Merge pull request #1047 from griffithlab/retraction_watch2

Fetch retracted status from Retraction Watch and display information; Consistently fetch flagged/deprecated/status tag attributes
griffithlab · May 1, 2024 · 644571f · 644571f
2 parents 4743338 + 37f78d9
commit 644571f
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Showing 130 changed files with 2,888 additions and 511 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
@@ -27,37 +27,50 @@
           <ng-template #activityHeaderTemplate>
             <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>
-            ·
+            @switch (activity.subject.__typename) {
+              @case ('Feature') {
+                <cvc-feature-tag
+                  [feature]="activity.subject"></cvc-feature-tag>
+              }
+              @case ('Assertion') {
+                <cvc-assertion-tag
+                  [assertion]="activity.subject"></cvc-assertion-tag>
+              }
+              @case ('EvidenceItem') {
+                <cvc-evidence-tag
+                  [evidence]="activity.subject"></cvc-evidence-tag>
+              }
+              @case ('GeneVariant') {
+                <cvc-feature-variant-tag
+                  [variant]="activity.subject"></cvc-feature-variant-tag>
+              }
+              @case ('FactorVariant') {
+                <cvc-feature-variant-tag
+                  [variant]="activity.subject"></cvc-feature-variant-tag>
+              }
+              @case ('Revision') {
+                <cvc-revision-tag
+                  [revision]="$any(activity.subject)"></cvc-revision-tag>
+              }
+              @case ('VariantGroup') {
+                <cvc-variant-group-tag
+                  [variantgroup]="activity.subject"></cvc-variant-group-tag>
+              }
+              @case ('Source') {
+                <cvc-source-tag
+                  mode="concise"
+                  [source]="$any(activity.subject)"></cvc-source-tag>
+              }
+              @case ('MolecularProfile') {
+                <cvc-molecular-profile-tag
+                  [molecularProfile]="
+                    activity.subject
+                  "></cvc-molecular-profile-tag>
+              }
+              @default {
+                <span *ngSwitchDefault>{{ activity.subject.name }}</span>
+              }
+            }
             <span
               nz-tooltip
               nzTooltipPlacement="top"

diff --git a/client/src/app/components/activities/activity-feed/activity-feed.gql b/client/src/app/components/activities/activity-feed/activity-feed.gql
@@ -108,23 +108,36 @@ fragment activityFeedNode on ActivityInterface {
     }
     ... on EvidenceItem {
       status
+      flagged
     }
     ... on Assertion {
       status
+      flagged
     }
     ... on Revision {
       revisionSetId
     }
     ... on VariantInterface {
       deprecated
+      flagged
       feature {
         id
         name
         link
+        deprecated
+        flagged
       }
     }
     ... on MolecularProfile {
       deprecated
+      flagged
+    }
+    ... on Feature {
+      deprecated
+      flagged
+    }
+    ... on VariantGroup {
+      flagged
     }
     __typename
   }

diff --git a/client/src/app/components/assertions/assertions-popover/assertion-popover.query.gql b/client/src/app/components/assertions/assertions-popover/assertion-popover.query.gql
@@ -34,12 +34,14 @@ fragment assertionPopover on Assertion {
     id
     name
     link
+    deprecated
   }
   therapyInteractionType
   disease {
     id
     name
     link
+    deprecated
   }
   phenotypes {
     id
@@ -53,6 +55,8 @@ fragment assertionPopover on Assertion {
     parsedName {
       ...MolecularProfileParsedName
     }
+    deprecated
+    flagged
   }
   flags(state: OPEN) {
     totalCount

diff --git a/client/src/app/components/assertions/assertions-table/assertions-table.query.gql b/client/src/app/components/assertions/assertions-table/assertions-table.query.gql
@@ -75,16 +75,19 @@ fragment AssertionBrowseFields on Assertion {
     parsedName {
       ...MolecularProfileParsedName
     }
+    deprecated
   }
   disease {
     id
     name
     link
+    deprecated
   }
   therapies {
     id
     name
     link
+    deprecated
   }
   therapyInteractionType
   summary

diff --git a/client/src/app/components/assertions/assertions-tag/assertion-tag.component.ts b/client/src/app/components/assertions/assertions-tag/assertion-tag.component.ts
@@ -6,8 +6,8 @@ export interface LinkableAssertion {
   id: number
   name: string
   link: string
-  status?: EvidenceStatus
-  flagged?: boolean
+  status: EvidenceStatus
+  flagged: boolean
 }
 
 @Component({

diff --git a/client/src/app/components/comments/comment-body/comment-body.component.html b/client/src/app/components/comments/comment-body/comment-body.component.html
@@ -5,58 +5,29 @@
   <ng-container *ngIf="c.__typename == 'User'">
     <cvc-user-tag [user]="c"></cvc-user-tag>
   </ng-container>
-  <ng-container *ngIf="c.__typename == 'CommentTagSegment'">
+  <ng-container *ngIf="c.__typename == 'CommentTagSegmentFlagged'">
     <ng-container [ngSwitch]="c.tagType">
-      <span *ngSwitchCase="'REVISION'">
-        <!--<cvc-revision-tag-->
-        <!--[revision]="{-->
-        <!--id: c.entityId,-->
-        <!--name: c.displayName,-->
-        <!--link: c.link,-->
-        <!--revisionSetId: c.revisionSetId!-->
-        <!--}"></cvc-revision-tag>-->
-        <nz-tag>
-          <i
-            nz-icon
-            nzType="civic-revision"
-            nzTheme="twotone"
-            nzTwotoneColor="#F0673A"></i>
-          {{ c.displayName }}
-        </nz-tag>
-      </span>
-      <span *ngSwitchCase="'FEATURE'">
-        <cvc-feature-tag
-          [feature]="{
-            id: c.entityId,
-            name: c.displayName,
-            link: c.link
-          }"></cvc-feature-tag>
-      </span>
-      <span *ngSwitchCase="'VARIANT'">
-        <cvc-feature-variant-tag
-          [variant]="{
-            id: c.entityId,
-            name: c.displayName,
-            link: c.link,
-            deprecated: c.deprecated,
-            feature: c.feature
-          }"></cvc-feature-variant-tag>
-      </span>
       <span *ngSwitchCase="'VARIANT_GROUP'">
         <cvc-variant-group-tag
           [variantgroup]="{
             id: c.entityId,
             name: c.displayName,
-            link: c.link
+            link: c.link,
+            flagged: c.flagged
           }"></cvc-variant-group-tag>
       </span>
+    </ng-container>
+  </ng-container>
+  <ng-container *ngIf="c.__typename == 'CommentTagSegmentFlaggedAndWithStatus'">
+    <ng-container [ngSwitch]="c.tagType">
       <span *ngSwitchCase="'EVIDENCE_ITEM'">
         <cvc-evidence-tag
           [evidence]="{
             id: c.entityId,
             name: c.displayName,
             status: c.status,
-            link: c.link
+            link: c.link,
+            flagged: c.flagged
           }"></cvc-evidence-tag>
       </span>
       <span *ngSwitchCase="'ASSERTION'">
@@ -65,25 +36,73 @@
             id: c.entityId,
             name: c.displayName,
             status: c.status,
-            link: c.link
+            link: c.link,
+            flagged: c.flagged
           }"></cvc-assertion-tag>
       </span>
-      <span *ngSwitchCase="'ORGANIZATION'">
-        <cvc-organization-tag
-          [org]="{
+    </ng-container>
+  </ng-container>
+  <ng-container *ngIf="c.__typename == 'CommentTagSegmentFlaggedAndDeprecated'">
+    <ng-container [ngSwitch]="c.tagType">
+      <span *ngSwitchCase="'VARIANT'">
+        <cvc-feature-variant-tag
+          [variant]="{
             id: c.entityId,
-            name: c.displayName
-          }"></cvc-organization-tag>
+            name: c.displayName,
+            link: c.link,
+            deprecated: c.deprecated,
+            feature: c.feature,
+            flagged: c.flagged
+          }"></cvc-feature-variant-tag>
       </span>
       <span *ngSwitchCase="'MOLECULAR_PROFILE'">
         <cvc-molecular-profile-tag
           [molecularProfile]="{
             id: c.entityId,
             name: c.displayName,
             link: c.link,
-            deprecated: c.deprecated
+            deprecated: c.deprecated,
+            flagged: c.flagged
           }"></cvc-molecular-profile-tag>
       </span>
+      <span *ngSwitchCase="'FEATURE'">
+        <cvc-feature-tag
+          [feature]="{
+            id: c.entityId,
+            name: c.displayName,
+            link: c.link,
+            deprecated: c.deprecated,
+            flagged: c.flagged
+          }"></cvc-feature-tag>
+      </span>
+    </ng-container>
+  </ng-container>
+  <ng-container *ngIf="c.__typename == 'CommentTagSegment'">
+    <ng-container [ngSwitch]="c.tagType">
+      <span *ngSwitchCase="'REVISION'">
+        <!--<cvc-revision-tag-->
+        <!--[revision]="{-->
+        <!--id: c.entityId,-->
+        <!--name: c.displayName,-->
+        <!--link: c.link,-->
+        <!--revisionSetId: c.revisionSetId!-->
+        <!--}"></cvc-revision-tag>-->
+        <nz-tag>
+          <i
+            nz-icon
+            nzType="civic-revision"
+            nzTheme="twotone"
+            nzTwotoneColor="#F0673A"></i>
+          {{ c.displayName }}
+        </nz-tag>
+      </span>
+      <span *ngSwitchCase="'ORGANIZATION'">
+        <cvc-organization-tag
+          [org]="{
+            id: c.entityId,
+            name: c.displayName
+          }"></cvc-organization-tag>
+      </span>
       <span *ngSwitchCase="'ROLE'">
         <nz-tag
           ><i

diff --git a/client/src/app/components/comments/comment-body/comment-body.component.ts b/client/src/app/components/comments/comment-body/comment-body.component.ts
@@ -1,6 +1,9 @@
 import { Component, Input, OnInit } from '@angular/core'
 import {
   CommentTagSegment,
+  CommentTagSegmentFlagged,
+  CommentTagSegmentFlaggedAndDeprecated,
+  CommentTagSegmentFlaggedAndWithStatus,
   CommentTextSegment,
 } from '@app/generated/civic.apollo'
 
@@ -14,6 +17,9 @@ interface CommentBodyUserSegment {
 export type CommentSegment =
   | CommentBodyUserSegment
   | CommentTagSegment
+  | CommentTagSegmentFlagged
+  | CommentTagSegmentFlaggedAndDeprecated
+  | CommentTagSegmentFlaggedAndWithStatus
   | CommentTextSegment
 
 @Component({