Merge branch 'develop' of github.com:stochss/stochss into develop

.github/workflows/pylint_on_pull_request.yml

@@ -22,7 +22,7 @@ jobs:
         BASE_REF: ${{ github.event.pull_request.base.ref }}
     - name: Get Base Lint Score
       run: |
-        echo ::set-env name=BASE_LINT::$(git diff --name-only --diff-filter=M $HEAD_REF | grep -E "\.py" | xargs pylint | grep -E -o "at [0-9.-]+" | grep -E -o [0-9.-]+)
+        echo BASE_LINT=$(git diff --name-only --diff-filter=M $HEAD_REF | grep -E "\.py" | xargs pylint | grep -E -o "at [0-9.-]+" | grep -E -o [0-9.-]+) >> $GITHUB_ENV
       env:
         HEAD_REF: ${{ github.event.pull_request.head.ref }}
       if: always()
@@ -31,17 +31,20 @@ jobs:
       env:
         HEAD_REF: ${{ github.event.pull_request.head.ref }}
     - name: Get Lint Delta Sign (+/-)
-      run: echo ::set-env name=PASSING_SCORE::$(git diff --name-only --diff-filter=M $BASE_REF | grep -E "\.py" | xargs pylint | grep -Eo "10, [+-]" | grep -Eo [+-] )
+      run: |
+        echo PASSING_SCORE=$(git diff --name-only --diff-filter=M $BASE_REF | grep -E "\.py" | xargs pylint | grep -Eo "10, [+-]" | grep -Eo [+-] ) >> $GITHUB_ENV
       env:
         BASE_REF: ${{ github.event.pull_request.base.ref }}
       if: always()
     - name: Get Head Lint Score
-      run: echo ::set-env name=HEAD_LINT::$(git diff --name-only --diff-filter=M $BASE_REF | grep -E "\.py" | xargs pylint | grep -E -o "at [0-9.-]+" | grep -E -o [0-9.-]+)
+      run: |
+        echo HEAD_LINT=$(git diff --name-only --diff-filter=M $BASE_REF | grep -E "\.py" | xargs pylint | grep -E -o "at [0-9.-]+" | grep -E -o [0-9.-]+) >> $GITHUB_ENV
       env:
         BASE_REF: ${{ github.event.pull_request.base.ref }}
       if: always()
     - name: Get Added Files Lint Score
-      run: echo ::set-env name=ADDED_LINT::$(git diff --name-only --diff-filter=A $BASE_REF | grep -E "\.py" | xargs pylint | grep -E -o "at [0-9.-]+" | grep -E -o [0-9.-]+)
+      run: |
+        echo ADDED_LINT=$(git diff --name-only --diff-filter=A $BASE_REF | grep -E "\.py" | xargs pylint | grep -E -o "at [0-9.-]+" | grep -E -o [0-9.-]+) >> $GITHUB_ENV
       env:
         BASE_REF: ${{ github.event.pull_request.base.ref }}
       if: always()

.gitignore

@@ -8,6 +8,12 @@ stochss-model-editor.html
 stochss-workflow-manager.html
 stochss-workflow-selection.html
 stochss-project-manager.html
+multiple-plots-page.html
+stochss-domain-editor.html
+stochss-loading-page.html
+stochss-project-browser.html
+stochss-quick-start.html
+stochss-user-home.html
 *.swp
 *.swo
 package-lock.json

__version__.py

@@ -5,7 +5,7 @@
 # @website https://github.com/stochss/stochss
 # =============================================================================
 
-__version__ = '2.1.6'
+__version__ = '2.3.2'
 __title__ = 'StochSS'
 __description__ = 'StochSS is an integrated development environment (IDE) \
                     for simulation of biochemical networks.'

client/app.js

@@ -17,7 +17,11 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
 
 //var config = require('./config.js')(process.env.NODE_ENV);
+let xhr = require('xhr');
+let $ = require('jquery');
 let path = require('path');
+//support files
+let modals = require('./modals');
 
 let routePrefix = 'stochss';
 let apiPrefix =  path.join(routePrefix, 'api');
@@ -77,14 +81,128 @@ var BrowserDetect = {
   ]
 };
 
+let changeCollapseButtonText = (view, e) => {
+  let source = e.target.dataset.hook;
+  let isBtn = $(view.queryByHook(source)).attr("class").includes("btn");
+  let collapseContainer = $(view.queryByHook(source).dataset.target);
+  if(isBtn && !collapseContainer.attr("class").includes("collapsing")) {
+    let collapseBtn = $(view.queryByHook(source));
+    let text = collapseBtn.text();
+    text === '+' ? collapseBtn.text('-') : collapseBtn.text('+');
+  }
+};
+
+let registerRenderSubview = (parent, view, hook) => {
+  parent.registerSubview(view);
+  parent.renderSubview(view, parent.queryByHook(hook));
+};
+
+let getXHR = (endpoint, {
+  always = function (err, response, body) {}, success = function (err, response, body) {},
+  error = function (err, response, body) {}}={}) => {
+  xhr({uri: endpoint, json: true}, function (err, response, body) {
+    if(response.statusCode < 400) {
+      success(err, response, body);
+    }else if(response.statusCode < 500) {
+      error(err, response, body);
+    }else{
+      console.log("Critical Error Detected");
+    }
+    always(err, response, body);
+  });
+};
+
+let postXHR = (endpoint, data, {
+  always = function (err, response, body) {}, success = function (err, response, body) {},
+  error = function (err, response, body) {}}={}, isJSON) => {
+  xhr({uri: endpoint, json: isJSON !== undefined ? isJSON : true, method: "post", body: data}, function (err, response, body) {
+    if(response.statusCode < 400) {
+      success(err, response, body);
+    }else if(response.statusCode < 500) {
+      error(err, response, body);
+    }else{
+      console.log("Critical Error Detected");
+    }
+    always(err, response, body);
+  });
+};
+
 let getBrowser = () => {
   BrowserDetect.init();
   return {"name":BrowserDetect.browser,"version":BrowserDetect.version};
 }
 
+let validateName = (input, rename = false) => {
+  var error = ""
+  if(input.endsWith('/')) {
+    error = 'forward'
+  }
+  var invalidChars = "`~!@#$%^&*=+[{]}\"|:;'<,>?\\"
+  if(rename) {
+    invalidChars += "/"
+  }
+  for(var i = 0; i < input.length; i++) {
+    if(invalidChars.includes(input.charAt(i))) {
+      error = error === "" || error === "special" ? "special" : "both"
+    }
+  }
+  return error
+}
+
+let newWorkflow = (parent, mdlPath, isSpatial, type) => {
+  if(document.querySelector('#newWorkflowModal')) {
+    document.querySelector('#newWorkflowModal').remove()
+  }
+  let self = parent;
+  let ext = isSpatial ? /.smdl/g : /.mdl/g
+  let name = mdlPath.split('/').pop().replace(ext, "")
+  let modal = $(modals.newWorkflowHtml(name, type)).modal();
+  let okBtn = document.querySelector('#newWorkflowModal .ok-model-btn');
+  let input = document.querySelector('#newWorkflowModal #workflowNameInput');
+  okBtn.disabled = false;
+  input.addEventListener("keyup", function (event) {
+    if(event.keyCode === 13){
+      event.preventDefault();
+      okBtn.click();
+    }
+  });
+  input.addEventListener("input", function (e) {
+    let endErrMsg = document.querySelector('#newWorkflowModal #workflowNameInputEndCharError')
+    let charErrMsg = document.querySelector('#newWorkflowModal #workflowNameInputSpecCharError')
+    let error = validateName(input.value)
+    okBtn.disabled = error !== "" || input.value.trim() === ""
+    charErrMsg.style.display = error === "both" || error === "special" ? "block" : "none"
+    endErrMsg.style.display = error === "both" || error === "forward" ? "block" : "none"
+  });
+  okBtn.addEventListener('click', function (e) {
+    modal.modal("hide");
+    let typeCode = type === "Ensemble Simulation" ? "_ES" : "_PS";
+    let wkflFile = input.value.trim() + typeCode + ".wkfl";
+    if(mdlPath.includes(".proj") && !mdlPath.includes(".wkgp")){
+      var wkflPath = path.join(path.dirname(mdlPath), "WorkflowGroup1.wkgp", wkflFile);
+    }else{
+      var wkflPath = path.join(path.dirname(mdlPath), wkflFile);
+    }
+    let queryString = "?path=" + wkflPath + "&model=" + mdlPath + "&type=" + type;
+    let endpoint = path.join(getApiPath(), "workflow/new") + queryString;
+    getXHR(endpoint, {
+      success: function (err, response, body) {
+        window.location.href = path.join(getBasePath(), "stochss/workflow/edit") + "?path=" + body.path;
+      }
+    });
+  });
+}
+
 module.exports = {
     routePrefix: routePrefix,
     getApiPath: getApiPath,
     getBasePath: getBasePath,
-    getBrowser: getBrowser
+    getBrowser: getBrowser,
+    registerRenderSubview: registerRenderSubview,
+    changeCollapseButtonText: changeCollapseButtonText,
+    newWorkflow: newWorkflow,
+    getXHR: getXHR,
+    postXHR: postXHR
 };
+
+

client/modals.js

@@ -190,6 +190,39 @@ let templates = {
                     </div>
                   </div>
                 </div>`
+        },
+        fileSelect : (modalID, fileID, locationID, title, label, files) => {
+            return `
+                <div id=${modalID} class="modal" tabindex="-1" role="dialog">
+                  <div class="modal-dialog" role="document">
+                    <div class="modal-content">
+                      <div class="modal-header">
+                        <h5 class="modal-title">${title}</h5>
+                        <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+                          <span aria-hidden="true">&times;</span>
+                        </button>
+                      </div>
+                      <div class="modal-body">
+                        <div>
+                          <label for=${fileID}>${label}</label>
+                          <select id=${fileID} name=${fileID} autofocus>
+                            ${files}
+                          </select>
+                        </div>
+                        <div id="location-container" style="display: none;">
+                          <div class="text-info">This model was found in multiple locations</div>
+                          <label for=${locationID}>Location: </label>
+                          <select id=${locationID} name=${locationID} autofocus>
+                          </select>
+                        </div>
+                      </div>
+                      <div class="modal-footer">
+                        <button type="button" class="btn btn-primary ok-model-btn box-shadow" disabled>OK</button>
+                        <button type="button" class="btn btn-secondary box-shadow" data-dismiss="modal">Close</button>
+                      </div>
+                    </div>
+                  </div>
+                </div>`
         }
     }
 
@@ -200,10 +233,14 @@ module.exports = {
 
         return templates.confirmation(modalID, title)
     },
-    moveToTrashConfirmHtml : (fileType) => {
+    moveToTrashConfirmHtml : (fileType, newProjectFormat=false) => {
         let modalID = "moveToTrashConfirmModal"
         let title = `Move this ${fileType} to trash?`
 
+        if(newProjectFormat) {
+          let message = "The workflows for this model will be archived"
+          return templates.confirmation_with_message(modalID, title, message);
+        }
         return templates.confirmation(modalID, title)
     },
     emptyTrashConfirmHtml : () => {
@@ -237,17 +274,19 @@ module.exports = {
 
       return templates.input(modalID, inputID, title, label, value)
     },
-    newProjectModelHtml : (options) => {
+    newProjectModelHtml : (files) => {
       let modalID = "newProjectModelModal"
-      let selectID = "modelPathInput"
+      let fileID = "modelFileInput"
+      let locationID = "modelPathInput"
       let title = "Add Existing Model to Project"
-      let label = "Path to the Model"
-      options = options.map(function (name) {
-        return `<option value="${name}">${name}</option>`
+      let label = "Models: "
+      files = files.map(function (file) {
+        return `<option value="${file[0]}">${file[1]}</option>`
       })
-      options = options.join(" ")
+      files.unshift(`<option value="">-- Select a model --</option>`)
+      files = files.join(" ")
 
-      return templates.select(modalID, selectID, title, label, options)
+      return templates.fileSelect(modalID, fileID, locationID, title, label, files)
     },
     newProjectModelSuccessHtml : (message) => {
       let modalID = "newProjectModelSuccessModal"
@@ -428,6 +467,28 @@ module.exports = {
 
       return templates.message(modalID, title, message)
     },
+    newWorkflowHtml: (name, type) => {
+      let modalID = "newWorkflowModal"
+      let inputID = "workflowNameInput"
+      let title = `New ${type} Workflow`
+      let label = "Name:"
+      let value = name
+
+      return templates.input(modalID, inputID, title, label, value);
+    },
+    updateFormatHtml: (fileType) => {
+      let modalID = `update${fileType}FormatModal`
+      let title = `Update ${fileType} Format`
+      if(fileType === "Project") {
+        fileType += "s and Workflow";
+        var target = "project and its workflows";
+      }else{
+        var target = "workflow";
+      }
+      let message = `StochSS ${fileType}s have a new format.  Would you like to update this ${target} to the new format?`
+
+      return templates.confirmation_with_message(modalID, title, message);
+    },
     renderDefaultModeModalHtml : () => {
         let concentrationDesciption = `Variables will only be represented using continuous (floating point) values.`;
         let populationDescription = `Population - Variables will only be represented using discrete (integer count) values.`;

client/models/creator.js

@@ -24,7 +24,8 @@ module.exports = State.extend({
     fname: 'string',
     lname: 'string',
     email: 'string',
-    organization: 'string'
+    organization: 'string',
+    elementID: 'string'
   },
   initialize: function(attrs, options) {
     State.prototype.initialize.apply(this, arguments)

client/models/models.js → client/models/creators.js

@@ -16,11 +16,24 @@ You should have received a copy of the GNU General Public License
 along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
 
-var app = require('ampersand-app');
-var RestCollection = require('ampersand-rest-collection');
-var Model = require('./model');
-var path = require('path');
+//collections
+let Collection = require('ampersand-collection');
+//models
+let Creator = require('./creator');
 
-module.exports = RestCollection.extend({
-  model: Model
+module.exports = Collection.extend({
+  model: Creator,
+  indexes: ["elementID"],
+  addCreator: function (creatorInfo) {
+  	let elementID = "C" + (this.length + 1);
+  	let creator = new Creator({
+  	  fname: creatorInfo.fname,
+  	  lname: creatorInfo.lname,
+  	  email: creatorInfo.email,
+  	  organization: creatorInfo.organization,
+  	  elementID: elementID
+  	});
+  	this.add(creator);
+  	return creator;
+  }
 });

client/models/domain.js

@@ -32,7 +32,8 @@ module.exports = State.extend({
     size: 'number',
     x_lim: 'object',
     y_lim: 'object',
-    z_lim: 'object'
+    z_lim: 'object',
+    static: 'boolean'
   },
   collections: {
     types: Types,