Fix general regression issues and implement other requested changes

backend/iblapi.py

@@ -250,6 +250,10 @@ def handle_q(subpath, args, proj, fetch_args=None, **kwargs):
             training_status='training_status', good_enough_for_brainwide_map='good_enough_for_brainwide_map',
             keep_all_rows=True
             )
+        subj = subject.Subject().aggr(
+            subject.Death().proj('death_date') * dj.U('death_date'),
+            death_date='IFNULL(death_date, NULL)',
+            keep_all_rows=True)
         regions = kwargs.get('brain_regions', None)
         #   expected format of brain_regions = ["AB", "ABCa", "CS of TCV"]
         if regions is not None and len(regions) > 0: 
@@ -268,7 +272,7 @@ def handle_q(subpath, args, proj, fetch_args=None, **kwargs):
         #       subject.SubjectLab() * subject.SubjectUser() *
         #       analyses_behavior.SessionTrainingStatus()) & args & brain_restriction)
 
-        q = ((acquisition.Session() * sess_proj * psych_curve * ephys_data * subject.Subject() *
+        q = ((acquisition.Session() * sess_proj * psych_curve * ephys_data * subj *
               subject.SubjectLab() * subject.SubjectUser() * trainingStatus) & args & brain_restriction)
         q = q.proj(*proj) if proj else q
         dj.conn().query("SET SESSION max_join_size={}".format('18446744073709551615'))

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

@@ -7,56 +7,60 @@ <h5>Mouse <{{ mouse?.subject_nickname }}> Info</h5>
     </div>
     <div class="row mouse-info-table">
       <table class="table col-lg-4 col-sm-6 col-xs-12 table-striped table-bordered table-sm">
-        <tr>
-          <th>Mouse Nickname</th>
-          <td>{{ mouse?.subject_nickname }}</td>
-        </tr>
-        <tr>
-          <th>Mouse UUID</th>
-          <td>{{ mouse?.subject_uuid }}</td>
-        </tr>
-        <tr>
-          <th>Mouse DOB</th>
-          <td>{{ mouse?.subject_birth_date }}</td>
-        </tr>
-        <tr>
-          <th>Lab</th>
-          <td>{{ mouse?.lab_name }}</td>
-        </tr>
-        <tr>
-          <th>Sex</th>
-          <td>{{ mouse?.sex }}</td>
-        </tr>
-        <tr>
-          <th>Project</th>
-          <td>{{ mouse?.projects }}</td>
-        </tr>
-        <tr>
-          <th>User</th>
-          <td>{{ mouse?.responsible_user }}</td>
-        </tr>
+        <tbody>
+          <tr>
+            <th>Mouse Nickname</th>
+            <td>{{ mouse?.subject_nickname }}</td>
+          </tr>
+          <tr>
+            <th>Mouse UUID</th>
+            <td>{{ mouse?.subject_uuid }}</td>
+          </tr>
+          <tr>
+            <th>Mouse DOB</th>
+            <td>{{ mouse?.subject_birth_date }}</td>
+          </tr>
+          <tr>
+            <th>Lab</th>
+            <td>{{ mouse?.lab_name }}</td>
+          </tr>
+          <tr>
+            <th>Sex</th>
+            <td>{{ mouse?.sex }}</td>
+          </tr>
+          <tr>
+            <th>Project</th>
+            <td>{{ mouse?.projects }}</td>
+          </tr>
+          <tr>
+            <th>User</th>
+            <td>{{ mouse?.responsible_user }}</td>
+          </tr>
+        </tbody>
       </table>
       <table class="table col-lg-3 col-sm-6 col-xs-12 table-striped table-bordered table-sm">
-        <tr>
-          <th>Ear Mark</th>
-          <td>{{ mouse?.ear_mark }}</td>
-        </tr>
-        <tr>
-          <th>Mouse Line</th>
-          <td>{{ mouse?.subject_line }}</td>
-        </tr>
-        <tr>
-          <th>Source</th>
-          <td>{{ mouse?.subject_source }}</td>
-        </tr>
-        <tr>
-          <th>Protocol Number</th>
-          <td>{{ mouse?.protocol_number }}</td>
-        </tr>
-        <tr>
-          <th>Description</th>
-          <td>{{ mouse?.subject_description }}</td>
-        </tr>
+        <tbody>  
+          <tr>
+            <th>Ear Mark</th>
+            <td>{{ mouse?.ear_mark }}</td>
+          </tr>
+          <tr>
+            <th>Mouse Line</th>
+            <td>{{ mouse?.subject_line }}</td>
+          </tr>
+          <tr>
+            <th>Source</th>
+            <td>{{ mouse?.subject_source }}</td>
+          </tr>
+          <tr>
+            <th>Protocol Number</th>
+            <td>{{ mouse?.protocol_number }}</td>
+          </tr>
+          <tr>
+            <th>Description</th>
+            <td>{{ mouse?.subject_description }}</td>
+          </tr>
+        </tbody>
       </table>
       <div class="spinning-brain-container col-xs-12 col-sm-6 col-lg-4" *ngIf="mouse">
         <app-spinning-brain [mouseInfo]="mouse"></app-spinning-brain>

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

@@ -139,6 +139,14 @@ label {
     position: relative;
     overflow-x: auto;
 }
+
+.flipped, .flipped .col-12
+{
+    transform:rotateX(180deg);
+    -ms-transform:rotateX(180deg); /* IE 9 */
+    -webkit-transform:rotateX(180deg); /* Safari and Chrome */
+}
+
 td.mat-cell, 
 td.mat-footer-cell, 
 th.mat-header-cell {

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

@@ -155,11 +155,23 @@ <h4>
             </mat-autocomplete>
           </mat-form-field>
 
+          <div class="date-range-toggler">
+            <label for="isAlive">Mouse Vital Status</label>
+            <div>
+              Deceased&nbsp;<mat-slide-toggle name="isAlive" [checked]="isAlive" (change)="isAlive=!isAlive">Alive
+              </mat-slide-toggle>
+            </div>
+          </div>
+
           <!-- // Brain Tree Selection Area -->
           <div class="brain-tree-zone">
             <mat-form-field>
               <label>Brain Regions</label>
-              <input matInput (input)="filterChanged($event.target.value.toLowerCase())">
+              <input matInput type="text" name="brain_regions" formControlName="brain_regions">
+                <mat-autocomplete #autoCompRU="matAutocomplete">
+                  <mat-option *ngFor="let responsible_user of dropDownMenuOptions.filteredResponsibleUserOptions | async"[value]="brain_regions"
+                    (click)="updateMenu()">{{ brain_regions }}</mat-option>
+                </mat-autocomplete>
             </mat-form-field>
            <!-- <div>Selected Brain Region:
               <div class="chip-list">
@@ -219,7 +231,7 @@ <h4>
             <button mat-raised-button class="btn btn-refresh" (click)="refreshData()">Refresh Data</button>
           </div>
         </div>
-        <!-- <div class="checkbox-filters">
+        <div class="checkbox-filters">
           <div class="chbox-filter">
             <mat-checkbox class="nplot_status_chbox" [checked]="hideMissingPlots" (change)="toggleNplotStatus()">
               Only show sessions with behavior plots
@@ -235,15 +247,15 @@ <h4>
               Only show sessions with ephys data
             </mat-checkbox>
           </div>
-        </div> -->
+        </div>
       </div>
     </form>
 
     <div [class]="isLoading && initialLoad ? 'loading-icon loading initial': isLoading ? 'loading-icon loading': 'loading-icon'">
       <img src="assets/images/loading_icon.gif">
       <p [class]="initialLoad ? 'session-list-loading-message show' : 'session-list-loading-message'"></p>
     </div>
-    <div class="table-container">
+    <div class="table-container flipped">
       <div class="session-list-loading-shade"
           *ngIf="isLoadingTable">
         <mat-spinner *ngIf="isLoadingTable"></mat-spinner>
@@ -304,6 +316,11 @@ <h4>
         <td mat-cell *matCellDef="let session"class="to-center"> {{session.sex}} </td>
       </ng-container>
 
+      <ng-container matColumnDef="death_date">
+        <th mat-header-cell *matHeaderCellDef mat-sort-header> Mouse Vital Status </th>
+        <td mat-cell *matCellDef="let session"class="to-center"> {{session.death_date}} </td>
+      </ng-container>
+
       <ng-container matColumnDef="nplot">
         <th mat-header-cell *matHeaderCellDef> Plot Availability </th>
         <td mat-cell *matCellDef="let session" class="to-center"> {{session.nplot.toString() | i18nSelect: nplotMap}} </td>

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

@@ -51,7 +51,9 @@ export class SessionListComponent implements OnInit, OnDestroy {
     sex: new FormArray([new FormControl(), new FormControl(), new FormControl()]),
     subject_birth_date: new FormControl(),
     subject_line: new FormControl(),
-    responsible_user: new FormControl()
+    responsible_user: new FormControl(),
+    brain_regions: new FormControl(),
+    death_date: new FormControl()
   });
   isLoading;
   isLoadingTable = true;
@@ -65,6 +67,7 @@ export class SessionListComponent implements OnInit, OnDestroy {
   sessionMinDate: Date;
   sessionMaxDate: Date;
   isSessionDateUsingRange: boolean;
+  isAlive: boolean
   dropDownMenuOptions: any = {};
   // filteredTaskProtocolOptions: Observable<string[]>;
   // filteredSessionUuidOptions: Observable<string[]>;
@@ -83,7 +86,7 @@ export class SessionListComponent implements OnInit, OnDestroy {
   // setup for the table columns
   displayedColumns: string[] = ['session_lab', 'subject_nickname', 'subject_birth_date', 'session_start_time',
                               'task_protocol', 'subject_line', 'responsible_user',
-                              'session_uuid', 'sex', 'subject_uuid', 'nplot', 'nprobe', 'session_project', 'good4bmap'];
+                              'session_uuid', 'sex', 'death_date', 'subject_uuid', 'nplot', 'nprobe', 'session_project', 'good4bmap'];
   nplotMap: any = { '0': '', '1': '\u2714' };
   // setup for the paginator
   dataSource;
@@ -338,52 +341,82 @@ export class SessionListComponent implements OnInit, OnDestroy {
       .pipe(
         startWith({}),
         switchMap(() => {
+          let dj_restriction_conditions = [];
+
           this.isLoadingTable = true;
           if(this.sort.direction == ''){
-            this.sort.active = 'session_start_time';
+            this.sort.active = 'nprobe';
             this.sort.direction = 'desc'
           }
           let filter = Object.assign({}, this.session_filter_form.getRawValue());
-          let newFilter = JSON.stringify(filter)
+
+          if(this.hideMissingPlots){
+            filter["nplot"] = 1;
+          }
+
+          if(this.hideNG4BrainMap){
+            filter["good_enough_for_brainwide_map"] = 1;
+          }
+
+          if(this.hideNotReady4Delay){
+            filter["training_status"] = "ready4delay";
+          }
+
+          if(this.hideMissingEphys){
+            dj_restriction_conditions.push("nprobe>0");
+          }
 
           for (const [key, value] of Object.entries(filter)) {
             if(key == 'sex'){
               if(value[0] == true){
-                newObject[key] = 'F'
+                newObject[key] = 'F';
                 //female
-                continue
+                continue;
               }
               else if (value[1] == true){
-                newObject[key] = 'M'
+                newObject[key] = 'M';
                 //male
-                continue
+                continue;
               }
               else if (value[2] == true){
-                newObject[key] = 'U'
+                newObject[key] = 'U';
                 //undefined
-                continue
+                continue;
               }
               else{
-                continue
+                continue;
               }
             }
             if(key == 'session_range_filter'){
               for( const [key2, val] of Object.entries(value)){
                 if(val !== null){
-                  newObject[key2] = val
+                  newObject[key2] = val;
                 }
-                continue
+                continue;
               }
             }
+            if(key == 'brain_regions' && value !== null && value !== ""){
+              newObject["__json_kwargs"] = `{"brain_regions": ["${value}"]}`;
+              continue;
+            }
+            if(this.isAlive){
+              dj_restriction_conditions.push("death_date is null");
+              continue;
+            }
+            if(!this.isAlive){
+              dj_restriction_conditions.push("death_date is not null");
+              continue;
+            }
             if(value !== null){
-              newObject[key] = value
+              newObject[key] = value;
             }
           }
           this.isLoadingResults = true;
 
           newObject["__page"] = this.paginator.pageIndex + 1;
           newObject["__limit"] = this.paginator.pageSize;
-          newObject["__order"] = this.sort.active + ' ' + this.sort.direction
+          newObject["__order"] = this.sort.active + ' ' + this.sort.direction;
+          newObject["__json"] = JSON.stringify(dj_restriction_conditions);
           return this.sessionService!.getSessions(
               newObject)
             .pipe(catchError(() => observableOf(null)));
@@ -474,7 +507,7 @@ export class SessionListComponent implements OnInit, OnDestroy {
   private createMenu(restrictedSessions: Array<any>) {
     const keys = ['task_protocol', 'session_start_time',
     'session_uuid', 'session_lab', 'subject_birth_date', 'subject_line',
-    'subject_uuid', 'sex', 'subject_nickname', 'responsible_user', 'session_project'];
+    'subject_uuid', 'sex', 'subject_nickname', 'responsible_user', 'session_project', 'brain_regions', 'death_date'];
 
     keys.forEach(key => {
       this.uniqueValuesForEachAttribute[key] = new Set();
@@ -545,6 +578,8 @@ export class SessionListComponent implements OnInit, OnDestroy {
     this.setDropDownFormOptions('filteredTaskProtocolOptions',  this.session_filter_form.controls.task_protocol, 'task_protocol');
     this.setDropDownFormOptions('filteredSubjectLineOptions',  this.session_filter_form.controls.subject_line, 'subject_line');
     this.setDropDownFormOptions('filteredResponsibleUserOptions',  this.session_filter_form.controls.responsible_user, 'responsible_user');
+    this.setDropDownFormOptions('filteredBrainRegionsOptions',  this.session_filter_form.controls.brain_regions, 'brain_regions');
+    this.setDropDownFormOptions('filteredDeathDateOptions',  this.session_filter_form.controls.death_date, 'death_date');
   }
 
   /**
@@ -574,7 +609,7 @@ export class SessionListComponent implements OnInit, OnDestroy {
             // The unique value does include the user restrction string, thus we need to add it to the validUniqueValues array
             validUniqueValues.push(uniqueValue);
           }
-    
+
           if (validUniqueValues.length > MAX_NUMBER_OF_SUGGESTIONS) {
             return;
           }
@@ -1157,27 +1192,31 @@ export class SessionListComponent implements OnInit, OnDestroy {
   }
   ​
   toggleNplotStatus() {
-    // hide or show sessions that have missing session plots
     this.hideMissingPlots = !this.hideMissingPlots;
-    this.updateSelection();
+    this.isLoading = false; 
+    this.paginator.pageIndex = 0; 
+    this.ngAfterViewInit();
   }
   ​
   toggleNprobeStatus() {
-    // hide or show sessions that have missing ephys data (based on existence of probe insertion)
     this.hideMissingEphys = !this.hideMissingEphys;
-    this.updateSelection();
+    this.isLoading = false; 
+    this.paginator.pageIndex = 0; 
+    this.ngAfterViewInit();
   }
 
   toggleG4BMviewStatus() {
-    // hide or show sessions that are not good enough for brain map
     this.hideNG4BrainMap = !this.hideNG4BrainMap;
-    this.updateSelection();
+    this.isLoading = false; 
+    this.paginator.pageIndex = 0; 
+    this.ngAfterViewInit();
   }
 
   toggleR4DviewStatus() {
-    // hide or show session that are not ready for delay
     this.hideNotReady4Delay = !this.hideNotReady4Delay;
-    this.updateSelection();
+    this.isLoading = false; 
+    this.paginator.pageIndex = 0; 
+    this.ngAfterViewInit();
   }
 
   //==**==**==**==**+=**+== [START] brain tree functions **==**==**==**==**==**==**==**==**==**+=//