Workflow Manager Updates

client/job-view/job-view.js

@@ -46,10 +46,10 @@ module.exports = View.extend({
   },
   render: function (attrs, options) {
   	View.prototype.render.apply(this, arguments);
-  	if(this.model.status !== "error") {
+  	if(this.model.status === "complete") {
       this.renderResultsView();
     }
-    if(!this.readOnly) {
+    if(!this.readOnly && this.model.status !== "running") {
       this.renderLogsView();
     }
     this.renderSettingsView();

client/models/job.js

@@ -74,6 +74,13 @@ module.exports = State.extend({
         // timeZone = timeZone.replace('(', '').replace(')', '') // remove the '()' from the timezone
         return  stamp + hours + ":" + minutes + " " + ampm + " " + timeZone;
       }
+    },
+    sortTime: {
+      deps: ["startTime"],
+      fn: function () {
+        let date = new Date(this.startTime);
+        return Math.round(date.getTime() / 1000);
+      }
     }
   }
 });

client/models/jobs.js

@@ -22,5 +22,6 @@ let Collection = require('ampersand-collection');
 let Job = require('./job');
 
 module.exports = Collection.extend({
-  model: Job
+  model: Job,
+  comparator: 'sortTime'
 });

client/pages/workflow-manager.js

@@ -49,12 +49,14 @@ let WorkflowManager = PageView.extend({
     'click [data-target=start-job]'  : 'clickStartJobHandler',
     'click [data-hook=edit-model]' : 'clickEditModelHandler',
     'click [data-hook=collapse-jobs]' : 'changeCollapseButtonText',
-    'click [data-hook=return-to-project-btn]' : 'handleReturnToProject'
+    'click [data-hook=return-to-project-btn]' : 'handleReturnToProject',
+    'click [data-hook=manual-view-control]' : 'setActiveJobViewControl'
   },
   initialize: function (attrs, options) {
     PageView.prototype.initialize.apply(this, arguments);
     let urlParams = new URLSearchParams(window.location.search);
     let jobID = urlParams.has('job') ? urlParams.get('job') : null;
+    this.viewingActiveJob = false;
     this.model = new Workflow({
       directory: urlParams.get('path')
     });
@@ -227,8 +229,9 @@ let WorkflowManager = PageView.extend({
     this.jobListingView = this.renderCollection(
       this.model.jobs,
       JobListingView,
-      this.queryByHook("job-listing")
+      this.queryByHook("job-listing"),
     );
+    this.setActiveJobIndicator();
   },
   renderModelLocationSelectView: function (model) {
     if(this.modelLocationSelectView) {
@@ -287,14 +290,13 @@ let WorkflowManager = PageView.extend({
     }else if(this.model.activeJob.status !== "ready") {
       this.renderStatusView();
     }
-    let detailsStatus = ["error", "complete"];
     if(jobID !== null) {
       let activeJob = this.model.jobs.filter((job) => { return job.name === jobID; })[0] || null;
       if(activeJob !== null) {
         this.model.activeJob = activeJob;
       }
     }
-    if(this.model.activeJob && detailsStatus.includes(this.model.activeJob.status)) {
+    if(this.model.activeJob) {
       this.renderActiveJob();
     }
   },
@@ -309,8 +311,20 @@ let WorkflowManager = PageView.extend({
   setActiveJob: function (job) {
     this.removeActiveJob();
     this.model.activeJob = job;
+    this.viewingActiveJob = false;
+    this.setActiveJobViewControl();
     this.renderActiveJob();
   },
+  setActiveJobIndicator: function () {
+    this.jobListingView.views.forEach((view) => {
+      view.updateActiveJob(this.model.activeJob.directory);
+    });
+  },
+  setActiveJobViewControl: function (e) {
+    this.viewingActiveJob = !this.viewingActiveJob;
+    $(this.queryByHook("manual-view-control")).text(this.viewingActiveJob ? "Finished" : "View");
+    this.setActiveJobIndicator();
+  },
   setupSettingsView: function () {
     if(!this.model.newFormat) {
       $(this.queryByHook("of-start-job")).css('display', 'inline-block');
@@ -375,31 +389,46 @@ let WorkflowManager = PageView.extend({
         let runEndpoint = `${path.join(app.getApiPath(), "workflow/run-job")}${runQuery}`;
         app.getXHR(runEndpoint, {
           success: (err, response, body) => {
-            this.updateWorkflow(true);
+            this.updateWorkflow({newJob: true});
           }
         });
       }
     });
   },
-  updateWorkflow: function (newJob) {
-    let self = this;
+  updateWorkflow: function ({newJob=false}={}) {
     if(this.model.newFormat) {
-      let hadActiveJob = Boolean(this.model.activeJob.status)
       app.getXHR(this.model.url(), {
-        success: function (err, response, body) {
-          self.model.set({jobs: body.jobs, activeJob: body.activeJob});
-          if(!Boolean(self.model.activeJob.status)){
-            self.removeActiveJob();
-          }else if(!hadActiveJob && Boolean(self.model.activeJob.status)) {
-            self.renderActiveJob();
+        success: (err, response, body) => {
+          this.model.set({jobs: body.jobs});
+          if(newJob || this.viewingActiveJob) {
+            setTimeout(() => { this.setActiveJobIndicator(); });
+          }else if (!Boolean(body.activeJob.status)) {
+            this.removeActiveJob();
+          }else {
+            this.model.set({activeJob: body.activeJob});
+            this.setActiveJobViewControl();
+            this.renderActiveJob();
+          }
+          if(newJob) {
+            setTimeout(() => { this.setActiveJobIndicator(); });
+          }else {
+            if(!Boolean(this.model.activeJob.status)) {
+              this.removeActiveJob();
+            }else if(!this.viewingActiveJob){
+              this.model.set({activeJob: body.activeJob});
+              this.renderActiveJob();
+              this.setActiveJobViewControl();
+            }else {
+              setTimeout(() => { this.setActiveJobIndicator(); });
+            }
           }
         }
       });
     }else if(!this.model.newFormat){
       app.getXHR(this.model.url(), {
-        success: function (err, response, body) {
-          self.model.set(body)
-          self.renderSubviews();
+        success: (err, response, body) => {
+          this.model.set(body)
+          this.renderSubviews();
         }
       });
     }

client/settings-view/views/well-mixed-settings-view.js

@@ -63,7 +63,8 @@ module.exports = View.extend({
     }else {
       if(!this.model.isAutomatic){
         $(this.queryByHook('select-ode')).prop('checked', Boolean(this.model.algorithm === "ODE"));
-        $(this.queryByHook('select-ssa')).prop('checked', Boolean(this.model.algorithm === "SSA")); 
+        $(this.queryByHook('select-ssa')).prop('checked', Boolean(this.model.algorithm === "SSA"));
+        $(this.queryByHook('select-cle')).prop('checked', Boolean(this.model.algorithm === "CLE"));
         $(this.queryByHook('select-tau-leaping')).prop('checked', Boolean(this.model.algorithm === "Tau-Leaping"));
         $(this.queryByHook('select-hybrid-tau')).prop('checked', Boolean(this.model.algorithm === "Hybrid-Tau-Leaping"));
       }else{

client/styles/styles.css

@@ -884,4 +884,19 @@ input:checked + .slider:before {
   position: absolute;
   left: 15px;
   top: 40%;
-}
+}
+
+.active-job-listing {
+  background-color: rgba(0, 255, 255, 1.0);
+}
+
+.job-listing-btn {
+  color: rgb(108, 117, 125);
+  background-color: rgb(255, 255, 255) !important;
+}
+
+.job-listing-btn:hover {
+  color: rgb(255, 255, 255);
+  background-color: rgb(108, 117, 125) !important;
+}
+

client/templates/includes/jobListing.pug

@@ -3,24 +3,26 @@ div(data-hook=this.model.elementID)
   if(this.model.collection.indexOf(this.model) !== 0)
     hr
 
-  div.row
+  div.py-1.pl-1(data-hook="is-active-job")
 
-    div.col-md-3
+    div.row
 
-      button.btn.btn-outline-secondary.box-shadow(data-hook=this.model.elementID + "-open" style="width: 100%")=this.model.name
+      div.col-md-3
 
-    div.col-md-4
+        button.btn.btn-outline-secondary.box-shadow.job-listing-btn(data-hook=this.model.elementID + "-open" style="width: 100%")=this.model.name
 
-      div.py-2=this.model.fmtStartTime
+      div.col-md-4
 
-    div.col-md-3
+        div.py-2=this.model.fmtStartTime
 
-      div.py-2
+      div.col-md-3
 
-        div.inline(data-hook=this.model.elementID + "-status")=this.model.status
+        div.py-2
 
-        div.inline.spinner-border.status(data-hook=this.model.elementID + "-running-spinner")
+          div.inline(data-hook=this.model.elementID + "-status")=this.model.status
 
-    div.col-md-2
+          div.inline.spinner-border.status(data-hook=this.model.elementID + "-running-spinner")
 
-      button.btn.btn-outline-secondary.box-shadow(data-hook=this.model.elementID + "-remove") X
+      div.col-md-2
+
+        button.btn.btn-outline-secondary.box-shadow.job-listing-btn(data-hook=this.model.elementID + "-remove") X

client/templates/pages/workflowManager.pug

@@ -106,7 +106,13 @@ section.page
 
   div.mt-4(data-hook="active-job-header-container" style="display: none")
 
-    h2(data-hook="active-job-header") Job:
+    div.inline
+
+      h2(data-hook="active-job-header") Job:
+
+    div.mr-3.inline(style="float: right;")
+
+      button.btn.btn-outline-secondary.box-shadow(data-hook="manual-view-control") View
 
   div(data-hook="active-job-container")
 

client/views/job-listing.js

@@ -36,11 +36,15 @@ module.exports = View.extend({
   },
   initialize: function (attrs, options) {
     View.prototype.initialize.apply(this, arguments);
+    this.isActiveJob = false;
+    console.log(this.model.startTime, this.model.sortTime)
   },
   render: function (attrs, options) {
     View.prototype.render.apply(this, arguments);
+    if(this.isActiveJob) {
+      $(this.queryByHook("is-active-job")).addClass("active-job-listing");
+    }
     if(this.model.status === "running") {
-      $(this.queryByHook(this.model.elementID + "-open")).prop("disabled", true);
       this.getJobStatus();
     }else{
       $(this.queryByHook(this.model.elementID + '-running-spinner')).css('display', "none")
@@ -80,5 +84,13 @@ module.exports = View.extend({
   },
   openActiveJob: function (e) {
     this.parent.setActiveJob(this.model);
+  },
+  updateActiveJob: function (activeJob) {
+    this.isActiveJob = Boolean(activeJob) && activeJob === this.model.directory;
+    if(this.isActiveJob) {
+      $(this.queryByHook("is-active-job")).addClass("active-job-listing");
+    }else {
+      $(this.queryByHook("is-active-job")).removeClass("active-job-listing");
+    }
   }
 });

client/views/workflow-group-listing.js

@@ -44,12 +44,14 @@ module.exports = View.extend({
   initialize: function (attrs, options) {
     View.prototype.initialize.apply(this, arguments);
     let links = [];
-    this.model.model.refLinks.forEach((link) => {
-      links.push(
-        `<a class="text-break" href='stochss/workflow/edit?path=${link.path}&type=none'>${link.name}</a>`
-      );
-    });
-    this.htmlLinks = links.join('')
+    if(this.model.model.refLinks) {
+      this.model.model.refLinks.forEach((link) => {
+        links.push(
+          `<a class="text-break" href='stochss/workflow/edit?path=${link.path}&type=none'>${link.name}</a>`
+        );
+      });
+    }
+    this.htmlLinks = links.join('');
   },
   render: function (attrs, options) {
     View.prototype.render.apply(this, arguments);

jupyterhub/.env

@@ -5,7 +5,7 @@ JUPYTER_CONFIG_DIR=/opt/stochss-config/.jupyter
 
 #AUTH_CLASS=jupyterhub.auth.DummyAuthenticator
 
-JUPYTERHUB_VERSION=1.1.0
+JUPYTERHUB_VERSION=3.1.1
 
 DOCKER_HUB_IMAGE=stochss-hub
 

stochss/handlers/util/stochss_job.py

@@ -692,6 +692,18 @@ def get_time_stamp(self):
             return time_stamp
         return None
 
+    def get_update_time(self):
+        os.chdir(self.get_path(full=True))
+        if os.path.exists("COMPLETE"):
+            mod_time = os.path.getctime("COMPLETE")
+        elif os.path.exists("ERROR"):
+            mod_time = os.path.getctime("ERROR")
+        elif os.path.exists("RUNNING"):
+            mod_time = os.path.getctime("RUNNING")
+        else:
+            mod_time = None
+        os.chdir(self.user_dir)
+        return mod_time
 
     def load(self, new=False):
         '''

stochss/handlers/util/stochss_workflow.py

@@ -165,20 +165,21 @@ def __load_annotation(self):
 
     def __load_jobs(self):
         self.workflow['jobs'] = []
-        time = 0
+        mrm_time = 0
         last_job = None
         for file_obj in os.listdir(self.get_path(full=True)):
             if file_obj.startswith("job_"):
                 path = os.path.join(self.path, file_obj)
-                job = StochSSJob(path=path).load()
-                self.workflow['jobs'].append(job)
-                if os.path.getmtime(path) > time and job['status'] != "running":
-                    time = os.path.getmtime(path)
-                    last_job = job
+                job = StochSSJob(path=path)
+                self.workflow['jobs'].append(job.load())
+                cm_time = job.get_update_time()
+                if cm_time > mrm_time:
+                    mrm_time = cm_time
+                    last_job = len(self.workflow['jobs']) - 1
         if last_job is None:
             self.workflow['activeJob'] = None
         else:
-            self.workflow['activeJob'] = last_job
+            self.workflow['activeJob'] = self.workflow['jobs'][last_job]
 
 
     def __load_settings(self):