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
index 27ff32791..2beccaab6 100644
--- 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 @@
{{ activity.verbiage }}
-
-
-
-
-
-
-
-
-
- {{ activity.subject.name }}
-
- ยท
+ @switch (activity.subject.__typename) {
+ @case ('Feature') {
+
+ }
+ @case ('Assertion') {
+
+ }
+ @case ('EvidenceItem') {
+
+ }
+ @case ('GeneVariant') {
+
+ }
+ @case ('FactorVariant') {
+
+ }
+ @case ('Revision') {
+
+ }
+ @case ('VariantGroup') {
+
+ }
+ @case ('Source') {
+
+ }
+ @case ('MolecularProfile') {
+
+ }
+ @default {
+ {{ activity.subject.name }}
+ }
+ }
-
+
-
-
-
-
-
-
-
-
-
-
- {{ c.displayName }}
-
-
-
-
-
-
-
-
+
+
+
+
@@ -65,15 +36,24 @@
id: c.entityId,
name: c.displayName,
status: c.status,
- link: c.link
+ link: c.link,
+ flagged: c.flagged
}">
-
-
+
+
+
+
+
+ name: c.displayName,
+ link: c.link,
+ deprecated: c.deprecated,
+ feature: c.feature,
+ flagged: c.flagged
+ }">
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ {{ c.displayName }}
+
+
+
+
+
commented on
-
-
-
-
-
+ @switch (c.commentable.__typename) {
+ @case ('Feature') {
+
+ }
+ @case ('Assertion') {
+
+ }
+ @case ('EvidenceItem') {
+
+ }
+ @case ('Variant') {
+
+ }
-
-
- {{ c.commentable.name }}
-
+ @case ('Revision') {
+
+ }
+ @case ('Source') {
+
+ }
+ @default {
+ {{ c.commentable.name }}
+ }
+ }
{{ c.createdAt | timeAgo }}
diff --git a/client/src/app/components/comments/comment-popover/comment-popover.query.gql b/client/src/app/components/comments/comment-popover/comment-popover.query.gql
index b0986e637..1dec70393 100644
--- a/client/src/app/components/comments/comment-popover/comment-popover.query.gql
+++ b/client/src/app/components/comments/comment-popover/comment-popover.query.gql
@@ -25,7 +25,26 @@ fragment commentPopover on Comment {
id
name
link
+ deprecated
+ flagged
}
+ flagged
+ }
+ ...on Feature {
+ deprecated
+ flagged
+ }
+ ...on Source {
+ deprecated
+ sourceType
+ }
+ ...on Assertion {
+ flagged
+ status
+ }
+ ...on EvidenceItem {
+ flagged
+ status
}
__typename
}
diff --git a/client/src/app/components/diseases/cvc-disease-popover/cvc-disease-popover.query.gql b/client/src/app/components/diseases/cvc-disease-popover/cvc-disease-popover.query.gql
index 41dfbcf17..5b275a182 100644
--- a/client/src/app/components/diseases/cvc-disease-popover/cvc-disease-popover.query.gql
+++ b/client/src/app/components/diseases/cvc-disease-popover/cvc-disease-popover.query.gql
@@ -10,5 +10,6 @@ query DiseasePopover($diseaseId: Int!) {
evidenceItemCount
molecularProfileCount
link
+ deprecated
}
}
diff --git a/client/src/app/components/diseases/cvc-disease-tag/cvc-disease-tag.component.html b/client/src/app/components/diseases/cvc-disease-tag/cvc-disease-tag.component.html
index 0d400fbf9..c4e8fca70 100644
--- a/client/src/app/components/diseases/cvc-disease-tag/cvc-disease-tag.component.html
+++ b/client/src/app/components/diseases/cvc-disease-tag/cvc-disease-tag.component.html
@@ -6,6 +6,7 @@
-
-
-
-
-
-
-
-
-
- {{ subject.name }}
+ *ngIf="tagDisplay != 'hideSubject' && event.subject as subject">
+ @switch (subject.__typename) {
+ @case ('Feature') {
+
+ }
+ @case ('Assertion') {
+
+ }
+ @case ('EvidenceItem') {
+
+ }
+ @case ('GeneVariant') {
+
+ }
+ @case ('FactorVariant') {
+
+ }
+ @case ('Revision') {
+
+ }
+ @case ('VariantGroup') {
+
+ }
+ @case ('Source') {
+
+ }
+ @case ('MolecularProfile') {
+
+ }
+ @default {
+ {{ subject.name }}
+ }
+ }
diff --git a/client/src/app/components/evidence/evidence-popover/evidence-popover.query.gql b/client/src/app/components/evidence/evidence-popover/evidence-popover.query.gql
index 6411846a4..f09102e5e 100644
--- a/client/src/app/components/evidence/evidence-popover/evidence-popover.query.gql
+++ b/client/src/app/components/evidence/evidence-popover/evidence-popover.query.gql
@@ -18,12 +18,14 @@ fragment evidencePopover on EvidenceItem {
id
name
link
+ deprecated
}
therapyInteractionType
disease {
id
name
link
+ deprecated
}
phenotypes {
id
@@ -36,6 +38,7 @@ fragment evidencePopover on EvidenceItem {
name
link
deprecated
+ flagged
parsedName {
...MolecularProfileParsedName
}
@@ -46,6 +49,7 @@ fragment evidencePopover on EvidenceItem {
sourceType
displayType
link
+ deprecated
}
flags(state: OPEN) {
totalCount
diff --git a/client/src/app/components/evidence/evidence-table/evidence-table.query.gql b/client/src/app/components/evidence/evidence-table/evidence-table.query.gql
index df0e53c09..07657bba0 100644
--- a/client/src/app/components/evidence/evidence-table/evidence-table.query.gql
+++ b/client/src/app/components/evidence/evidence-table/evidence-table.query.gql
@@ -80,11 +80,13 @@ fragment EvidenceGridFields on EvidenceItem {
id
name
link
+ deprecated
}
therapies {
id
name
link
+ deprecated
}
molecularProfile {
id
@@ -93,6 +95,7 @@ fragment EvidenceGridFields on EvidenceItem {
parsedName {
...MolecularProfileParsedName
}
+ deprecated
}
status
flagged
diff --git a/client/src/app/components/evidence/evidence-tag/evidence-tag.component.ts b/client/src/app/components/evidence/evidence-tag/evidence-tag.component.ts
index 4367c475d..b78337ba0 100644
--- a/client/src/app/components/evidence/evidence-tag/evidence-tag.component.ts
+++ b/client/src/app/components/evidence/evidence-tag/evidence-tag.component.ts
@@ -6,8 +6,8 @@ import { EvidenceStatus, Maybe } from '@app/generated/civic.apollo'
export interface LinkableEvidence {
id: number
name: string
- status?: EvidenceStatus
- flagged?: boolean
+ status: EvidenceStatus
+ flagged: boolean
link: string
}
diff --git a/client/src/app/components/features/feature-tag/feature-tag.component.ts b/client/src/app/components/features/feature-tag/feature-tag.component.ts
index 625b7a725..e7a5882df 100644
--- a/client/src/app/components/features/feature-tag/feature-tag.component.ts
+++ b/client/src/app/components/features/feature-tag/feature-tag.component.ts
@@ -12,8 +12,8 @@ export interface LinkableFeature {
id: number
name: string
link: string
- flagged?: boolean
- deprecated?: boolean
+ flagged: boolean
+ deprecated: boolean
}
@Component({
diff --git a/client/src/app/components/features/features-table/features-table.query.gql b/client/src/app/components/features/features-table/features-table.query.gql
index f794d455d..8e0cf6175 100644
--- a/client/src/app/components/features/features-table/features-table.query.gql
+++ b/client/src/app/components/features/features-table/features-table.query.gql
@@ -45,17 +45,20 @@ fragment BrowseFeaturesFields on BrowseFeature {
id
name
link
+ deprecated
flagged
featureAliases
diseases {
name
id
link
+ deprecated
}
therapies {
name
id
link
+ deprecated
}
variantCount
evidenceItemCount
diff --git a/client/src/app/components/flags/flag-list-and-filter/flag-list-and-filter.gql b/client/src/app/components/flags/flag-list-and-filter/flag-list-and-filter.gql
index c8184c980..5f52671a4 100644
--- a/client/src/app/components/flags/flag-list-and-filter/flag-list-and-filter.gql
+++ b/client/src/app/components/flags/flag-list-and-filter/flag-list-and-filter.gql
@@ -57,6 +57,15 @@ fragment flag on Flag {
id
name
link
+ ... on Variant {
+ deprecated
+ }
+ ... on Feature {
+ deprecated
+ }
+ ... on MolecularProfile {
+ deprecated
+ }
}
openActivity {
id
diff --git a/client/src/app/components/flags/flag-popover/flag-popover.component.html b/client/src/app/components/flags/flag-popover/flag-popover.component.html
index 23728522e..25fc7e708 100644
--- a/client/src/app/components/flags/flag-popover/flag-popover.component.html
+++ b/client/src/app/components/flags/flag-popover/flag-popover.component.html
@@ -22,29 +22,36 @@
-
-
-
-
-
-
- {{ f.flaggable.name }}
-
+ @switch (f.flaggable.__typename) {
+ @case ('Feature') {
+
+ }
+ @case ('Assertion') {
+
+ }
+ @case ('EvidenceItem') {
+
+ }
+ @case ('Variant') {
+
+ }
+ @case ('VariantGroup') {
+
+ }
+ @default {
+ {{ f.flaggable.name }}
+ }
+ }
-
+
+
+
{{ molecularProfile.name! | truncate : this.truncationLength }}
diff --git a/client/src/app/components/molecular-profiles/molecular-profile-tag/molecular-profile-tag.component.ts b/client/src/app/components/molecular-profiles/molecular-profile-tag/molecular-profile-tag.component.ts
index 584ca7a91..7f806eac9 100644
--- a/client/src/app/components/molecular-profiles/molecular-profile-tag/molecular-profile-tag.component.ts
+++ b/client/src/app/components/molecular-profiles/molecular-profile-tag/molecular-profile-tag.component.ts
@@ -12,7 +12,8 @@ export interface LinkableMolecularProfile {
id: number
name: string
link: string
- deprecated?: boolean
+ deprecated: boolean
+ flagged: boolean
}
export interface LinkableMolecularProfileSegments {
@@ -20,7 +21,8 @@ export interface LinkableMolecularProfileSegments {
segments: MolecularProfileSegment[]
link: string
name?: string
- deprecated?: boolean
+ deprecated: boolean
+ flagged: boolean
}
@Component({
diff --git a/client/src/app/components/molecular-profiles/molecular-profile-tag/molecular-profile-tag.module.ts b/client/src/app/components/molecular-profiles/molecular-profile-tag/molecular-profile-tag.module.ts
index cb95ff8ad..6b13008e3 100644
--- a/client/src/app/components/molecular-profiles/molecular-profile-tag/molecular-profile-tag.module.ts
+++ b/client/src/app/components/molecular-profiles/molecular-profile-tag/molecular-profile-tag.module.ts
@@ -7,6 +7,7 @@ import { NzIconModule } from 'ng-zorro-antd/icon'
import { NzPopoverModule } from 'ng-zorro-antd/popover'
import { CvcPipesModule } from '@app/core/pipes/pipes.module'
import { CvcMolecularProfilePopoverModule } from '../molecular-profile-popover/molecular-profile-popover.module'
+import { CvcIconBadgesModule } from '@app/components/shared/icon-badges/icon-badges.module'
@NgModule({
declarations: [CvcMolecularProfileTagComponent],
@@ -18,6 +19,7 @@ import { CvcMolecularProfilePopoverModule } from '../molecular-profile-popover/m
NzIconModule,
CvcPipesModule,
CvcMolecularProfilePopoverModule,
+ CvcIconBadgesModule,
],
exports: [CvcMolecularProfileTagComponent],
})
diff --git a/client/src/app/components/molecular-profiles/molecular-profiles-menu/molecular-profiles-menu.gql b/client/src/app/components/molecular-profiles/molecular-profiles-menu/molecular-profiles-menu.gql
index be7aedfea..9d4075285 100644
--- a/client/src/app/components/molecular-profiles/molecular-profiles-menu/molecular-profiles-menu.gql
+++ b/client/src/app/components/molecular-profiles/molecular-profiles-menu/molecular-profiles-menu.gql
@@ -39,4 +39,5 @@ fragment menuMolecularProfile on MolecularProfile {
name
link
flagged
+ deprecated
}
diff --git a/client/src/app/components/revisions/revision-list/revision-list.component.html b/client/src/app/components/revisions/revision-list/revision-list.component.html
index 8478bff11..9df4edbea 100644
--- a/client/src/app/components/revisions/revision-list/revision-list.component.html
+++ b/client/src/app/components/revisions/revision-list/revision-list.component.html
@@ -37,7 +37,9 @@
[feature]="{
id: item.id,
name: item.displayName,
- link: item.link
+ link: item.link,
+ deprecated: item.deprecated,
+ flagged: item.flagged
}">
@@ -64,7 +66,8 @@
[disease]="{
id: item.id,
name: item.displayName,
- link: item.link
+ link: item.link,
+ deprecated: item.deprecated,
}">
@@ -80,7 +83,9 @@
[molecularProfile]="{
id: item.id,
name: item.displayName,
- link: item.link
+ link: item.link,
+ deprecated: item.deprecated,
+ flagged: item.flagged
}">
@@ -96,7 +101,8 @@
[therapy]="{
id: item.id,
name: item.displayName,
- link: item.link
+ link: item.link,
+ deprecated: item.deprecated
}">
@@ -112,7 +118,8 @@
[therapy]="{
id: item.id,
name: item.displayName,
- link: item.link
+ link: item.link,
+ deprecated: item.deprecated
}">
@@ -266,7 +273,8 @@
name: item.displayName,
link: item.link,
feature: item.feature,
- deprecated: item.deprecated
+ deprecated: item.deprecated,
+ flagged: item.flagged
}">
@@ -284,7 +292,8 @@
name: item.displayName,
link: item.link,
feature: item.feature,
- deprecated: item.deprecated
+ deprecated: item.deprecated,
+ flagged: item.flagged
}">
@@ -312,7 +321,8 @@
id: item.id,
name: item.displayName,
link: item.link,
- status: item.status
+ status: item.status,
+ flagged: item.flagged
}">
diff --git a/client/src/app/components/revisions/revision-popover/revision-popover.component.html b/client/src/app/components/revisions/revision-popover/revision-popover.component.html
index c9594fd01..b5a80bd56 100644
--- a/client/src/app/components/revisions/revision-popover/revision-popover.component.html
+++ b/client/src/app/components/revisions/revision-popover/revision-popover.component.html
@@ -22,29 +22,36 @@
-
-
-
-
-
-
- {{ r.subject.name }}
-
+ @switch (r.subject.__typename) {
+ @case ('Feature') {
+
+ }
+ @case ('Assertion') {
+
+ }
+ @case ('EvidenceItem') {
+
+ }
+ @case ('Variant') {
+
+ }
+ @case ('VariantGroup') {
+
+ }
+ @default {
+ {{ r.subject.name }}
+ }
+ }
+
+
+ {{ retractionNature | titlecase }}
+
+
+
+
+ {{ retractionDate | timeAgo }}
+
+
+
+ {{ reason.replace('+', '') }}
+
+
+
+
+
+ Retraction Watch Homepage
+
+
+ Retraction Watch Database
+
+
+
+
diff --git a/client/src/app/components/shared/retraction-status-tag/retraction-status-tag.component.less b/client/src/app/components/shared/retraction-status-tag/retraction-status-tag.component.less
new file mode 100644
index 000000000..1bf0271a0
--- /dev/null
+++ b/client/src/app/components/shared/retraction-status-tag/retraction-status-tag.component.less
@@ -0,0 +1 @@
+@import 'themes/overrides/descriptions-overrides.less';
\ No newline at end of file
diff --git a/client/src/app/components/shared/retraction-status-tag/retraction-status-tag.component.ts b/client/src/app/components/shared/retraction-status-tag/retraction-status-tag.component.ts
new file mode 100644
index 000000000..29137bd7e
--- /dev/null
+++ b/client/src/app/components/shared/retraction-status-tag/retraction-status-tag.component.ts
@@ -0,0 +1,55 @@
+import { Component, Input, OnInit } from '@angular/core'
+import {
+ Maybe,
+} from '@app/generated/civic.apollo'
+
+@Component({
+ selector: 'cvc-retraction-status-tag',
+ templateUrl: './retraction-status-tag.component.html',
+ styleUrls: ['./retraction-status-tag.component.less'],
+})
+
+export class CvcRetractionStatusTagComponent implements OnInit {
+ private _retractionNature?: string
+
+ @Input() set retractionNature(value: Maybe) {
+ this._retractionNature = value
+ if (value) {
+ if (value == 'Retraction') {
+ this.tagStatus = 'error'
+ this.retracted = true
+ } else {
+ this.tagStatus = 'warning'
+ this.retracted = false
+ }
+ }
+ }
+ @Input() retractionDate!: string
+ @Input() retractionReasons!: string
+ @Input() enablePopover: boolean = true
+
+ get retractionNature(): Maybe {
+ return this._retractionNature
+ }
+
+ tagStatus?: string
+ retracted?: boolean
+
+ ngOnInit(): void {
+ if (this.retractionNature === undefined) {
+ throw new Error(
+ 'Must pass a valid retractionNature to cvc-status-tag component'
+ )
+ }
+ if (this.retractionDate === undefined) {
+ throw new Error(
+ 'Must pass a valid retractionDate to cvc-status-tag component'
+ )
+ }
+ if (this.retractionReasons === undefined) {
+ throw new Error(
+ 'Must pass a valid retractionReasons to cvc-status-tag component'
+ )
+ }
+ }
+}
diff --git a/client/src/app/components/shared/retraction-status-tag/retraction-status-tag.module.ts b/client/src/app/components/shared/retraction-status-tag/retraction-status-tag.module.ts
new file mode 100644
index 000000000..8def1a0bb
--- /dev/null
+++ b/client/src/app/components/shared/retraction-status-tag/retraction-status-tag.module.ts
@@ -0,0 +1,26 @@
+import { NgModule } from '@angular/core'
+import { CommonModule } from '@angular/common'
+import { CvcRetractionStatusTagComponent } from './retraction-status-tag.component'
+import { NzTagModule } from 'ng-zorro-antd/tag'
+import { NzIconModule } from 'ng-zorro-antd/icon'
+import { NzPopoverModule } from 'ng-zorro-antd/popover'
+import { NzDescriptionsModule } from 'ng-zorro-antd/descriptions'
+import { NzListModule } from 'ng-zorro-antd/list'
+import { CvcPipesModule } from '@app/core/pipes/pipes.module'
+import { CvcLinkTagModule } from '../link-tag/link-tag.module'
+
+@NgModule({
+ declarations: [CvcRetractionStatusTagComponent],
+ imports: [
+ CommonModule,
+ NzTagModule,
+ NzIconModule,
+ NzPopoverModule,
+ NzDescriptionsModule,
+ NzListModule,
+ CvcPipesModule,
+ CvcLinkTagModule
+ ],
+ exports: [CvcRetractionStatusTagComponent],
+})
+export class CvcRetractionStatusTagModule {}
diff --git a/client/src/app/components/shared/status-tag/status-tag.component.ts b/client/src/app/components/shared/status-tag/status-tag.component.ts
index b1bd59758..e62a661d5 100644
--- a/client/src/app/components/shared/status-tag/status-tag.component.ts
+++ b/client/src/app/components/shared/status-tag/status-tag.component.ts
@@ -42,7 +42,7 @@ export class CvcStatusTagComponent implements OnInit {
ngOnInit(): void {
if (this.status === undefined) {
throw new Error(
- 'Must pass a valid EvidenceStatus or RevisionStatus to cvc-status-tag component'
+ 'Must pass a valid EvidenceStatus, RevisionStatus, or FlagState to cvc-status-tag component'
)
}
}
diff --git a/client/src/app/components/source-suggestions/source-suggestions-table/source-suggestions-table.query.gql b/client/src/app/components/source-suggestions/source-suggestions-table/source-suggestions-table.query.gql
index 350b39981..85c704a0a 100644
--- a/client/src/app/components/source-suggestions/source-suggestions-table/source-suggestions-table.query.gql
+++ b/client/src/app/components/source-suggestions/source-suggestions-table/source-suggestions-table.query.gql
@@ -56,11 +56,13 @@ fragment BrowseSourceSuggestionRowFields on SourceSuggestion {
id
name
link
+ deprecated
}
disease {
id
name
link
+ deprecated
}
source {
link
@@ -70,6 +72,7 @@ fragment BrowseSourceSuggestionRowFields on SourceSuggestion {
sourceType
sourceUrl
displayType
+ deprecated
}
user {
id
diff --git a/client/src/app/components/sources/source-popover/source-popover.component.html b/client/src/app/components/sources/source-popover/source-popover.component.html
index c1583b2dd..e990be67d 100644
--- a/client/src/app/components/sources/source-popover/source-popover.component.html
+++ b/client/src/app/components/sources/source-popover/source-popover.component.html
@@ -19,6 +19,7 @@
[tooltip]="'View on ' + s.displayType">
{{ s.displayType + ':' + s.citationId }}
+
diff --git a/client/src/app/components/variants/variants-table/variants-table.query.gql b/client/src/app/components/variants/variants-table/variants-table.query.gql
index 8ee06a060..eb76e36fe 100644
--- a/client/src/app/components/variants/variants-table/variants-table.query.gql
+++ b/client/src/app/components/variants/variants-table/variants-table.query.gql
@@ -59,15 +59,19 @@ fragment BrowseVariantsFields on BrowseVariant {
featureName
featureLink
category
+ featureDeprecated
+ featureFlagged
diseases {
id
name
link
+ deprecated
}
therapies {
id
name
link
+ deprecated
}
aliases {
name
@@ -77,4 +81,6 @@ fragment BrowseVariantsFields on BrowseVariant {
name
link
}
+ deprecated
+ flagged
}
diff --git a/client/src/app/forms/components/variant-deprecate/variant-deprecate.query.gql b/client/src/app/forms/components/variant-deprecate/variant-deprecate.query.gql
index 3c25c3fb0..9c7822d99 100644
--- a/client/src/app/forms/components/variant-deprecate/variant-deprecate.query.gql
+++ b/client/src/app/forms/components/variant-deprecate/variant-deprecate.query.gql
@@ -32,6 +32,8 @@ query MolecularProfilesForVariant($variantId: Int!) {
submittedCount
acceptedCount
}
+ deprecated
+ flagged
}
}
}
diff --git a/client/src/app/forms/config/evidence-submit/evidence-submit.query.gql b/client/src/app/forms/config/evidence-submit/evidence-submit.query.gql
index b4b1dde21..5480ad6d3 100644
--- a/client/src/app/forms/config/evidence-submit/evidence-submit.query.gql
+++ b/client/src/app/forms/config/evidence-submit/evidence-submit.query.gql
@@ -24,6 +24,7 @@ query EvidenceFieldsFromSourceSuggestion(
citationId
citation
link
+ deprecated
}
}
}
@@ -48,6 +49,7 @@ fragment SubmittableEvidenceFields on EvidenceItem {
id
citation
sourceType
+ deprecated
}
phenotypes {
id
diff --git a/client/src/app/forms/types/evidence-select/evidence-manager/evidence-manager.query.gql b/client/src/app/forms/types/evidence-select/evidence-manager/evidence-manager.query.gql
index 64c98664d..8f44f30f5 100644
--- a/client/src/app/forms/types/evidence-select/evidence-manager/evidence-manager.query.gql
+++ b/client/src/app/forms/types/evidence-select/evidence-manager/evidence-manager.query.gql
@@ -84,11 +84,13 @@ fragment EvidenceManagerFields on EvidenceItem {
id
name
link
+ deprecated
}
therapies {
id
name
link
+ deprecated
}
molecularProfile {
id
@@ -97,6 +99,7 @@ fragment EvidenceManagerFields on EvidenceItem {
parsedName {
...MolecularProfileParsedName
}
+ deprecated
}
status
flagged
diff --git a/client/src/app/forms/types/molecular-profile-select/molecular-profile-select.query.gql b/client/src/app/forms/types/molecular-profile-select/molecular-profile-select.query.gql
index 57a1017df..179f52732 100644
--- a/client/src/app/forms/types/molecular-profile-select/molecular-profile-select.query.gql
+++ b/client/src/app/forms/types/molecular-profile-select/molecular-profile-select.query.gql
@@ -17,4 +17,6 @@ fragment MolecularProfileSelectTypeaheadFields on MolecularProfile {
name
link
molecularProfileAliases
-}
+ deprecated
+ flagged
+}
\ No newline at end of file
diff --git a/client/src/app/forms/types/molecular-profile-select/mp-expression-editor/mp-expression-editor.query.gql b/client/src/app/forms/types/molecular-profile-select/mp-expression-editor/mp-expression-editor.query.gql
index 459555d46..f71997721 100644
--- a/client/src/app/forms/types/molecular-profile-select/mp-expression-editor/mp-expression-editor.query.gql
+++ b/client/src/app/forms/types/molecular-profile-select/mp-expression-editor/mp-expression-editor.query.gql
@@ -7,6 +7,8 @@ query PreviewMolecularProfileName2(
id
name
link
+ deprecated
+ flagged
}
segments {
...PreviewMpName2
@@ -15,6 +17,8 @@ query PreviewMolecularProfileName2(
id
name
link
+ deprecated
+ flagged
}
}
}
@@ -26,6 +30,8 @@ query MpExpressionEditorPrepopulate($mpId: Int!) {
...MolecularProfileParsedName
}
rawName
+ deprecated
+ flagged
}
}
@@ -39,6 +45,8 @@ mutation CreateMolecularProfile2(
id
name
link
+ deprecated
+ flagged
}
}
}
@@ -53,10 +61,14 @@ fragment PreviewMpName2 on MolecularProfileSegment {
id
name
link
+ deprecated
+ flagged
}
... on Variant {
id
name
link
+ deprecated
+ flagged
}
}
diff --git a/client/src/app/forms/types/source-select/source-select.query.gql b/client/src/app/forms/types/source-select/source-select.query.gql
index fe8382c38..7fd7a94ab 100644
--- a/client/src/app/forms/types/source-select/source-select.query.gql
+++ b/client/src/app/forms/types/source-select/source-select.query.gql
@@ -20,4 +20,5 @@ fragment SourceSelectTypeaheadFields on Source {
citation
citationId
sourceType
+ deprecated
}
diff --git a/client/src/app/forms/types/variant-select/variant-manager/variant-manager.query.gql b/client/src/app/forms/types/variant-select/variant-manager/variant-manager.query.gql
index 71d9ad889..9756a0e03 100644
--- a/client/src/app/forms/types/variant-select/variant-manager/variant-manager.query.gql
+++ b/client/src/app/forms/types/variant-select/variant-manager/variant-manager.query.gql
@@ -54,11 +54,13 @@ fragment VariantManagerFields on BrowseVariant {
id
name
link
+ deprecated
}
therapies {
id
name
link
+ deprecated
}
aliases {
name
diff --git a/client/src/app/generated/civic.apollo-helpers.ts b/client/src/app/generated/civic.apollo-helpers.ts
index 2fbc5b4ee..bc6aada76 100644
--- a/client/src/app/generated/civic.apollo-helpers.ts
+++ b/client/src/app/generated/civic.apollo-helpers.ts
@@ -164,9 +164,10 @@ export type BrowseClinicalTrialEdgeFieldPolicy = {
cursor?: FieldPolicy | FieldReadFunction,
node?: FieldPolicy | FieldReadFunction
};
-export type BrowseDiseaseKeySpecifier = ('assertionCount' | 'diseaseUrl' | 'displayName' | 'doid' | 'evidenceItemCount' | 'featureCount' | 'features' | 'id' | 'link' | 'name' | 'variantCount' | BrowseDiseaseKeySpecifier)[];
+export type BrowseDiseaseKeySpecifier = ('assertionCount' | 'deprecated' | 'diseaseUrl' | 'displayName' | 'doid' | 'evidenceItemCount' | 'featureCount' | 'features' | 'id' | 'link' | 'name' | 'variantCount' | BrowseDiseaseKeySpecifier)[];
export type BrowseDiseaseFieldPolicy = {
assertionCount?: FieldPolicy | FieldReadFunction,
+ deprecated?: FieldPolicy | FieldReadFunction,
diseaseUrl?: FieldPolicy | FieldReadFunction,
displayName?: FieldPolicy | FieldReadFunction,
doid?: FieldPolicy | FieldReadFunction,
@@ -193,9 +194,10 @@ export type BrowseDiseaseEdgeFieldPolicy = {
cursor?: FieldPolicy | FieldReadFunction,
node?: FieldPolicy | FieldReadFunction
};
-export type BrowseFeatureKeySpecifier = ('assertionCount' | 'description' | 'diseases' | 'evidenceItemCount' | 'featureAliases' | 'featureInstanceId' | 'featureInstanceType' | 'flagged' | 'flags' | 'id' | 'link' | 'molecularProfileCount' | 'name' | 'therapies' | 'variantCount' | BrowseFeatureKeySpecifier)[];
+export type BrowseFeatureKeySpecifier = ('assertionCount' | 'deprecated' | 'description' | 'diseases' | 'evidenceItemCount' | 'featureAliases' | 'featureInstanceId' | 'featureInstanceType' | 'flagged' | 'flags' | 'id' | 'link' | 'molecularProfileCount' | 'name' | 'therapies' | 'variantCount' | BrowseFeatureKeySpecifier)[];
export type BrowseFeatureFieldPolicy = {
assertionCount?: FieldPolicy | FieldReadFunction,
+ deprecated?: FieldPolicy | FieldReadFunction,
description?: FieldPolicy | FieldReadFunction,
diseases?: FieldPolicy | FieldReadFunction,
evidenceItemCount?: FieldPolicy | FieldReadFunction,
@@ -226,10 +228,11 @@ export type BrowseFeatureEdgeFieldPolicy = {
cursor?: FieldPolicy | FieldReadFunction,
node?: FieldPolicy | FieldReadFunction
};
-export type BrowseMolecularProfileKeySpecifier = ('aliases' | 'assertionCount' | 'diseases' | 'evidenceItemCount' | 'id' | 'link' | 'molecularProfileScore' | 'name' | 'therapies' | 'variantCount' | 'variants' | BrowseMolecularProfileKeySpecifier)[];
+export type BrowseMolecularProfileKeySpecifier = ('aliases' | 'assertionCount' | 'deprecated' | 'diseases' | 'evidenceItemCount' | 'id' | 'link' | 'molecularProfileScore' | 'name' | 'therapies' | 'variantCount' | 'variants' | BrowseMolecularProfileKeySpecifier)[];
export type BrowseMolecularProfileFieldPolicy = {
aliases?: FieldPolicy | FieldReadFunction,
assertionCount?: FieldPolicy | FieldReadFunction,
+ deprecated?: FieldPolicy | FieldReadFunction,
diseases?: FieldPolicy | FieldReadFunction,
evidenceItemCount?: FieldPolicy | FieldReadFunction,
id?: FieldPolicy | FieldReadFunction,
@@ -280,12 +283,13 @@ export type BrowsePhenotypeEdgeFieldPolicy = {
cursor?: FieldPolicy | FieldReadFunction,
node?: FieldPolicy | FieldReadFunction
};
-export type BrowseSourceKeySpecifier = ('authors' | 'citation' | 'citationId' | 'clinicalTrials' | 'displayType' | 'evidenceItemCount' | 'id' | 'journal' | 'link' | 'name' | 'openAccess' | 'publicationYear' | 'sourceSuggestionCount' | 'sourceType' | 'sourceUrl' | BrowseSourceKeySpecifier)[];
+export type BrowseSourceKeySpecifier = ('authors' | 'citation' | 'citationId' | 'clinicalTrials' | 'deprecated' | 'displayType' | 'evidenceItemCount' | 'id' | 'journal' | 'link' | 'name' | 'openAccess' | 'publicationYear' | 'retractionNature' | 'sourceSuggestionCount' | 'sourceType' | 'sourceUrl' | BrowseSourceKeySpecifier)[];
export type BrowseSourceFieldPolicy = {
authors?: FieldPolicy | FieldReadFunction,
citation?: FieldPolicy | FieldReadFunction,
citationId?: FieldPolicy | FieldReadFunction,
clinicalTrials?: FieldPolicy | FieldReadFunction,
+ deprecated?: FieldPolicy | FieldReadFunction,
displayType?: FieldPolicy | FieldReadFunction,
evidenceItemCount?: FieldPolicy | FieldReadFunction,
id?: FieldPolicy | FieldReadFunction,
@@ -294,6 +298,7 @@ export type BrowseSourceFieldPolicy = {
name?: FieldPolicy | FieldReadFunction,
openAccess?: FieldPolicy | FieldReadFunction,
publicationYear?: FieldPolicy | FieldReadFunction,
+ retractionNature?: FieldPolicy | FieldReadFunction,
sourceSuggestionCount?: FieldPolicy | FieldReadFunction,
sourceType?: FieldPolicy | FieldReadFunction,
sourceUrl?: FieldPolicy | FieldReadFunction
@@ -313,9 +318,10 @@ export type BrowseSourceEdgeFieldPolicy = {
cursor?: FieldPolicy | FieldReadFunction,
node?: FieldPolicy | FieldReadFunction
};
-export type BrowseTherapyKeySpecifier = ('assertionCount' | 'evidenceCount' | 'id' | 'link' | 'name' | 'ncitId' | 'therapyUrl' | BrowseTherapyKeySpecifier)[];
+export type BrowseTherapyKeySpecifier = ('assertionCount' | 'deprecated' | 'evidenceCount' | 'id' | 'link' | 'name' | 'ncitId' | 'therapyUrl' | BrowseTherapyKeySpecifier)[];
export type BrowseTherapyFieldPolicy = {
assertionCount?: FieldPolicy | FieldReadFunction,
+ deprecated?: FieldPolicy | FieldReadFunction,
evidenceCount?: FieldPolicy | FieldReadFunction,
id?: FieldPolicy | FieldReadFunction,
link?: FieldPolicy | FieldReadFunction,
@@ -338,14 +344,18 @@ export type BrowseTherapyEdgeFieldPolicy = {
cursor?: FieldPolicy | FieldReadFunction,
node?: FieldPolicy | FieldReadFunction
};
-export type BrowseVariantKeySpecifier = ('aliases' | 'category' | 'diseases' | 'featureId' | 'featureLink' | 'featureName' | 'id' | 'link' | 'name' | 'therapies' | 'variantTypes' | BrowseVariantKeySpecifier)[];
+export type BrowseVariantKeySpecifier = ('aliases' | 'category' | 'deprecated' | 'diseases' | 'featureDeprecated' | 'featureFlagged' | 'featureId' | 'featureLink' | 'featureName' | 'flagged' | 'id' | 'link' | 'name' | 'therapies' | 'variantTypes' | BrowseVariantKeySpecifier)[];
export type BrowseVariantFieldPolicy = {
aliases?: FieldPolicy | FieldReadFunction,
category?: FieldPolicy | FieldReadFunction,
+ deprecated?: FieldPolicy | FieldReadFunction,
diseases?: FieldPolicy | FieldReadFunction,
+ featureDeprecated?: FieldPolicy | FieldReadFunction,
+ featureFlagged?: FieldPolicy | FieldReadFunction,
featureId?: FieldPolicy | FieldReadFunction,
featureLink?: FieldPolicy | FieldReadFunction,
featureName?: FieldPolicy | FieldReadFunction,
+ flagged?: FieldPolicy | FieldReadFunction,
id?: FieldPolicy | FieldReadFunction,
link?: FieldPolicy | FieldReadFunction,
name?: FieldPolicy | FieldReadFunction,
@@ -501,12 +511,42 @@ export type CommentEdgeFieldPolicy = {
cursor?: FieldPolicy | FieldReadFunction,
node?: FieldPolicy | FieldReadFunction
};
-export type CommentTagSegmentKeySpecifier = ('deprecated' | 'displayName' | 'entityId' | 'feature' | 'link' | 'revisionSetId' | 'status' | 'tagType' | CommentTagSegmentKeySpecifier)[];
+export type CommentTagSegmentKeySpecifier = ('displayName' | 'entityId' | 'feature' | 'link' | 'revisionSetId' | 'tagType' | CommentTagSegmentKeySpecifier)[];
export type CommentTagSegmentFieldPolicy = {
+ displayName?: FieldPolicy | FieldReadFunction,
+ entityId?: FieldPolicy | FieldReadFunction,
+ feature?: FieldPolicy | FieldReadFunction,
+ link?: FieldPolicy | FieldReadFunction,
+ revisionSetId?: FieldPolicy | FieldReadFunction,
+ tagType?: FieldPolicy | FieldReadFunction
+};
+export type CommentTagSegmentFlaggedKeySpecifier = ('displayName' | 'entityId' | 'feature' | 'flagged' | 'link' | 'revisionSetId' | 'tagType' | CommentTagSegmentFlaggedKeySpecifier)[];
+export type CommentTagSegmentFlaggedFieldPolicy = {
+ displayName?: FieldPolicy | FieldReadFunction,
+ entityId?: FieldPolicy | FieldReadFunction,
+ feature?: FieldPolicy | FieldReadFunction,
+ flagged?: FieldPolicy | FieldReadFunction,
+ link?: FieldPolicy | FieldReadFunction,
+ revisionSetId?: FieldPolicy | FieldReadFunction,
+ tagType?: FieldPolicy | FieldReadFunction
+};
+export type CommentTagSegmentFlaggedAndDeprecatedKeySpecifier = ('deprecated' | 'displayName' | 'entityId' | 'feature' | 'flagged' | 'link' | 'revisionSetId' | 'tagType' | CommentTagSegmentFlaggedAndDeprecatedKeySpecifier)[];
+export type CommentTagSegmentFlaggedAndDeprecatedFieldPolicy = {
deprecated?: FieldPolicy | FieldReadFunction,
displayName?: FieldPolicy | FieldReadFunction,
entityId?: FieldPolicy | FieldReadFunction,
feature?: FieldPolicy | FieldReadFunction,
+ flagged?: FieldPolicy | FieldReadFunction,
+ link?: FieldPolicy | FieldReadFunction,
+ revisionSetId?: FieldPolicy | FieldReadFunction,
+ tagType?: FieldPolicy | FieldReadFunction
+};
+export type CommentTagSegmentFlaggedAndWithStatusKeySpecifier = ('displayName' | 'entityId' | 'feature' | 'flagged' | 'link' | 'revisionSetId' | 'status' | 'tagType' | CommentTagSegmentFlaggedAndWithStatusKeySpecifier)[];
+export type CommentTagSegmentFlaggedAndWithStatusFieldPolicy = {
+ displayName?: FieldPolicy | FieldReadFunction,
+ entityId?: FieldPolicy | FieldReadFunction,
+ feature?: FieldPolicy | FieldReadFunction,
+ flagged?: FieldPolicy | FieldReadFunction,
link?: FieldPolicy | FieldReadFunction,
revisionSetId?: FieldPolicy | FieldReadFunction,
status?: FieldPolicy | FieldReadFunction,
@@ -678,8 +718,9 @@ export type DeprecateVariantPayloadFieldPolicy = {
newlyDeprecatedMolecularProfiles?: FieldPolicy | FieldReadFunction,
variant?: FieldPolicy | FieldReadFunction
};
-export type DiseaseKeySpecifier = ('diseaseAliases' | 'diseaseUrl' | 'displayName' | 'doid' | 'id' | 'link' | 'myDiseaseInfo' | 'name' | DiseaseKeySpecifier)[];
+export type DiseaseKeySpecifier = ('deprecated' | 'diseaseAliases' | 'diseaseUrl' | 'displayName' | 'doid' | 'id' | 'link' | 'myDiseaseInfo' | 'name' | DiseaseKeySpecifier)[];
export type DiseaseFieldPolicy = {
+ deprecated?: FieldPolicy | FieldReadFunction,
diseaseAliases?: FieldPolicy | FieldReadFunction,
diseaseUrl?: FieldPolicy | FieldReadFunction,
displayName?: FieldPolicy | FieldReadFunction,
@@ -689,9 +730,10 @@ export type DiseaseFieldPolicy = {
myDiseaseInfo?: FieldPolicy | FieldReadFunction,
name?: FieldPolicy | FieldReadFunction
};
-export type DiseasePopoverKeySpecifier = ('assertionCount' | 'diseaseAliases' | 'diseaseUrl' | 'displayName' | 'doid' | 'evidenceItemCount' | 'id' | 'link' | 'molecularProfileCount' | 'myDiseaseInfo' | 'name' | DiseasePopoverKeySpecifier)[];
+export type DiseasePopoverKeySpecifier = ('assertionCount' | 'deprecated' | 'diseaseAliases' | 'diseaseUrl' | 'displayName' | 'doid' | 'evidenceItemCount' | 'id' | 'link' | 'molecularProfileCount' | 'myDiseaseInfo' | 'name' | DiseasePopoverKeySpecifier)[];
export type DiseasePopoverFieldPolicy = {
assertionCount?: FieldPolicy | FieldReadFunction,
+ deprecated?: FieldPolicy | FieldReadFunction,
diseaseAliases?: FieldPolicy | FieldReadFunction,
diseaseUrl?: FieldPolicy | FieldReadFunction,
displayName?: FieldPolicy | FieldReadFunction,
@@ -1164,28 +1206,33 @@ export type LeaderboardUserEdgeFieldPolicy = {
cursor?: FieldPolicy | FieldReadFunction,
node?: FieldPolicy | FieldReadFunction
};
-export type LinkableDiseaseKeySpecifier = ('id' | 'link' | 'name' | LinkableDiseaseKeySpecifier)[];
+export type LinkableDiseaseKeySpecifier = ('deprecated' | 'id' | 'link' | 'name' | LinkableDiseaseKeySpecifier)[];
export type LinkableDiseaseFieldPolicy = {
+ deprecated?: FieldPolicy | FieldReadFunction,
id?: FieldPolicy | FieldReadFunction,
link?: FieldPolicy | FieldReadFunction,
name?: FieldPolicy | FieldReadFunction
};
-export type LinkableFeatureKeySpecifier = ('id' | 'link' | 'name' | LinkableFeatureKeySpecifier)[];
+export type LinkableFeatureKeySpecifier = ('deprecated' | 'flagged' | 'id' | 'link' | 'name' | LinkableFeatureKeySpecifier)[];
export type LinkableFeatureFieldPolicy = {
+ deprecated?: FieldPolicy | FieldReadFunction,
+ flagged?: FieldPolicy | FieldReadFunction,
id?: FieldPolicy | FieldReadFunction,
link?: FieldPolicy | FieldReadFunction,
name?: FieldPolicy | FieldReadFunction
};
-export type LinkableTherapyKeySpecifier = ('id' | 'link' | 'name' | LinkableTherapyKeySpecifier)[];
+export type LinkableTherapyKeySpecifier = ('deprecated' | 'id' | 'link' | 'name' | LinkableTherapyKeySpecifier)[];
export type LinkableTherapyFieldPolicy = {
+ deprecated?: FieldPolicy | FieldReadFunction,
id?: FieldPolicy | FieldReadFunction,
link?: FieldPolicy | FieldReadFunction,
name?: FieldPolicy | FieldReadFunction
};
-export type LinkableVariantKeySpecifier = ('deprecated' | 'feature' | 'id' | 'link' | 'matchText' | 'name' | LinkableVariantKeySpecifier)[];
+export type LinkableVariantKeySpecifier = ('deprecated' | 'feature' | 'flagged' | 'id' | 'link' | 'matchText' | 'name' | LinkableVariantKeySpecifier)[];
export type LinkableVariantFieldPolicy = {
deprecated?: FieldPolicy | FieldReadFunction,
feature?: FieldPolicy | FieldReadFunction,
+ flagged?: FieldPolicy | FieldReadFunction,
id?: FieldPolicy | FieldReadFunction,
link?: FieldPolicy | FieldReadFunction,
matchText?: FieldPolicy