Merge pull request #37 from vathes/dev

merging dev to master for official deploy

Author: guzman-raphael

backend/iblapi.py

@@ -24,7 +24,6 @@
 API_PREFIX = '/v{}'.format(API_VERSION)
 is_gunicorn = "gunicorn" in os.environ.get("SERVER_SOFTWARE", "")
 
-
 def mkvmod(mod):
     return dj.create_virtual_module(
         mod, dj.config.get('database.prefix', '') + 'ibl_{}'.format(mod))
@@ -243,9 +242,14 @@ def handle_q(subpath, args, proj, fetch_args=None, **kwargs):
         #   expected format of brain_regions = ["AB", "ABCa", "CS of TCV"]
         if regions is not None and len(regions) > 0: 
             region_restr = [{'acronym': v} for v in regions]
-            brain_restriction = histology.ProbeBrainRegionTemp() & region_restr
-            # keep the temp table for internal site since temp table has more entries for internal users to see
-            # for public site replace ProbeBrainRegionTemp() with ProbeBrainRegion() table.
+            
+            if os.environ.get('API_MODE') in ['private', None]:
+                brain_restriction = histology.ProbeBrainRegionTemp() & region_restr
+            elif os.environ.get('API_MODE') == 'public':
+                brain_restriction = histology.ProbeBrainRegion() & region_restr
+            else:
+                raise Exception('Invalid API_MODE, it should either be not defined / private / public, please check your environment variables.')
+            
         else:
             brain_restriction = {}
         # q = ((acquisition.Session() * sess_proj * psych_curve * ephys_data * subject.Subject()*
@@ -323,17 +327,19 @@ def handle_q(subpath, args, proj, fetch_args=None, **kwargs):
         q = (ephys.DefaultCluster & args).proj(..., *exclude_attrs) * ephys.DefaultCluster.Metrics.proj('firing_rate') 
         print(q)
     elif subpath == 'probetrajectory':
-        # keep the provenance and temp table for internal site
-        traj = histology.ProbeTrajectoryTemp * histology.Provenance
+        if os.environ.get('API_MODE') in ['private', None]:
+            traj = histology.ProbeTrajectoryTemp * histology.Provenance
 
-        traj_latest = traj * (dj.U('subject_uuid', 'session_start_time', 'probe_idx', 'provenance') & \
-                      (ephys.ProbeInsertion & args).aggr(traj, provenance='max(provenance)'))
+            traj_latest = traj * (dj.U('subject_uuid', 'session_start_time', 'probe_idx', 'provenance') & \
+                        (ephys.ProbeInsertion & args).aggr(traj, provenance='max(provenance)'))
 
-        q = traj * (dj.U('subject_uuid', 'session_start_time', 'probe_idx', 'provenance') & \
-                      (ephys.ProbeInsertion & args).aggr(traj, provenance='max(provenance)'))
+            q = traj * (dj.U('subject_uuid', 'session_start_time', 'probe_idx', 'provenance') & \
+                        (ephys.ProbeInsertion & args).aggr(traj, provenance='max(provenance)'))
+        elif os.environ.get('API_MODE') == 'public':
+            q = histology.ProbeTrajectory & args
+        else:
+            raise Exception('Invalid API_MODE, it should either be not defined / private / public, please check your environment variables.')
 
-        # for public site we don't need the trajectory source info (uses provenance) anymore so -> traj = histology.ProbeTrajectory
-        # or basically for public -> q = histology.ProbeTrajectory & args
     elif subpath == 'rasterlight':
         # q = plotting_ephys.RasterLinkS3 & args
         q = plotting_ephys.Raster & args # temp test table
@@ -430,12 +436,6 @@ def post_process(ret):
                 parsed_items.append(parsed_item)
             return parsed_items
     elif subpath == 'depthbrainregions':
-        # depth_region = histology.DepthBrainRegionTemp * histology.Provenance
-
-        # q = depth_region * (dj.U('subject_uuid', 'session_start_time', 'probe_idx', 'provenance') & 
-        #             (ephys.ProbeInsertion & args).aggr(depth_region, provenance='max(provenance)'))
-                
-        # NEW: test this before deploy to internal
         q = histology.DepthBrainRegion & args
     elif subpath == 'spinningbrain':
         q = plotting_histology.SubjectSpinningBrain & args

docker-compose-base.yml

@@ -8,7 +8,7 @@ x-net: &net
 services:
   iblapi:
     <<: *net
-    image: registry.vathes.com/ibl-navigator/iblapi:v0.5.0 # for internal demo
+    image: registry.vathes.com/ibl-navigator/iblapi:v0.5.1 # for internal demo
     # image: registry.vathes.com/ibl-navigator/iblapi:v0.1.0-public # for public demo
     environment:
     - DJ_USER=maho
@@ -31,7 +31,7 @@ services:
     #cpu_period: 100ms
   ibl-navigator:
     <<: *net
-    image: registry.vathes.com/ibl-navigator/frontend:v0.4.0 # for internal demo
+    image: registry.vathes.com/ibl-navigator/frontend:v0.4.1 # for internal demo
     # image: registry.vathes.com/ibl-navigator/frontend:v0.1.0-public # for public demo
     healthcheck:
       test: curl --fail http://localhost:9000 || exit 1

ibl-frontend/frontend-content/src/app/cell-list/cell-list.component.css

@@ -122,6 +122,16 @@ td span.oi {
     margin-top: 15px;
 }
 
+.depth-peth-not-available {
+    border: 1px solid gray;
+    margin: 12px;
+    width: 400px;
+    height: 300px;
+    display: flex;
+    justify-content: center;
+    align-items: center;
+}
+
 .order-button-content .radio-option,
 .alternative_plot_buttons .radio-option  {
     padding-right: 15px;
@@ -154,6 +164,9 @@ td span.oi {
     padding-right: 10px;
 }
 
+.cluster-nav-plot-area {
+    padding-left: 12px;
+}
 .cluster-nav-plot-area > .yaxis-selector-plot-area {
     display: flex;
     flex-direction: row;

ibl-frontend/frontend-content/src/app/cell-list/cell-list.component.html

@@ -67,7 +67,7 @@ <h6>(Total clusters for probe {{probeIndex}}: {{cellsByProbeIns.length}})</h6>
 
   <div class="row">
     <br />
-    <div class="cluster-nav-plot-area col-10 col-xl-6">
+    <div class="cluster-nav-plot-area">
       <div *ngIf="plot_data_processed && plot_data_processed[0]" class="yaxis-selector-plot-area">
         <div class="alternative_plot_buttons y_axis">
           <label for="y_label"><b>y axis</b></label>
@@ -106,7 +106,7 @@ <h6>(Total clusters for probe {{probeIndex}}: {{cellsByProbeIns.length}})</h6>
       </div> 
     </div>
 
-    <div class="depth-peth-plot-area col-10 col-xl-4" *ngIf="depthPethLookup[eventType]['layout']">
+    <div class="depth-peth-plot-area">
       <div class="order-buttons col-10">
 
         <div class="order-button-content">
@@ -125,9 +125,12 @@ <h6>(Total clusters for probe {{probeIndex}}: {{cellsByProbeIns.length}})</h6>
           </div>    
         </div>  
       </div>
-      <div>
+      <div *ngIf="!depthPethIsLoading && depthPethLookup[eventType] && depthPethLookup[eventType]['data']">
         <plotly-plot [data]="depthPethLookup[eventType]['data']" [layout]="depthPethLookup[eventType]['layout']" [config]="depthPethLookup[eventType]['config']"></plotly-plot> 
       </div>
+      <div *ngIf="!depthPethIsLoading && (!depthPethLookup[eventType] || !depthPethLookup[eventType]['data'])" class="depth-peth-not-available">
+        <p>Depth PETH plot not available for this session</p> 
+      </div>
     </div>
     <div [class]="minimizeController? 'plots-navigator minimize': 'plots-navigator'" *ngIf="showController">
       <div *ngIf="cells" class="clusterListContainer">
@@ -160,7 +163,7 @@ <h3><span class="oi oi-arrow-circle-top" (click)="navigate_cell_plots($event, 'u
         <h3><span class="oi oi-arrow-circle-bottom" (click)="navigate_cell_plots($event, 'down')"></span></h3>
       </div>
     </div>
-
+    <br />
     <div class="rasterPlotSelectors col-8">
       <div class="order-buttons col-4">
         <label for="event"><b>Event</b></label>

ibl-frontend/frontend-content/src/app/cell-list/cell-list.component.ts

@@ -92,6 +92,7 @@ export class CellListComponent implements OnInit, OnDestroy, DoCheck {
   depthPETH;
   depthPethTemplates = {};
   depthPethLookup = {};
+  depthPethIsLoading = false;
 
   spikeAmpTimeLookup = {};
   spikeAmpTime;
@@ -674,6 +675,7 @@ export class CellListComponent implements OnInit, OnDestroy, DoCheck {
 
           /////++++++///// start of grabbing depth PETH plot info /////++++++/////
           this.cellListService.getDepthPethTemplate();
+          this.depthPethIsLoading = true;
           this.depthPethTemplateSubscription = this.cellListService.getDepthPethTemplateLoadedListener()
             .subscribe((dpTemplates) => {
               // console.log('depth PETH templates retrieved: ', dpTemplates[0]);
@@ -691,12 +693,8 @@ export class CellListComponent implements OnInit, OnDestroy, DoCheck {
           }
           this.depthPethSubscription = this.cellListService.getDepthPethLoadedListener()
             .subscribe((plotInfo) => {
-              this.depthPETHtimeB = new Date()
-              // console.log('retrieved depth PETH data - took ', this.depthPETHtimeB-this.depthPETHtimeA, 'ms')
               this.depthPETH = deepCopy(plotInfo);
-              // console.log('depth PETH retrieved for session: ', plotInfo);
               for (let plot of Object.values(plotInfo)) {
-                // console.log("this.depthPethTemplates[plot['depth_peth_template_idx']]: ", this.depthPethTemplates)
                 this.depthPethLookup[plot['event']]['data'] = deepCopy(this.depthPethTemplates[plot['depth_peth_template_idx']]['data'])
                 this.depthPethLookup[plot['event']]['layout'] = deepCopy(this.depthPethTemplates[plot['depth_peth_template_idx']]['layout'])
                 let depth_peth_config_copy = {...this.depthPETH_config};
@@ -724,15 +722,12 @@ export class CellListComponent implements OnInit, OnDestroy, DoCheck {
 
                 this.depthPethLookup[plot['event']]['config'] = depth_peth_config_copy
               }
-              // console.log('this.DepthPethLookup: ', this.depthPethLookup)
               if (this.depthPethLookup['movement'] && Object.keys(this.depthPethLookup['movement']).length == 0) {
                 this.depthPethEventLacksMovement = true;
               } else {
                 this.depthPethEventLacksMovement = false;
               }
-              // console.log('depthPethEventLacksMovement: ', this.depthPethEventLacksMovement);
-              this.depthPETHtimeC = new Date()
-              // console.log('depth PETH done plotting - took: ', this.depthPETHtimeC-this.depthPETHtimeB, 'ms')
+              this.depthPethIsLoading = false;
             });
 
 

ibl-frontend/frontend-content/src/app/session-list/session-list.component.ts

@@ -532,7 +532,6 @@ export class SessionListComponent implements OnInit, OnDestroy {
    * @returns 
    */
   getFiltersRequests(focusedField?: string) {
-    // console.log("shoulnd't be using getFIltersREquest anymore returning")
     return;
     const filterList = Object.entries(this.session_filter_form.getRawValue());
     const brainRegionRequest = this.requested_BR;
@@ -786,7 +785,6 @@ export class SessionListComponent implements OnInit, OnDestroy {
    * @returns 
    */
   async applyFilter(focusFieldKey?: string) {
-    let t0 = performance.now()
     if (!this.allSessions) {
       return [];
     }
@@ -801,7 +799,7 @@ export class SessionListComponent implements OnInit, OnDestroy {
 
     // Check if there is a brain region request, if so override the tupleToRestrict reference
     const brainRegionRequest = this.requested_BR;
-    if (brainRegionRequest !== []) {
+    if (brainRegionRequest.length !== 0) {
       // BrainRegionRequest is not empty, thus query the backend for it
       let requestFilter = {}
       let BR_JSONstring = '';
@@ -822,6 +820,9 @@ export class SessionListComponent implements OnInit, OnDestroy {
         requestFilter['__json_kwargs'] = '{ "brain_regions": ' + BR_JSONstring + '}';
       }
 
+      // Add the default sorting for the api request
+      requestFilter['__order'] = 'session_start_time DESC';
+
       // Query back end
       tupleToRestrict = await this.allSessionsService.fetchSessions(requestFilter).toPromise();
     }
@@ -1089,7 +1090,7 @@ export class SessionListComponent implements OnInit, OnDestroy {
     return newData;
   }
 
-  filterNode(node, word, selectAll){
+  filterNode(node, word, selectAll) {
     let children = []
     let newNode = {
       display: node.display,