Merge pull request #1274 from StochSS/develop

Release 2.4.2
StochSS · Nov 10, 2021 · 82d8e6a · 82d8e6a
2 parents f93e193 + b77ad45
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diff --git a/EXAMPLE_DIRECTORY.md b/EXAMPLE_DIRECTORY.md
@@ -0,0 +1,90 @@
+# Example Directory
+
+This file contains a directory to all GillesPy2 and SpatialPy example notebooks.
+
+## GillesPy2
+
+["Start Here" Model](https://github.com/StochSS/GillesPy2/blob/main/examples/StartHere.ipynb)
+
+### Starting Models
+
+- [Michaelis Menten](https://github.com/StochSS/GillesPy2/tree/main/examples/StartingModels/MichaelisMenten)
+    - [SSA C Solver](https://github.com/StochSS/GillesPy2/blob/main/examples/StartingModels/MichaelisMenten/Michaelis-Menten_SSA_C.ipynb)
+    - [SSA NumPy Solver](https://github.com/StochSS/GillesPy2/blob/main/examples/StartingModels/MichaelisMenten/Michaelis-Menten_NumPy_SSA.ipynb)
+    - [Tau Leaping NumPy](https://github.com/StochSS/GillesPy2/blob/main/examples/StartingModels/MichaelisMenten/Michaelis-Menten_Basic_Tau_Leaping.ipynb)
+    - [Tau Hybrid NumPy](https://github.com/StochSS/GillesPy2/blob/main/examples/StartingModels/MichaelisMenten/Michaelis-Menten_Basic_Tau_Hybrid.ipynb)
+
+- [Vilar Oscillator](https://github.com/StochSS/GillesPy2/tree/main/examples/StartingModels/VilarOscillator)
+    - [SSA](https://github.com/StochSS/GillesPy2/blob/main/examples/StartingModels/VilarOscillator/VilarOscillator_SSA.ipynb)
+    - [Tau Leaping](https://github.com/StochSS/GillesPy2/blob/main/examples/StartingModels/VilarOscillator/VilarOscillator_Tau_Leaping.ipynb)
+    - [Tau Hybrid](https://github.com/StochSS/GillesPy2/blob/main/examples/StartingModels/VilarOscillator/VilarOscillator_Tau_Hybrid.ipynb)
+
+
+### Results Management
+
+- [Basic Results Management](https://github.com/StochSS/GillesPy2/blob/main/examples/ResultsManagement/basic-results-management.ipynb)
+- [Single Trajectory to CSV](https://github.com/StochSS/GillesPy2/blob/main/examples/ResultsManagement/to_csv-single-trajectory.ipynb)
+- [Multiple Trajectories to CSV](https://github.com/StochSS/GillesPy2/blob/main/examples/ResultsManagement/to_csv-multi-trajectory.ipynb)
+- [Using Pickle](https://github.com/StochSS/GillesPy2/blob/main/examples/ResultsManagement/using-pickle.ipynb)
+
+
+### Data Visualization
+
+- [Data Visualization](https://github.com/StochSS/GillesPy2/blob/main/examples/DataVisualization/DataVisualization.ipynb)
+- [Live Output](https://github.com/StochSS/GillesPy2/blob/main/examples/DataVisualization/LiveOutput.ipynb)
+
+
+### Advanced Features
+
+- [Events](https://github.com/StochSS/GillesPy2/blob/main/examples/AdvancedFeatures/Events.ipynb)
+- [Kinetic Model for Styrene Polymerization](https://github.com/StochSS/GillesPy2/blob/main/examples/AdvancedFeatures/KineticModelForStyrenePolymerization.ipynb)
+- [Photosynthesis](https://github.com/StochSS/GillesPy2/blob/main/examples/AdvancedFeatures/Photosynthesis.ipynb)
+- [GillesPy2 in Parallel](https://github.com/StochSS/GillesPy2/blob/main/examples/AdvancedFeatures/Run%20GillesPy2%20Simulations%20in%20Parallel.ipynb)
+- [SBML Import](https://github.com/StochSS/GillesPy2/blob/main/examples/AdvancedFeatures/SBML_Import_Test.ipynb)
+- [Variable Inputs (SSA)](https://github.com/StochSS/GillesPy2/blob/main/examples/AdvancedFeatures/Variable_SSA_C_Example.ipynb)
+- [Volume Test](https://github.com/StochSS/GillesPy2/blob/main/examples/AdvancedFeatures/Volume_test.py)
+- [Hybrid Continuous Species](https://github.com/StochSS/GillesPy2/blob/main/examples/AdvancedFeatures/hybrid_continuous_species.ipynb)
+- [Hybrid Switching](https://github.com/StochSS/GillesPy2/blob/main/examples/AdvancedFeatures/hybrid_switching_example.ipynb)
+- [Parameter Changing](https://github.com/StochSS/GillesPy2/blob/main/examples/AdvancedFeatures/parameter_changing.py)
+
+
+### Extra Models
+
+- [Brusselator](https://github.com/StochSS/GillesPy2/blob/main/examples/ExtraModels/Brusselator.ipynb)
+- [Genetic Toggle Switch](https://github.com/StochSS/GillesPy2/blob/main/examples/ExtraModels/GeneticToggleSwitch.ipynb)
+- [Opioid Model](https://github.com/StochSS/GillesPy2/blob/main/examples/ExtraModels/Opioid_Model.ipynb)
+- [Oregonator](https://github.com/StochSS/GillesPy2/blob/main/examples/ExtraModels/Oregonator.ipynb)
+- [Tyson Oscillator](https://github.com/StochSS/GillesPy2/blob/main/examples/ExtraModels/Tyson%20Oscillator.ipynb)
+- [Degradation Model](https://github.com/StochSS/GillesPy2/blob/main/examples/ExtraModels/degradation_example.py)
+- [Dimer Model](https://github.com/StochSS/GillesPy2/blob/main/examples/ExtraModels/dimer_example.py)
+- [Tyson Oscillator](https://github.com/StochSS/GillesPy2/blob/main/examples/ExtraModels/tyson_oscillator.py)
+
+
+
+## SpatialPy
+
+### General Examples
+
+- [Bistable Elf Ehrenberg](https://github.com/StochSS/SpatialPy/blob/develop/examples/Bistable_Biochem_Elf_Ehrenberg/Bistable_Biochem_Elf_Ehrenberg.ipynb)
+- [Boundary Conditions](https://github.com/StochSS/SpatialPy/blob/develop/examples/BoundaryCondition/BoundaryCondition.ipynb)
+- [SpatialPy Gravity](https://github.com/StochSS/SpatialPy/blob/develop/examples/Gravity/Spatialpy_gravity.ipynb)
+- [Coral Reef](https://github.com/StochSS/SpatialPy/blob/develop/examples/coral_reef/CoralModel.ipynb)
+- [3D Cylinder Diffusion](https://github.com/StochSS/SpatialPy/blob/develop/examples/cylinderDemo/SpatialPy_cylinderDemo3D.ipynb)
+- [hes1](https://github.com/StochSS/SpatialPy/blob/develop/examples/hes1/hes1.ipynb)
+- [Lid Driven Cavity](https://github.com/StochSS/SpatialPy/blob/develop/examples/lid_driven_cavity/Lid%20driven%20cavity.ipynb)
+- [MinCDE](https://github.com/StochSS/SpatialPy/blob/develop/examples/mincde/mincde.ipynb)
+- [Turing Pattern (Old)](https://github.com/StochSS/SpatialPy/blob/develop/examples/turing_pattern/turing_pattern.ipynb)
+- [Turing Pattern (New)](https://github.com/StochSS/SpatialPy/blob/develop/examples/turing_pattern/new_turing_pattern.ipynb)
+- [Weir](https://github.com/StochSS/SpatialPy/blob/develop/examples/weir/weir.ipynb)
+- [Yeast Polarization](https://github.com/StochSS/SpatialPy/tree/develop/examples/yeast_polarization)
+    - [G-Protein 1D](https://github.com/StochSS/SpatialPy/blob/develop/examples/yeast_polarization/G-Protein_1D.ipynb)
+    - [Polarisome 1D](https://github.com/StochSS/SpatialPy/blob/develop/examples/yeast_polarization/Polarisome_1D.ipynb)
+    - [cdc42](https://github.com/StochSS/SpatialPy/blob/develop/examples/yeast_polarization/cdc42.ipynb)
+
+### Tests
+
+- [Diffusion Validation](https://github.com/StochSS/SpatialPy/blob/develop/examples/tests/Diffusion_validation.ipynb)
+- [Spatial Birth-Death](https://github.com/StochSS/SpatialPy/blob/develop/examples/tests/Spatial_Birth_Death.ipynb)
+- [Compile Time Test](https://github.com/StochSS/SpatialPy/blob/develop/examples/tests/compile_time_comparison.ipynb)
+- [Read Meshes](https://github.com/StochSS/SpatialPy/blob/develop/examples/tests/read_meshes.ipynb)
+
diff --git a/__version__.py b/__version__.py
@@ -5,7 +5,7 @@
 # @website https://github.com/stochss/stochss
 # =============================================================================
 
-__version__ = '2.4.1'
+__version__ = '2.4.2'
 __title__ = 'StochSS'
 __description__ = 'StochSS is an integrated development environment (IDE) \
                     for simulation of biochemical networks.'

diff --git a/client/models/presentation.js b/client/models/presentation.js
@@ -20,8 +20,10 @@ let State = require('ampersand-state');
 
 module.exports = State.extend({
   session: {
+    ctime: 'string',
     file: 'string',
     link: 'string',
+    name: 'string',
     size: 'number',
     tag: 'string'
   },

diff --git a/client/pages/loading-page.js b/client/pages/loading-page.js
@@ -91,7 +91,7 @@ let LoadingPage = PageView.extend({
         $(self.queryByHook("loading-spinner")).css("display", "none");
         let modal = $(modals.errorHtml(body.reason, body.message)).modal();
         modal.on('hidden.bs.modal', function (e) {
-          window.location.href = this.homeLink;
+          window.location.href = self.homeLink;
         });
       }
       app.getXHR(endpoint, {

diff --git a/client/pages/model-editor.js b/client/pages/model-editor.js
@@ -197,17 +197,22 @@ let ModelEditor = PageView.extend({
             errorCB(err, response, body);
           }
           else if(!body.Running){
+            Plotly.purge(this.queryByHook('preview-plot-container'));
             if(body.Results.timeout){
               $(this.queryByHook('model-timeout-message')).collapse('show');
             }
             this.plotResults(body.Results.results);
           }else{
+            if(body.Results) {
+              Plotly.purge(this.queryByHook('preview-plot-container'));
+              this.plotResults(body.Results.results);
+            }
             this.getResults();
           }
         },
         error: errorCB
       });
-    }, 2000);
+    }, 1000);
   },
   handlePresentationClick: function (e) {
     let errorMsg = $(this.queryByHook("error-detected-msg"));

diff --git a/client/pages/project-manager.js b/client/pages/project-manager.js
@@ -92,8 +92,8 @@ let ProjectManager = PageView.extend({
       always: function (err, response, body) {
         let modal = $(modals.importModelHtml(body.files)).modal();
         let okBtn = document.querySelector('#importModelModal .ok-model-btn');
-        let select = document.querySelector('#importModelModal #modelFileInput');
-        let location = document.querySelector('#importModelModal #modelPathInput');
+        let select = document.querySelector('#importModelModal #modelFileSelect');
+        let location = document.querySelector('#importModelModal #modelPathSelect');
         select.addEventListener("change", function (e) {
           okBtn.disabled = e.target.value && body.paths[e.target.value].length >= 2;
           if(body.paths[e.target.value].length >= 2) {
@@ -314,7 +314,7 @@ let ProjectManager = PageView.extend({
     }
   },
   handleUploadModelClick: function (e) {
-    this.projectFileBrowser.uploadFile(undefined, "model")
+    this.projectFileBrowser.uploadFile(null, this.model.directory, "model", true)
   },
   renderArchiveCollection: function () {
     if(this.archiveCollectionView) {

diff --git a/client/project-config.js b/client/project-config.js
@@ -151,7 +151,7 @@ let getNotebookContext = (view, node) => {
     open: open,
     publish: view.getPublishNotebookContext(node),
     download: download, rename: rename,
-    duplicate: duplicate, delete: deleteFile
+    duplicate: duplicate, moveToTrash: moveToTrash
   }
 }
 

diff --git a/client/templates/body.pug b/client/templates/body.pug
@@ -64,6 +64,8 @@ body
 
                 button.my-0.btn.btn-outline-collapse.inline(data-hook="user-logs-collapse") +
 
+                button.my-0.btn.btn-light.inline(data-hook="clear-user-logs" style="float: right;") clear
+
               div.pl-1.overflow-auto(id="user-logs")
 
       main.col-sm-12.col-md-10.col-xl-9.col-xxl-6.body(role="main" data-hook="page-main")

diff --git a/client/templates/includes/presentationView.pug b/client/templates/includes/presentationView.pug
@@ -5,14 +5,18 @@ div.mx-1
 
   div.row
 
-    div.col-sm-6
+    div.col-sm-4
 
-      a.pl-2(href=this.model.link)=this.model.file
+      a.pl-2(href=this.model.link)=this.model.name
 
     div.col-sm-2
 
       button.btn.btn-outline-secondary.box-shadow(data-hook="copy-link") Copy Link
 
+    div.col-sm-2
+
+      div=this.model.ctime
+
     div.col-sm-2
 
       div=this.model.size + " " + this.model.tag

diff --git a/client/templates/pages/browser.pug b/client/templates/pages/browser.pug
@@ -36,7 +36,9 @@ section.page
 
         div.mx-1.row.head.align-items-baseline
 
-          div.col-sm-8: h6 <b>File</b>
+          div.col-sm-6: h6 <b>File</b>
+
+          div.col-sm-2: h6 <b>Date</b>
 
           div.col-sm-2: h6 <b>Size</b>
 

diff --git a/client/views/jstree-view.js b/client/views/jstree-view.js
@@ -900,7 +900,7 @@ module.exports = View.extend({
             msg.html(reason);
             msg.css("display", "inline-block");
           }
-          app.copyToClipboard(links.presentation, onFulfilled, onReject);
+          app.copyToClipboard(body.links.presentation, onFulfilled, onReject);
         });
       },
       error: (err, response, body) => {

diff --git a/client/views/main.js b/client/views/main.js
@@ -38,67 +38,6 @@ String.prototype.toHtmlEntities = function() {
   });
 };
 
-let operationInfoModalHtml = (infoKey) => {
-  let fileBrowserInfo = `
-    <p>In StochSS we use custom file extensions for a number of files we work with.  Here is a list of our extentions with the files they are associated with:</p>
-    <table style="margin-left: 2em;">
-      <tr>
-        <td width=200> StochSS Model </td>
-        <td> .mdl </td>
-      </tr>
-      <tr>
-        <td width=200> StochSS Spatial Model </td>
-        <td> .smdl </td>
-      </tr>
-      <tr>
-        <td width=200> SBML Model </td>
-        <td> .sbml </td>
-      </tr>
-      <tr>
-        <td width=200> Workflows </td>
-        <td> .wkfl </td>
-      </tr>
-    </table>
-    <br>
-    <p>Other useful file extensions include the following:</p>
-    <table style="margin-left: 2em;">
-      <tr>
-        <td width=200> Jupyter Notebook </td>
-        <td> .ipynb </td>
-      </tr>
-    </table>
-  `;
-  let modelInfo = `
-    Model Information
-  `;
-  let workflowInfo = `
-    Workflow Information
-  `;
-
-  let infoList = {"File Browser":fileBrowserInfo, "Models":modelInfo, "Workflows":workflowInfo}
-
-  return `
-    <div id="operationInfoModal" class="modal" tabindex="-1" role="dialog">
-      <div class="modal-dialog" role="document">
-        <div class="modal-content info">
-          <div class="modal-header">
-            <h5 class="modal-title"> Working with ${infoKey} </h5>
-            <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-              <span aria-hidden="true">&times;</span>
-            </button>
-          </div>
-          <div class="modal-body">
-            <p> ${infoList[infoKey]} </p>
-          </div>
-          <div class="modal-footer">
-            <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-          </div>
-        </div>
-      </div>
-    </div>
-  ` 
-}
-
 module.exports = View.extend({
   template: bodyTemplate,
   autoRender: true,
@@ -109,8 +48,8 @@ module.exports = View.extend({
   },
   events: {
     'click [data-hook=registration-link-button]' : 'handleRegistrationLinkClick',
-    'click [data-hook=user-logs-collapse]' : 'collapseExpandLogs'
-    //'click a[href]': 'handleLinkClick'
+    'click [data-hook=user-logs-collapse]' : 'collapseExpandLogs',
+    'click [data-hook=clear-user-logs]' : 'clearUserLogs'
   },
   render: function () {
 
@@ -132,18 +71,7 @@ module.exports = View.extend({
     if(app.getBasePath() === "/") {
       $("#presentation-nav-link").css("display", "none");
     }
-    let self = this;
-    let message = app.getBasePath() === "/" ? "Welcome to StochSS!" : "Welcome to StochSS Live!";
-    $("#user-logs").html(message)
-    this.logBlock = [];
-    this.logs = [];
-    this.getUserLogs();
-    this.scrolled = false;
-    this.scrollCount = 0;
-    $("#user-logs").on("mousewheel", function(e) {
-      self.scrolled = true;
-      self.scrollCount = 0;
-    });
+    this.setupUserLogs();
     return this;
   },
   addNewLogBlock: function () {
@@ -172,6 +100,14 @@ module.exports = View.extend({
     });
     this.addNewLogBlock();
   },
+  clearUserLogs: function (e) {
+    let endpoint = path.join(app.getApiPath(), "clear-user-logs");
+    app.getXHR(endpoint, {
+      success: (err, response, body) => {
+        this.setupUserLogs({getLogs: false});
+      }
+    });
+  },
   collapseExpandLogs: function (e) {
     let logs = $("#user-logs");
     let classes = logs.attr("class").split(/\s+/);
@@ -249,6 +185,21 @@ module.exports = View.extend({
   navigate: function (page) {
     window.location = url;
   },
+  setupUserLogs: function ({getLogs = true}={}) {
+    let message = app.getBasePath() === "/" ? "Welcome to StochSS!" : "Welcome to StochSS Live!";
+    $("#user-logs").html(message)
+    this.logBlock = [];
+    this.logs = [];
+    this.scrolled = false;
+    this.scrollCount = 0;
+    if(getLogs) {
+      this.getUserLogs();
+      $("#user-logs").on("mousewheel", (e) => {
+        this.scrolled = true;
+        this.scrollCount = 0;
+      });
+    }
+  },
   updateUserLogs: function () {
     setTimeout(_.bind(this.getUserLogs, this), 1000);
   }

diff --git a/launch_webbrowser.py b/launch_webbrowser.py
@@ -4,6 +4,9 @@
 import sys
 import time
 import webbrowser
+
+MAX_WAIT_TIME = 60
+
 try:
     import docker
 except ImportError:
@@ -25,11 +28,15 @@
 #time.sleep(10)
 print("Checking for running StochSS container: stochss-lab")
 container_started = False
+poll_start_time = time.time()
 while not container_started:
+    if (time.time() - MAX_WAIT_TIME) > poll_start_time:
+        print(f"Stopped checking for running StochSS container after {MAX_WAIT_TIME}s")
+        sys.exit(1)
     time.sleep(1)
     try:
         stochss_container=docker_client.containers.get("stochss-lab")
-        print("Generating StochSS webpage...")
+        print("Checking to see if the server is active.")
         jupyter_url_generator=stochss_container.exec_run("jupyter notebook list", demux=False)
         url_regex = r"(?i)\b((?:https?://|www\d{0,3}[.]|[a-z0-9.\-]+[.][a-z]{2,4}/)(?:[^\s()<>]+|\(([^\s()<>]+|(\([^\s()<>]+\)))*\))+(?:\(([^\s()<>]+|(\([^\s()<>]+\)))*\)|[^\s`!()\[\]{};:'\".,<>?«»“”‘’]))"
         jupyter_url_bytes = jupyter_url_generator.output
@@ -40,6 +47,7 @@
         jupyter_url=jupyter_url_sequence[0]
         jupyter_url=jupyter_url.replace('0.0.0.0','127.0.0.1')
         print(f"Opening StochSS webpage...\n")
+        time.sleep(1)
         webbrowser.open_new_tab(jupyter_url)
         print("Welcome to StochSS!\n\nYou can access your local StochSS service with this URL:\n\n")
         print(jupyter_url+"\n")