Merge pull request #1221 from StochSS/develop

Release 2.3.11

.win32.env

@@ -0,0 +1,5 @@
+DOCKER_STOCHSS_IMAGE=stochss-lab
+
+DOCKER_BASE_IMAGE=jupyter/minimal-notebook:latest
+
+JUPYTER_CONFIG_DIR=/opt/stochss-config/.jupyter

Dockerfile

@@ -29,20 +29,20 @@ COPY --chown=jovyan:users jupyter_notebook_config.py $JUPYTER_CONFIG_DIR/jupyter
 
 USER root
 
-RUN wget -q https://julialang-s3.julialang.org/bin/linux/x64/1.4/julia-1.4.2-linux-x86_64.tar.gz
-RUN tar -xvzf julia-1.4.2-linux-x86_64.tar.gz
-RUN mv julia-1.4.2 /usr/local/
-RUN chown -R jovyan:users /usr/local/julia-1.4.2/
+#RUN wget -q https://julialang-s3.julialang.org/bin/linux/x64/1.4/julia-1.4.2-linux-x86_64.tar.gz
+#RUN tar -xvzf julia-1.4.2-linux-x86_64.tar.gz
+#RUN mv julia-1.4.2 /usr/local/
+#RUN chown -R jovyan:users /usr/local/julia-1.4.2/
 
 USER jovyan
 
-ENV PATH="/usr/local/julia-1.4.2/bin:${PATH}"
+#ENV PATH="/usr/local/julia-1.4.2/bin:${PATH}"
 
-RUN julia -e 'using Pkg; Pkg.add("IJulia")'
-RUN julia -e 'using Pkg; Pkg.add(PackageSpec(url="https://github.com/stochss/gillespy2lia", rev="main"))'
+#RUN julia -e 'using Pkg; Pkg.add("IJulia")'
+#RUN julia -e 'using Pkg; Pkg.add(PackageSpec(url="https://github.com/stochss/gillespy2lia", rev="main"))'
 
 RUN pip install --no-cache-dir -e .
 
 RUN rm -r /home/jovyan/work
 
-WORKDIR /home/jovyan
+WORKDIR /home/jovyan

Makefile

@@ -152,4 +152,4 @@ update:
 	docker exec -it $(DOCKER_STOCHSS_IMAGE) python -m pip install -e /stochss
 
 
-.PHONY: network volumes check-files pull notebook_image build
+.PHONY: network volumes check-files pull notebook_image build

__version__.py

@@ -5,7 +5,7 @@
 # @website https://github.com/stochss/stochss
 # =============================================================================
 
-__version__ = '2.3.9'
+__version__ = '2.3.11'
 __title__ = 'StochSS'
 __description__ = 'StochSS is an integrated development environment (IDE) \
                     for simulation of biochemical networks.'

client/app.js

@@ -212,29 +212,14 @@ documentSetup = () => {
   });
 }
 
-copyToClipboard = (text) => {
-    if (window.clipboardData && window.clipboardData.setData) {
-        // Internet Explorer-specific code path to prevent textarea being shown while dialog is visible.
-        return window.clipboardData.setData("Text", text);
-
-    }
-    else if (document.queryCommandSupported && document.queryCommandSupported("copy")) {
-        var textarea = document.createElement("textarea");
-        textarea.textContent = text;
-        textarea.style.display = 'none';  // Prevent scrolling to bottom of page in Microsoft Edge.
-        document.body.appendChild(textarea);
-        textarea.select();
-        try {
-            return document.execCommand("copy");  // Security exception may be thrown by some browsers.
-        }
-        catch (ex) {
-            console.warn("Copy to clipboard failed.", ex);
-            return false;
-        }
-        finally {
-            document.body.removeChild(textarea);
-        }
-    }
+copyToClipboard = (text, success, error) => {
+  if (window.clipboardData && window.clipboardData.setData) {
+    // Internet Explorer-specific code path to prevent textarea being shown while dialog is visible.
+    return window.clipboardData.setData("Text", text);
+  }
+  else {
+    navigator.clipboard.writeText(text).then(success, error)
+  }
 }
 
 module.exports = {

client/modals.js

@@ -224,7 +224,7 @@ let templates = {
                   </div>
                 </div>`
         },
-        presentationLinks : (modalID, title, name, headers, links) => {
+        presentationLinks : (modalID, title, headers, links) => {
           return `
             <div id=${modalID} class="modal" tabindex="-1" role="dialog">
               <div class="modal-dialog" role="document">
@@ -238,8 +238,10 @@ let templates = {
                   <div class="modal-body">
                     <h4><u>${headers}</u></h4>
                     <div>
-                      <a class="inline" data-hook="view-present-link" href="${links.presentation}" target="_blank"> View ${name} Presentation</a>
+                      <a class="btn btn-primary box-shadow inline" role="button" data-hook="view-present-link" href="${links.presentation}" target="_blank">View</a>
                       <button type="button" class="btn btn-primary box-shadow inline" id="copy-to-clipboard">Copy Link</button>
+                      <div class="text-success" id="copy-link-success" style="display: none;"> Link copied to clipboard</div>
+                      <div class="text-danger" id="copy-link-failed" style="display: none;"></div>
                     </div>
                   </div>
                   <div class="modal-footer">
@@ -567,9 +569,14 @@ module.exports = {
               </div>
             </div>`
     },
-    presentationLinks : (title, name, headers, links) => {
+    presentationLinks : (title, headers, links) => {
       let modalID = "presentationLinksModal"
 
-      return templates.presentationLinks(modalID, title, name, headers, links);
+      return templates.presentationLinks(modalID, title, headers, links);
+    },
+    modelErrorHtml: (title, message) => {
+      let modalID = "modelErrorModal";
+
+      return templates.message(modalID, title, message);
     }
 }

client/models/domain-type.js

@@ -36,6 +36,7 @@ module.exports = State.extend({
     this.numParticles = 0;
   },
   validate: function () {
+    if((!/^[a-zA-Z0-9_]+$/.test(this.name))) return false;
     return true;
   }
 });

client/models/event.js

@@ -51,6 +51,7 @@ module.exports = State.extend({
   validateComponent: function () {
     advanced_error = false;
     if(!this.name.trim() || this.name.match(/^\d/)) return false;
+    if((!/^[a-zA-Z0-9_]+$/.test(this.name))) return false;
     if(!this.triggerExpression.trim()) return false;
     if(!this.priority.trim()) {
       this.advanced_error = true;

client/models/parameter.js

@@ -38,6 +38,7 @@ module.exports = State.extend({
   },
   validateComponent: function () {
     if(!this.name.trim() || this.name.match(/^\d/)) return false;
+    if((!/^[a-zA-Z0-9_]+$/.test(this.name))) return false;
     if(this.expression === "" || isNaN(this.expression)) return false
     return true;
   }

client/models/reaction.js

@@ -165,6 +165,7 @@ module.exports = State.extend({
   },
   validateComponent: function () {
     if(!this.name.trim() || this.name.match(/^\d/)) return false;
+    if((!/^[a-zA-Z0-9_]+$/.test(this.name))) return false;
     if(!this.propensity.trim() && this.reactionType === "custom-propensity") return false;
     if(this.reactionType.startsWith('custom')) {
       if(this.reactants.length <= 0 && this.products.length <= 0) return false;

client/models/rule.js

@@ -33,6 +33,7 @@ module.exports = State.extend({
   },
   validateComponent: function () {
     if(!this.name.trim() || this.name.match(/^\d/)) return false;
+    if((!/^[a-zA-Z0-9_]+$/.test(this.name))) return false;
     if(!this.expression.trim()) return false;
     return true;
   }

client/models/specie.js

@@ -44,6 +44,7 @@ module.exports = State.extend({
   },
   validateComponent: function () {
     if(!this.name.trim() || this.name.match(/^\d/)) return false;
+    if((!/^[a-zA-Z0-9_]+$/.test(this.name))) return false;
     if(this.value === "" || isNaN(this.value)) return false;
     if(this.mode === "dynamic") {
       if(this.isSwitchTol && (this.switchTol === "" || isNaN(this.switchTol))) return false;

client/models/sweep-parameter.js

@@ -29,6 +29,9 @@ module.exports = State.extend({
     steps: 'any',
     hasChangedRange: 'boolean' 
   },
+  session: {
+    fixed: 'boolean'
+  },
   derived: {
     elementID: {
       deps: ["collection"],

client/pages/file-browser.js

@@ -23,6 +23,8 @@ let _ = require('underscore');
 //support files
 let app = require('../app');
 let modals = require('../modals');
+//models
+let Model = require('../models/model');
 //views
 let PageView = require('./base');
 //templates
@@ -660,7 +662,23 @@ let FileBrowser = PageView.extend({
     });
   },
   newWorkflow: function (o, type) {
-    app.newWorkflow(this, o.original._path, o.type === "spatial", type);
+    let model = new Model({
+      directory: o.original._path
+    });
+    app.getXHR(model.url(), {
+      success: function (err, response, body) {
+        model.set(body);
+        model.updateValid();
+        if(model.valid){
+          app.newWorkflow(this, o.original._path, o.type === "spatial", type);
+        }else{
+          let title = "Model Errors Detected";
+          let endpoint = path.join(app.getBasePath(), "stochss/models/edit") + '?path=' + model.directory;
+          let message = 'Errors were detected in you model <a href="' + endpoint + '">click here to fix your model<a/>';
+          $(modals.modelErrorHtml(title, message)).modal();
+        }
+      }
+    });
   },
   addExistingModel: function (o) {
     var self = this
@@ -904,13 +922,20 @@ let FileBrowser = PageView.extend({
     app.getXHR(endpoint, {
       success: function (err, response, body) {
         let title = body.message;
-        let linkHeaders = "Shareable Presentation Link";
+        let linkHeaders = "Shareable Presentation";
         let links = body.links;
-        let name = o.original._path.split('/').pop().split('.ipynb')[0];
-        $(modals.presentationLinks(title, name, linkHeaders, links)).modal();
+        $(modals.presentationLinks(title, linkHeaders, links)).modal();
         let copyBtn = document.querySelector('#presentationLinksModal #copy-to-clipboard');
         copyBtn.addEventListener('click', function (e) {
-          app.copyToClipboard(links.presentation)
+          let onFulfilled = (value) => {
+            $("#copy-link-success").css("display", "inline-block");
+          } 
+          let onReject = (reason) => {
+            let msg = $("#copy-link-failed");
+            msg.html(reason);
+            msg.css("display", "inline-block");
+          }
+          app.copyToClipboard(links.presentation, onFulfilled, onReject);
         });
       },
       error: function (err, response, body) {

client/pages/job-presentation.js

@@ -27,7 +27,7 @@ let Job = require("../models/job");
 //views
 let PageView = require('./base');
 let ModelView = require('../model-view/model-view');
-let ResultsView = require('../views/workflow-results');
+let ResultsView = require('../views/job-results-view');
 let SettingsView = require('../views/settings-viewer');
 //templates
 let template = require('../templates/pages/jobPresentation.pug');

client/pages/loading-page.js

@@ -35,7 +35,7 @@ let LoadingPage = PageView.extend({
     let urlParams = new URLSearchParams(window.location.search)
     this.filePath = urlParams.get("path");
     this.action = urlParams.get("action");
-    this.homeLink = path.append(app.getBasePath(), 'stochss/home');
+    this.homeLink = path.join(app.getBasePath(), 'stochss/home');
   },
   render: function (attrs, options) {
     PageView.prototype.render.apply(this, arguments);

client/pages/model-presentation.js

@@ -29,18 +29,21 @@ let PageView = require('./base');
 let ModelView = require('../model-view/model-view');
 //templates
 let template = require('../templates/pages/modelPresentation.pug');
+let loadingTemplate = require('../templates/pages/loadingPage.pug');
+let errorTemplate = require('../templates/pages/errorTemplate.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,
+  template: loadingTemplate,
   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.fileType = file.endsWith(".mdl") ? "Model" : "Spatial Model";
     this.model = new Model({
       directory: file,
       for: "presentation"
@@ -51,16 +54,31 @@ let ModelPresentationPage = PageView.extend({
     app.getXHR(endpoint, {
       success: function (err, response, body) {
         self.model.set(body);
-        self.renderSubviews();
+        self.renderSubviews(false);
+      },
+      error: function (err, response, body) {
+        self.notFound = true;
+        self.renderSubviews(true);
       }
     });
     let downloadStart = "https://live.stochss.org/stochss/download_presentation";
     this.downloadLink = downloadStart + "/" + owner + "/" + file;
     this.openLink = "https://open.stochss.org?open=" + this.downloadLink;
   },
-  renderSubviews: function () {
+  render: function (attrs, options) {
     PageView.prototype.render.apply(this, arguments);
-    this.renderModelView();
+    $(this.queryByHook("loading-header")).html(`Loading ${this.fileType}`);
+    $(this.queryByHook("loading-target")).css("display", "none");
+    $(this.queryByHook("loading-spinner")).css("display", "block");
+    let message = `This ${this.fileType} can be downloaded or opened in your own StochSS Live! account using the buttons at the bottom of the page.`;
+    $(this.queryByHook("loading-message")).html(message);
+  },
+  renderSubviews: function (notFound) {
+    this.template = notFound ? errorTemplate : template
+    PageView.prototype.render.apply(this, arguments);
+    if(!notFound) {
+      this.renderModelView();
+    }
   },
   renderModelView: function () {
     let modelView = new ModelView({

client/pages/notebook-presentation.js

@@ -25,44 +25,61 @@ let app = require('../app');
 //views
 let PageView = require('./base');
 //templates
+let loadingTemplate = require('../templates/pages/loadingPage.pug');
+let errorTemplate = require('../templates/pages/errorTemplate.pug');
 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,
+  template: loadingTemplate,
   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.fileType = "Notebook";
     let self = this;
     let queryStr = "?owner=" + owner + "&file=" + file;
     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);
+        self.renderSubviews(false, body.html);
+      },
+      error: function (err, response, body) {
+        self.renderSubviews(true, null);
       }
     });
     let downloadStart = "https://live.stochss.org/stochss/notebook/download_presentation";
     this.downloadLink = downloadStart + "/" + owner + "/" + file;
     this.openLink = "https://open.stochss.org?open=" + this.downloadLink;
   },
-  renderSubviews: function (html) {
+  render: function (attrs, options) {
+    PageView.prototype.render.apply(this, arguments);
+    $(this.queryByHook("loading-header")).html(`Loading ${this.fileType}`);
+    $(this.queryByHook("loading-spinner")).css("display", "block");
+    $(this.queryByHook("loading-target")).css("display", "none");
+    let message = `This ${this.fileType} can be downloaded or opened in your own StochSS Live! account using the buttons at the bottom of the page.`;
+    $(this.queryByHook("loading-message")).html(message);
+  },
+  renderSubviews: function (notFound, html) {
+    this.template = notFound ? errorTemplate : template;
   	PageView.prototype.render.apply(this, arguments);
-    let iframe = document.getElementById('notebook');
-    let iframedoc = iframe.document;
-    if (iframe.contentDocument) {
-      iframedoc = iframe.contentDocument;
-    }else if (iframe.contentWindow) {
-      iframedoc = iframe.contentWindow.document;
-    }
-    if (iframedoc) {
-      iframedoc.write(html);
-      iframedoc.close();
+    if(!notFound){
+      let iframe = document.getElementById('notebook');
+      let iframedoc = iframe.document;
+      if (iframe.contentDocument) {
+        iframedoc = iframe.contentDocument;
+      }else if (iframe.contentWindow) {
+        iframedoc = iframe.contentWindow.document;
+      }
+      if (iframedoc) {
+        iframedoc.write(html);
+        iframedoc.close();
+      }
     }
   }
 });