Merge pull request #1111 from StochSS/develop

2.3.2 Release

.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__ = '2.3'
+__version__ = '2.3.2'
 __title__ = 'StochSS'
 __description__ = 'StochSS is an integrated development environment (IDE) \
                     for simulation of biochemical networks.'

client/pages/domain-editor.js

@@ -669,19 +669,28 @@ let DomainEditor = PageView.extend({
       let projBC = $(this.queryByHook("grandparent-breadcrumb"));
       projBC.text(breadData.project.name);
       projBC.prop("href", breadData.project.href);
+      $(this.queryByHook("return-to-project")).prop("href", breadData.project.href);
       let mdlBC = $(this.queryByHook("parent-two-breadcrumb"));
       mdlBC.text(breadData.model.name);
       mdlBC.prop("href", breadData.model.href);
+      $(this.queryByHook("return-to-model")).prop("href", breadData.model.href);
     }else if(breadData.model || breadData.project) {
       $(this.queryByHook("one-parent-breadcrumb-links")).css("display", "block");
       let breadcrumb = $(this.queryByHook("parent-one-breadcrumb"));
       if(breadData.project) {
         breadcrumb.text(breadData.project.name)
         breadcrumb.prop("href", breadData.project.href);
+        $(this.queryByHook("return-to-project")).prop("href", breadData.project.href);
+        $(this.queryByHook("return-to-model")).css("display", "none");
       }else {
         breadcrumb.text(breadData.model.name)
         breadcrumb.prop("href", breadData.model.href);
+        $(this.queryByHook("return-to-project")).css("display", "none");
+        $(this.queryByHook("return-to-model")).prop("href", breadData.model.href);
       }
+    }else{
+      $(this.queryByHook("return-to-model")).css("display", "none");
+      $(this.queryByHook("return-to-project")).css("display", "none");
     }
     this.renderDomainProperties();
     this.renderDomainLimitations();

client/pages/file-browser.js

@@ -44,6 +44,7 @@ let FileBrowser = PageView.extend({
     'click [data-hook=file-browser-help]' : function () {
       let modal = $(modals.operationInfoModalHtml('file-browser')).modal();
     },
+    'click [data-hook=empty-trash]' : 'emptyTrash'
   },
   initialize: function (attrs, options) {
     PageView.prototype.initialize.apply(this, arguments)
@@ -78,7 +79,10 @@ let FileBrowser = PageView.extend({
           if(op === 'move_node' && more && more.ref && more.ref.type && !(more.ref.type == 'folder' || more.ref.type == 'root')){
             return false
           }
-          if(op === 'move_node' && more && more.ref && more.ref.type && more.ref.type === 'folder'){
+          if(op === 'move_node' && more && more.ref && more.ref.original && path.dirname(more.ref.original._path).split("/").includes("trash")){
+            return false
+          }
+          if(op === 'move_node' && more && more.ref && more.ref.type && more.ref.type === 'folder' && more.ref.text !== "trash"){
             if(!more.ref.state.loaded){
               return false
             }
@@ -110,6 +114,11 @@ let FileBrowser = PageView.extend({
                 node.original._path = path.join(newDir, file);
                 if(node.type === "folder") {
                   $('#models-jstree').jstree().refresh_node(node);
+                }else if(newDir.endsWith("trash")) {
+                  $(self.queryByHook('empty-trash')).prop('disabled', false);
+                  $('#models-jstree').jstree().refresh_node(par);
+                }else if(oldPath.split("/").includes("trash")) {
+                  $('#models-jstree').jstree().refresh_node(par);
                 }
               },
               error: function (err, response, body) {
@@ -639,16 +648,9 @@ let FileBrowser = PageView.extend({
         var endpoint = path.join(app.getApiPath(), "project/new-project")+"?path="+projectPath
         app.getXHR(endpoint, {
           success: function (err, response, body) {
-            if(o){//directory was created with context menu option
-              var node = $('#models-jstree').jstree().get_node(o);
-              if(node.type === "root"){
-                self.refreshJSTree();
-              }else{          
-                $('#models-jstree').jstree().refresh_node(node);
-              }
-            }else{//directory was created with create directory button
-              self.refreshJSTree();
-            }
+            let queryStr = "?path=" + body.path;
+            let endpoint = path.join(app.getBasePath(), 'stochss/project/manager') + queryStr;
+            window.location.href = endpoint;
           },
           error: function (err, response, body) {
             let errorModel = $(modals.newProjectOrWorkflowGroupErrorHtml(body.Reason, body.Message)).modal();
@@ -770,7 +772,6 @@ let FileBrowser = PageView.extend({
         if(o && o.original && o.original.type !== "root"){
           parentPath = o.original._path
         }
-        console.log(parentPath)
         if(isModel) {
           let ext = isSpatial ? ".smdl" : ".mdl"
           let modelName = o && o.type === "project" ? input.value.trim().split("/").pop() + ext : input.value.trim() + ext;
@@ -860,6 +861,43 @@ let FileBrowser = PageView.extend({
       }
     });
   },
+  moveToTrash: function (o) {
+    if(document.querySelector('#moveToTrashConfirmModal')) {
+      document.querySelector('#moveToTrashConfirmModal').remove();
+    }
+    let self = this;
+    let modal = $(modals.moveToTrashConfirmHtml("model")).modal();
+    let yesBtn = document.querySelector('#moveToTrashConfirmModal .yes-modal-btn');
+    yesBtn.addEventListener('click', function (e) {
+      modal.modal('hide');
+      let queryStr = "?srcPath=" + o.original._path + "&dstPath=" + path.join("trash", o.text)
+      let endpoint = path.join(app.getApiPath(), "file/move") + queryStr
+      app.getXHR(endpoint, {
+        always: function (err, response, body) {
+          $(self.queryByHook('empty-trash')).prop('disabled', false);
+          $('#models-jstree').jstree().refresh();
+        }
+      });
+    });
+  },
+  emptyTrash: function (e) {
+    if(document.querySelector("#emptyTrashConfirmModal")) {
+      document.querySelector("#emptyTrashConfirmModal").remove()
+    }
+    let self = this;
+    let modal = $(modals.emptyTrashConfirmHtml()).modal();
+    let yesBtn = document.querySelector('#emptyTrashConfirmModal .yes-modal-btn');
+    yesBtn.addEventListener('click', function (e) {
+      modal.modal('hide');
+      let endpoint = path.join(app.getApiPath(), "file/empty-trash") + "?path=trash";
+      app.getXHR(endpoint, {
+        success: function (err, response, body) {
+          self.refreshJSTree();
+          $(self.queryByHook('empty-trash')).prop('disabled', true);
+        }
+      });
+    });
+  },
   setupJstree: function () {
     var self = this;
     $.jstree.defaults.contextmenu.items = (o, cb) => {
@@ -905,6 +943,17 @@ let FileBrowser = PageView.extend({
             self.duplicateFileOrDirectory(o, null)
           }
         },
+        "MoveToTrash" : {
+          "label" : "Move To Trash",
+          "_disabled" : false,
+          "separator_before" : false,
+          "separator_after" : false,
+          "action" : function (data) {
+            self.moveToTrash(o);
+          }
+        }
+      }
+      let delete_node = {
         "Delete" : {
           "label" : "Delete",
           "_disabled" : false,
@@ -1268,6 +1317,12 @@ let FileBrowser = PageView.extend({
       if (o.type === 'root'){
         return folder
       }
+      if (o.text === "trash") {
+        return {"Refresh": folder.Refresh}
+      }
+      if (o.original._path.split("/")[0] === "trash") {
+        return delete_node
+      }
       if (o.type ===  'folder') {
         return $.extend(folder, common)
       }
@@ -1326,26 +1381,28 @@ let FileBrowser = PageView.extend({
       var file = e.target.text
       var node = $('#models-jstree').jstree().get_node(e.target)
       var _path = node.original._path;
-      if(file.endsWith('.mdl') || file.endsWith('.smdl')){
-        window.location.href = path.join(app.getBasePath(), "stochss/models/edit")+"?path="+_path;
-      }else if(file.endsWith('.ipynb')){
-        var notebookPath = path.join(app.getBasePath(), "notebooks", _path)
-        window.open(notebookPath, '_blank')
-      }else if(file.endsWith('.sbml')){
-        var openPath = path.join(app.getBasePath(), "edit", _path)
-        window.open(openPath, '_blank')
-      }else if(file.endsWith('.proj')){
-        window.location.href = path.join(app.getBasePath(), "stochss/project/manager")+"?path="+_path;
-      }else if(file.endsWith('.wkfl')){
-        window.location.href = path.join(app.getBasePath(), "stochss/workflow/edit")+"?path="+_path+"&type=none";
-      }else if(file.endsWith('.domn')) {
-        let queryStr = "?domainPath=" + _path
-        window.location.href = path.join(app.getBasePath(), "stochss/domain/edit") + queryStr
-      }else if(node.type === "folder" && $('#models-jstree').jstree().is_open(node) && $('#models-jstree').jstree().is_loaded(node)){
-        $('#models-jstree').jstree().refresh_node(node)
-      }else if(node.type === "other"){
-        var openPath = path.join(app.getBasePath(), "view", _path);
-        window.open(openPath, "_blank");
+      if(!(_path.split("/")[0] === "trash")) {
+        if(file.endsWith('.mdl') || file.endsWith('.smdl')){
+          window.location.href = path.join(app.getBasePath(), "stochss/models/edit")+"?path="+_path;
+        }else if(file.endsWith('.ipynb')){
+          var notebookPath = path.join(app.getBasePath(), "notebooks", _path)
+          window.open(notebookPath, '_blank')
+        }else if(file.endsWith('.sbml')){
+          var openPath = path.join(app.getBasePath(), "edit", _path)
+          window.open(openPath, '_blank')
+        }else if(file.endsWith('.proj')){
+          window.location.href = path.join(app.getBasePath(), "stochss/project/manager")+"?path="+_path;
+        }else if(file.endsWith('.wkfl')){
+          window.location.href = path.join(app.getBasePath(), "stochss/workflow/edit")+"?path="+_path+"&type=none";
+        }else if(file.endsWith('.domn')) {
+          let queryStr = "?domainPath=" + _path
+          window.location.href = path.join(app.getBasePath(), "stochss/domain/edit") + queryStr
+        }else if(node.type === "folder" && $('#models-jstree').jstree().is_open(node) && $('#models-jstree').jstree().is_loaded(node)){
+          $('#models-jstree').jstree().refresh_node(node)
+        }else if(node.type === "other"){
+          var openPath = path.join(app.getBasePath(), "view", _path);
+          window.open(openPath, "_blank");
+        }
       }
     });
   }

client/pages/multiple-plots.js

@@ -0,0 +1,61 @@
+/*
+StochSS is a platform for simulating biochemical systems
+Copyright (C) 2019-2020 StochSS developers.
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+let path = require('path');
+//support files
+let app = require('../app');
+let Plotly = require('../lib/plotly');
+//views
+var PageView = require('../pages/base');
+//templates
+let template = require("../templates/pages/multiplePlots.pug");
+
+import initPage from './page.js';
+
+let ModelEditor = PageView.extend({
+  template: template,
+  initialize: function (attrs, options) {
+    PageView.prototype.initialize.apply(this, arguments);
+    let urlParams = new URLSearchParams(window.location.search);
+    this.workflow = urlParams.get("wkfl");
+    this.job = urlParams.get("job");
+    this.path = urlParams.get("path");
+    this.data = urlParams.get("data");
+  },
+  render: function (attrs, options) {
+    PageView.prototype.render.apply(this, arguments);
+    let queryStr = "?path=" + this.path + "&data=" + this.data;
+    let endpoint = path.join(app.getApiPath(), "workflow/plot-results") + queryStr;
+    let self = this;
+    app.getXHR(endpoint, {
+      success: function (err, response, body) {
+        self.plotFigure(body);
+      },
+      error: function (err, response, body) {
+        console.log(body)
+      }
+    });
+  },
+  plotFigure: function (figure) {
+    let el = this.queryByHook("figures");
+    let config = {"responsive":true};
+    Plotly.newPlot(el, figure, config);
+  }
+});
+
+initPage(ModelEditor);

client/pages/project-manager.js

@@ -229,7 +229,7 @@ let ProjectManager = PageView.extend({
     let yesBtn = document.querySelector('#emptyTrashConfirmModal .yes-modal-btn');
     yesBtn.addEventListener('click', function (e) {
       modal.modal('hide');
-      let endpoint = path.join(app.getApiPath(), "project/empty-trash")+"?path="+path.join(self.model.directory, "trash");
+      let endpoint = path.join(app.getApiPath(), "file/empty-trash")+"?path="+path.join(self.model.directory, "trash");
       app.getXHR(endpoint, {
         success: function (err, response, body) {
           $(self.queryByHook('empty-project-trash')).prop('disabled', true);

client/templates/includes/gillespyResultsEnsemble.pug

@@ -83,6 +83,8 @@ div#workflow-results.card.card-body
 
         button.btn.btn-primary.box-shadow(data-hook="trajectories-edit-plot" data-target="edit-plot" disabled) Edit Plot
 
+        button.btn.btn-primary.box-shadow(data-hook="multiple-plots", data-type="mltplplt" disabled) Multiple Plots
+
         button.btn.btn-primary.box-shadow(
           data-hook="trajectories-download-png-custom"
           data-target="download-png-custom"

client/templates/includes/parameterScanResults.pug

@@ -50,6 +50,8 @@ div#workflow-results.card.card-body
 
             button.btn.btn-primary.box-shadow(data-hook="ts-psweep-edit-plot" data-target="edit-plot" disabled) Edit Plot
 
+            button.btn.btn-primary.box-shadow(data-hook="multiple-plots" data-type="ts-psweep-mp" style="display: none;" disabled) Multiple Plots
+
             button.btn.btn-primary.box-shadow(
               data-hook="ts-psweep-download-png-custom"
               data-target="download-png-custom"

client/templates/includes/parameterSweepResults.pug

@@ -64,6 +64,8 @@ div#workflow-results.card.card-body
 
               button.btn.btn-primary.box-shadow(data-hook="ts-psweep-edit-plot" data-target="edit-plot" disabled) Edit Plot
 
+              button.btn.btn-primary.box-shadow(data-hook="multiple-plots" data-type="ts-psweep-mp" style="display: none;" disabled) Multiple Plots
+
               button.btn.btn-primary.box-shadow(
                 data-hook="ts-psweep-download-png-custom"
                 data-target="download-png-custom"

client/templates/pages/domainEditor.pug

@@ -319,6 +319,10 @@ section.page
       li.dropdown-item(data-hook="save-to-model") to Model
       li.dropdown-item(data-hook="save-to-file") to File (.domn)
 
+  a.btn.btn-primary.box-shadow.text-break(role="button" data-hook="return-to-project") Return to Project
+
+  a.btn.btn-primary.box-shadow.text-break(role="button" data-hook="return-to-model") Return to Model
+
   div.mdl-edit-btn.saving-status.inline(data-hook="sd-in-progress")
 
     div.spinner-grow.mr-2

client/templates/pages/fileBrowser.pug

@@ -35,4 +35,6 @@ section.page
 
   button.btn.btn-primary.box-shadow(id="options-for-node" data-hook="options-for-node" disabled) Actions
 
-  button.btn.btn-primary.inline.box-shadow(id="refresh-jstree" data-hook="refresh-jstree") Refresh
+  button.btn.btn-primary.inline.box-shadow(id="refresh-jstree" data-hook="refresh-jstree") Refresh
+
+  button.btn.btn-primary.inline.box-shadow(id="empty-trash" data-hook="empty-trash") Empty Trash

client/templates/pages/multiplePlots.pug

@@ -0,0 +1,11 @@
+section.page
+
+  h3="Workflow: "+this.workflow
+
+  h4="Job: "+this.job
+
+  div.card.card-body
+
+    h5 Plot Trajectories: Multiple Graphs
+
+    div(data-hook="figures")