Merge branch 'features' into staging

griffithlab · Jan 10, 2024 · 5e07517 · 5e07517
2 parents cf9c87e + 63a77ff
commit 5e07517
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Showing 315 changed files with 5,526 additions and 3,290 deletions.
diff --git a/client/src/app/components/activities/activity-feed/activity-feed.component.html b/client/src/app/components/activities/activity-feed/activity-feed.component.html
@@ -8,69 +8,72 @@
           *ngIf="activity"
           [nzDot]="timelineDotTemplate">
           <ng-template #timelineDotTemplate>
-            <nz-avatar nzIcon="user" [nzSrc]="activity.user.profileImagePath"></nz-avatar>
+            <nz-avatar
+              nzIcon="user"
+              [nzSrc]="activity.user.profileImagePath"></nz-avatar>
           </ng-template>
           <nz-collapse
             [nzBordered]="false"
             nzExpandIconPosition="right">
-            <cvc-collapsible-card [header]="activityHeaderTemplate" [contents]="activityContentTemplate"></cvc-collapsible-card>
+            <cvc-collapsible-card
+              [header]="activityHeaderTemplate"
+              [contents]="activityContentTemplate"></cvc-collapsible-card>
           </nz-collapse>
 
           <ng-template #activityContentTemplate>
             <cvc-activity-card [activityId]="activity.id"></cvc-activity-card>
           </ng-template>
 
           <ng-template #activityHeaderTemplate>
-
-          <cvc-user-tag [user]="activity.user"></cvc-user-tag>
-          {{ activity.verbiage }}
-          <ng-container
-            [ngSwitch]="activity.subject.__typename">
-            <cvc-gene-tag
-              *ngSwitchCase="'Gene'"
-              [gene]="activity.subject"></cvc-gene-tag>
-            <cvc-assertion-tag
-              *ngSwitchCase="'Assertion'"
-              [assertion]="activity.subject"></cvc-assertion-tag>
-            <cvc-evidence-tag
-              *ngSwitchCase="'EvidenceItem'"
-              [evidence]="activity.subject"></cvc-evidence-tag>
-            <cvc-variant-tag
-              *ngSwitchCase="'Variant'"
-              [variant]="activity.subject"></cvc-variant-tag>
-            <cvc-revision-tag
-              *ngSwitchCase="'Revision'"
-              [revision]="$any(activity.subject)"></cvc-revision-tag>
-            <cvc-variant-group-tag
-              *ngSwitchCase="'VariantGroup'"
-              [variantgroup]="activity.subject"></cvc-variant-group-tag>
-            <cvc-source-tag
-              *ngSwitchCase="'Source'"
-              mode="concise"
-              [source]="$any(activity.subject)"></cvc-source-tag>
-            <cvc-molecular-profile-tag
-              *ngSwitchCase="'MolecularProfile'"
-              [molecularProfile]="activity.subject"></cvc-molecular-profile-tag>
-            <span *ngSwitchDefault>{{ activity.subject.name }}</span>
-          </ng-container>
-          ·
-          <span
-            nz-tooltip
-            nzTooltipPlacement="top"
-            [nzTooltipTitle]="activity.createdAt | date">
-            {{ activity.createdAt | timeAgo }}
-          </span>
+            <cvc-user-tag [user]="activity.user"></cvc-user-tag>
+            {{ activity.verbiage }}
+            <ng-container [ngSwitch]="activity.subject.__typename">
+              <cvc-feature-tag
+                *ngSwitchCase="'Feature'"
+                [feature]="activity.subject"></cvc-feature-tag>
+              <cvc-assertion-tag
+                *ngSwitchCase="'Assertion'"
+                [assertion]="activity.subject"></cvc-assertion-tag>
+              <cvc-evidence-tag
+                *ngSwitchCase="'EvidenceItem'"
+                [evidence]="activity.subject"></cvc-evidence-tag>
+              <cvc-feature-variant-tag
+                *ngSwitchCase="'Variant'"
+                [variant]="activity.subject"></cvc-feature-variant-tag>
+              <cvc-revision-tag
+                *ngSwitchCase="'Revision'"
+                [revision]="$any(activity.subject)"></cvc-revision-tag>
+              <cvc-variant-group-tag
+                *ngSwitchCase="'VariantGroup'"
+                [variantgroup]="activity.subject"></cvc-variant-group-tag>
+              <cvc-source-tag
+                *ngSwitchCase="'Source'"
+                mode="concise"
+                [source]="$any(activity.subject)"></cvc-source-tag>
+              <cvc-molecular-profile-tag
+                *ngSwitchCase="'MolecularProfile'"
+                [molecularProfile]="
+                  activity.subject
+                "></cvc-molecular-profile-tag>
+              <span *ngSwitchDefault>{{ activity.subject.name }}</span>
+            </ng-container>
+            ·
+            <span
+              nz-tooltip
+              nzTooltipPlacement="top"
+              [nzTooltipTitle]="activity.createdAt | date">
+              {{ activity.createdAt | timeAgo }}
+            </span>
           </ng-template>
-    
-<!--           <cvc-event-timeline-item
+
+          <!--           <cvc-event-timeline-item
             [event]="event!"
             [tagDisplay]="tagDisplay"></cvc-event-timeline-item> -->
         </nz-timeline-item>
       </ng-container>
     </nz-timeline>
   </ng-container>
 
-
   <!-- <ng-container
     *ngIf="this.unfilteredCount$ | ngrxPush as count; else noEvents">
     <nz-row [nzGutter]="16">

diff --git a/client/src/app/components/activities/activity-feed/activity-feed.component.ts b/client/src/app/components/activities/activity-feed/activity-feed.component.ts
@@ -4,12 +4,9 @@ import {
   ActivityFeedNodeFragment,
   ActivityFeedQuery,
   ActivityFeedQueryVariables,
-  EventAction,
   Maybe,
-  NotificationOrganizationFragment,
   NotificationOriginatingUsersFragment,
   PageInfo,
-  SubscribableQueryInput,
 } from '@app/generated/civic.apollo'
 import { QueryRef } from 'apollo-angular'
 import { ApolloQueryResult } from '@apollo/client/core'
@@ -19,16 +16,9 @@ import {
   filter,
   map,
   pluck,
-  startWith,
-  take,
-  takeUntil,
 } from 'rxjs/operators'
-import { TagLinkableOrganization } from '@app/components/organizations/organization-tag/organization-tag.component'
-import { TagLinkableUser } from '@app/components/users/user-tag/user-tag.component'
-import { environment } from 'environments/environment'
 import { isNonNulled } from 'rxjs-etc'
-import { tag } from 'rxjs-spy/cjs/operators'
-import { UntilDestroy, untilDestroyed } from '@ngneat/until-destroy'
+import { UntilDestroy } from '@ngneat/until-destroy'
 
 // interface SelectableAction {
 //   id: EventAction
@@ -130,7 +120,7 @@ export class CvcActivityFeedComponent implements OnInit, OnDestroy {
 
     // this.unfilteredCount$
     //   .pipe(
-    //     take(1), 
+    //     take(1),
     //     untilDestroyed(this))
     //   .subscribe(value => this.originalEventCount = value)
 

diff --git a/client/src/app/components/activities/activity-feed/activity-feed.gql b/client/src/app/components/activities/activity-feed/activity-feed.gql
@@ -117,6 +117,11 @@ fragment activityFeedNode on ActivityInterface {
     }
     ... on Variant {
       deprecated
+      feature {
+        id
+        name
+        link
+      }
     }
     ... on MolecularProfile {
       deprecated
@@ -125,7 +130,7 @@ fragment activityFeedNode on ActivityInterface {
   }
   ... on FlagEntityActivity {
     flag {
-      id 
+      id
       name
       link
     }

diff --git a/client/src/app/components/activities/activity-feed/activity-feed.module.ts b/client/src/app/components/activities/activity-feed/activity-feed.module.ts
@@ -21,7 +21,6 @@ import { NzBadgeModule } from 'ng-zorro-antd/badge'
 import { NzToolTipModule } from 'ng-zorro-antd/tooltip'
 import { NzTimelineModule } from 'ng-zorro-antd/timeline'
 import { CvcUserTagModule } from '@app/components/users/user-tag/user-tag.module'
-import { CvcGeneTagModule } from '@app/components/genes/gene-tag/gene-tag.module'
 import { CvcAssertionsTagModule } from '@app/components/assertions/assertions-tag/assertions-tag.module'
 import { CvcEvidenceTagModule } from '@app/components/evidence/evidence-tag/evidence-tag.module'
 import { CvcVariantTagModule } from '@app/components/variants/variant-tag/variant-tag.module'
@@ -32,6 +31,8 @@ import { CvcRevisionTagModule } from '@app/components/revisions/revision-tag/rev
 import { NzCollapseModule } from 'ng-zorro-antd/collapse'
 import { CvcActivityCardModule } from '../activity-card/activity-card.module'
 import { CvcCollapsibleCardModule } from '../collapsible-card/collapsible-card.module'
+import { CvcFeatureTagModule } from '@app/components/features/feature-tag/feature-tag.module'
+import { CvcFeatureVariantTagModule } from '@app/components/shared/feature-variant-tag/feature-variant-tag.module'
 
 @NgModule({
   declarations: [CvcActivityFeedComponent],
@@ -60,7 +61,7 @@ import { CvcCollapsibleCardModule } from '../collapsible-card/collapsible-card.m
     CvcParticipantListModule,
     CvcPipesModule,
     CvcUserTagModule,
-    CvcGeneTagModule,
+    CvcFeatureTagModule,
     CvcAssertionsTagModule,
     CvcEvidenceTagModule,
     CvcVariantTagModule,
@@ -69,7 +70,8 @@ import { CvcCollapsibleCardModule } from '../collapsible-card/collapsible-card.m
     CvcMolecularProfileTagModule,
     CvcRevisionTagModule,
     CvcActivityCardModule,
-    CvcCollapsibleCardModule
+    CvcCollapsibleCardModule,
+    CvcFeatureVariantTagModule
   ],
   exports: [CvcActivityFeedComponent],
 })

diff --git a/client/src/app/components/assertions/assertion-card/assertion-card.component.html b/client/src/app/components/assertions/assertion-card/assertion-card.component.html
diff --git a/client/src/app/components/assertions/assertion-card/assertion-card.component.ts b/client/src/app/components/assertions/assertion-card/assertion-card.component.ts
diff --git a/client/src/app/components/assertions/assertion-card/assertion-card.module.ts b/client/src/app/components/assertions/assertion-card/assertion-card.module.ts