Merge branch 'main' into release

griffithlab · Apr 16, 2024 · ecc7817 · ecc7817
2 parents 747853b + f7443e5
commit ecc7817
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Showing 495 changed files with 29,644 additions and 14,849 deletions.
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -9,9 +9,6 @@ jobs:
   backend_tests:
     name: Backend Tests
     runs-on: 'ubuntu-latest'
-    strategy:
-      matrix:
-        ruby: ['3.0', '3.2']
     services:
         postgres:
           image: postgres:13
@@ -30,7 +27,7 @@ jobs:
         uses: ruby/setup-ruby@v1
         with:
           bundler-cache: true
-          ruby-version: ${{ matrix.ruby }}
+          ruby-version: '3.3'
           working-directory: ./server
 
       - name: Setup DB

diff --git a/client/angular.json b/client/angular.json
@@ -99,12 +99,12 @@
         "serve": {
           "builder": "@angular-devkit/build-angular:dev-server",
           "options": {
-            "browserTarget": "main:build",
-            "proxyConfig": "proxy.config.json"
+            "proxyConfig": "proxy.config.json",
+            "buildTarget": "main:build"
           },
           "configurations": {
             "production": {
-              "browserTarget": "main:build:production"
+              "buildTarget": "main:build:production"
             }
           }
         },

diff --git a/client/package.json b/client/package.json
@@ -23,35 +23,35 @@
     "error-stack-parser": "2.0.6"
   },
   "dependencies": {
-    "@angular-devkit/schematics": "16.1.4",
-    "@angular/animations": "^16.1.5",
-    "@angular/common": "^16.1.5",
-    "@angular/compiler": "^16.1.5",
-    "@angular/core": "^16.1.5",
-    "@angular/forms": "^16.1.5",
-    "@angular/platform-browser": "^16.1.5",
-    "@angular/platform-browser-dynamic": "^16.1.5",
-    "@angular/router": "^16.1.5",
+    "@angular-devkit/schematics": "17.0.10",
+    "@angular/animations": "^17.0.9",
+    "@angular/common": "^17.0.9",
+    "@angular/compiler": "^17.0.9",
+    "@angular/core": "^17.0.9",
+    "@angular/forms": "^17.0.9",
+    "@angular/platform-browser": "^17.0.9",
+    "@angular/platform-browser-dynamic": "^17.0.9",
+    "@angular/router": "^17.0.9",
     "@apollo/client": "^3.7.17",
     "@ngneat/until-destroy": "^9.1.2",
-    "@ngrx/component": "^16.1.0",
+    "@ngrx/component": "^17.0.1",
     "@ngx-formly/core": "^6.2.2",
     "@ngx-formly/ng-zorro-antd": "^6.2.2",
     "apollo-angular": "^5.0.0",
-    "ng-zorro-antd": "^16.1.0",
+    "ng-zorro-antd": "17.0.0",
     "ngx-cookie-service": "^16.0.0",
     "rxjs": "^7.8.1",
     "rxjs-etc": "^10.6.2",
     "rxjs-spy": "^8.0.2",
     "ts-enum-util": "^4.0.2",
     "ts-mixin-extended": "^1.1.1",
-    "zone.js": "~0.13.1"
+    "zone.js": "0.14.3"
   },
   "devDependencies": {
-    "@angular-devkit/build-angular": "^16.1.4",
-    "@angular-eslint/schematics": "^16.1.0",
-    "@angular/cli": "^16.1.4",
-    "@angular/compiler-cli": "16.1.5",
+    "@angular-devkit/build-angular": "^17.0.10",
+    "@angular-eslint/schematics": "^16.1.2",
+    "@angular/cli": "^17.0.10",
+    "@angular/compiler-cli": "17.0.9",
     "@graphql-codegen/add": "^3.2.3",
     "@graphql-codegen/cli": "^2.16.4",
     "@graphql-codegen/fragment-matcher": "^3.3.3",
@@ -65,18 +65,18 @@
     "graphql": "^16.8.1",
     "mustache": "^4.2.0",
     "ngx-json-viewer": "^3.0.2",
-    "prettier": "^2.5.1",
+    "prettier": "^3.2.4",
     "svg-to-ts": "^9.0.0",
     "svgo": "^3.0.2",
     "ts-node": "~10.9.1",
     "tslib": "^2.3.1",
     "tslint": "~6.1.0",
-    "typescript": "^4.9.4",
+    "typescript": "5.2.2",
     "webpack-bundle-analyzer": "^4.5.0"
   },
   "overrides": {
     "rxjs-spy": {
       "error-stack-parser": "2.0.6"
     }
   }
-}
+}
diff --git a/client/src/app/components/activities/activity-card/activity-card.module.ts b/client/src/app/components/activities/activity-card/activity-card.module.ts
@@ -1,20 +1,20 @@
-import { CommonModule } from "@angular/common";
-import { NgModule } from "@angular/core";
-import { PushModule } from "@ngrx/component";
-import { NzCardModule } from "ng-zorro-antd/card";
-import { CvcActivityCardComponent } from "./activity-card.component";
-import { CvcCommentBodyModule } from "@app/components/comments/comment-body/comment-body.module";
-import { NzDividerModule } from "ng-zorro-antd/divider";
+import { CommonModule } from '@angular/common'
+import { NgModule } from '@angular/core'
+import { PushPipe } from '@ngrx/component'
+import { NzCardModule } from 'ng-zorro-antd/card'
+import { CvcActivityCardComponent } from './activity-card.component'
+import { CvcCommentBodyModule } from '@app/components/comments/comment-body/comment-body.module'
+import { NzDividerModule } from 'ng-zorro-antd/divider'
 
 @NgModule({
   declarations: [CvcActivityCardComponent],
   imports: [
     CommonModule,
-    PushModule,
+    PushPipe,
     NzCardModule,
     NzDividerModule,
-    CvcCommentBodyModule
+    CvcCommentBodyModule,
   ],
   exports: [CvcActivityCardComponent],
 })
-export class CvcActivityCardModule {}
+export class CvcActivityCardModule {}
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
@@ -32,7 +32,7 @@ query ActivityFeed(
   $last: Int
   $before: String
   $after: String
-  $userId: Int
+  $userId: [Int!]
   #$organizationId: Int
   #$eventType: EventAction
   #$mode: EventFeedMode
@@ -115,8 +115,13 @@ fragment activityFeedNode on ActivityInterface {
     ... on Revision {
       revisionSetId
     }
-    ... on Variant {
+    ... on VariantInterface {
       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
@@ -1,7 +1,7 @@
 import { NgModule } from '@angular/core'
 import { CommonModule } from '@angular/common'
 import { CvcActivityFeedComponent } from './activity-feed.component'
-import { LetModule, PushModule } from '@ngrx/component'
+import { LetDirective, PushPipe } from '@ngrx/component'
 import { NzCardModule } from 'ng-zorro-antd/card'
 import { NzIconModule } from 'ng-zorro-antd/icon'
 import { NzFormModule } from 'ng-zorro-antd/form'
@@ -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'
@@ -32,14 +31,16 @@ 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],
   imports: [
     CommonModule,
     FormsModule,
-    LetModule,
-    PushModule,
+    LetDirective,
+    PushPipe,
     NzButtonModule,
     NzCardModule,
     NzIconModule,
@@ -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],
 })