EditFunctionDefinition = require('./function-definition-view'); +let View = require('ampersand-view'); +let EditFunctionDefinition = require('./function-definition-view'); //templates -var template = require('../templates/includes/sbmlComponentsView.pug'); +let template = require('../templates/includes/sbmlComponentsView.pug'); module.exports = View.extend({ template: template, @@ -54,6 +54,9 @@ module.exports = View.extend({ } this.renderViewFunctionDefinitionView(); }, + changeCollapseButtonText: function (e) { + app.changeCollapseButtonText(this, e); + }, renderEditFunctionDefinitionView: function () { if(this.editFunctionDefinitionView){ this.editFunctionDefinitionView.remove(); @@ -63,12 +66,7 @@ module.exports = View.extend({ EditFunctionDefinition, this.queryByHook('edit-function-definition-list') ); - $(function () { - $('[data-toggle="tooltip"]').tooltip(); - $('[data-toggle="tooltip"]').click(function () { - $('[data-toggle="tooltip"]').tooltip("hide"); - }); - }); + app.tooltipSetup(); }, renderViewFunctionDefinitionView: function () { if(this.viewFunctionDefinitionView) { @@ -87,14 +85,6 @@ module.exports = View.extend({ this.queryByHook('view-function-definition-list'), options ); - $(function () { - $('[data-toggle="tooltip"]').tooltip(); - $('[data-toggle="tooltip"]').click(function () { - $('[data-toggle="tooltip"]').tooltip("hide"); - }); - }); - }, - changeCollapseButtonText: function (e) { - app.changeCollapseButtonText(this, e); - }, + app.tooltipSetup(); + } }); \ No newline at end of file From 712066748cb867dd189a7692ee201ab484e23494 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 16 Jul 2021 15:42:54 -0400 Subject: [PATCH 170/192] Moved all species view, template, and subview files to the new model view directory. --- client/{views => model-view}/model-view.js | 2 +- .../templates}/editSpatialSpecies.pug | 0 .../templates}/editSpecies.pug | 0 .../templates}/reactionTypeTemplate.pug | 0 .../templates}/spatialSpeciesView.pug | 0 .../templates}/speciesTypeTemplate.pug | 0 .../templates}/speciesView.pug | 0 .../templates}/viewSpatialSpecies.pug | 0 .../templates}/viewSpecies.pug | 0 client/{ => model-view}/views/component-types.js | 4 ++-- client/{ => model-view}/views/specie-view.js | 16 ++++++++-------- client/{ => model-view}/views/species-view.js | 8 ++++---- client/pages/model-editor.js | 2 +- 13 files changed, 16 insertions(+), 16 deletions(-) rename client/{views => model-view}/model-view.js (99%) rename client/{templates/includes => model-view/templates}/editSpatialSpecies.pug (100%) rename client/{templates/includes => model-view/templates}/editSpecies.pug (100%) rename client/{templates/includes => model-view/templates}/reactionTypeTemplate.pug (100%) rename client/{templates/includes => model-view/templates}/spatialSpeciesView.pug (100%) rename client/{templates/includes => model-view/templates}/speciesTypeTemplate.pug (100%) rename client/{templates/includes => model-view/templates}/speciesView.pug (100%) rename client/{templates/includes => model-view/templates}/viewSpatialSpecies.pug (100%) rename client/{templates/includes => model-view/templates}/viewSpecies.pug (100%) rename client/{ => model-view}/views/component-types.js (91%) rename client/{ => model-view}/views/specie-view.js (96%) rename client/{ => model-view}/views/species-view.js (96%) diff --git a/client/views/model-view.js b/client/model-view/model-view.js similarity index 99% rename from client/views/model-view.js rename to client/model-view/model-view.js index 88c5a4e947..0a5da88db3 100644 --- a/client/views/model-view.js +++ b/client/model-view/model-view.js @@ -30,7 +30,7 @@ let View = require('ampersand-view'); let InputView = require('../views/input'); let RulesView = require('../views/rules-view'); let EventsView = require('../views/events-view'); -let SpeciesView = require('../views/species-view'); +let SpeciesView = require('./views/species-view'); let DomainViewer = require('../views/domain-viewer'); let ReactionsView = require('../views/reactions-view'); let ParametersView = require('../views/parameters-view'); diff --git a/client/templates/includes/editSpatialSpecies.pug b/client/model-view/templates/editSpatialSpecies.pug similarity index 100% rename from client/templates/includes/editSpatialSpecies.pug rename to client/model-view/templates/editSpatialSpecies.pug diff --git a/client/templates/includes/editSpecies.pug b/client/model-view/templates/editSpecies.pug similarity index 100% rename from client/templates/includes/editSpecies.pug rename to client/model-view/templates/editSpecies.pug diff --git a/client/templates/includes/reactionTypeTemplate.pug b/client/model-view/templates/reactionTypeTemplate.pug similarity index 100% rename from client/templates/includes/reactionTypeTemplate.pug rename to client/model-view/templates/reactionTypeTemplate.pug diff --git a/client/templates/includes/spatialSpeciesView.pug b/client/model-view/templates/spatialSpeciesView.pug similarity index 100% rename from client/templates/includes/spatialSpeciesView.pug rename to client/model-view/templates/spatialSpeciesView.pug diff --git a/client/templates/includes/speciesTypeTemplate.pug b/client/model-view/templates/speciesTypeTemplate.pug similarity index 100% rename from client/templates/includes/speciesTypeTemplate.pug rename to client/model-view/templates/speciesTypeTemplate.pug diff --git a/client/templates/includes/speciesView.pug b/client/model-view/templates/speciesView.pug similarity index 100% rename from client/templates/includes/speciesView.pug rename to client/model-view/templates/speciesView.pug diff --git a/client/templates/includes/viewSpatialSpecies.pug b/client/model-view/templates/viewSpatialSpecies.pug similarity index 100% rename from client/templates/includes/viewSpatialSpecies.pug rename to client/model-view/templates/viewSpatialSpecies.pug diff --git a/client/templates/includes/viewSpecies.pug b/client/model-view/templates/viewSpecies.pug similarity index 100% rename from client/templates/includes/viewSpecies.pug rename to client/model-view/templates/viewSpecies.pug diff --git a/client/views/component-types.js b/client/model-view/views/component-types.js similarity index 91% rename from client/views/component-types.js rename to client/model-view/views/component-types.js index f96375fa28..f04a3d4247 100644 --- a/client/views/component-types.js +++ b/client/model-view/views/component-types.js @@ -20,8 +20,8 @@ let $ = require("jquery"); //views var View = require('ampersand-view'); //templates -var specTypeTemplate = require('../templates/includes/speciesTypeTemplate.pug'); -var reacTypeTemplate = require('../templates/includes/reactionTypeTemplate.pug'); +var specTypeTemplate = require('../templates/speciesTypeTemplate.pug'); +var reacTypeTemplate = require('../templates/reactionTypeTemplate.pug'); module.exports = View.extend({ events: { diff --git a/client/views/specie-view.js b/client/model-view/views/specie-view.js similarity index 96% rename from client/views/specie-view.js rename to client/model-view/views/specie-view.js index be1d092944..1540fccb08 100644 --- a/client/views/specie-view.js +++ b/client/model-view/views/specie-view.js @@ -19,19 +19,19 @@ along with this program. If not, see . let $ = require('jquery'); let _ = require('underscore'); //support files -let app = require('../app'); -let tests = require('./tests'); -let modals = require('../modals'); +let app = require('../../app'); +let tests = require('../../views/tests'); +let modals = require('../../modals'); //views -let InputView = require('./input'); +let InputView = require('../../views/input'); let View = require('ampersand-view'); let TypesView = require('./component-types'); let SelectView = require('ampersand-select-view'); //templates -let editTemplate = require('../templates/includes/editSpecies.pug'); -let editSpatialTemplate = require('../templates/includes/editSpatialSpecies.pug'); -let viewTemplate = require('../templates/includes/viewSpecies.pug'); -let viewSpatialTemplate = require('../templates/includes/viewSpatialSpecies.pug'); +let editTemplate = require('../templates/editSpecies.pug'); +let editSpatialTemplate = require('../templates/editSpatialSpecies.pug'); +let viewTemplate = require('../templates/viewSpecies.pug'); +let viewSpatialTemplate = require('../templates/viewSpatialSpecies.pug'); module.exports = View.extend({ bindings: { diff --git a/client/views/species-view.js b/client/model-view/views/species-view.js similarity index 96% rename from client/views/species-view.js rename to client/model-view/views/species-view.js index 05b659aea0..f9aca59ac9 100644 --- a/client/views/species-view.js +++ b/client/model-view/views/species-view.js @@ -18,14 +18,14 @@ along with this program. If not, see . let $ = require('jquery'); //support files -let app = require('../app'); -let Tooltips = require('../tooltips'); +let app = require('../../app'); +let Tooltips = require('../../tooltips'); //views let View = require('ampersand-view'); let SpecieView = require('./specie-view'); //templates -let speciesTemplate = require('../templates/includes/speciesView.pug'); -let spatialSpeciesTemplate = require('../templates/includes/spatialSpeciesView.pug'); +let speciesTemplate = require('../templates/speciesView.pug'); +let spatialSpeciesTemplate = require('../templates/spatialSpeciesView.pug'); module.exports = View.extend({ events: { diff --git a/client/pages/model-editor.js b/client/pages/model-editor.js index 604b7988c4..2c6826b4c0 100644 --- a/client/pages/model-editor.js +++ b/client/pages/model-editor.js @@ -25,7 +25,7 @@ var modals = require('../modals'); let Tooltips = require("../tooltips"); //views var PageView = require('../pages/base'); -let ModelView = require('../views/model-view'); +let ModelView = require('../model-view/model-view'); var ParticleViewer = require('../views/view-particle'); var TimespanSettingsView = require('../views/timespan-settings'); var ModelStateButtonsView = require('../views/model-state-buttons'); From a80c36e55a8f6bc89ffe6db70ed619a765bf4b2b Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 16 Jul 2021 15:51:52 -0400 Subject: [PATCH 171/192] Moved all initial condition view, template, and subview files to the new model view directory. --- client/model-view/model-view.js | 2 +- .../templates}/editInitialCondition.pug | 0 .../templates}/initialConditionsView.pug | 0 .../templates}/viewInitialCondition.pug | 0 .../{ => model-view}/views/initial-condition-view.js | 12 ++++++------ .../views/initial-conditions-view.js | 6 +++--- 6 files changed, 10 insertions(+), 10 deletions(-) rename client/{templates/includes => model-view/templates}/editInitialCondition.pug (100%) rename client/{templates/includes => model-view/templates}/initialConditionsView.pug (100%) rename client/{templates/includes => model-view/templates}/viewInitialCondition.pug (100%) rename client/{ => model-view}/views/initial-condition-view.js (95%) rename client/{ => model-view}/views/initial-conditions-view.js (96%) diff --git a/client/model-view/model-view.js b/client/model-view/model-view.js index 0a5da88db3..a30cba0e5f 100644 --- a/client/model-view/model-view.js +++ b/client/model-view/model-view.js @@ -35,7 +35,7 @@ let DomainViewer = require('../views/domain-viewer'); let ReactionsView = require('../views/reactions-view'); let ParametersView = require('../views/parameters-view'); let SBMLComponentsView = require('../views/sbml-components-view'); -let InitialConditionsView = require('../views/initial-conditions-view'); +let InitialConditionsView = require('./views/initial-conditions-view'); let BoundaryConditionsView = require('../views/boundary-conditions-view'); //templates let template = require('../templates/includes/modelView.pug'); diff --git a/client/templates/includes/editInitialCondition.pug b/client/model-view/templates/editInitialCondition.pug similarity index 100% rename from client/templates/includes/editInitialCondition.pug rename to client/model-view/templates/editInitialCondition.pug diff --git a/client/templates/includes/initialConditionsView.pug b/client/model-view/templates/initialConditionsView.pug similarity index 100% rename from client/templates/includes/initialConditionsView.pug rename to client/model-view/templates/initialConditionsView.pug diff --git a/client/templates/includes/viewInitialCondition.pug b/client/model-view/templates/viewInitialCondition.pug similarity index 100% rename from client/templates/includes/viewInitialCondition.pug rename to client/model-view/templates/viewInitialCondition.pug diff --git a/client/views/initial-condition-view.js b/client/model-view/views/initial-condition-view.js similarity index 95% rename from client/views/initial-condition-view.js rename to client/model-view/views/initial-condition-view.js index 0d1fa6c3d3..bd45098172 100644 --- a/client/views/initial-condition-view.js +++ b/client/model-view/views/initial-condition-view.js @@ -19,17 +19,17 @@ along with this program. If not, see . let $ = require('jquery'); let _ = require('underscore'); //support files -let app = require('../app'); -let tests = require('./tests'); -let modals = require('../modals'); +let app = require('../../app'); +let tests = require('../../views/tests'); +let modals = require('../../modals'); //views -let InputView = require('./input'); +let InputView = require('../../views/input'); let View = require('ampersand-view'); let TypesView = require('./component-types'); let SelectView = require('ampersand-select-view'); //templates -let editTemplate = require('../templates/includes/editInitialCondition.pug'); -let viewTemplate = require('../templates/includes/viewInitialCondition.pug'); +let editTemplate = require('../templates/editInitialCondition.pug'); +let viewTemplate = require('../templates/viewInitialCondition.pug'); module.exports = View.extend({ events: { diff --git a/client/views/initial-conditions-view.js b/client/model-view/views/initial-conditions-view.js similarity index 96% rename from client/views/initial-conditions-view.js rename to client/model-view/views/initial-conditions-view.js index caa473fc9a..c842157d1e 100644 --- a/client/views/initial-conditions-view.js +++ b/client/model-view/views/initial-conditions-view.js @@ -18,13 +18,13 @@ along with this program. If not, see . let $ = require('jquery'); //support files -let app = require('../app'); -let Tooltips = require('../tooltips'); +let app = require('../../app'); +let Tooltips = require('../../tooltips'); //views let View = require('ampersand-view'); let InitialConditionView = require('./initial-condition-view'); //templates -let template = require('../templates/includes/initialConditionsView.pug'); +let template = require('../templates/initialConditionsView.pug'); module.exports = View.extend({ template: template, From b01dddc0b372a1a613d72e80d0e2317530fcccc2 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 16 Jul 2021 16:19:10 -0400 Subject: [PATCH 172/192] Moved all reaction view, template, and subview files to the new model view directory. --- client/model-view/model-view.js | 4 ++-- .../{templates/includes => model-view}/modelView.pug | 0 .../templates}/editCustomStoichSpecie.pug | 0 .../templates}/editStoichSpecie.pug | 0 .../templates}/reactantProduct.pug | 0 .../templates}/reactionDetails.pug | 0 .../templates}/reactionListing.pug | 0 .../templates}/reactionTypes.pug | 0 .../templates}/reactionsView.pug | 0 .../templates}/viewReactions.pug | 0 .../views/edit-custom-stoich-specie.js | 2 +- client/{ => model-view}/views/edit-stoich-specie.js | 2 +- client/{ => model-view}/views/reactant-product.js | 4 ++-- client/{ => model-view}/views/reaction-details.js | 10 +++++----- client/{ => model-view}/views/reaction-listing.js | 12 ++++++------ client/{ => model-view}/views/reaction-types.js | 2 +- client/{ => model-view}/views/reactions-view.js | 10 +++++----- 17 files changed, 23 insertions(+), 23 deletions(-) rename client/{templates/includes => model-view}/modelView.pug (100%) rename client/{templates/includes => model-view/templates}/editCustomStoichSpecie.pug (100%) rename client/{templates/includes => model-view/templates}/editStoichSpecie.pug (100%) rename client/{templates/includes => model-view/templates}/reactantProduct.pug (100%) rename client/{templates/includes => model-view/templates}/reactionDetails.pug (100%) rename client/{templates/includes => model-view/templates}/reactionListing.pug (100%) rename client/{templates/includes => model-view/templates}/reactionTypes.pug (100%) rename client/{templates/includes => model-view/templates}/reactionsView.pug (100%) rename client/{templates/includes => model-view/templates}/viewReactions.pug (100%) rename client/{ => model-view}/views/edit-custom-stoich-specie.js (98%) rename client/{ => model-view}/views/edit-stoich-specie.js (96%) rename client/{ => model-view}/views/reactant-product.js (97%) rename client/{ => model-view}/views/reaction-details.js (97%) rename client/{ => model-view}/views/reaction-listing.js (93%) rename client/{ => model-view}/views/reaction-types.js (95%) rename client/{ => model-view}/views/reactions-view.js (97%) diff --git a/client/model-view/model-view.js b/client/model-view/model-view.js index a30cba0e5f..e176c74d7d 100644 --- a/client/model-view/model-view.js +++ b/client/model-view/model-view.js @@ -32,13 +32,13 @@ let RulesView = require('../views/rules-view'); let EventsView = require('../views/events-view'); let SpeciesView = require('./views/species-view'); let DomainViewer = require('../views/domain-viewer'); -let ReactionsView = require('../views/reactions-view'); +let ReactionsView = require('./views/reactions-view'); let ParametersView = require('../views/parameters-view'); let SBMLComponentsView = require('../views/sbml-components-view'); let InitialConditionsView = require('./views/initial-conditions-view'); let BoundaryConditionsView = require('../views/boundary-conditions-view'); //templates -let template = require('../templates/includes/modelView.pug'); +let template = require('./modelView.pug'); module.exports = View.extend({ template: template, diff --git a/client/templates/includes/modelView.pug b/client/model-view/modelView.pug similarity index 100% rename from client/templates/includes/modelView.pug rename to client/model-view/modelView.pug diff --git a/client/templates/includes/editCustomStoichSpecie.pug b/client/model-view/templates/editCustomStoichSpecie.pug similarity index 100% rename from client/templates/includes/editCustomStoichSpecie.pug rename to client/model-view/templates/editCustomStoichSpecie.pug diff --git a/client/templates/includes/editStoichSpecie.pug b/client/model-view/templates/editStoichSpecie.pug similarity index 100% rename from client/templates/includes/editStoichSpecie.pug rename to client/model-view/templates/editStoichSpecie.pug diff --git a/client/templates/includes/reactantProduct.pug b/client/model-view/templates/reactantProduct.pug similarity index 100% rename from client/templates/includes/reactantProduct.pug rename to client/model-view/templates/reactantProduct.pug diff --git a/client/templates/includes/reactionDetails.pug b/client/model-view/templates/reactionDetails.pug similarity index 100% rename from client/templates/includes/reactionDetails.pug rename to client/model-view/templates/reactionDetails.pug diff --git a/client/templates/includes/reactionListing.pug b/client/model-view/templates/reactionListing.pug similarity index 100% rename from client/templates/includes/reactionListing.pug rename to client/model-view/templates/reactionListing.pug diff --git a/client/templates/includes/reactionTypes.pug b/client/model-view/templates/reactionTypes.pug similarity index 100% rename from client/templates/includes/reactionTypes.pug rename to client/model-view/templates/reactionTypes.pug diff --git a/client/templates/includes/reactionsView.pug b/client/model-view/templates/reactionsView.pug similarity index 100% rename from client/templates/includes/reactionsView.pug rename to client/model-view/templates/reactionsView.pug diff --git a/client/templates/includes/viewReactions.pug b/client/model-view/templates/viewReactions.pug similarity index 100% rename from client/templates/includes/viewReactions.pug rename to client/model-view/templates/viewReactions.pug diff --git a/client/views/edit-custom-stoich-specie.js b/client/model-view/views/edit-custom-stoich-specie.js similarity index 98% rename from client/views/edit-custom-stoich-specie.js rename to client/model-view/views/edit-custom-stoich-specie.js index 0e842387eb..bbc71ca80e 100644 --- a/client/views/edit-custom-stoich-specie.js +++ b/client/model-view/views/edit-custom-stoich-specie.js @@ -20,7 +20,7 @@ var $ = require('jquery'); //views var SelectView = require('ampersand-select-view'); //templates -var template = require('../templates/includes/editCustomStoichSpecie.pug'); +var template = require('../templates/editCustomStoichSpecie.pug'); module.exports = SelectView.extend({ // SelectView expects a string template, so pre-render it diff --git a/client/views/edit-stoich-specie.js b/client/model-view/views/edit-stoich-specie.js similarity index 96% rename from client/views/edit-stoich-specie.js rename to client/model-view/views/edit-stoich-specie.js index 4f276620aa..b4acc31af6 100644 --- a/client/views/edit-stoich-specie.js +++ b/client/model-view/views/edit-stoich-specie.js @@ -20,7 +20,7 @@ var $ = require('jquery'); //views var SelectView = require('ampersand-select-view'); //templates -var template = require('../templates/includes/editStoichSpecie.pug'); +var template = require('../templates/editStoichSpecie.pug'); module.exports = SelectView.extend({ // SelectView expects a string template, so pre-render it diff --git a/client/views/reactant-product.js b/client/model-view/views/reactant-product.js similarity index 97% rename from client/views/reactant-product.js rename to client/model-view/views/reactant-product.js index e2866f4e9f..bdd1bfc183 100644 --- a/client/views/reactant-product.js +++ b/client/model-view/views/reactant-product.js @@ -18,14 +18,14 @@ along with this program. If not, see . let $ = require('jquery'); //models -let StoichSpecie = require('../models/stoich-specie'); +let StoichSpecie = require('../../models/stoich-specie'); //views let View = require('ampersand-view'); let SelectView = require('ampersand-select-view'); let EditStoichSpecieView = require('./edit-stoich-specie'); let EditCustomStoichSpecieView = require('./edit-custom-stoich-specie'); //templates -let template = require('../templates/includes/reactantProduct.pug'); +let template = require('../templates/reactantProduct.pug'); module.exports = View.extend({ template: template, diff --git a/client/views/reaction-details.js b/client/model-view/views/reaction-details.js similarity index 97% rename from client/views/reaction-details.js rename to client/model-view/views/reaction-details.js index 042a3d768d..91dfe74735 100644 --- a/client/views/reaction-details.js +++ b/client/model-view/views/reaction-details.js @@ -20,18 +20,18 @@ let $ = require('jquery'); let katex = require('katex'); let _ = require('underscore'); //support files -let app = require('../app'); -let ReactionTypes = require('../reaction-types'); +let app = require('../../app'); +let ReactionTypes = require('../../reaction-types'); //models -let StoichSpecie = require('../models/stoich-specie'); +let StoichSpecie = require('../../models/stoich-specie'); //views -let InputView = require('./input'); +let InputView = require('../../views/input'); let View = require('ampersand-view'); let SelectView = require('ampersand-select-view'); let ReactionTypesView = require('./reaction-types'); let ReactantProductView = require('./reactant-product'); //templates -let template = require('../templates/includes/reactionDetails.pug'); +let template = require('../templates/reactionDetails.pug'); module.exports = View.extend({ template: template, diff --git a/client/views/reaction-listing.js b/client/model-view/views/reaction-listing.js similarity index 93% rename from client/views/reaction-listing.js rename to client/model-view/views/reaction-listing.js index c59aaea928..a0b2c426f2 100644 --- a/client/views/reaction-listing.js +++ b/client/model-view/views/reaction-listing.js @@ -20,15 +20,15 @@ let $ = require('jquery'); let katex = require('katex'); let _ = require('underscore'); //support files -let app = require('../app'); -let tests = require('./tests'); -let modals = require('../modals'); +let app = require('../../app'); +let tests = require('../../views/tests'); +let modals = require('../../modals'); //views -let InputView = require('./input'); +let InputView = require('../../views/input'); let View = require('ampersand-view'); //templates -let viewTemplate = require('../templates/includes/viewReactions.pug'); -let editTemplate = require('../templates/includes/reactionListing.pug'); +let viewTemplate = require('../templates/viewReactions.pug'); +let editTemplate = require('../templates/reactionListing.pug'); module.exports = View.extend({ bindings: { diff --git a/client/views/reaction-types.js b/client/model-view/views/reaction-types.js similarity index 95% rename from client/views/reaction-types.js rename to client/model-view/views/reaction-types.js index a744e809ad..9bf2fc4e07 100644 --- a/client/views/reaction-types.js +++ b/client/model-view/views/reaction-types.js @@ -20,7 +20,7 @@ along with this program. If not, see . let View = require('ampersand-view'); let TypesView = require('./component-types'); //templates -let template = require('../templates/includes/reactionTypes.pug'); +let template = require('../templates/reactionTypes.pug'); module.exports = View.extend({ template: template, diff --git a/client/views/reactions-view.js b/client/model-view/views/reactions-view.js similarity index 97% rename from client/views/reactions-view.js rename to client/model-view/views/reactions-view.js index 4ecb155570..1d25ba3347 100644 --- a/client/views/reactions-view.js +++ b/client/model-view/views/reactions-view.js @@ -20,18 +20,18 @@ let $ = require('jquery'); let katex = require('katex'); let _ = require('underscore'); //support files -let app = require('../app'); -let Tooltips = require('../tooltips'); -let ReactionTypes = require('../reaction-types'); +let app = require('../../app'); +let Tooltips = require('../../tooltips'); +let ReactionTypes = require('../../reaction-types'); //models -let StoichSpeciesCollection = require('../models/stoich-species'); +let StoichSpeciesCollection = require('../../models/stoich-species'); //views let View = require('ampersand-view'); let ViewSwitcher = require('ampersand-view-switcher'); let ReactionListingView = require('./reaction-listing'); let ReactionDetailsView = require('./reaction-details'); //templates -let template = require('../templates/includes/reactionsView.pug'); +let template = require('../templates/reactionsView.pug'); module.exports = View.extend({ template: template, From 65f099c10b518c259ac66d936421b88ff1479462 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 16 Jul 2021 16:33:32 -0400 Subject: [PATCH 173/192] Moved the domain viewer and template files to the new model view directory . --- client/model-view/model-view.js | 2 +- .../templates}/domainViewer.pug | 0 client/{ => model-view}/views/domain-viewer.js | 12 ++++++------ 3 files changed, 7 insertions(+), 7 deletions(-) rename client/{templates/includes => model-view/templates}/domainViewer.pug (100%) rename client/{ => model-view}/views/domain-viewer.js (96%) diff --git a/client/model-view/model-view.js b/client/model-view/model-view.js index e176c74d7d..99a55eeb35 100644 --- a/client/model-view/model-view.js +++ b/client/model-view/model-view.js @@ -31,7 +31,7 @@ let InputView = require('../views/input'); let RulesView = require('../views/rules-view'); let EventsView = require('../views/events-view'); let SpeciesView = require('./views/species-view'); -let DomainViewer = require('../views/domain-viewer'); +let DomainViewer = require('./views/domain-viewer'); let ReactionsView = require('./views/reactions-view'); let ParametersView = require('../views/parameters-view'); let SBMLComponentsView = require('../views/sbml-components-view'); diff --git a/client/templates/includes/domainViewer.pug b/client/model-view/templates/domainViewer.pug similarity index 100% rename from client/templates/includes/domainViewer.pug rename to client/model-view/templates/domainViewer.pug diff --git a/client/views/domain-viewer.js b/client/model-view/views/domain-viewer.js similarity index 96% rename from client/views/domain-viewer.js rename to client/model-view/views/domain-viewer.js index 2a439109c6..619347c0f5 100644 --- a/client/views/domain-viewer.js +++ b/client/model-view/views/domain-viewer.js @@ -20,16 +20,16 @@ var $ = require('jquery'); let path = require('path'); var _ = require('underscore'); //support files -var app = require('../app'); -var Plotly = require('../lib/plotly'); -var Tooltips = require('../tooltips'); +var app = require('../../app'); +var Plotly = require('../../lib/plotly'); +var Tooltips = require('../../tooltips'); //views var View = require('ampersand-view'); -var TypesViewer = require('./edit-domain-type'); +var TypesViewer = require('../../views/edit-domain-type'); var SelectView = require('ampersand-select-view'); -var ParticleViewer = require('./view-particle'); +var ParticleViewer = require('../../views/view-particle'); //templates -var template = require('../templates/includes/domainViewer.pug'); +var template = require('../templates/domainViewer.pug'); module.exports = View.extend({ template: template, From f9570959655cd3d95b49ee39c2434e20853871e1 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 16 Jul 2021 16:42:18 -0400 Subject: [PATCH 174/192] Moved all parameter view, template, and subview files to the new model view directory. --- client/model-view/model-view.js | 2 +- .../templates}/editParameter.pug | 0 .../templates}/parametersView.pug | 0 .../templates/viewParameter.pug} | 0 client/{ => model-view}/views/parameter-view.js | 12 ++++++------ client/{ => model-view}/views/parameters-view.js | 6 +++--- 6 files changed, 10 insertions(+), 10 deletions(-) rename client/{templates/includes => model-view/templates}/editParameter.pug (100%) rename client/{templates/includes => model-view/templates}/parametersView.pug (100%) rename client/{templates/includes/viewParameters.pug => model-view/templates/viewParameter.pug} (100%) rename client/{ => model-view}/views/parameter-view.js (93%) rename client/{ => model-view}/views/parameters-view.js (96%) diff --git a/client/model-view/model-view.js b/client/model-view/model-view.js index 99a55eeb35..3141150029 100644 --- a/client/model-view/model-view.js +++ b/client/model-view/model-view.js @@ -33,7 +33,7 @@ let EventsView = require('../views/events-view'); let SpeciesView = require('./views/species-view'); let DomainViewer = require('./views/domain-viewer'); let ReactionsView = require('./views/reactions-view'); -let ParametersView = require('../views/parameters-view'); +let ParametersView = require('./views/parameters-view'); let SBMLComponentsView = require('../views/sbml-components-view'); let InitialConditionsView = require('./views/initial-conditions-view'); let BoundaryConditionsView = require('../views/boundary-conditions-view'); diff --git a/client/templates/includes/editParameter.pug b/client/model-view/templates/editParameter.pug similarity index 100% rename from client/templates/includes/editParameter.pug rename to client/model-view/templates/editParameter.pug diff --git a/client/templates/includes/parametersView.pug b/client/model-view/templates/parametersView.pug similarity index 100% rename from client/templates/includes/parametersView.pug rename to client/model-view/templates/parametersView.pug diff --git a/client/templates/includes/viewParameters.pug b/client/model-view/templates/viewParameter.pug similarity index 100% rename from client/templates/includes/viewParameters.pug rename to client/model-view/templates/viewParameter.pug diff --git a/client/views/parameter-view.js b/client/model-view/views/parameter-view.js similarity index 93% rename from client/views/parameter-view.js rename to client/model-view/views/parameter-view.js index 61c8159643..0dd0df630a 100644 --- a/client/views/parameter-view.js +++ b/client/model-view/views/parameter-view.js @@ -19,15 +19,15 @@ along with this program. If not, see . let $ = require('jquery'); let _ = require('underscore'); //support files -let app = require('../app'); -let tests = require('./tests'); -let modals = require('../modals') +let app = require('../../app'); +let tests = require('../../views/tests'); +let modals = require('../../modals'); //views -let InputView = require('./input'); +let InputView = require('../../views/input'); let View = require('ampersand-view'); //templates -let editTemplate = require('../templates/includes/editParameter.pug'); -let viewTemplate = require('../templates/includes/viewParameters.pug'); +let editTemplate = require('../templates/editParameter.pug'); +let viewTemplate = require('../templates/viewParameter.pug'); module.exports = View.extend({ bindings: { diff --git a/client/views/parameters-view.js b/client/model-view/views/parameters-view.js similarity index 96% rename from client/views/parameters-view.js rename to client/model-view/views/parameters-view.js index 7e51981fd1..13bdf608a9 100644 --- a/client/views/parameters-view.js +++ b/client/model-view/views/parameters-view.js @@ -18,13 +18,13 @@ along with this program. If not, see . let $ = require('jquery'); //support files -let app = require('../app'); -let Tooltips = require('../tooltips'); +let app = require('../../app'); +let Tooltips = require('../../tooltips'); //views let View = require('ampersand-view'); let EditParameterView = require('./parameter-view'); //templates -let template = require('../templates/includes/parametersView.pug'); +let template = require('../templates/parametersView.pug'); module.exports = View.extend({ template: template, From 6796659a857a567171cb20a6ca936117df5a2fdf Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Fri, 16 Jul 2021 16:58:11 -0400 Subject: [PATCH 175/192] Moved all event view, template, and subview files to the new model view directory. --- client/model-view/model-view.js | 2 +- .../templates}/editEventAssignment.pug | 0 ...{editSpatialSpecies.pug => editSpatialSpecie.pug} | 0 .../templates/{editSpecies.pug => editSpecie.pug} | 0 .../templates}/eventAssignmentsView.pug | 0 .../templates}/eventDetails.pug | 0 .../templates/eventListing.pug} | 0 .../includes => model-view/templates}/eventsView.pug | 0 .../templates/viewEvent.pug} | 0 .../templates}/viewEventAssignment.pug | 0 .../{viewReactions.pug => viewReaction.pug} | 0 ...{viewSpatialSpecies.pug => viewSpatialSpecie.pug} | 0 .../templates/{viewSpecies.pug => viewSpecie.pug} | 0 .../{ => model-view}/views/event-assignment-view.js | 8 ++++---- .../{ => model-view}/views/event-assignments-view.js | 4 ++-- client/{ => model-view}/views/event-details.js | 8 ++++---- .../views/event-listing.js} | 12 ++++++------ client/{ => model-view}/views/events-view.js | 8 ++++---- client/model-view/views/reaction-listing.js | 2 +- client/model-view/views/specie-view.js | 8 ++++---- 20 files changed, 26 insertions(+), 26 deletions(-) rename client/{templates/includes => model-view/templates}/editEventAssignment.pug (100%) rename client/model-view/templates/{editSpatialSpecies.pug => editSpatialSpecie.pug} (100%) rename client/model-view/templates/{editSpecies.pug => editSpecie.pug} (100%) rename client/{templates/includes => model-view/templates}/eventAssignmentsView.pug (100%) rename client/{templates/includes => model-view/templates}/eventDetails.pug (100%) rename client/{templates/includes/eventListings.pug => model-view/templates/eventListing.pug} (100%) rename client/{templates/includes => model-view/templates}/eventsView.pug (100%) rename client/{templates/includes/viewEvents.pug => model-view/templates/viewEvent.pug} (100%) rename client/{templates/includes => model-view/templates}/viewEventAssignment.pug (100%) rename client/model-view/templates/{viewReactions.pug => viewReaction.pug} (100%) rename client/model-view/templates/{viewSpatialSpecies.pug => viewSpatialSpecie.pug} (100%) rename client/model-view/templates/{viewSpecies.pug => viewSpecie.pug} (100%) rename client/{ => model-view}/views/event-assignment-view.js (94%) rename client/{ => model-view}/views/event-assignments-view.js (96%) rename client/{ => model-view}/views/event-details.js (96%) rename client/{views/event-listings.js => model-view/views/event-listing.js} (93%) rename client/{ => model-view}/views/events-view.js (96%) diff --git a/client/model-view/model-view.js b/client/model-view/model-view.js index 3141150029..100839fe6f 100644 --- a/client/model-view/model-view.js +++ b/client/model-view/model-view.js @@ -29,7 +29,7 @@ let Domain = require('../models/domain'); let View = require('ampersand-view'); let InputView = require('../views/input'); let RulesView = require('../views/rules-view'); -let EventsView = require('../views/events-view'); +let EventsView = require('./views/events-view'); let SpeciesView = require('./views/species-view'); let DomainViewer = require('./views/domain-viewer'); let ReactionsView = require('./views/reactions-view'); diff --git a/client/templates/includes/editEventAssignment.pug b/client/model-view/templates/editEventAssignment.pug similarity index 100% rename from client/templates/includes/editEventAssignment.pug rename to client/model-view/templates/editEventAssignment.pug diff --git a/client/model-view/templates/editSpatialSpecies.pug b/client/model-view/templates/editSpatialSpecie.pug similarity index 100% rename from client/model-view/templates/editSpatialSpecies.pug rename to client/model-view/templates/editSpatialSpecie.pug diff --git a/client/model-view/templates/editSpecies.pug b/client/model-view/templates/editSpecie.pug similarity index 100% rename from client/model-view/templates/editSpecies.pug rename to client/model-view/templates/editSpecie.pug diff --git a/client/templates/includes/eventAssignmentsView.pug b/client/model-view/templates/eventAssignmentsView.pug similarity index 100% rename from client/templates/includes/eventAssignmentsView.pug rename to client/model-view/templates/eventAssignmentsView.pug diff --git a/client/templates/includes/eventDetails.pug b/client/model-view/templates/eventDetails.pug similarity index 100% rename from client/templates/includes/eventDetails.pug rename to client/model-view/templates/eventDetails.pug diff --git a/client/templates/includes/eventListings.pug b/client/model-view/templates/eventListing.pug similarity index 100% rename from client/templates/includes/eventListings.pug rename to client/model-view/templates/eventListing.pug diff --git a/client/templates/includes/eventsView.pug b/client/model-view/templates/eventsView.pug similarity index 100% rename from client/templates/includes/eventsView.pug rename to client/model-view/templates/eventsView.pug diff --git a/client/templates/includes/viewEvents.pug b/client/model-view/templates/viewEvent.pug similarity index 100% rename from client/templates/includes/viewEvents.pug rename to client/model-view/templates/viewEvent.pug diff --git a/client/templates/includes/viewEventAssignment.pug b/client/model-view/templates/viewEventAssignment.pug similarity index 100% rename from client/templates/includes/viewEventAssignment.pug rename to client/model-view/templates/viewEventAssignment.pug diff --git a/client/model-view/templates/viewReactions.pug b/client/model-view/templates/viewReaction.pug similarity index 100% rename from client/model-view/templates/viewReactions.pug rename to client/model-view/templates/viewReaction.pug diff --git a/client/model-view/templates/viewSpatialSpecies.pug b/client/model-view/templates/viewSpatialSpecie.pug similarity index 100% rename from client/model-view/templates/viewSpatialSpecies.pug rename to client/model-view/templates/viewSpatialSpecie.pug diff --git a/client/model-view/templates/viewSpecies.pug b/client/model-view/templates/viewSpecie.pug similarity index 100% rename from client/model-view/templates/viewSpecies.pug rename to client/model-view/templates/viewSpecie.pug diff --git a/client/views/event-assignment-view.js b/client/model-view/views/event-assignment-view.js similarity index 94% rename from client/views/event-assignment-view.js rename to client/model-view/views/event-assignment-view.js index 5fb865389b..69193ac7ec 100644 --- a/client/views/event-assignment-view.js +++ b/client/model-view/views/event-assignment-view.js @@ -18,14 +18,14 @@ along with this program. If not, see . let $ = require('jquery'); //support files -let app = require('../app'); +let app = require('../../app'); //views -let InputView = require('./input'); +let InputView = require('../../views/input'); let View = require('ampersand-view'); let SelectView = require('ampersand-select-view'); //templates -let editTemplate = require('../templates/includes/editEventAssignment.pug'); -let viewTemplate = require('../templates/includes/viewEventAssignment.pug'); +let editTemplate = require('../templates/editEventAssignment.pug'); +let viewTemplate = require('../templates/viewEventAssignment.pug'); module.exports = View.extend({ events: { diff --git a/client/views/event-assignments-view.js b/client/model-view/views/event-assignments-view.js similarity index 96% rename from client/views/event-assignments-view.js rename to client/model-view/views/event-assignments-view.js index ab53de27a3..7d604f8ac7 100644 --- a/client/views/event-assignments-view.js +++ b/client/model-view/views/event-assignments-view.js @@ -18,12 +18,12 @@ along with this program. If not, see . let $ = require('jquery'); //support files -let app = require('../app'); +let app = require('../../app'); //views var View = require('ampersand-view'); var EditEventAssignment = require('./event-assignment-view'); //templates -var template = require('../templates/includes/eventAssignmentsView.pug'); +var template = require('../templates/eventAssignmentsView.pug'); module.exports = View.extend({ template: template, diff --git a/client/views/event-details.js b/client/model-view/views/event-details.js similarity index 96% rename from client/views/event-details.js rename to client/model-view/views/event-details.js index 8aabc4823e..b6ea87febd 100644 --- a/client/views/event-details.js +++ b/client/model-view/views/event-details.js @@ -18,14 +18,14 @@ along with this program. If not, see . let $ = require('jquery'); //support files -let app = require('../app'); -let tests = require('./tests'); +let app = require('../../app'); +let tests = require('../../views/tests'); //views -let InputView = require('./input'); +let InputView = require('../../views/input'); let View = require('ampersand-view'); let EventAssignment = require('./event-assignments-view'); //templates -let template = require('../templates/includes/eventDetails.pug'); +let template = require('../templates/eventDetails.pug'); module.exports = View.extend({ template: template, diff --git a/client/views/event-listings.js b/client/model-view/views/event-listing.js similarity index 93% rename from client/views/event-listings.js rename to client/model-view/views/event-listing.js index f0885a7c3c..7776033d03 100644 --- a/client/views/event-listings.js +++ b/client/model-view/views/event-listing.js @@ -19,16 +19,16 @@ along with this program. If not, see . let $ = require('jquery'); let _ = require('underscore'); //support files -let app = require('../app'); -let tests = require('./tests'); -let modals = require('../modals'); +let app = require('../../app'); +let tests = require('../../views/tests'); +let modals = require('../../modals'); //views -let InputView = require('./input'); +let InputView = require('../../views/input'); let View = require('ampersand-view'); let EventAssignment = require('./event-assignments-view'); //templates -let viewTemplate = require('../templates/includes/viewEvents.pug'); -let editTemplate = require('../templates/includes/eventListings.pug'); +let viewTemplate = require('../templates/viewEvent.pug'); +let editTemplate = require('../templates/eventListing.pug'); module.exports = View.extend({ bindings: { diff --git a/client/views/events-view.js b/client/model-view/views/events-view.js similarity index 96% rename from client/views/events-view.js rename to client/model-view/views/events-view.js index a3af64889e..629470944a 100644 --- a/client/views/events-view.js +++ b/client/model-view/views/events-view.js @@ -18,15 +18,15 @@ along with this program. If not, see . let $ = require('jquery'); //support files -let app = require('../app'); -let Tooltips = require("../tooltips"); +let app = require('../../app'); +let Tooltips = require("../../tooltips"); //views let View = require('ampersand-view'); let EventDetails = require('./event-details'); -let EventListings = require('./event-listings'); +let EventListings = require('./event-listing'); let ViewSwitcher = require('ampersand-view-switcher'); //templates -let template = require('../templates/includes/eventsView.pug'); +let template = require('../templates/eventsView.pug'); module.exports = View.extend({ template: template, diff --git a/client/model-view/views/reaction-listing.js b/client/model-view/views/reaction-listing.js index a0b2c426f2..2493684a78 100644 --- a/client/model-view/views/reaction-listing.js +++ b/client/model-view/views/reaction-listing.js @@ -27,7 +27,7 @@ let modals = require('../../modals'); let InputView = require('../../views/input'); let View = require('ampersand-view'); //templates -let viewTemplate = require('../templates/viewReactions.pug'); +let viewTemplate = require('../templates/viewReaction.pug'); let editTemplate = require('../templates/reactionListing.pug'); module.exports = View.extend({ diff --git a/client/model-view/views/specie-view.js b/client/model-view/views/specie-view.js index 1540fccb08..633890e2f6 100644 --- a/client/model-view/views/specie-view.js +++ b/client/model-view/views/specie-view.js @@ -28,10 +28,10 @@ let View = require('ampersand-view'); let TypesView = require('./component-types'); let SelectView = require('ampersand-select-view'); //templates -let editTemplate = require('../templates/editSpecies.pug'); -let editSpatialTemplate = require('../templates/editSpatialSpecies.pug'); -let viewTemplate = require('../templates/viewSpecies.pug'); -let viewSpatialTemplate = require('../templates/viewSpatialSpecies.pug'); +let editTemplate = require('../templates/editSpecie.pug'); +let editSpatialTemplate = require('../templates/editSpatialSpecie.pug'); +let viewTemplate = require('../templates/viewSpecie.pug'); +let viewSpatialTemplate = require('../templates/viewSpatialSpecie.pug'); module.exports = View.extend({ bindings: { From 8a67ee7f51ca40bc38c32d198018e5573ba57007 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Mon, 19 Jul 2021 09:58:22 -0400 Subject: [PATCH 176/192] Moved the rules view and template files to the new model view directory. --- client/model-view/model-view.js | 2 +- .../includes => model-view/templates}/editRule.pug | 0 .../includes => model-view/templates}/rulesView.pug | 0 .../templates/viewRule.pug} | 0 client/{ => model-view}/views/rule-view.js | 12 ++++++------ client/{ => model-view}/views/rules-view.js | 6 +++--- 6 files changed, 10 insertions(+), 10 deletions(-) rename client/{templates/includes => model-view/templates}/editRule.pug (100%) rename client/{templates/includes => model-view/templates}/rulesView.pug (100%) rename client/{templates/includes/viewRules.pug => model-view/templates/viewRule.pug} (100%) rename client/{ => model-view}/views/rule-view.js (95%) rename client/{ => model-view}/views/rules-view.js (96%) diff --git a/client/model-view/model-view.js b/client/model-view/model-view.js index 100839fe6f..ce94c7b160 100644 --- a/client/model-view/model-view.js +++ b/client/model-view/model-view.js @@ -28,7 +28,7 @@ let Domain = require('../models/domain'); //views let View = require('ampersand-view'); let InputView = require('../views/input'); -let RulesView = require('../views/rules-view'); +let RulesView = require('./views/rules-view'); let EventsView = require('./views/events-view'); let SpeciesView = require('./views/species-view'); let DomainViewer = require('./views/domain-viewer'); diff --git a/client/templates/includes/editRule.pug b/client/model-view/templates/editRule.pug similarity index 100% rename from client/templates/includes/editRule.pug rename to client/model-view/templates/editRule.pug diff --git a/client/templates/includes/rulesView.pug b/client/model-view/templates/rulesView.pug similarity index 100% rename from client/templates/includes/rulesView.pug rename to client/model-view/templates/rulesView.pug diff --git a/client/templates/includes/viewRules.pug b/client/model-view/templates/viewRule.pug similarity index 100% rename from client/templates/includes/viewRules.pug rename to client/model-view/templates/viewRule.pug diff --git a/client/views/rule-view.js b/client/model-view/views/rule-view.js similarity index 95% rename from client/views/rule-view.js rename to client/model-view/views/rule-view.js index 8febcb192b..40b755826a 100644 --- a/client/views/rule-view.js +++ b/client/model-view/views/rule-view.js @@ -19,16 +19,16 @@ along with this program. If not, see . let $ = require('jquery'); let _ = require('underscore'); //support files -let app = require('../app'); -let tests = require('./tests'); -let modals = require('../modals'); +let app = require('../../app'); +let tests = require('../../views/tests'); +let modals = require('../../modals'); //views -let InputView = require('./input'); +let InputView = require('../../views/input'); let View = require('ampersand-view'); let SelectView = require('ampersand-select-view'); //templates -let editTemplate = require('../templates/includes/editRule.pug'); -let viewTemplate = require('../templates/includes/viewRules.pug'); +let editTemplate = require('../templates/editRule.pug'); +let viewTemplate = require('../templates/viewRule.pug'); module.exports = View.extend({ events: { diff --git a/client/views/rules-view.js b/client/model-view/views/rules-view.js similarity index 96% rename from client/views/rules-view.js rename to client/model-view/views/rules-view.js index b3f68b6519..8b82069cc7 100644 --- a/client/views/rules-view.js +++ b/client/model-view/views/rules-view.js @@ -18,13 +18,13 @@ along with this program. If not, see . let $ = require('jquery'); //support files -let app = require('../app'); -let Tooltips = require('../tooltips'); +let app = require('../../app'); +let Tooltips = require('../../tooltips'); //views let View = require('ampersand-view'); let RuleView = require('./rule-view'); //templates -let template = require('../templates/includes/rulesView.pug'); +let template = require('../templates/rulesView.pug'); module.exports = View.extend({ template: template, From 94fafd547bf2eb7d25a98e364ce403871c1d9995 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Mon, 19 Jul 2021 10:09:03 -0400 Subject: [PATCH 177/192] Moved the sbml components and function definition view and template files to the new model view directory. --- client/model-view/model-view.js | 2 +- .../templates}/editFunctionDefinition.pug | 0 .../templates}/sbmlComponentsView.pug | 0 .../templates}/viewFunctionDefinition.pug | 0 client/{ => model-view}/views/function-definition-view.js | 8 ++++---- client/{ => model-view}/views/sbml-components-view.js | 6 +++--- 6 files changed, 8 insertions(+), 8 deletions(-) rename client/{templates/includes => model-view/templates}/editFunctionDefinition.pug (100%) rename client/{templates/includes => model-view/templates}/sbmlComponentsView.pug (100%) rename client/{templates/includes => model-view/templates}/viewFunctionDefinition.pug (100%) rename client/{ => model-view}/views/function-definition-view.js (91%) rename client/{ => model-view}/views/sbml-components-view.js (95%) diff --git a/client/model-view/model-view.js b/client/model-view/model-view.js index ce94c7b160..6af2baee36 100644 --- a/client/model-view/model-view.js +++ b/client/model-view/model-view.js @@ -34,7 +34,7 @@ let SpeciesView = require('./views/species-view'); let DomainViewer = require('./views/domain-viewer'); let ReactionsView = require('./views/reactions-view'); let ParametersView = require('./views/parameters-view'); -let SBMLComponentsView = require('../views/sbml-components-view'); +let SBMLComponentsView = require('./views/sbml-components-view'); let InitialConditionsView = require('./views/initial-conditions-view'); let BoundaryConditionsView = require('../views/boundary-conditions-view'); //templates diff --git a/client/templates/includes/editFunctionDefinition.pug b/client/model-view/templates/editFunctionDefinition.pug similarity index 100% rename from client/templates/includes/editFunctionDefinition.pug rename to client/model-view/templates/editFunctionDefinition.pug diff --git a/client/templates/includes/sbmlComponentsView.pug b/client/model-view/templates/sbmlComponentsView.pug similarity index 100% rename from client/templates/includes/sbmlComponentsView.pug rename to client/model-view/templates/sbmlComponentsView.pug diff --git a/client/templates/includes/viewFunctionDefinition.pug b/client/model-view/templates/viewFunctionDefinition.pug similarity index 100% rename from client/templates/includes/viewFunctionDefinition.pug rename to client/model-view/templates/viewFunctionDefinition.pug diff --git a/client/views/function-definition-view.js b/client/model-view/views/function-definition-view.js similarity index 91% rename from client/views/function-definition-view.js rename to client/model-view/views/function-definition-view.js index ed94e9aab0..dd6f3d6f89 100644 --- a/client/views/function-definition-view.js +++ b/client/model-view/views/function-definition-view.js @@ -18,13 +18,13 @@ along with this program. If not, see . let $ = require('jquery'); //support files -let app = require('../app'); -let modals = require('../modals'); +let app = require('../../app'); +let modals = require('../../modals'); //views let View = require('ampersand-view'); //templates -let editTemplate = require('../templates/includes/editFunctionDefinition.pug'); -let viewTemplate = require('../templates/includes/viewFunctionDefinition.pug'); +let editTemplate = require('../templates/editFunctionDefinition.pug'); +let viewTemplate = require('../templates/viewFunctionDefinition.pug'); module.exports = View.extend({ events: { diff --git a/client/views/sbml-components-view.js b/client/model-view/views/sbml-components-view.js similarity index 95% rename from client/views/sbml-components-view.js rename to client/model-view/views/sbml-components-view.js index 61fd44d858..a7257a35c5 100644 --- a/client/views/sbml-components-view.js +++ b/client/model-view/views/sbml-components-view.js @@ -18,13 +18,13 @@ along with this program. If not, see . let $ = require('jquery'); //support files -let app = require('../app'); -let Tooltips = require('../tooltips'); +let app = require('../../app'); +let Tooltips = require('../../tooltips'); //views let View = require('ampersand-view'); let EditFunctionDefinition = require('./function-definition-view'); //templates -let template = require('../templates/includes/sbmlComponentsView.pug'); +let template = require('../templates/sbmlComponentsView.pug'); module.exports = View.extend({ template: template, From 1c2c31a2f9c7a96755ed6d711fdc6b6b197aef5d Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Mon, 19 Jul 2021 10:15:04 -0400 Subject: [PATCH 178/192] Moved the boundary conditions view and template files to the new model view directory. --- client/model-view/model-view.js | 2 +- .../templates}/boundaryConditionsView.pug | 0 .../templates}/editBoundaryCondition.pug | 0 .../templates}/viewBoundaryCondition.pug | 0 .../{ => model-view}/views/boundary-condition-view.js | 8 ++++---- .../{ => model-view}/views/boundary-conditions-view.js | 10 +++++----- 6 files changed, 10 insertions(+), 10 deletions(-) rename client/{templates/includes => model-view/templates}/boundaryConditionsView.pug (100%) rename client/{templates/includes => model-view/templates}/editBoundaryCondition.pug (100%) rename client/{templates/includes => model-view/templates}/viewBoundaryCondition.pug (100%) rename client/{ => model-view}/views/boundary-condition-view.js (92%) rename client/{ => model-view}/views/boundary-conditions-view.js (98%) diff --git a/client/model-view/model-view.js b/client/model-view/model-view.js index 6af2baee36..ab7d5a0129 100644 --- a/client/model-view/model-view.js +++ b/client/model-view/model-view.js @@ -36,7 +36,7 @@ let ReactionsView = require('./views/reactions-view'); let ParametersView = require('./views/parameters-view'); let SBMLComponentsView = require('./views/sbml-components-view'); let InitialConditionsView = require('./views/initial-conditions-view'); -let BoundaryConditionsView = require('../views/boundary-conditions-view'); +let BoundaryConditionsView = require('./views/boundary-conditions-view'); //templates let template = require('./modelView.pug'); diff --git a/client/templates/includes/boundaryConditionsView.pug b/client/model-view/templates/boundaryConditionsView.pug similarity index 100% rename from client/templates/includes/boundaryConditionsView.pug rename to client/model-view/templates/boundaryConditionsView.pug diff --git a/client/templates/includes/editBoundaryCondition.pug b/client/model-view/templates/editBoundaryCondition.pug similarity index 100% rename from client/templates/includes/editBoundaryCondition.pug rename to client/model-view/templates/editBoundaryCondition.pug diff --git a/client/templates/includes/viewBoundaryCondition.pug b/client/model-view/templates/viewBoundaryCondition.pug similarity index 100% rename from client/templates/includes/viewBoundaryCondition.pug rename to client/model-view/templates/viewBoundaryCondition.pug diff --git a/client/views/boundary-condition-view.js b/client/model-view/views/boundary-condition-view.js similarity index 92% rename from client/views/boundary-condition-view.js rename to client/model-view/views/boundary-condition-view.js index 43d5f3332d..21b37c246e 100644 --- a/client/views/boundary-condition-view.js +++ b/client/model-view/views/boundary-condition-view.js @@ -18,13 +18,13 @@ along with this program. If not, see . let $ = require('jquery'); //support files -let app = require('../app'); -let modals = require('../modals'); +let app = require('../../app'); +let modals = require('../../modals'); //views let View = require('ampersand-view'); //templates -let editTemplate = require('../templates/includes/editBoundaryCondition.pug'); -let viewTemplate = require('../templates/includes/viewBoundaryCondition.pug'); +let editTemplate = require('../templates/editBoundaryCondition.pug'); +let viewTemplate = require('../templates/viewBoundaryCondition.pug'); module.exports = View.extend({ events: { diff --git a/client/views/boundary-conditions-view.js b/client/model-view/views/boundary-conditions-view.js similarity index 98% rename from client/views/boundary-conditions-view.js rename to client/model-view/views/boundary-conditions-view.js index 5fc85bbc1e..557273ce52 100644 --- a/client/views/boundary-conditions-view.js +++ b/client/model-view/views/boundary-conditions-view.js @@ -19,16 +19,16 @@ along with this program. If not, see . let $ = require('jquery'); let path = require('path'); //support files -let app = require('../app'); -let tests = require('./tests'); -let Tooltips = require('../tooltips'); +let app = require('../../app'); +let tests = require('../../views/tests'); +let Tooltips = require('../../tooltips'); //views -let InputView = require('./input'); +let InputView = require('../../views/input'); let View = require('ampersand-view'); let SelectView = require('ampersand-select-view'); let BoundaryConditionView = require('./boundary-condition-view'); //templates -let template = require('../templates/includes/boundaryConditionsView.pug'); +let template = require('../templates/boundaryConditionsView.pug'); module.exports = View.extend({ template: template, From 8ab9ae734a0785c5e0199fe5a89420b97342d4e1 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Mon, 19 Jul 2021 10:56:31 -0400 Subject: [PATCH 179/192] Switched the review model section of the workflow manager to use the new model view file in read only instead of the model viewer. Added the necessary headers to the new review model section. Removed the dead files for the model viewer. --- client/pages/workflow-manager.js | 22 +++-- client/templates/includes/modelViewer.pug | 23 ------ client/templates/pages/workflowManager.pug | 14 +++- client/views/model-viewer.js | 96 ---------------------- 4 files changed, 25 insertions(+), 130 deletions(-) delete mode 100644 client/templates/includes/modelViewer.pug delete mode 100644 client/views/model-viewer.js diff --git a/client/pages/workflow-manager.js b/client/pages/workflow-manager.js index 0e1696a6b0..42c982255a 100644 --- a/client/pages/workflow-manager.js +++ b/client/pages/workflow-manager.js @@ -29,9 +29,9 @@ let PageView = require('./base'); let SettingsView = require('../views/settings'); let LogsView = require('../views/workflow-info'); let SelectView = require('ampersand-select-view'); +let ModelView = require('../model-view/model-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 @@ -47,6 +47,7 @@ let WorkflowManager = PageView.extend({ 'click [data-hook=project-breadcrumb]' : 'handleReturnToProject', 'click [data-hook=save-model]' : 'handleSaveWorkflow', 'click [data-hook=collapse-jobs]' : 'changeCollapseButtonText', + 'click [data-hook=collapse-model]' : 'changeCollapseButtonText', 'click [data-hook=return-to-project-btn]' : 'handleReturnToProject' }, initialize: function (attrs, options) { @@ -146,7 +147,7 @@ let WorkflowManager = PageView.extend({ } if(this.logsView) { this.logsView.remove(); - this.modelViewerView.remove(); + this.modelView.remove(); this.settingsViewerView.remove(); } }, @@ -160,7 +161,7 @@ let WorkflowManager = PageView.extend({ } this.renderLogsView(); this.renderSettingsViewerView(); - this.renderModelViewerView(); + this.renderModelView(); }, renderJobListingView: function () { if(this.jobListingView) { @@ -208,14 +209,17 @@ let WorkflowManager = PageView.extend({ }); app.registerRenderSubview(this, modelSelectView, "model-file"); }, - renderModelViewerView: function () { - if(this.modelViewerView) { - this.modelViewerView.remove(); + renderModelView: function () { + if(this.modelView) { + this.modelView.remove(); } - this.modelViewerView = new ModelViewerView({ - model: this.model.activeJob.model + let header = "Review Model: " + this.model.activeJob.model.name; + $("#model-viewer-header").html(header); + this.modelView = new ModelView({ + model: this.model.activeJob.model, + readOnly: true }); - app.registerRenderSubview(this, this.modelViewerView, "model-viewer-container"); + app.registerRenderSubview(this, this.modelView, "model-viewer-container"); }, renderResultsView: function () { if(this.resultsView) { diff --git a/client/templates/includes/modelViewer.pug b/client/templates/includes/modelViewer.pug deleted file mode 100644 index 9559e2a1f8..0000000000 --- a/client/templates/includes/modelViewer.pug +++ /dev/null @@ -1,23 +0,0 @@ -div.card.card-body - - div(id="model-viewer-header") - - h3.inline="Review Model: "+this.model.name - - 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") - - div(data-hook="parameters-viewer-container") - - div(data-hook="reactions-viewer-container") - - div(data-hook="events-viewer-container") - - div(data-hook="rules-viewer-container") - - div(data-hook="sbml-components-viewer-container") - - div.card.card-body="System Volume: "+this.model.volume diff --git a/client/templates/pages/workflowManager.pug b/client/templates/pages/workflowManager.pug index b4f85bdb30..ff45f09c82 100644 --- a/client/templates/pages/workflowManager.pug +++ b/client/templates/pages/workflowManager.pug @@ -69,9 +69,19 @@ section.page div(data-hook="settings-viewer-container") - div(data-hook="model-viewer-container") + div.card - div(data-hook="computational-resources-container") + div.card-header + + h3.inline(id="model-viewer-header") "Review Model: " + + button.btn.btn-outline-collapse(data-toggle="collapse" data-target="#collapse-model" data-hook="collapse-model") + + + div.collapse(id="collapse-model") + + div.card-body(data-hook="model-viewer-container") + + div.mb-2(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/views/model-viewer.js b/client/views/model-viewer.js deleted file mode 100644 index c1919f2440..0000000000 --- a/client/views/model-viewer.js +++ /dev/null @@ -1,96 +0,0 @@ -/* -StochSS is a platform for simulating biochemical systems -Copyright (C) 2019-2021 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 . -*/ - -//support files -let app = require('../app'); -//views -let View = require('ampersand-view'); -let EventsViewer = require('./events-editor'); -let RulesViewer = require('./rules-editor'); -let SpeciesViewer = require('./species-editor'); -let ReactionsViewer = require('./reactions-editor'); -let ParametersViewer = require('./parameters-editor'); -let SBMLComponentsView = require('./sbml-component-editor'); -//templates -let template = require('../templates/includes/modelViewer.pug'); - -module.exports = View.extend({ - template: template, - events: { - 'click [data-hook=collapse-model]' : 'changeCollapseButtonText' - }, - initialize: function (attrs, options) { - View.prototype.initialize.apply(this, arguments); - }, - render: function () { - View.prototype.render.apply(this, arguments); - this.renderSpeciesView(); - this.renderParametersView(); - this.renderReactionsView(); - this.renderEventsView(); - this.renderRulesView(); - this.renderSBMLComponentsView(); - }, - renderEventsView: function () { - let eventsViewer = new EventsViewer({ - collection: this.model.eventsCollection, - readOnly: true - }); - app.registerRenderSubview(this, eventsViewer, "events-viewer-container"); - }, - renderParametersView: function () { - let parametersViewer = new ParametersViewer({ - collection: this.model.parameters, - readOnly: true - }); - app.registerRenderSubview(this, parametersViewer, "parameters-viewer-container"); - }, - renderReactionsView: function () { - let reactionsViewer = new ReactionsViewer({ - collection: this.model.reactions, - readOnly: true - }); - app.registerRenderSubview(this, reactionsViewer, "reactions-viewer-container"); - }, - renderRulesView: function () { - let rulesViewer = new RulesViewer({ - collection: this.model.rules, - readOnly: true - }); - app.registerRenderSubview(this, rulesViewer, "rules-viewer-container"); - }, - renderSBMLComponentsView: function () { - let sbmlComponentsView = new SBMLComponentsView({ - functionDefinitions: this.model.functionDefinitions, - readOnly: true - }); - app.registerRenderSubview(this, sbmlComponentsView, "sbml-components-viewer-container"); - }, - renderSpeciesView: function () { - let speciesViewer = new SpeciesViewer({ - collection: this.model.species, - spatial: this.model.is_spatial, - defaultMode: this.model.defaultMode, - readOnly: true - }); - app.registerRenderSubview(this, speciesViewer, "species-viewer-container"); - }, - changeCollapseButtonText: function (e) { - app.changeCollapseButtonText(this, e); - } -}); From 9075d61cd3abbf20e2dc74420184a2075b4278f9 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Wed, 21 Jul 2021 11:07:21 -0400 Subject: [PATCH 180/192] Wrote unit tests for the stochss file class. --- stochss/tests/test_stochss_file.py | 270 +++++++++++++++++++++++++++++ 1 file changed, 270 insertions(+) create mode 100644 stochss/tests/test_stochss_file.py diff --git a/stochss/tests/test_stochss_file.py b/stochss/tests/test_stochss_file.py new file mode 100644 index 0000000000..e7d8949be1 --- /dev/null +++ b/stochss/tests/test_stochss_file.py @@ -0,0 +1,270 @@ +''' +StochSS is a platform for simulating biochemical systems +Copyright (C) 2019-2021 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 logging +import zipfile +import unittest +import tempfile +# import datetime + +from unittest import mock +from pathlib import Path + +from stochss.handlers import StochSSFile +from stochss.handlers.util.stochss_errors import StochSSFileNotFoundError, StochSSUnzipError, \ + StochSSFileExistsError, StochSSPermissionsError + +os.chdir('/stochss') + +# pylint: disable=too-many-public-methods +# pylint: disable=line-too-long +class TestStochSSFileObject(unittest.TestCase): + ''' + ################################################################################################ + Unit tests for the StochSS file class. + ################################################################################################ + ''' + def setUp(self): + ''' Create a temporary directory with a file for each file test. ''' + self.tempdir = tempfile.TemporaryDirectory() + StochSSFile.user_dir = self.tempdir.name + self.test_filepath = os.path.join(self.tempdir.name, "test_file") + Path(self.test_filepath).touch() + + + def tearDown(self): + ''' Cleanup the temp directory after each test. ''' + self.tempdir.cleanup() + StochSSFile.user_dir = os.path.expanduser("~") + + ################################################################################################ + # Unit tests for the StochSS file class __init__ function. + ################################################################################################ + + def test_init__new_file__unique(self): + ''' Check if the new file is written correctly. ''' + StochSSFile(path="test_new_file", new=True) + self.assertIn("test_new_file", os.listdir(self.tempdir.name)) + + + def test_init__new_binary_file__unique(self): + ''' Check if the new binary file is writen correctly. ''' + StochSSFile(path="test_new_file", new=True, body="test body".encode()) + self.assertIn("test_new_file", os.listdir(self.tempdir.name)) + + + def test_init__new_file__not_unique(self): + ''' Check if the new file is writen correctly with a unique name. ''' + StochSSFile(path="test_file", new=True) + self.assertIn("test_file(1)", os.listdir(self.tempdir.name)) + + ################################################################################################ + # Unit tests for the StochSS file class delete function. + ################################################################################################ + + def test_delete(self): + ''' Check if the file is deleted successfully. ''' + test_file = StochSSFile(path=self.test_filepath) + test_resp = test_file.delete() + self.assertNotIn("test_file", os.listdir(self.tempdir.name)) + self.assertIsInstance(test_resp, str) + + + def test_delete__file_not_found_error(self): + ''' Check if the StochSSFileNotFoundError is raised when the target file is missing. ''' + test_file = StochSSFile(path=self.test_filepath) + with mock.patch("os.remove", mock.mock_open()) as mock_remove: + mock_remove.side_effect = FileNotFoundError + with self.assertRaises(StochSSFileNotFoundError): + test_file.delete() + + + def test_delete_permission_error(self): + ''' Check if the StochSSPermissionsError is raised when the user doesn't have the correct permissions. ''' + test_file = StochSSFile(path=self.test_filepath) + with mock.patch("os.remove") as mock_remove: + mock_remove.side_effect = PermissionError + with self.assertRaises(StochSSPermissionsError): + test_file.delete() + + ################################################################################################ + # Unit tests for the StochSS file class duplicate function. + ################################################################################################ + + def test_dulpicate(self): + ''' Check if the file is copied successfully. ''' + test_file = StochSSFile(path=self.test_filepath) + test_resp = test_file.duplicate() + self.assertIn("Message", test_resp.keys()) + self.assertIn("File", test_resp.keys()) + self.assertIn("test_file-copy", os.listdir(self.tempdir.name)) + + + def test_duplicate__model_in_new_format_project(self): + ''' Check if a model in a new format project is copied successfully. ''' + test_proj_path = os.path.join(self.tempdir.name, "test.proj") + test_wkgp_path = os.path.join(test_proj_path, "test.wkgp") + test_model_path = os.path.join(test_wkgp_path, "test.mdl") + os.makedirs(test_wkgp_path) + Path(test_model_path).touch() + test_file = StochSSFile(path=test_model_path) + test_resp = test_file.duplicate() + self.assertIn("Message", test_resp.keys()) + self.assertIn("File", test_resp.keys()) + self.assertIn("test-copy.wkgp", os.listdir(test_proj_path)) + self.assertIn("test-copy.mdl", os.listdir(os.path.join(test_proj_path, "test-copy.wkgp"))) + + + def test_duplicate__file_not_found_error(self): + ''' Check if the StochSSFileNotFoundError is raised when the target file is missing. ''' + test_file = StochSSFile(path=self.test_filepath) + with mock.patch("shutil.copyfile", mock.mock_open()) as mock_copyfile: + mock_copyfile.side_effect = FileNotFoundError + with self.assertRaises(StochSSFileNotFoundError): + test_file.duplicate() + + + def test_duplicate_permission_error(self): + ''' Check if the StochSSPermissionsError is raised when the user doesn't have the correct permissions. ''' + test_file = StochSSFile(path=self.test_filepath) + with mock.patch("shutil.copyfile") as mock_copyfile: + mock_copyfile.side_effect = PermissionError + with self.assertRaises(StochSSPermissionsError): + test_file.duplicate() + + ################################################################################################ + # Unit tests for the StochSS file class move function. + ################################################################################################ + + def test_move(self): + ''' Check if the file is moved successfully. ''' + test_location = os.path.join(self.tempdir.name, "test_location") + test_file_path = os.path.join(test_location, "test_file") + os.mkdir(test_location) + test_file = StochSSFile(path=self.test_filepath) + test_resp = test_file.move(location=test_file_path) + self.assertIsInstance(test_resp, str) + self.assertIn("test_file", os.listdir(test_location)) + + + def test_move__file_not_found_error(self): + ''' Check if the StochSSFileNotFoundError is raised when the target file is missing. ''' + test_file = StochSSFile(path=self.test_filepath) + with mock.patch("os.rename", mock.mock_open()) as mock_rename: + mock_rename.side_effect = FileNotFoundError + with self.assertRaises(StochSSFileNotFoundError): + test_file.move("test_folder") + + + def test_move_permission_error(self): + ''' Check if the StochSSPermissionsError is raised when the user doesn't have the correct permissions. ''' + test_file = StochSSFile(path=self.test_filepath) + with mock.patch("os.rename") as mock_rename: + mock_rename.side_effect = PermissionError + with self.assertRaises(StochSSPermissionsError): + test_file.move("test_folder") + + ################################################################################################ + # Unit tests for the StochSS file class read function. + ################################################################################################ + + def test_read(self): + ''' Check if the file is read successfully. ''' + test_file = StochSSFile(path=self.test_filepath) + with mock.patch("builtins.open", mock.mock_open(read_data="Test Contents"), create=True) as mock_file: + test_data = test_file.read() + mock_file.assert_called_once_with(self.test_filepath, "r") + self.assertEqual(test_data, "Test Contents") + + + def test_read__file_not_found_error(self): + ''' Check if the StochSSFileNotFoundError is raised when the target file is missing. ''' + test_file = StochSSFile(path=self.test_filepath) + with mock.patch("builtins.open", mock.mock_open()) as mock_file: + mock_file.side_effect = FileNotFoundError + with self.assertRaises(StochSSFileNotFoundError): + test_file.read() + + ################################################################################################ + # Unit tests for the StochSS file class unzip function. + ################################################################################################ + + def test_unzip__from_upload_true(self): + ''' Check the return for unzipping an uploaded file. ''' + test_dir_path = os.path.join(self.tempdir.name, "test_folder") + os.mkdir(test_dir_path) + test_file_path = os.path.join(test_dir_path, "test_file") + Path(test_file_path).touch() + test_archive = shutil.make_archive(os.path.join(self.tempdir.name, "test_zip"), "zip", self.tempdir.name, test_dir_path) + shutil.rmtree(test_dir_path) + test_file = StochSSFile(path=test_archive) + test_resp = test_file.unzip() + self.assertIsInstance(test_resp, list) + self.assertFalse(len(test_resp)) + + + def test_unzip__from_upload_false(self): + ''' Check the return for unzipping a file. ''' + test_dir_path = os.path.join(self.tempdir.name, "test_folder") + os.mkdir(test_dir_path) + test_file_path = os.path.join(test_dir_path, "test_file") + Path(test_file_path).touch() + test_archive = shutil.make_archive(os.path.join(self.tempdir.name, "test_zip"), "zip", self.tempdir.name, test_dir_path) + shutil.rmtree(test_dir_path) + test_file = StochSSFile(path=test_archive) + test_resp = test_file.unzip(from_upload=False) + self.assertIsInstance(test_resp, dict) + self.assertIn("message", test_resp.keys()) + + + def test_unzip__file_exists_error(self): + ''' Check if the StochSSFileExistsError is raised when the contents of the archive already exist. ''' + test_dir_path = os.path.join(self.tempdir.name, "test_folder") + os.mkdir(test_dir_path) + test_file_path = os.path.join(test_dir_path, "test_file") + Path(test_file_path).touch() + shutil.make_archive(os.path.join(self.tempdir.name, "test_zip"), "zip", self.tempdir.name, "test_folder") + test_file = StochSSFile(path="test_zip.zip") + with self.assertRaises(StochSSFileExistsError): + test_file.unzip() + + + def test_unzip__bad_zip_file_error__from_upload_true(self): + ''' Check if an error list is returned when the target file cannot be unzipped. ''' + test_file_path = os.path.join(self.tempdir.name, "test_file.zip") + Path(test_file_path).touch() + test_file = StochSSFile(path=test_file_path) + with mock.patch("zipfile.ZipFile.extractall", mock.mock_open()) as mock_extractall: + mock_extractall.side_effect = zipfile.BadZipFile + errors = test_file.unzip() + self.assertIsInstance(errors, list) + self.assertTrue(len(errors) == 1) + + + def test_unzip__bad_zip_file_error__from_upload_false(self): + ''' Check if the StochSSUnzipError is raised when the target file cannot be unzipped. ''' + test_file_path = os.path.join(self.tempdir.name, "test_file.zip") + Path(test_file_path).touch() + test_file = StochSSFile(path=test_file_path) + with mock.patch("zipfile.ZipFile.extractall", mock.mock_open()) as mock_extractall: + mock_extractall.side_effect = zipfile.BadZipFile + with self.assertRaises(StochSSUnzipError): + test_file.unzip(from_upload=False) From db4f14429ec76cfc8d7ea443bc1af64489621429 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Wed, 21 Jul 2021 11:07:54 -0400 Subject: [PATCH 181/192] Added stochss file test to the test suite. --- stochss/tests/run_tests.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/stochss/tests/run_tests.py b/stochss/tests/run_tests.py index 896b1a3be4..b551054521 100755 --- a/stochss/tests/run_tests.py +++ b/stochss/tests/run_tests.py @@ -37,13 +37,15 @@ import test_model_template import test_settings_template import test_stochss_base + import test_stochss_file import test_gillespy2 modules = [ test_model_template, test_settings_template, test_gillespy2, - test_stochss_base + test_stochss_base, + test_stochss_file ] for module in modules: From 946f5cdfe478c90debe59ee99cab938a80fdb8e9 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Wed, 21 Jul 2021 11:43:04 -0400 Subject: [PATCH 182/192] Refactored the presentation functions to always return the links. --- stochss/handlers/file_browser.py | 9 ++++++--- stochss/handlers/models.py | 9 ++++++--- stochss/handlers/util/stochss_model.py | 8 ++++---- stochss/handlers/util/stochss_notebook.py | 13 +++++++------ 4 files changed, 23 insertions(+), 16 deletions(-) diff --git a/stochss/handlers/file_browser.py b/stochss/handlers/file_browser.py index 5d1b7f4ffd..b488081f81 100644 --- a/stochss/handlers/file_browser.py +++ b/stochss/handlers/file_browser.py @@ -752,9 +752,12 @@ async def get(self): try: notebook = StochSSNotebook(path=path) log.info("Publishing the %s presentation", notebook.get_name()) - links = notebook.publish_presentation() - resp = {"message": f"Successfully published the {notebook.get_name()} presentation", - "links": links} + links, exists = notebook.publish_presentation() + if exists: + message = f"A presentation for {notebook.get_name()} already exists." + else: + message = f"Successfully published the {notebook.get_name()} presentation" + resp = {"message": message, "links": links} log.info(resp['message']) log.debug("Response Message: %s", resp) self.write(resp) diff --git a/stochss/handlers/models.py b/stochss/handlers/models.py index 24e9114a27..1900659ece 100644 --- a/stochss/handlers/models.py +++ b/stochss/handlers/models.py @@ -431,9 +431,12 @@ async def get(self): model = file_objs[ext](path=path) log.info("Publishing the %s presentation", model.get_name()) links, data = model.publish_presentation() - file_objs[ext](**data) - resp = {"message": f"Successfully published the {model.get_name()} presentation", - "links": links} + if data is None: + message = f"A presentation for {model.get_name()} already exists." + else: + message = f"Successfully published the {model.get_name()} presentation." + file_objs[ext](**data) + resp = {"message": message, "links": links} log.info(resp['message']) log.debug("Response Message: %s", resp) self.write(resp) diff --git a/stochss/handlers/util/stochss_model.py b/stochss/handlers/util/stochss_model.py index cc562540cc..e499c027b2 100644 --- a/stochss/handlers/util/stochss_model.py +++ b/stochss/handlers/util/stochss_model.py @@ -32,7 +32,7 @@ from .stochss_base import StochSSBase from .stochss_errors import StochSSAPIError, StochSSFileNotFoundError, FileNotJSONFormatError, \ - StochSSModelFormatError, StochSSFileExistsError, StochSSPermissionsError + StochSSModelFormatError, StochSSPermissionsError class StochSSModel(StochSSBase): ''' @@ -483,15 +483,15 @@ def publish_presentation(self): file = f"{hashlib.md5(model.encode('utf-8')).hexdigest()}.mdl" dst = os.path.join(present_dir, file) if os.path.exists(dst): - message = "A presentation with this name already exists" - raise StochSSFileExistsError(message) + data = None + else: + data = {"path": dst, "new":True, "model":self.model} query_str = f"?owner={hostname}&file={file}" present_link = f"https://staging.stochss.org/stochss/present-model{query_str}" downloadlink = os.path.join("https://staging.stochss.org/stochss/download_presentation", hostname, file) open_link = f"https://staging.stochss.org?open={downloadlink}" links = {"presentation": present_link, "download": downloadlink, "open": open_link} - data = {"path": dst, "new":True, "model":self.model} return links, data except PermissionError as err: message = f"You do not have permission to publish this file: {str(err)}" diff --git a/stochss/handlers/util/stochss_notebook.py b/stochss/handlers/util/stochss_notebook.py index e4fd63bc89..bb71f45896 100644 --- a/stochss/handlers/util/stochss_notebook.py +++ b/stochss/handlers/util/stochss_notebook.py @@ -29,7 +29,7 @@ from .stochss_base import StochSSBase from .stochss_errors import StochSSFileNotFoundError, StochSSModelFormatError, \ - StochSSPermissionsError, StochSSFileExistsError + StochSSPermissionsError class StochSSNotebook(StochSSBase): ''' @@ -1047,12 +1047,13 @@ def publish_presentation(self): file = f"{hashlib.md5(nb_str.encode('utf-8')).hexdigest()}.ipynb" dst = os.path.join(present_dir, file) if os.path.exists(dst): - message = "A presentation with this name already exists" - raise StochSSFileExistsError(message) + exists = True + else: + exists = False + with open(dst, "w") as presentation_file: + json.dump(notebook_pres, presentation_file) links = self.__get_presentation_links(hostname, file) - with open(dst, "w") as presentation_file: - json.dump(notebook_pres, presentation_file) - return links + return links, exists except PermissionError as err: message = f"You do not have permission to publish this file: {str(err)}" raise StochSSPermissionsError(message, traceback.format_exc()) from err From acec781698f820c0e8fb06d544482658592bf38b Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Wed, 21 Jul 2021 11:43:39 -0400 Subject: [PATCH 183/192] Fixed syntax error in model presentation page. --- client/pages/model-presentation.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/client/pages/model-presentation.js b/client/pages/model-presentation.js index 64ba808e22..b26b515cdc 100644 --- a/client/pages/model-presentation.js +++ b/client/pages/model-presentation.js @@ -95,7 +95,7 @@ let ModelPresentationPage = PageView.extend({ }, renderRulesContainer: function () { let rules = new Rules({ - collection: this.model.rules + collection: this.model.rules, readOnly: true }); app.registerRenderSubview(this, rules, "model-rules"); From eff14e6e9d8668ecab3111ac49c4fbdca20a613a Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Wed, 21 Jul 2021 11:51:59 -0400 Subject: [PATCH 184/192] Removed 'Presentation' from the publish presentation buttons and context menu options. --- client/pages/file-browser.js | 4 ++-- client/templates/includes/gillespyResults.pug | 2 +- client/templates/includes/gillespyResultsEnsemble.pug | 2 +- client/templates/includes/modelStateButtons.pug | 2 +- client/templates/includes/parameterSweepResults.pug | 2 +- client/views/file-browser-view.js | 4 ++-- 6 files changed, 8 insertions(+), 8 deletions(-) diff --git a/client/pages/file-browser.js b/client/pages/file-browser.js index bb488e43ca..15d3d04d28 100644 --- a/client/pages/file-browser.js +++ b/client/pages/file-browser.js @@ -1331,8 +1331,8 @@ let FileBrowser = PageView.extend({ } } let notebook = { - "publishPresentation" : { - "label" : "Publish Presentation", + "publish" : { + "label" : "Publish", "_disabled" : false, "separator_before" : false, "separator_after" : false, diff --git a/client/templates/includes/gillespyResults.pug b/client/templates/includes/gillespyResults.pug index a37a6c6858..ec7dc3f17e 100644 --- a/client/templates/includes/gillespyResults.pug +++ b/client/templates/includes/gillespyResults.pug @@ -64,7 +64,7 @@ div#workflow-results.card.card-body button.btn.btn-primary.box-shadow(id="download-results-csv" data-hook="download-results-csv") Download Results as .csv - button.btn.btn-primary.box-shadow(id="job-presentation" data-hook="job-presentation") Publish Presentation + button.btn.btn-primary.box-shadow(id="job-presentation" data-hook="job-presentation") Publish div.saving-status(data-hook="job-action-start") diff --git a/client/templates/includes/gillespyResultsEnsemble.pug b/client/templates/includes/gillespyResultsEnsemble.pug index f7feb8ab88..87282e234a 100644 --- a/client/templates/includes/gillespyResultsEnsemble.pug +++ b/client/templates/includes/gillespyResultsEnsemble.pug @@ -177,7 +177,7 @@ div#workflow-results.card.card-body button.btn.btn-primary.box-shadow(id="download-results-csv" data-hook="download-results-csv") Download Results as .csv - button.btn.btn-primary.box-shadow(id="job-presentation" data-hook="job-presentation") Publish Presentation + button.btn.btn-primary.box-shadow(id="job-presentation" data-hook="job-presentation") Publish div.saving-status(data-hook="job-action-start") diff --git a/client/templates/includes/modelStateButtons.pug b/client/templates/includes/modelStateButtons.pug index 32d0ce7f0d..5cc08474a9 100644 --- a/client/templates/includes/modelStateButtons.pug +++ b/client/templates/includes/modelStateButtons.pug @@ -38,5 +38,5 @@ div.mdl-edit-btn li.dropdown-item(id="stochss-ps" data-hook="stochss-ps" data-type="psweep") Parameter Sweep li.dropdown-item(data-hook="new-workflow" data-type="notebook") Jupyter Notebook - button.btn.btn-primary.box-shadow(data-hook="presentation") Publish Presentation + button.btn.btn-primary.box-shadow(data-hook="presentation") Publish \ No newline at end of file diff --git a/client/templates/includes/parameterSweepResults.pug b/client/templates/includes/parameterSweepResults.pug index a837022517..ccd407c306 100644 --- a/client/templates/includes/parameterSweepResults.pug +++ b/client/templates/includes/parameterSweepResults.pug @@ -161,7 +161,7 @@ div#workflow-results.card.card-body button.btn.btn-primary.box-shadow(id="download-results-csv" data-hook="download-results-csv") Download Results as .csv - button.btn.btn-primary.box-shadow(id="job-presentation" data-hook="job-presentation") Publish Presentation + button.btn.btn-primary.box-shadow(id="job-presentation" data-hook="job-presentation") Publish div.saving-status(data-hook="job-action-start") diff --git a/client/views/file-browser-view.js b/client/views/file-browser-view.js index ab054333ef..edb54b2307 100644 --- a/client/views/file-browser-view.js +++ b/client/views/file-browser-view.js @@ -1390,8 +1390,8 @@ module.exports = View.extend({ } } let notebook = { - "publishPresentation" : { - "label" : "Publish Presentation", + "publish" : { + "label" : "Publish", "_disabled" : false, "separator_before" : false, "separator_after" : false, From e97efaf77f74d50a63bbc6adac8a847e8297c7ec Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Wed, 21 Jul 2021 11:52:57 -0400 Subject: [PATCH 185/192] disabled the event listener for job publishing presentations. --- client/views/workflow-results.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/client/views/workflow-results.js b/client/views/workflow-results.js index 308e44dece..95dc9fba28 100644 --- a/client/views/workflow-results.js +++ b/client/views/workflow-results.js @@ -51,7 +51,7 @@ module.exports = View.extend({ 'click [data-target=download-json]' : 'handleDownloadJSONClick', 'click [data-hook=convert-to-notebook]' : 'handleConvertToNotebookClick', 'click [data-hook=download-results-csv]' : 'handleDownloadResultsCsvClick', - 'click [data-hook=job-presentation]' : 'handlePresentationClick' + // 'click [data-hook=job-presentation]' : 'handlePresentationClick' }, initialize: function (attrs, options) { View.prototype.initialize.apply(this, arguments); From 8138f637c5c208ed011744c251b411124c811943 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Wed, 21 Jul 2021 13:12:14 -0400 Subject: [PATCH 186/192] Fixed download links and routes. --- client/modals.js | 12 +++++++++--- client/pages/model-presentation.js | 4 ++-- client/pages/notebook-presentation.js | 4 ++-- jupyterhub/jupyterhub_config.py | 2 +- 4 files changed, 14 insertions(+), 8 deletions(-) diff --git a/client/modals.js b/client/modals.js index bb2acf9a1c..f1eb40c27a 100644 --- a/client/modals.js +++ b/client/modals.js @@ -237,13 +237,19 @@ let templates = {

${headers[0]}

- Open ${name} Presentation +

${headers[1]}

- Download ${name} Presentation +

${headers[2]}

- Open ${name} Presentation +
diff --git a/client/pages/model-presentation.js b/client/pages/model-presentation.js index b26b515cdc..72070bc154 100644 --- a/client/pages/model-presentation.js +++ b/client/pages/model-presentation.js @@ -60,8 +60,8 @@ let ModelPresentationPage = PageView.extend({ } }); let downloadStart = "https://staging.stochss.org/stochss/download_presentation"; - this.downloadLink = path.join(downloadStart, owner, file); - this.openLink = "open.stochss.org?open=" + this.downloadLink; + this.downloadLink = downloadStart + "/" + owner + "/" + file; + this.openLink = "https://open.stochss.org?open=" + this.downloadLink; }, renderSubviews: function () { PageView.prototype.render.apply(this, arguments); diff --git a/client/pages/notebook-presentation.js b/client/pages/notebook-presentation.js index 0817d71136..54b3e49e0e 100644 --- a/client/pages/notebook-presentation.js +++ b/client/pages/notebook-presentation.js @@ -48,8 +48,8 @@ let NotebookPresentationPage = PageView.extend({ } }); let downloadStart = "https://staging.stochss.org/stochss/notebook/download_presentation"; - this.downloadLink = path.join(downloadStart, owner, file); - this.openLink = "open.stochss.org?open=" + this.downloadLink; + this.downloadLink = downloadStart + "/" + owner + "/" + file; + this.openLink = "https://open.stochss.org?open=" + this.downloadLink; }, renderSubviews: function (html) { PageView.prototype.render.apply(this, arguments); diff --git a/jupyterhub/jupyterhub_config.py b/jupyterhub/jupyterhub_config.py index 7da4a96ffb..1b09d4e43e 100644 --- a/jupyterhub/jupyterhub_config.py +++ b/jupyterhub/jupyterhub_config.py @@ -91,7 +91,7 @@ (r"/stochss/api/file/json-data\/?", JsonFileAPIHandler), (r"/stochss/presentation-download/(\w+)/(.+)\/?", DownModelPresentationAPIHandler), (r"/stochss/api/notebook/load\/?", NotebookAPIHandler), - (r"/stochss/notebook/presentation-download/(\w+)/(.+)\/?", + (r"/stochss/notebook/download_presentation/(\w+)/(.+)\/?", DownNotebookPresentationAPIHandler) ] From d9fd3c38436ef740ac605436a1b011480de4edcd Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Wed, 21 Jul 2021 15:09:11 -0400 Subject: [PATCH 187/192] Fixed the anchor tags for the presentation links. --- client/modals.js | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/client/modals.js b/client/modals.js index f1eb40c27a..b9ccd2ff77 100644 --- a/client/modals.js +++ b/client/modals.js @@ -238,7 +238,7 @@ let templates = {

${headers[0]}

${headers[1]}

@@ -248,7 +248,7 @@ let templates = {

${headers[2]}

From 45b5f3d65b83aa47886a47896073eef026c49d64 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Wed, 21 Jul 2021 15:13:01 -0400 Subject: [PATCH 188/192] Fixed route for model presentation downloads. --- jupyterhub/jupyterhub_config.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/jupyterhub/jupyterhub_config.py b/jupyterhub/jupyterhub_config.py index 1b09d4e43e..091e9602ab 100644 --- a/jupyterhub/jupyterhub_config.py +++ b/jupyterhub/jupyterhub_config.py @@ -89,7 +89,7 @@ (r"/stochss/present-model\/?", ModelPresentationHandler), (r"/stochss/present-notebook\/?", NotebookPresentationHandler), (r"/stochss/api/file/json-data\/?", JsonFileAPIHandler), - (r"/stochss/presentation-download/(\w+)/(.+)\/?", DownModelPresentationAPIHandler), + (r"/stochss/download_presentation/(\w+)/(.+)\/?", DownModelPresentationAPIHandler), (r"/stochss/api/notebook/load\/?", NotebookAPIHandler), (r"/stochss/notebook/download_presentation/(\w+)/(.+)\/?", DownNotebookPresentationAPIHandler) From a39ba758c517c3fe381cb25abb34ed9cbd7fcb70 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Wed, 21 Jul 2021 16:25:44 -0400 Subject: [PATCH 189/192] Refactored the tooltip setup function to use an event listener instead of the deprecated click function. --- client/app.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/client/app.js b/client/app.js index 5fd33ed0e3..c4db96216a 100644 --- a/client/app.js +++ b/client/app.js @@ -196,7 +196,7 @@ let newWorkflow = (parent, mdlPath, isSpatial, type) => { tooltipSetup = () => { $(function () { $('[data-toggle="tooltip"]').tooltip(); - $('[data-toggle="tooltip"]').click(function () { + $('[data-toggle="tooltip"]').on('click ', function () { $('[data-toggle="tooltip"]').tooltip("hide"); }); }); From 11d69f5323a16026effaf3737bc573c12b1e7525 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Wed, 21 Jul 2021 16:26:14 -0400 Subject: [PATCH 190/192] Removed commented code. --- client/model-view/views/reactions-view.js | 1 - 1 file changed, 1 deletion(-) diff --git a/client/model-view/views/reactions-view.js b/client/model-view/views/reactions-view.js index 1d25ba3347..912745f565 100644 --- a/client/model-view/views/reactions-view.js +++ b/client/model-view/views/reactions-view.js @@ -90,7 +90,6 @@ module.exports = View.extend({ if (this.collection.length) { this.setSelectedReaction(this.collection.at(0)); this.collection.trigger("select", this.selectedReaction); - // this.collection.trigger("change"); } this.toggleAddReactionButton(); if(this.collection.parent.parameters.length > 0){ From 59a992fe8ef44be02b05b1c2c45c32f76fb01376 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Thu, 22 Jul 2021 08:06:41 -0400 Subject: [PATCH 191/192] Switched the links to live. --- client/pages/model-presentation.js | 2 +- client/pages/notebook-presentation.js | 2 +- stochss/handlers/util/stochss_model.py | 6 +++--- stochss/handlers/util/stochss_notebook.py | 6 +++--- 4 files changed, 8 insertions(+), 8 deletions(-) diff --git a/client/pages/model-presentation.js b/client/pages/model-presentation.js index 72070bc154..e3a55256dc 100644 --- a/client/pages/model-presentation.js +++ b/client/pages/model-presentation.js @@ -59,7 +59,7 @@ let ModelPresentationPage = PageView.extend({ self.renderSubviews(); } }); - let downloadStart = "https://staging.stochss.org/stochss/download_presentation"; + let downloadStart = "https://live.stochss.org/stochss/download_presentation"; this.downloadLink = downloadStart + "/" + owner + "/" + file; this.openLink = "https://open.stochss.org?open=" + this.downloadLink; }, diff --git a/client/pages/notebook-presentation.js b/client/pages/notebook-presentation.js index 54b3e49e0e..932b2175bc 100644 --- a/client/pages/notebook-presentation.js +++ b/client/pages/notebook-presentation.js @@ -47,7 +47,7 @@ let NotebookPresentationPage = PageView.extend({ self.renderSubviews(body.html); } }); - let downloadStart = "https://staging.stochss.org/stochss/notebook/download_presentation"; + let downloadStart = "https://live.stochss.org/stochss/notebook/download_presentation"; this.downloadLink = downloadStart + "/" + owner + "/" + file; this.openLink = "https://open.stochss.org?open=" + this.downloadLink; }, diff --git a/stochss/handlers/util/stochss_model.py b/stochss/handlers/util/stochss_model.py index e499c027b2..29e4d4b1ab 100644 --- a/stochss/handlers/util/stochss_model.py +++ b/stochss/handlers/util/stochss_model.py @@ -487,10 +487,10 @@ def publish_presentation(self): else: data = {"path": dst, "new":True, "model":self.model} query_str = f"?owner={hostname}&file={file}" - present_link = f"https://staging.stochss.org/stochss/present-model{query_str}" - downloadlink = os.path.join("https://staging.stochss.org/stochss/download_presentation", + present_link = f"https://live.stochss.org/stochss/present-model{query_str}" + downloadlink = os.path.join("https://live.stochss.org/stochss/download_presentation", hostname, file) - open_link = f"https://staging.stochss.org?open={downloadlink}" + open_link = f"https://live.stochss.org?open={downloadlink}" links = {"presentation": present_link, "download": downloadlink, "open": open_link} return links, data except PermissionError as err: diff --git a/stochss/handlers/util/stochss_notebook.py b/stochss/handlers/util/stochss_notebook.py index bb71f45896..5397d599d8 100644 --- a/stochss/handlers/util/stochss_notebook.py +++ b/stochss/handlers/util/stochss_notebook.py @@ -873,10 +873,10 @@ def __get_gillespy2_solver_name(self): @classmethod def __get_presentation_links(cls, hostname, file): query_str = f"?owner={hostname}&file={file}" - present_link = f"https://staging.stochss.org/stochss/present-notebook{query_str}" - dl_link_base = "https://staging.stochss.org/stochss/notebook/download_presentation" + present_link = f"https://live.stochss.org/stochss/present-notebook{query_str}" + dl_link_base = "https://live.stochss.org/stochss/notebook/download_presentation" download_link = os.path.join(dl_link_base, hostname, file) - open_link = f"https://staging.stochss.org?open={download_link}" + open_link = f"https://live.stochss.org?open={download_link}" return {"presentation": present_link, "download": download_link, "open": open_link} def create_1dps_notebook(self): From 41fc3b55b73d9dd073459d4deb0113f6edeac7be Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Thu, 22 Jul 2021 08:12:51 -0400 Subject: [PATCH 192/192] Updated the gillespy2 version to 1.6.3. --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 630c67b797..876eceebc1 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==1.6.2 +gillespy2==1.6.3 sciope==0.4 pygmsh==5.0.2 meshio==2.3.10