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Fetch retracted status from Retraction Watch and display information; Consistently fetch flagged/deprecated/status tag attributes #1047

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merged 9 commits into from
May 1, 2024
Merged

Fetch retracted status from Retraction Watch and display information; Consistently fetch flagged/deprecated/status tag attributes #1047

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939151f
Fetch retracted status from Retraction Watch and display information
susannasiebert Mar 5, 2024
98320f6
Update source tags to show retracted sources in grey, update retracti…
susannasiebert Mar 15, 2024
c3aef8c
return custom deprecated field on Sources and use it instead of retra…
susannasiebert Mar 18, 2024
4b8ff03
Fix class name typo
susannasiebert Mar 19, 2024
d24ccc8
Consisitently require deprecated attribute when displaying various tags
susannasiebert Apr 26, 2024
554ec63
Consistently require flagged attribute when displaying various tags
susannasiebert Mar 22, 2024
04cb2e1
Consistently require status attribute when displaying various tags
susannasiebert Mar 25, 2024
f9ccf38
Update server/app/lib/importer/retraction_watch.rb
acoffman Apr 25, 2024
37f78d9
Merge remote-tracking branch 'origin/main' into retraction_watch2
susannasiebert Apr 26, 2024
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75 changes: 44 additions & 31 deletions client/src/app/components/activities/activity-feed/activity-feed.component.html
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Original file line number Diff line number Diff line change
Expand Up @@ -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"
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13 changes: 13 additions & 0 deletions client/src/app/components/activities/activity-feed/activity-feed.gql
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Original file line number Diff line number Diff line change
Expand Up @@ -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
}
Expand Down
4 changes: 4 additions & 0 deletions client/src/app/components/assertions/assertions-popover/assertion-popover.query.gql
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Expand Up @@ -34,12 +34,14 @@ fragment assertionPopover on Assertion {
id
name
link
deprecated
}
therapyInteractionType
disease {
id
name
link
deprecated
}
phenotypes {
id
Expand All @@ -53,6 +55,8 @@ fragment assertionPopover on Assertion {
parsedName {
...MolecularProfileParsedName
}
deprecated
flagged
}
flags(state: OPEN) {
totalCount
Expand Down
3 changes: 3 additions & 0 deletions client/src/app/components/assertions/assertions-table/assertions-table.query.gql
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Expand Up @@ -75,16 +75,19 @@ fragment AssertionBrowseFields on Assertion {
parsedName {
...MolecularProfileParsedName
}
deprecated
}
disease {
id
name
link
deprecated
}
therapies {
id
name
link
deprecated
}
therapyInteractionType
summary
Expand Down
4 changes: 2 additions & 2 deletions client/src/app/components/assertions/assertions-tag/assertion-tag.component.ts
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Expand Up @@ -6,8 +6,8 @@ export interface LinkableAssertion {
id: number
name: string
link: string
status?: EvidenceStatus
flagged?: boolean
status: EvidenceStatus
flagged: boolean
}

@Component({
Expand Down
109 changes: 64 additions & 45 deletions client/src/app/components/comments/comment-body/comment-body.component.html
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Original file line number Diff line number Diff line change
Expand Up @@ -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'">
Expand All @@ -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
Expand Down
6 changes: 6 additions & 0 deletions client/src/app/components/comments/comment-body/comment-body.component.ts
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Original file line number Diff line number Diff line change
@@ -1,6 +1,9 @@
import { Component, Input, OnInit } from '@angular/core'
import {
CommentTagSegment,
CommentTagSegmentFlagged,
CommentTagSegmentFlaggedAndDeprecated,
CommentTagSegmentFlaggedAndWithStatus,
CommentTextSegment,
} from '@app/generated/civic.apollo'

Expand All @@ -14,6 +17,9 @@ interface CommentBodyUserSegment {
export type CommentSegment =
| CommentBodyUserSegment
| CommentTagSegment
| CommentTagSegmentFlagged
| CommentTagSegmentFlaggedAndDeprecated
| CommentTagSegmentFlaggedAndWithStatus
| CommentTextSegment

@Component({
Expand Down
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