From cce032dc16bf40499f1aebbe644611214308d2b3 Mon Sep 17 00:00:00 2001 From: Susanna Kiwala Date: Tue, 4 Feb 2025 11:45:55 -0600 Subject: [PATCH 1/9] Add OpenCRAVAT predictor annotations --- .../gene-variant-summary.page.html | 42 +++--- .../gene-variant-summary.page.ts | 2 + .../open-cravat-annotations.component.html | 121 ++++++++++++++++++ .../open-cravat-annotations.component.less | 15 +++ .../open-cravat-annotations.component.ts | 26 ++++ .../open-cravat-annotations.module.ts | 29 +++++ .../src/app/generated/civic.apollo-helpers.ts | 3 +- client/src/app/generated/civic.apollo.ts | 14 +- client/src/app/generated/server.model.graphql | 1 + client/src/app/generated/server.schema.json | 12 ++ .../variants-summary.query.gql | 1 + .../types/variants/gene_variant_type.rb | 11 ++ server/app/jobs/generate_open_cravat_link.rb | 12 +- server/app/models/open_cravat.rb | 93 ++++++++++++++ ...ravat_url_to_open_cravat_url_parameters.rb | 5 + server/db/schema.rb | 4 +- 16 files changed, 356 insertions(+), 35 deletions(-) create mode 100644 client/src/app/components/variants/open-cravat-annotations/open-cravat-annotations.component.html create mode 100644 client/src/app/components/variants/open-cravat-annotations/open-cravat-annotations.component.less create mode 100644 client/src/app/components/variants/open-cravat-annotations/open-cravat-annotations.component.ts create mode 100644 client/src/app/components/variants/open-cravat-annotations/open-cravat-annotations.module.ts create mode 100644 server/app/models/open_cravat.rb create mode 100644 server/db/migrate/20250128191951_rename_open_cravat_url_to_open_cravat_url_parameters.rb diff --git a/client/src/app/components/variants/gene-variant-summary/gene-variant-summary.page.html b/client/src/app/components/variants/gene-variant-summary/gene-variant-summary.page.html index 4876ecf36..62ec8c925 100644 --- a/client/src/app/components/variants/gene-variant-summary/gene-variant-summary.page.html +++ b/client/src/app/components/variants/gene-variant-summary/gene-variant-summary.page.html @@ -160,7 +160,7 @@ @@ -233,35 +233,39 @@ > - - - - Variant Report - - - - + + - - - - + + - - + + + + + + @if (variant.openCravatAnnotations && variant.openCravatUrl) { + + + } @else { + + + + + } + diff --git a/client/src/app/components/variants/gene-variant-summary/gene-variant-summary.page.ts b/client/src/app/components/variants/gene-variant-summary/gene-variant-summary.page.ts index 8f25c021c..7512e4e7f 100644 --- a/client/src/app/components/variants/gene-variant-summary/gene-variant-summary.page.ts +++ b/client/src/app/components/variants/gene-variant-summary/gene-variant-summary.page.ts @@ -17,6 +17,7 @@ import { VariantSummaryFieldsFragment } from '@app/generated/civic.apollo' import { CvcUserTagModule } from '@app/components/users/user-tag/user-tag.module' import { CvcFeatureTagModule } from '@app/components/features/feature-tag/feature-tag.module' import { CvcPipesModule } from '@app/core/pipes/pipes.module' +import { CvcOpenCravatAnnotationsModule } from '../open-cravat-annotations/open-cravat-annotations.module' @Component({ standalone: true, @@ -39,6 +40,7 @@ import { CvcPipesModule } from '@app/core/pipes/pipes.module' CvcFeatureTagModule, CvcMolecularProfilesTableModule, CvcMyVariantInfoModule, + CvcOpenCravatAnnotationsModule, CvcPipesModule, ], }) diff --git a/client/src/app/components/variants/open-cravat-annotations/open-cravat-annotations.component.html b/client/src/app/components/variants/open-cravat-annotations/open-cravat-annotations.component.html new file mode 100644 index 000000000..56844440a --- /dev/null +++ b/client/src/app/components/variants/open-cravat-annotations/open-cravat-annotations.component.html @@ -0,0 +1,121 @@ + + + + + Variant Report + + + + + + + + + + + + + + +
+
+ + @if ((openCravatAnnotations.benignity_counts|keyvalue).length === 0) { +
+ No Annotations +
+ } + @for (keypar of openCravatAnnotations.benignity_counts|keyvalue; track keypar.key) { +
+ {{ keypar.key }} ({{ keypar.value }}) +
+ } + +
+
+ + @if ((openCravatAnnotations.pathogenicity_counts|keyvalue).length === 0) { +
+ None +
+ } + @for (keypar of openCravatAnnotations.pathogenicity_counts|keyvalue; track keypar.key) { +
+ {{ keypar.key }} ({{ keypar.value }}) +
+ } + +
+
+ + + + + + + Predictor + Annotation + + + + @for (keypar of openCravatAnnotations.benignity|keyvalue; track keypar.key) { + + {{ keypar.key }} + + {{ keypar.value | ifEmpty : '--' }} + + + } + + + + + + + + + Predictor + Annotation + + + + @for (keypar of openCravatAnnotations.pathogenicity|keyvalue; track keypar.key) { + + {{ keypar.key }} + + {{ keypar.value | ifEmpty : '--' }} + + + } + + + + + + \ No newline at end of file diff --git a/client/src/app/components/variants/open-cravat-annotations/open-cravat-annotations.component.less b/client/src/app/components/variants/open-cravat-annotations/open-cravat-annotations.component.less new file mode 100644 index 000000000..30681b7cc --- /dev/null +++ b/client/src/app/components/variants/open-cravat-annotations/open-cravat-annotations.component.less @@ -0,0 +1,15 @@ +:host { + display: block; +} + +nz-card { + width: 100%; +} + +.key-col { + text-align: right; + font-weight: bold; +} +.button-col { + text-align: right; +} diff --git a/client/src/app/components/variants/open-cravat-annotations/open-cravat-annotations.component.ts b/client/src/app/components/variants/open-cravat-annotations/open-cravat-annotations.component.ts new file mode 100644 index 000000000..fe300cc54 --- /dev/null +++ b/client/src/app/components/variants/open-cravat-annotations/open-cravat-annotations.component.ts @@ -0,0 +1,26 @@ +import { Component, Input, OnDestroy } from '@angular/core' +import { Maybe } from '@app/generated/civic.apollo' +import { BehaviorSubject } from 'rxjs' + +@Component({ + selector: 'cvc-open-cravat-annotations', + templateUrl: './open-cravat-annotations.component.html', + styleUrls: ['./open-cravat-annotations.component.less'], +}) +export class CvcOpenCravatAnnotationsComponent implements OnDestroy { + @Input() openCravatAnnotations: any + @Input() openCravatUrl: Maybe + + tabIndex = new BehaviorSubject(0) + + constructor() { + } + + tabChange(index: number): void { + this.tabIndex.next(index) + } + + ngOnDestroy(): void { + this.tabIndex.unsubscribe() + } +} diff --git a/client/src/app/components/variants/open-cravat-annotations/open-cravat-annotations.module.ts b/client/src/app/components/variants/open-cravat-annotations/open-cravat-annotations.module.ts new file mode 100644 index 000000000..d5d5040f1 --- /dev/null +++ b/client/src/app/components/variants/open-cravat-annotations/open-cravat-annotations.module.ts @@ -0,0 +1,29 @@ +import { NgModule } from '@angular/core' +import { CommonModule } from '@angular/common' +import { CvcOpenCravatAnnotationsComponent } from './open-cravat-annotations.component' +import { NzTabsModule } from 'ng-zorro-antd/tabs' +import { NzCardModule } from 'ng-zorro-antd/card' +import { NzGridModule } from 'ng-zorro-antd/grid' +import { NzTableModule } from 'ng-zorro-antd/table' +import { CvcPipesModule } from '@app/core/pipes/pipes.module' +import { CvcLinkTagModule } from '@app/components/shared/link-tag/link-tag.module' +import { NzToolTipModule } from 'ng-zorro-antd/tooltip' +import { CvcEmptyValueModule } from '@app/forms/components/empty-value/empty-value.module' +import { NzTypographyModule } from 'ng-zorro-antd/typography' + +@NgModule({ + declarations: [CvcOpenCravatAnnotationsComponent], + imports: [ + CommonModule, + NzTabsModule, + NzTableModule, + NzCardModule, + NzToolTipModule, + NzGridModule, + NzTypographyModule, + CvcLinkTagModule, + CvcPipesModule, + ], + exports: [CvcOpenCravatAnnotationsComponent], +}) +export class CvcOpenCravatAnnotationsModule {} diff --git a/client/src/app/generated/civic.apollo-helpers.ts b/client/src/app/generated/civic.apollo-helpers.ts index 8435ab739..389b9545c 100644 --- a/client/src/app/generated/civic.apollo-helpers.ts +++ b/client/src/app/generated/civic.apollo-helpers.ts @@ -1302,7 +1302,7 @@ export type GeneEdgeFieldPolicy = { cursor?: FieldPolicy | FieldReadFunction, node?: FieldPolicy | FieldReadFunction }; -export type GeneVariantKeySpecifier = ('alleleRegistryId' | 'clinvarIds' | 'comments' | 'coordinates' | 'creationActivity' | 'deprecated' | 'deprecationActivity' | 'deprecationReason' | 'events' | 'feature' | 'flagged' | 'flags' | 'hgvsDescriptions' | 'id' | 'lastAcceptedRevisionEvent' | 'lastCommentEvent' | 'lastSubmittedRevisionEvent' | 'link' | 'maneSelectTranscript' | 'molecularProfiles' | 'myVariantInfo' | 'name' | 'openCravatUrl' | 'openRevisionCount' | 'primaryCoordinates' | 'revisions' | 'singleVariantMolecularProfile' | 'singleVariantMolecularProfileId' | 'variantAliases' | 'variantTypes' | GeneVariantKeySpecifier)[]; +export type GeneVariantKeySpecifier = ('alleleRegistryId' | 'clinvarIds' | 'comments' | 'coordinates' | 'creationActivity' | 'deprecated' | 'deprecationActivity' | 'deprecationReason' | 'events' | 'feature' | 'flagged' | 'flags' | 'hgvsDescriptions' | 'id' | 'lastAcceptedRevisionEvent' | 'lastCommentEvent' | 'lastSubmittedRevisionEvent' | 'link' | 'maneSelectTranscript' | 'molecularProfiles' | 'myVariantInfo' | 'name' | 'openCravatAnnotations' | 'openCravatUrl' | 'openRevisionCount' | 'primaryCoordinates' | 'revisions' | 'singleVariantMolecularProfile' | 'singleVariantMolecularProfileId' | 'variantAliases' | 'variantTypes' | GeneVariantKeySpecifier)[]; export type GeneVariantFieldPolicy = { alleleRegistryId?: FieldPolicy | FieldReadFunction, clinvarIds?: FieldPolicy | FieldReadFunction, @@ -1326,6 +1326,7 @@ export type GeneVariantFieldPolicy = { molecularProfiles?: FieldPolicy | FieldReadFunction, myVariantInfo?: FieldPolicy | FieldReadFunction, name?: FieldPolicy | FieldReadFunction, + openCravatAnnotations?: FieldPolicy | FieldReadFunction, openCravatUrl?: FieldPolicy | FieldReadFunction, openRevisionCount?: FieldPolicy | FieldReadFunction, primaryCoordinates?: FieldPolicy | FieldReadFunction, diff --git a/client/src/app/generated/civic.apollo.ts b/client/src/app/generated/civic.apollo.ts index bcf025ea7..001b27dd2 100644 --- a/client/src/app/generated/civic.apollo.ts +++ b/client/src/app/generated/civic.apollo.ts @@ -3352,6 +3352,7 @@ export type GeneVariant = Commentable & EventOriginObject & EventSubject & Flagg molecularProfiles: MolecularProfileConnection; myVariantInfo?: Maybe; name: Scalars['String']['output']; + openCravatAnnotations?: Maybe; openCravatUrl?: Maybe; openRevisionCount: Scalars['Int']['output']; /** @deprecated The new Fusion variant type means Gene variants no longer have primary and secondary coordinates. Use 'coordinates' instead. */ @@ -9665,9 +9666,9 @@ export type MolecularProfileSummaryQueryVariables = Exact<{ }>; -export type MolecularProfileSummaryQuery = { __typename: 'Query', molecularProfile?: { __typename: 'MolecularProfile', id: number, name: string, description?: string | undefined, molecularProfileAliases: Array, molecularProfileScore: number, sources: Array<{ __typename: 'Source', id: number, citation?: string | undefined, link: string, sourceType: SourceSource, deprecated: boolean }>, variants: Array<{ __typename: 'FactorVariant', id: number, name: string, link: string, deprecated: boolean, flagged: boolean, variantAliases: Array, ncitId?: string | undefined, feature: { __typename: 'Feature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean }, molecularProfiles: { __typename: 'MolecularProfileConnection', totalCount: number, nodes: Array<{ __typename: 'MolecularProfile', id: number, link: string, name: string, deprecated: boolean, flagged: boolean }> }, variantTypes: Array<{ __typename: 'VariantType', id: number, link: string, soid: string, name: string }>, ncitDetails?: { __typename: 'NcitDetails', synonyms: Array<{ __typename: 'NcitSynonym', name: string, source: string }>, definitions: Array<{ __typename: 'NcitDefinition', definition: string, source: string }> } | undefined } | { __typename: 'FusionVariant', id: number, name: string, link: string, deprecated: boolean, flagged: boolean, variantAliases: Array, viccCompliantName: string, feature: { __typename: 'Feature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean }, molecularProfiles: { __typename: 'MolecularProfileConnection', totalCount: number, nodes: Array<{ __typename: 'MolecularProfile', id: number, link: string, name: string, deprecated: boolean, flagged: boolean }> }, variantTypes: Array<{ __typename: 'VariantType', id: number, link: string, soid: string, name: string }>, fusion: { __typename: 'Fusion', fivePrimePartnerStatus: FusionPartnerStatus, threePrimePartnerStatus: FusionPartnerStatus, fivePrimeGene?: { __typename: 'Gene', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined, threePrimeGene?: { __typename: 'Gene', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined }, fivePrimeCoordinates?: { __typename: 'VariantCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, referenceBases?: string | undefined, variantBases?: string | undefined, coordinateType: VariantCoordinateType } | undefined, threePrimeCoordinates?: { __typename: 'VariantCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, referenceBases?: string | undefined, variantBases?: string | undefined, coordinateType: VariantCoordinateType } | undefined, fivePrimeStartExonCoordinates?: { __typename: 'ExonCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, exon?: number | undefined, exonOffset?: number | undefined, exonOffsetDirection?: Direction | undefined, ensemblId?: string | undefined, strand?: Direction | undefined, coordinateType: ExonCoordinateType } | undefined, fivePrimeEndExonCoordinates?: { __typename: 'ExonCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, exon?: number | undefined, exonOffset?: number | undefined, exonOffsetDirection?: Direction | undefined, ensemblId?: string | undefined, strand?: Direction | undefined, coordinateType: ExonCoordinateType } | undefined, threePrimeStartExonCoordinates?: { __typename: 'ExonCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, exon?: number | undefined, exonOffset?: number | undefined, exonOffsetDirection?: Direction | undefined, ensemblId?: string | undefined, strand?: Direction | undefined, coordinateType: ExonCoordinateType } | undefined, threePrimeEndExonCoordinates?: { __typename: 'ExonCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, exon?: number | undefined, exonOffset?: number | undefined, exonOffsetDirection?: Direction | undefined, ensemblId?: string | undefined, strand?: Direction | undefined, coordinateType: ExonCoordinateType } | undefined } | { __typename: 'GeneVariant', id: number, name: string, link: string, deprecated: boolean, flagged: boolean, variantAliases: Array, alleleRegistryId?: string | undefined, openCravatUrl?: string | undefined, maneSelectTranscript?: string | undefined, hgvsDescriptions: Array, clinvarIds: Array, feature: { __typename: 'Feature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean }, molecularProfiles: { __typename: 'MolecularProfileConnection', totalCount: number, nodes: Array<{ __typename: 'MolecularProfile', id: number, link: string, name: string, deprecated: boolean, flagged: boolean }> }, variantTypes: Array<{ __typename: 'VariantType', id: number, link: string, soid: string, name: string }>, coordinates?: { __typename: 'VariantCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, referenceBases?: string | undefined, variantBases?: string | undefined, coordinateType: VariantCoordinateType } | undefined, myVariantInfo?: { __typename: 'MyVariantInfo', myVariantInfoId: string, caddConsequence: Array, caddDetail: Array, caddScore?: number | undefined, caddPhred?: number | undefined, clinvarClinicalSignificance: Array, clinvarHgvsCoding: Array, clinvarHgvsGenomic: Array, clinvarHgvsNonCoding: Array, clinvarHgvsProtein: Array, clinvarId?: number | undefined, clinvarOmim?: string | undefined, cosmicId?: string | undefined, dbnsfpInterproDomain: Array, dbsnpRsid?: string | undefined, eglClass?: string | undefined, eglHgvs: Array, eglProtein?: string | undefined, eglTranscript?: string | undefined, exacAlleleCount?: number | undefined, exacAlleleFrequency?: number | undefined, exacAlleleNumber?: number | undefined, fathmmMklPrediction?: string | undefined, fathmmMklScore?: number | undefined, fathmmPrediction: Array, fathmmScore: Array, fitconsScore?: number | undefined, gerp?: number | undefined, gnomadExomeAlleleCount?: number | undefined, gnomadExomeAlleleFrequency?: number | undefined, gnomadExomeAlleleNumber?: number | undefined, gnomadExomeFilter?: string | undefined, gnomadGenomeAlleleCount?: number | undefined, gnomadGenomeAlleleFrequency?: number | undefined, gnomadGenomeAlleleNumber?: number | undefined, gnomadGenomeFilter?: string | undefined, lrtPrediction?: string | undefined, lrtScore?: number | undefined, metalrPrediction?: string | undefined, metalrScore?: number | undefined, metasvmPrediction?: string | undefined, metasvmScore?: number | undefined, mutationassessorPrediction: Array, mutationassessorScore: Array, mutationtasterPrediction: Array, mutationtasterScore: Array, phastcons100way?: number | undefined, phastcons30way?: number | undefined, phyloP100way?: number | undefined, phyloP30way?: number | undefined, polyphen2HdivPrediction: Array, polyphen2HdivScore: Array, polyphen2HvarPrediction: Array, polyphen2HvarScore: Array, proveanPrediction: Array, proveanScore: Array, revelScore?: Array | undefined, siftPrediction: Array, siftScore: Array, siphy?: number | undefined, snpeffSnpEffect: Array, snpeffSnpImpact: Array } | undefined } | { __typename: 'Variant', id: number, name: string, link: string, deprecated: boolean, flagged: boolean, variantAliases: Array, feature: { __typename: 'Feature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean }, molecularProfiles: { __typename: 'MolecularProfileConnection', totalCount: number, nodes: Array<{ __typename: 'MolecularProfile', id: number, link: string, name: string, deprecated: boolean, flagged: boolean }> }, variantTypes: Array<{ __typename: 'VariantType', id: number, link: string, soid: string, name: string }> }>, parsedName: Array<{ __typename: 'Feature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | { __typename: 'MolecularProfileTextSegment', text: string } | { __typename: 'Variant', id: number, name: string, link: string, deprecated: boolean, flagged: boolean }>, complexMolecularProfileCreationActivity?: { __typename: 'CreateComplexMolecularProfileActivity', createdAt: any, user: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, variantDeprecationActivity?: { __typename: 'DeprecateVariantActivity', createdAt: any, user: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, complexMolecularProfileDeprecationActivity?: { __typename: 'DeprecateComplexMolecularProfileActivity', createdAt: any, user: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined }, parsedNote: Array<{ __typename: 'CommentTagSegment', entityId: number, displayName: string, tagType: TaggableEntity, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlagged', entityId: number, displayName: string, tagType: TaggableEntity, flagged: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlaggedAndDeprecated', entityId: number, displayName: string, tagType: TaggableEntity, flagged: boolean, deprecated: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlaggedAndWithStatus', entityId: number, displayName: string, tagType: TaggableEntity, status: EvidenceStatus, flagged: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTextSegment', text: string } | { __typename: 'User', id: number, username: string, displayName: string, name?: string | undefined, role: UserRole, profileImagePath?: string | undefined, organizations: Array<{ __typename: 'Organization', id: number, name: string, profileImagePath?: string | undefined }> }> } | undefined } | undefined }; +export type MolecularProfileSummaryQuery = { __typename: 'Query', molecularProfile?: { __typename: 'MolecularProfile', id: number, name: string, description?: string | undefined, molecularProfileAliases: Array, molecularProfileScore: number, sources: Array<{ __typename: 'Source', id: number, citation?: string | undefined, link: string, sourceType: SourceSource, deprecated: boolean }>, variants: Array<{ __typename: 'FactorVariant', id: number, name: string, link: string, deprecated: boolean, flagged: boolean, variantAliases: Array, ncitId?: string | undefined, feature: { __typename: 'Feature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean }, molecularProfiles: { __typename: 'MolecularProfileConnection', totalCount: number, nodes: Array<{ __typename: 'MolecularProfile', id: number, link: string, name: string, deprecated: boolean, flagged: boolean }> }, variantTypes: Array<{ __typename: 'VariantType', id: number, link: string, soid: string, name: string }>, ncitDetails?: { __typename: 'NcitDetails', synonyms: Array<{ __typename: 'NcitSynonym', name: string, source: string }>, definitions: Array<{ __typename: 'NcitDefinition', definition: string, source: string }> } | undefined } | { __typename: 'FusionVariant', id: number, name: string, link: string, deprecated: boolean, flagged: boolean, variantAliases: Array, viccCompliantName: string, feature: { __typename: 'Feature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean }, molecularProfiles: { __typename: 'MolecularProfileConnection', totalCount: number, nodes: Array<{ __typename: 'MolecularProfile', id: number, link: string, name: string, deprecated: boolean, flagged: boolean }> }, variantTypes: Array<{ __typename: 'VariantType', id: number, link: string, soid: string, name: string }>, fusion: { __typename: 'Fusion', fivePrimePartnerStatus: FusionPartnerStatus, threePrimePartnerStatus: FusionPartnerStatus, fivePrimeGene?: { __typename: 'Gene', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined, threePrimeGene?: { __typename: 'Gene', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined }, fivePrimeCoordinates?: { __typename: 'VariantCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, referenceBases?: string | undefined, variantBases?: string | undefined, coordinateType: VariantCoordinateType } | undefined, threePrimeCoordinates?: { __typename: 'VariantCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, referenceBases?: string | undefined, variantBases?: string | undefined, coordinateType: VariantCoordinateType } | undefined, fivePrimeStartExonCoordinates?: { __typename: 'ExonCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, exon?: number | undefined, exonOffset?: number | undefined, exonOffsetDirection?: Direction | undefined, ensemblId?: string | undefined, strand?: Direction | undefined, coordinateType: ExonCoordinateType } | undefined, fivePrimeEndExonCoordinates?: { __typename: 'ExonCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, exon?: number | undefined, exonOffset?: number | undefined, exonOffsetDirection?: Direction | undefined, ensemblId?: string | undefined, strand?: Direction | undefined, coordinateType: ExonCoordinateType } | undefined, threePrimeStartExonCoordinates?: { __typename: 'ExonCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, exon?: number | undefined, exonOffset?: number | undefined, exonOffsetDirection?: Direction | undefined, ensemblId?: string | undefined, strand?: Direction | undefined, coordinateType: ExonCoordinateType } | undefined, threePrimeEndExonCoordinates?: { __typename: 'ExonCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, exon?: number | undefined, exonOffset?: number | undefined, exonOffsetDirection?: Direction | undefined, ensemblId?: string | undefined, strand?: Direction | undefined, coordinateType: ExonCoordinateType } | undefined } | { __typename: 'GeneVariant', id: number, name: string, link: string, deprecated: boolean, flagged: boolean, variantAliases: Array, alleleRegistryId?: string | undefined, openCravatUrl?: string | undefined, maneSelectTranscript?: string | undefined, hgvsDescriptions: Array, clinvarIds: Array, openCravatAnnotations?: any | undefined, feature: { __typename: 'Feature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean }, molecularProfiles: { __typename: 'MolecularProfileConnection', totalCount: number, nodes: Array<{ __typename: 'MolecularProfile', id: number, link: string, name: string, deprecated: boolean, flagged: boolean }> }, variantTypes: Array<{ __typename: 'VariantType', id: number, link: string, soid: string, name: string }>, coordinates?: { __typename: 'VariantCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, referenceBases?: string | undefined, variantBases?: string | undefined, coordinateType: VariantCoordinateType } | undefined, myVariantInfo?: { __typename: 'MyVariantInfo', myVariantInfoId: string, caddConsequence: Array, caddDetail: Array, caddScore?: number | undefined, caddPhred?: number | undefined, clinvarClinicalSignificance: Array, clinvarHgvsCoding: Array, clinvarHgvsGenomic: Array, clinvarHgvsNonCoding: Array, clinvarHgvsProtein: Array, clinvarId?: number | undefined, clinvarOmim?: string | undefined, cosmicId?: string | undefined, dbnsfpInterproDomain: Array, dbsnpRsid?: string | undefined, eglClass?: string | undefined, eglHgvs: Array, eglProtein?: string | undefined, eglTranscript?: string | undefined, exacAlleleCount?: number | undefined, exacAlleleFrequency?: number | undefined, exacAlleleNumber?: number | undefined, fathmmMklPrediction?: string | undefined, fathmmMklScore?: number | undefined, fathmmPrediction: Array, fathmmScore: Array, fitconsScore?: number | undefined, gerp?: number | undefined, gnomadExomeAlleleCount?: number | undefined, gnomadExomeAlleleFrequency?: number | undefined, gnomadExomeAlleleNumber?: number | undefined, gnomadExomeFilter?: string | undefined, gnomadGenomeAlleleCount?: number | undefined, gnomadGenomeAlleleFrequency?: number | undefined, gnomadGenomeAlleleNumber?: number | undefined, gnomadGenomeFilter?: string | undefined, lrtPrediction?: string | undefined, lrtScore?: number | undefined, metalrPrediction?: string | undefined, metalrScore?: number | undefined, metasvmPrediction?: string | undefined, metasvmScore?: number | undefined, mutationassessorPrediction: Array, mutationassessorScore: Array, mutationtasterPrediction: Array, mutationtasterScore: Array, phastcons100way?: number | undefined, phastcons30way?: number | undefined, phyloP100way?: number | undefined, phyloP30way?: number | undefined, polyphen2HdivPrediction: Array, polyphen2HdivScore: Array, polyphen2HvarPrediction: Array, polyphen2HvarScore: Array, proveanPrediction: Array, proveanScore: Array, revelScore?: Array | undefined, siftPrediction: Array, siftScore: Array, siphy?: number | undefined, snpeffSnpEffect: Array, snpeffSnpImpact: Array } | undefined } | { __typename: 'Variant', id: number, name: string, link: string, deprecated: boolean, flagged: boolean, variantAliases: Array, feature: { __typename: 'Feature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean }, molecularProfiles: { __typename: 'MolecularProfileConnection', totalCount: number, nodes: Array<{ __typename: 'MolecularProfile', id: number, link: string, name: string, deprecated: boolean, flagged: boolean }> }, variantTypes: Array<{ __typename: 'VariantType', id: number, link: string, soid: string, name: string }> }>, parsedName: Array<{ __typename: 'Feature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | { __typename: 'MolecularProfileTextSegment', text: string } | { __typename: 'Variant', id: number, name: string, link: string, deprecated: boolean, flagged: boolean }>, complexMolecularProfileCreationActivity?: { __typename: 'CreateComplexMolecularProfileActivity', createdAt: any, user: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, variantDeprecationActivity?: { __typename: 'DeprecateVariantActivity', createdAt: any, user: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, complexMolecularProfileDeprecationActivity?: { __typename: 'DeprecateComplexMolecularProfileActivity', createdAt: any, user: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined }, parsedNote: Array<{ __typename: 'CommentTagSegment', entityId: number, displayName: string, tagType: TaggableEntity, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlagged', entityId: number, displayName: string, tagType: TaggableEntity, flagged: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlaggedAndDeprecated', entityId: number, displayName: string, tagType: TaggableEntity, flagged: boolean, deprecated: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlaggedAndWithStatus', entityId: number, displayName: string, tagType: TaggableEntity, status: EvidenceStatus, flagged: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTextSegment', text: string } | { __typename: 'User', id: number, username: string, displayName: string, name?: string | undefined, role: UserRole, profileImagePath?: string | undefined, organizations: Array<{ __typename: 'Organization', id: number, name: string, profileImagePath?: string | undefined }> }> } | undefined } | undefined }; -export type MolecularProfileSummaryFieldsFragment = { __typename: 'MolecularProfile', id: number, name: string, description?: string | undefined, molecularProfileAliases: Array, molecularProfileScore: number, sources: Array<{ __typename: 'Source', id: number, citation?: string | undefined, link: string, sourceType: SourceSource, deprecated: boolean }>, variants: Array<{ __typename: 'FactorVariant', id: number, name: string, link: string, deprecated: boolean, flagged: boolean, variantAliases: Array, ncitId?: string | undefined, feature: { __typename: 'Feature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean }, molecularProfiles: { __typename: 'MolecularProfileConnection', totalCount: number, nodes: Array<{ __typename: 'MolecularProfile', id: number, link: string, name: string, deprecated: boolean, flagged: boolean }> }, variantTypes: Array<{ __typename: 'VariantType', id: number, link: string, soid: string, name: string }>, ncitDetails?: { __typename: 'NcitDetails', synonyms: Array<{ __typename: 'NcitSynonym', name: string, source: string }>, definitions: Array<{ __typename: 'NcitDefinition', definition: string, source: string }> } | undefined } | { __typename: 'FusionVariant', id: number, name: string, link: string, deprecated: boolean, flagged: boolean, variantAliases: Array, viccCompliantName: string, feature: { __typename: 'Feature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean }, molecularProfiles: { __typename: 'MolecularProfileConnection', totalCount: number, nodes: Array<{ __typename: 'MolecularProfile', id: number, link: string, name: string, deprecated: boolean, flagged: boolean }> }, variantTypes: Array<{ __typename: 'VariantType', id: number, link: string, soid: string, name: string }>, fusion: { __typename: 'Fusion', fivePrimePartnerStatus: FusionPartnerStatus, threePrimePartnerStatus: FusionPartnerStatus, fivePrimeGene?: { __typename: 'Gene', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined, threePrimeGene?: { __typename: 'Gene', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined }, fivePrimeCoordinates?: { __typename: 'VariantCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, referenceBases?: string | undefined, variantBases?: string | undefined, coordinateType: VariantCoordinateType } | undefined, threePrimeCoordinates?: { __typename: 'VariantCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, referenceBases?: string | undefined, variantBases?: string | undefined, coordinateType: VariantCoordinateType } | undefined, fivePrimeStartExonCoordinates?: { __typename: 'ExonCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, exon?: number | undefined, exonOffset?: number | undefined, exonOffsetDirection?: Direction | undefined, ensemblId?: string | undefined, strand?: Direction | undefined, coordinateType: ExonCoordinateType } | undefined, fivePrimeEndExonCoordinates?: { __typename: 'ExonCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, exon?: number | undefined, exonOffset?: number | undefined, exonOffsetDirection?: Direction | undefined, ensemblId?: string | undefined, strand?: Direction | undefined, coordinateType: ExonCoordinateType } | undefined, threePrimeStartExonCoordinates?: { __typename: 'ExonCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, exon?: number | undefined, exonOffset?: number | undefined, exonOffsetDirection?: Direction | undefined, ensemblId?: string | undefined, strand?: Direction | undefined, coordinateType: ExonCoordinateType } | undefined, threePrimeEndExonCoordinates?: { __typename: 'ExonCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, exon?: number | undefined, exonOffset?: number | undefined, exonOffsetDirection?: Direction | undefined, ensemblId?: string | undefined, strand?: Direction | undefined, coordinateType: ExonCoordinateType } | undefined } | { __typename: 'GeneVariant', id: number, name: string, link: string, deprecated: boolean, flagged: boolean, variantAliases: Array, alleleRegistryId?: string | undefined, openCravatUrl?: string | undefined, maneSelectTranscript?: string | undefined, hgvsDescriptions: Array, clinvarIds: Array, feature: { __typename: 'Feature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean }, molecularProfiles: { __typename: 'MolecularProfileConnection', totalCount: number, nodes: Array<{ __typename: 'MolecularProfile', id: number, link: string, name: string, deprecated: boolean, flagged: boolean }> }, variantTypes: Array<{ __typename: 'VariantType', id: number, link: string, soid: string, name: string }>, coordinates?: { __typename: 'VariantCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, referenceBases?: string | undefined, variantBases?: string | undefined, coordinateType: VariantCoordinateType } | undefined, myVariantInfo?: { __typename: 'MyVariantInfo', myVariantInfoId: string, caddConsequence: Array, caddDetail: Array, caddScore?: number | undefined, caddPhred?: number | undefined, clinvarClinicalSignificance: Array, clinvarHgvsCoding: Array, clinvarHgvsGenomic: Array, clinvarHgvsNonCoding: Array, clinvarHgvsProtein: Array, clinvarId?: number | undefined, clinvarOmim?: string | undefined, cosmicId?: string | undefined, dbnsfpInterproDomain: Array, dbsnpRsid?: string | undefined, eglClass?: string | undefined, eglHgvs: Array, eglProtein?: string | undefined, eglTranscript?: string | undefined, exacAlleleCount?: number | undefined, exacAlleleFrequency?: number | undefined, exacAlleleNumber?: number | undefined, fathmmMklPrediction?: string | undefined, fathmmMklScore?: number | undefined, fathmmPrediction: Array, fathmmScore: Array, fitconsScore?: number | undefined, gerp?: number | undefined, gnomadExomeAlleleCount?: number | undefined, gnomadExomeAlleleFrequency?: number | undefined, gnomadExomeAlleleNumber?: number | undefined, gnomadExomeFilter?: string | undefined, gnomadGenomeAlleleCount?: number | undefined, gnomadGenomeAlleleFrequency?: number | undefined, gnomadGenomeAlleleNumber?: number | undefined, gnomadGenomeFilter?: string | undefined, lrtPrediction?: string | undefined, lrtScore?: number | undefined, metalrPrediction?: string | undefined, metalrScore?: number | undefined, metasvmPrediction?: string | undefined, metasvmScore?: number | undefined, mutationassessorPrediction: Array, mutationassessorScore: Array, mutationtasterPrediction: Array, mutationtasterScore: Array, phastcons100way?: number | undefined, phastcons30way?: number | undefined, phyloP100way?: number | undefined, phyloP30way?: number | undefined, polyphen2HdivPrediction: Array, polyphen2HdivScore: Array, polyphen2HvarPrediction: Array, polyphen2HvarScore: Array, proveanPrediction: Array, proveanScore: Array, revelScore?: Array | undefined, siftPrediction: Array, siftScore: Array, siphy?: number | undefined, snpeffSnpEffect: Array, snpeffSnpImpact: Array } | undefined } | { __typename: 'Variant', id: number, name: string, link: string, deprecated: boolean, flagged: boolean, variantAliases: Array, feature: { __typename: 'Feature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean }, molecularProfiles: { __typename: 'MolecularProfileConnection', totalCount: number, nodes: Array<{ __typename: 'MolecularProfile', id: number, link: string, name: string, deprecated: boolean, flagged: boolean }> }, variantTypes: Array<{ __typename: 'VariantType', id: number, link: string, soid: string, name: string }> }>, parsedName: Array<{ __typename: 'Feature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | { __typename: 'MolecularProfileTextSegment', text: string } | { __typename: 'Variant', id: number, name: string, link: string, deprecated: boolean, flagged: boolean }>, complexMolecularProfileCreationActivity?: { __typename: 'CreateComplexMolecularProfileActivity', createdAt: any, user: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, variantDeprecationActivity?: { __typename: 'DeprecateVariantActivity', createdAt: any, user: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, complexMolecularProfileDeprecationActivity?: { __typename: 'DeprecateComplexMolecularProfileActivity', createdAt: any, user: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined }, parsedNote: Array<{ __typename: 'CommentTagSegment', entityId: number, displayName: string, tagType: TaggableEntity, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlagged', entityId: number, displayName: string, tagType: TaggableEntity, flagged: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlaggedAndDeprecated', entityId: number, displayName: string, tagType: TaggableEntity, flagged: boolean, deprecated: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlaggedAndWithStatus', entityId: number, displayName: string, tagType: TaggableEntity, status: EvidenceStatus, flagged: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTextSegment', text: string } | { __typename: 'User', id: number, username: string, displayName: string, name?: string | undefined, role: UserRole, profileImagePath?: string | undefined, organizations: Array<{ __typename: 'Organization', id: number, name: string, profileImagePath?: string | undefined }> }> } | undefined }; +export type MolecularProfileSummaryFieldsFragment = { __typename: 'MolecularProfile', id: number, name: string, description?: string | undefined, molecularProfileAliases: Array, molecularProfileScore: number, sources: Array<{ __typename: 'Source', id: number, citation?: string | undefined, link: string, sourceType: SourceSource, deprecated: boolean }>, variants: Array<{ __typename: 'FactorVariant', id: number, name: string, link: string, deprecated: boolean, flagged: boolean, variantAliases: Array, ncitId?: string | undefined, feature: { __typename: 'Feature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean }, molecularProfiles: { __typename: 'MolecularProfileConnection', totalCount: number, nodes: Array<{ __typename: 'MolecularProfile', id: number, link: string, name: string, deprecated: boolean, flagged: boolean }> }, variantTypes: Array<{ __typename: 'VariantType', id: number, link: string, soid: string, name: string }>, ncitDetails?: { __typename: 'NcitDetails', synonyms: Array<{ __typename: 'NcitSynonym', name: string, source: string }>, definitions: Array<{ __typename: 'NcitDefinition', definition: string, source: string }> } | undefined } | { __typename: 'FusionVariant', id: number, name: string, link: string, deprecated: boolean, flagged: boolean, variantAliases: Array, viccCompliantName: string, feature: { __typename: 'Feature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean }, molecularProfiles: { __typename: 'MolecularProfileConnection', totalCount: number, nodes: Array<{ __typename: 'MolecularProfile', id: number, link: string, name: string, deprecated: boolean, flagged: boolean }> }, variantTypes: Array<{ __typename: 'VariantType', id: number, link: string, soid: string, name: string }>, fusion: { __typename: 'Fusion', fivePrimePartnerStatus: FusionPartnerStatus, threePrimePartnerStatus: FusionPartnerStatus, fivePrimeGene?: { __typename: 'Gene', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined, threePrimeGene?: { __typename: 'Gene', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined }, fivePrimeCoordinates?: { __typename: 'VariantCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, referenceBases?: string | undefined, variantBases?: string | undefined, coordinateType: VariantCoordinateType } | undefined, threePrimeCoordinates?: { __typename: 'VariantCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, referenceBases?: string | undefined, variantBases?: string | undefined, coordinateType: VariantCoordinateType } | undefined, fivePrimeStartExonCoordinates?: { __typename: 'ExonCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, exon?: number | undefined, exonOffset?: number | undefined, exonOffsetDirection?: Direction | undefined, ensemblId?: string | undefined, strand?: Direction | undefined, coordinateType: ExonCoordinateType } | undefined, fivePrimeEndExonCoordinates?: { __typename: 'ExonCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, exon?: number | undefined, exonOffset?: number | undefined, exonOffsetDirection?: Direction | undefined, ensemblId?: string | undefined, strand?: Direction | undefined, coordinateType: ExonCoordinateType } | undefined, threePrimeStartExonCoordinates?: { __typename: 'ExonCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, exon?: number | undefined, exonOffset?: number | undefined, exonOffsetDirection?: Direction | undefined, ensemblId?: string | undefined, strand?: Direction | undefined, coordinateType: ExonCoordinateType } | undefined, threePrimeEndExonCoordinates?: { __typename: 'ExonCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, exon?: number | undefined, exonOffset?: number | undefined, exonOffsetDirection?: Direction | undefined, ensemblId?: string | undefined, strand?: Direction | undefined, coordinateType: ExonCoordinateType } | undefined } | { __typename: 'GeneVariant', id: number, name: string, link: string, deprecated: boolean, flagged: boolean, variantAliases: Array, alleleRegistryId?: string | undefined, openCravatUrl?: string | undefined, maneSelectTranscript?: string | undefined, hgvsDescriptions: Array, clinvarIds: Array, openCravatAnnotations?: any | undefined, feature: { __typename: 'Feature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean }, molecularProfiles: { __typename: 'MolecularProfileConnection', totalCount: number, nodes: Array<{ __typename: 'MolecularProfile', id: number, link: string, name: string, deprecated: boolean, flagged: boolean }> }, variantTypes: Array<{ __typename: 'VariantType', id: number, link: string, soid: string, name: string }>, coordinates?: { __typename: 'VariantCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, referenceBases?: string | undefined, variantBases?: string | undefined, coordinateType: VariantCoordinateType } | undefined, myVariantInfo?: { __typename: 'MyVariantInfo', myVariantInfoId: string, caddConsequence: Array, caddDetail: Array, caddScore?: number | undefined, caddPhred?: number | undefined, clinvarClinicalSignificance: Array, clinvarHgvsCoding: Array, clinvarHgvsGenomic: Array, clinvarHgvsNonCoding: Array, clinvarHgvsProtein: Array, clinvarId?: number | undefined, clinvarOmim?: string | undefined, cosmicId?: string | undefined, dbnsfpInterproDomain: Array, dbsnpRsid?: string | undefined, eglClass?: string | undefined, eglHgvs: Array, eglProtein?: string | undefined, eglTranscript?: string | undefined, exacAlleleCount?: number | undefined, exacAlleleFrequency?: number | undefined, exacAlleleNumber?: number | undefined, fathmmMklPrediction?: string | undefined, fathmmMklScore?: number | undefined, fathmmPrediction: Array, fathmmScore: Array, fitconsScore?: number | undefined, gerp?: number | undefined, gnomadExomeAlleleCount?: number | undefined, gnomadExomeAlleleFrequency?: number | undefined, gnomadExomeAlleleNumber?: number | undefined, gnomadExomeFilter?: string | undefined, gnomadGenomeAlleleCount?: number | undefined, gnomadGenomeAlleleFrequency?: number | undefined, gnomadGenomeAlleleNumber?: number | undefined, gnomadGenomeFilter?: string | undefined, lrtPrediction?: string | undefined, lrtScore?: number | undefined, metalrPrediction?: string | undefined, metalrScore?: number | undefined, metasvmPrediction?: string | undefined, metasvmScore?: number | undefined, mutationassessorPrediction: Array, mutationassessorScore: Array, mutationtasterPrediction: Array, mutationtasterScore: Array, phastcons100way?: number | undefined, phastcons30way?: number | undefined, phyloP100way?: number | undefined, phyloP30way?: number | undefined, polyphen2HdivPrediction: Array, polyphen2HdivScore: Array, polyphen2HvarPrediction: Array, polyphen2HvarScore: Array, proveanPrediction: Array, proveanScore: Array, revelScore?: Array | undefined, siftPrediction: Array, siftScore: Array, siphy?: number | undefined, snpeffSnpEffect: Array, snpeffSnpImpact: Array } | undefined } | { __typename: 'Variant', id: number, name: string, link: string, deprecated: boolean, flagged: boolean, variantAliases: Array, feature: { __typename: 'Feature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean }, molecularProfiles: { __typename: 'MolecularProfileConnection', totalCount: number, nodes: Array<{ __typename: 'MolecularProfile', id: number, link: string, name: string, deprecated: boolean, flagged: boolean }> }, variantTypes: Array<{ __typename: 'VariantType', id: number, link: string, soid: string, name: string }> }>, parsedName: Array<{ __typename: 'Feature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | { __typename: 'MolecularProfileTextSegment', text: string } | { __typename: 'Variant', id: number, name: string, link: string, deprecated: boolean, flagged: boolean }>, complexMolecularProfileCreationActivity?: { __typename: 'CreateComplexMolecularProfileActivity', createdAt: any, user: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, variantDeprecationActivity?: { __typename: 'DeprecateVariantActivity', createdAt: any, user: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, complexMolecularProfileDeprecationActivity?: { __typename: 'DeprecateComplexMolecularProfileActivity', createdAt: any, user: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined }, parsedNote: Array<{ __typename: 'CommentTagSegment', entityId: number, displayName: string, tagType: TaggableEntity, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlagged', entityId: number, displayName: string, tagType: TaggableEntity, flagged: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlaggedAndDeprecated', entityId: number, displayName: string, tagType: TaggableEntity, flagged: boolean, deprecated: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlaggedAndWithStatus', entityId: number, displayName: string, tagType: TaggableEntity, status: EvidenceStatus, flagged: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTextSegment', text: string } | { __typename: 'User', id: number, username: string, displayName: string, name?: string | undefined, role: UserRole, profileImagePath?: string | undefined, organizations: Array<{ __typename: 'Organization', id: number, name: string, profileImagePath?: string | undefined }> }> } | undefined }; type MolecularProfileParsedName_Feature_Fragment = { __typename: 'Feature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean }; @@ -9681,7 +9682,7 @@ type VariantMolecularProfileCardFields_FactorVariant_Fragment = { __typename: 'F type VariantMolecularProfileCardFields_FusionVariant_Fragment = { __typename: 'FusionVariant', id: number, name: string, link: string, deprecated: boolean, flagged: boolean, variantAliases: Array, viccCompliantName: string, feature: { __typename: 'Feature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean }, molecularProfiles: { __typename: 'MolecularProfileConnection', totalCount: number, nodes: Array<{ __typename: 'MolecularProfile', id: number, link: string, name: string, deprecated: boolean, flagged: boolean }> }, variantTypes: Array<{ __typename: 'VariantType', id: number, link: string, soid: string, name: string }>, fusion: { __typename: 'Fusion', fivePrimePartnerStatus: FusionPartnerStatus, threePrimePartnerStatus: FusionPartnerStatus, fivePrimeGene?: { __typename: 'Gene', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined, threePrimeGene?: { __typename: 'Gene', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined }, fivePrimeCoordinates?: { __typename: 'VariantCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, referenceBases?: string | undefined, variantBases?: string | undefined, coordinateType: VariantCoordinateType } | undefined, threePrimeCoordinates?: { __typename: 'VariantCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, referenceBases?: string | undefined, variantBases?: string | undefined, coordinateType: VariantCoordinateType } | undefined, fivePrimeStartExonCoordinates?: { __typename: 'ExonCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, exon?: number | undefined, exonOffset?: number | undefined, exonOffsetDirection?: Direction | undefined, ensemblId?: string | undefined, strand?: Direction | undefined, coordinateType: ExonCoordinateType } | undefined, fivePrimeEndExonCoordinates?: { __typename: 'ExonCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, exon?: number | undefined, exonOffset?: number | undefined, exonOffsetDirection?: Direction | undefined, ensemblId?: string | undefined, strand?: Direction | undefined, coordinateType: ExonCoordinateType } | undefined, threePrimeStartExonCoordinates?: { __typename: 'ExonCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, exon?: number | undefined, exonOffset?: number | undefined, exonOffsetDirection?: Direction | undefined, ensemblId?: string | undefined, strand?: Direction | undefined, coordinateType: ExonCoordinateType } | undefined, threePrimeEndExonCoordinates?: { __typename: 'ExonCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, exon?: number | undefined, exonOffset?: number | undefined, exonOffsetDirection?: Direction | undefined, ensemblId?: string | undefined, strand?: Direction | undefined, coordinateType: ExonCoordinateType } | undefined }; -type VariantMolecularProfileCardFields_GeneVariant_Fragment = { __typename: 'GeneVariant', id: number, name: string, link: string, deprecated: boolean, flagged: boolean, variantAliases: Array, alleleRegistryId?: string | undefined, openCravatUrl?: string | undefined, maneSelectTranscript?: string | undefined, hgvsDescriptions: Array, clinvarIds: Array, feature: { __typename: 'Feature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean }, molecularProfiles: { __typename: 'MolecularProfileConnection', totalCount: number, nodes: Array<{ __typename: 'MolecularProfile', id: number, link: string, name: string, deprecated: boolean, flagged: boolean }> }, variantTypes: Array<{ __typename: 'VariantType', id: number, link: string, soid: string, name: string }>, coordinates?: { __typename: 'VariantCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, referenceBases?: string | undefined, variantBases?: string | undefined, coordinateType: VariantCoordinateType } | undefined, myVariantInfo?: { __typename: 'MyVariantInfo', myVariantInfoId: string, caddConsequence: Array, caddDetail: Array, caddScore?: number | undefined, caddPhred?: number | undefined, clinvarClinicalSignificance: Array, clinvarHgvsCoding: Array, clinvarHgvsGenomic: Array, clinvarHgvsNonCoding: Array, clinvarHgvsProtein: Array, clinvarId?: number | undefined, clinvarOmim?: string | undefined, cosmicId?: string | undefined, dbnsfpInterproDomain: Array, dbsnpRsid?: string | undefined, eglClass?: string | undefined, eglHgvs: Array, eglProtein?: string | undefined, eglTranscript?: string | undefined, exacAlleleCount?: number | undefined, exacAlleleFrequency?: number | undefined, exacAlleleNumber?: number | undefined, fathmmMklPrediction?: string | undefined, fathmmMklScore?: number | undefined, fathmmPrediction: Array, fathmmScore: Array, fitconsScore?: number | undefined, gerp?: number | undefined, gnomadExomeAlleleCount?: number | undefined, gnomadExomeAlleleFrequency?: number | undefined, gnomadExomeAlleleNumber?: number | undefined, gnomadExomeFilter?: string | undefined, gnomadGenomeAlleleCount?: number | undefined, gnomadGenomeAlleleFrequency?: number | undefined, gnomadGenomeAlleleNumber?: number | undefined, gnomadGenomeFilter?: string | undefined, lrtPrediction?: string | undefined, lrtScore?: number | undefined, metalrPrediction?: string | undefined, metalrScore?: number | undefined, metasvmPrediction?: string | undefined, metasvmScore?: number | undefined, mutationassessorPrediction: Array, mutationassessorScore: Array, mutationtasterPrediction: Array, mutationtasterScore: Array, phastcons100way?: number | undefined, phastcons30way?: number | undefined, phyloP100way?: number | undefined, phyloP30way?: number | undefined, polyphen2HdivPrediction: Array, polyphen2HdivScore: Array, polyphen2HvarPrediction: Array, polyphen2HvarScore: Array, proveanPrediction: Array, proveanScore: Array, revelScore?: Array | undefined, siftPrediction: Array, siftScore: Array, siphy?: number | undefined, snpeffSnpEffect: Array, snpeffSnpImpact: Array } | undefined }; +type VariantMolecularProfileCardFields_GeneVariant_Fragment = { __typename: 'GeneVariant', id: number, name: string, link: string, deprecated: boolean, flagged: boolean, variantAliases: Array, alleleRegistryId?: string | undefined, openCravatUrl?: string | undefined, maneSelectTranscript?: string | undefined, hgvsDescriptions: Array, clinvarIds: Array, openCravatAnnotations?: any | undefined, feature: { __typename: 'Feature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean }, molecularProfiles: { __typename: 'MolecularProfileConnection', totalCount: number, nodes: Array<{ __typename: 'MolecularProfile', id: number, link: string, name: string, deprecated: boolean, flagged: boolean }> }, variantTypes: Array<{ __typename: 'VariantType', id: number, link: string, soid: string, name: string }>, coordinates?: { __typename: 'VariantCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, referenceBases?: string | undefined, variantBases?: string | undefined, coordinateType: VariantCoordinateType } | undefined, myVariantInfo?: { __typename: 'MyVariantInfo', myVariantInfoId: string, caddConsequence: Array, caddDetail: Array, caddScore?: number | undefined, caddPhred?: number | undefined, clinvarClinicalSignificance: Array, clinvarHgvsCoding: Array, clinvarHgvsGenomic: Array, clinvarHgvsNonCoding: Array, clinvarHgvsProtein: Array, clinvarId?: number | undefined, clinvarOmim?: string | undefined, cosmicId?: string | undefined, dbnsfpInterproDomain: Array, dbsnpRsid?: string | undefined, eglClass?: string | undefined, eglHgvs: Array, eglProtein?: string | undefined, eglTranscript?: string | undefined, exacAlleleCount?: number | undefined, exacAlleleFrequency?: number | undefined, exacAlleleNumber?: number | undefined, fathmmMklPrediction?: string | undefined, fathmmMklScore?: number | undefined, fathmmPrediction: Array, fathmmScore: Array, fitconsScore?: number | undefined, gerp?: number | undefined, gnomadExomeAlleleCount?: number | undefined, gnomadExomeAlleleFrequency?: number | undefined, gnomadExomeAlleleNumber?: number | undefined, gnomadExomeFilter?: string | undefined, gnomadGenomeAlleleCount?: number | undefined, gnomadGenomeAlleleFrequency?: number | undefined, gnomadGenomeAlleleNumber?: number | undefined, gnomadGenomeFilter?: string | undefined, lrtPrediction?: string | undefined, lrtScore?: number | undefined, metalrPrediction?: string | undefined, metalrScore?: number | undefined, metasvmPrediction?: string | undefined, metasvmScore?: number | undefined, mutationassessorPrediction: Array, mutationassessorScore: Array, mutationtasterPrediction: Array, mutationtasterScore: Array, phastcons100way?: number | undefined, phastcons30way?: number | undefined, phyloP100way?: number | undefined, phyloP30way?: number | undefined, polyphen2HdivPrediction: Array, polyphen2HdivScore: Array, polyphen2HvarPrediction: Array, polyphen2HvarScore: Array, proveanPrediction: Array, proveanScore: Array, revelScore?: Array | undefined, siftPrediction: Array, siftScore: Array, siphy?: number | undefined, snpeffSnpEffect: Array, snpeffSnpImpact: Array } | undefined }; type VariantMolecularProfileCardFields_Variant_Fragment = { __typename: 'Variant', id: number, name: string, link: string, deprecated: boolean, flagged: boolean, variantAliases: Array, feature: { __typename: 'Feature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean }, molecularProfiles: { __typename: 'MolecularProfileConnection', totalCount: number, nodes: Array<{ __typename: 'MolecularProfile', id: number, link: string, name: string, deprecated: boolean, flagged: boolean }> }, variantTypes: Array<{ __typename: 'VariantType', id: number, link: string, soid: string, name: string }> }; @@ -9889,13 +9890,13 @@ export type VariantSummaryQueryVariables = Exact<{ }>; -export type VariantSummaryQuery = { __typename: 'Query', variant?: { __typename: 'FactorVariant', id: number, name: string, variantAliases: Array, ncitId?: string | undefined, feature: { __typename: 'Feature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean }, variantTypes: Array<{ __typename: 'VariantType', id: number, link: string, soid: string, name: string }>, flags: { __typename: 'FlagConnection', totalCount: number }, revisions: { __typename: 'RevisionConnection', totalCount: number }, comments: { __typename: 'CommentConnection', totalCount: number }, lastSubmittedRevisionEvent?: { __typename: 'Event', originatingUser: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, lastAcceptedRevisionEvent?: { __typename: 'Event', originatingUser: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, creationActivity?: { __typename: 'CreateVariantActivity', createdAt: any, user: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, deprecationActivity?: { __typename: 'DeprecateVariantActivity', createdAt: any, user: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined }, parsedNote: Array<{ __typename: 'CommentTagSegment', entityId: number, displayName: string, tagType: TaggableEntity, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlagged', entityId: number, displayName: string, tagType: TaggableEntity, flagged: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlaggedAndDeprecated', entityId: number, displayName: string, tagType: TaggableEntity, flagged: boolean, deprecated: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlaggedAndWithStatus', entityId: number, displayName: string, tagType: TaggableEntity, status: EvidenceStatus, flagged: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTextSegment', text: string } | { __typename: 'User', id: number, username: string, displayName: string, name?: string | undefined, role: UserRole, profileImagePath?: string | undefined, organizations: Array<{ __typename: 'Organization', id: number, name: string, profileImagePath?: string | undefined }> }> } | undefined, ncitDetails?: { __typename: 'NcitDetails', synonyms: Array<{ __typename: 'NcitSynonym', name: string, source: string }>, definitions: Array<{ __typename: 'NcitDefinition', definition: string, source: string }> } | undefined } | { __typename: 'FusionVariant', id: number, name: string, variantAliases: Array, viccCompliantName: string, feature: { __typename: 'Feature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean }, variantTypes: Array<{ __typename: 'VariantType', id: number, link: string, soid: string, name: string }>, flags: { __typename: 'FlagConnection', totalCount: number }, revisions: { __typename: 'RevisionConnection', totalCount: number }, comments: { __typename: 'CommentConnection', totalCount: number }, lastSubmittedRevisionEvent?: { __typename: 'Event', originatingUser: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, lastAcceptedRevisionEvent?: { __typename: 'Event', originatingUser: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, creationActivity?: { __typename: 'CreateVariantActivity', createdAt: any, user: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, deprecationActivity?: { __typename: 'DeprecateVariantActivity', createdAt: any, user: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined }, parsedNote: Array<{ __typename: 'CommentTagSegment', entityId: number, displayName: string, tagType: TaggableEntity, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlagged', entityId: number, displayName: string, tagType: TaggableEntity, flagged: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlaggedAndDeprecated', entityId: number, displayName: string, tagType: TaggableEntity, flagged: boolean, deprecated: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlaggedAndWithStatus', entityId: number, displayName: string, tagType: TaggableEntity, status: EvidenceStatus, flagged: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTextSegment', text: string } | { __typename: 'User', id: number, username: string, displayName: string, name?: string | undefined, role: UserRole, profileImagePath?: string | undefined, organizations: Array<{ __typename: 'Organization', id: number, name: string, profileImagePath?: string | undefined }> }> } | undefined, fusion: { __typename: 'Fusion', fivePrimePartnerStatus: FusionPartnerStatus, threePrimePartnerStatus: FusionPartnerStatus, fivePrimeGene?: { __typename: 'Gene', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined, threePrimeGene?: { __typename: 'Gene', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined }, fivePrimeCoordinates?: { __typename: 'VariantCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, referenceBases?: string | undefined, variantBases?: string | undefined, coordinateType: VariantCoordinateType } | undefined, threePrimeCoordinates?: { __typename: 'VariantCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, referenceBases?: string | undefined, variantBases?: string | undefined, coordinateType: VariantCoordinateType } | undefined, fivePrimeStartExonCoordinates?: { __typename: 'ExonCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, exon?: number | undefined, exonOffset?: number | undefined, exonOffsetDirection?: Direction | undefined, ensemblId?: string | undefined, strand?: Direction | undefined, coordinateType: ExonCoordinateType } | undefined, fivePrimeEndExonCoordinates?: { __typename: 'ExonCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, exon?: number | undefined, exonOffset?: number | undefined, exonOffsetDirection?: Direction | undefined, ensemblId?: string | undefined, strand?: Direction | undefined, coordinateType: ExonCoordinateType } | undefined, threePrimeStartExonCoordinates?: { __typename: 'ExonCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, exon?: number | undefined, exonOffset?: number | undefined, exonOffsetDirection?: Direction | undefined, ensemblId?: string | undefined, strand?: Direction | undefined, coordinateType: ExonCoordinateType } | undefined, threePrimeEndExonCoordinates?: { __typename: 'ExonCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, exon?: number | undefined, exonOffset?: number | undefined, exonOffsetDirection?: Direction | undefined, ensemblId?: string | undefined, strand?: Direction | undefined, coordinateType: ExonCoordinateType } | undefined } | { __typename: 'GeneVariant', id: number, name: string, variantAliases: Array, alleleRegistryId?: string | undefined, openCravatUrl?: string | undefined, maneSelectTranscript?: string | undefined, hgvsDescriptions: Array, clinvarIds: Array, feature: { __typename: 'Feature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean }, variantTypes: Array<{ __typename: 'VariantType', id: number, link: string, soid: string, name: string }>, flags: { __typename: 'FlagConnection', totalCount: number }, revisions: { __typename: 'RevisionConnection', totalCount: number }, comments: { __typename: 'CommentConnection', totalCount: number }, lastSubmittedRevisionEvent?: { __typename: 'Event', originatingUser: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, lastAcceptedRevisionEvent?: { __typename: 'Event', originatingUser: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, creationActivity?: { __typename: 'CreateVariantActivity', createdAt: any, user: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, deprecationActivity?: { __typename: 'DeprecateVariantActivity', createdAt: any, user: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined }, parsedNote: Array<{ __typename: 'CommentTagSegment', entityId: number, displayName: string, tagType: TaggableEntity, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlagged', entityId: number, displayName: string, tagType: TaggableEntity, flagged: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlaggedAndDeprecated', entityId: number, displayName: string, tagType: TaggableEntity, flagged: boolean, deprecated: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlaggedAndWithStatus', entityId: number, displayName: string, tagType: TaggableEntity, status: EvidenceStatus, flagged: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTextSegment', text: string } | { __typename: 'User', id: number, username: string, displayName: string, name?: string | undefined, role: UserRole, profileImagePath?: string | undefined, organizations: Array<{ __typename: 'Organization', id: number, name: string, profileImagePath?: string | undefined }> }> } | undefined, coordinates?: { __typename: 'VariantCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, referenceBases?: string | undefined, variantBases?: string | undefined, coordinateType: VariantCoordinateType } | undefined, myVariantInfo?: { __typename: 'MyVariantInfo', myVariantInfoId: string, caddConsequence: Array, caddDetail: Array, caddScore?: number | undefined, caddPhred?: number | undefined, clinvarClinicalSignificance: Array, clinvarHgvsCoding: Array, clinvarHgvsGenomic: Array, clinvarHgvsNonCoding: Array, clinvarHgvsProtein: Array, clinvarId?: number | undefined, clinvarOmim?: string | undefined, cosmicId?: string | undefined, dbnsfpInterproDomain: Array, dbsnpRsid?: string | undefined, eglClass?: string | undefined, eglHgvs: Array, eglProtein?: string | undefined, eglTranscript?: string | undefined, exacAlleleCount?: number | undefined, exacAlleleFrequency?: number | undefined, exacAlleleNumber?: number | undefined, fathmmMklPrediction?: string | undefined, fathmmMklScore?: number | undefined, fathmmPrediction: Array, fathmmScore: Array, fitconsScore?: number | undefined, gerp?: number | undefined, gnomadExomeAlleleCount?: number | undefined, gnomadExomeAlleleFrequency?: number | undefined, gnomadExomeAlleleNumber?: number | undefined, gnomadExomeFilter?: string | undefined, gnomadGenomeAlleleCount?: number | undefined, gnomadGenomeAlleleFrequency?: number | undefined, gnomadGenomeAlleleNumber?: number | undefined, gnomadGenomeFilter?: string | undefined, lrtPrediction?: string | undefined, lrtScore?: number | undefined, metalrPrediction?: string | undefined, metalrScore?: number | undefined, metasvmPrediction?: string | undefined, metasvmScore?: number | undefined, mutationassessorPrediction: Array, mutationassessorScore: Array, mutationtasterPrediction: Array, mutationtasterScore: Array, phastcons100way?: number | undefined, phastcons30way?: number | undefined, phyloP100way?: number | undefined, phyloP30way?: number | undefined, polyphen2HdivPrediction: Array, polyphen2HdivScore: Array, polyphen2HvarPrediction: Array, polyphen2HvarScore: Array, proveanPrediction: Array, proveanScore: Array, revelScore?: Array | undefined, siftPrediction: Array, siftScore: Array, siphy?: number | undefined, snpeffSnpEffect: Array, snpeffSnpImpact: Array } | undefined } | { __typename: 'Variant', id: number, name: string, variantAliases: Array, feature: { __typename: 'Feature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean }, variantTypes: Array<{ __typename: 'VariantType', id: number, link: string, soid: string, name: string }>, flags: { __typename: 'FlagConnection', totalCount: number }, revisions: { __typename: 'RevisionConnection', totalCount: number }, comments: { __typename: 'CommentConnection', totalCount: number }, lastSubmittedRevisionEvent?: { __typename: 'Event', originatingUser: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, lastAcceptedRevisionEvent?: { __typename: 'Event', originatingUser: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, creationActivity?: { __typename: 'CreateVariantActivity', createdAt: any, user: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, deprecationActivity?: { __typename: 'DeprecateVariantActivity', createdAt: any, user: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined }, parsedNote: Array<{ __typename: 'CommentTagSegment', entityId: number, displayName: string, tagType: TaggableEntity, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlagged', entityId: number, displayName: string, tagType: TaggableEntity, flagged: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlaggedAndDeprecated', entityId: number, displayName: string, tagType: TaggableEntity, flagged: boolean, deprecated: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlaggedAndWithStatus', entityId: number, displayName: string, tagType: TaggableEntity, status: EvidenceStatus, flagged: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTextSegment', text: string } | { __typename: 'User', id: number, username: string, displayName: string, name?: string | undefined, role: UserRole, profileImagePath?: string | undefined, organizations: Array<{ __typename: 'Organization', id: number, name: string, profileImagePath?: string | undefined }> }> } | undefined } | undefined }; +export type VariantSummaryQuery = { __typename: 'Query', variant?: { __typename: 'FactorVariant', id: number, name: string, variantAliases: Array, ncitId?: string | undefined, feature: { __typename: 'Feature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean }, variantTypes: Array<{ __typename: 'VariantType', id: number, link: string, soid: string, name: string }>, flags: { __typename: 'FlagConnection', totalCount: number }, revisions: { __typename: 'RevisionConnection', totalCount: number }, comments: { __typename: 'CommentConnection', totalCount: number }, lastSubmittedRevisionEvent?: { __typename: 'Event', originatingUser: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, lastAcceptedRevisionEvent?: { __typename: 'Event', originatingUser: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, creationActivity?: { __typename: 'CreateVariantActivity', createdAt: any, user: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, deprecationActivity?: { __typename: 'DeprecateVariantActivity', createdAt: any, user: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined }, parsedNote: Array<{ __typename: 'CommentTagSegment', entityId: number, displayName: string, tagType: TaggableEntity, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlagged', entityId: number, displayName: string, tagType: TaggableEntity, flagged: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlaggedAndDeprecated', entityId: number, displayName: string, tagType: TaggableEntity, flagged: boolean, deprecated: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlaggedAndWithStatus', entityId: number, displayName: string, tagType: TaggableEntity, status: EvidenceStatus, flagged: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTextSegment', text: string } | { __typename: 'User', id: number, username: string, displayName: string, name?: string | undefined, role: UserRole, profileImagePath?: string | undefined, organizations: Array<{ __typename: 'Organization', id: number, name: string, profileImagePath?: string | undefined }> }> } | undefined, ncitDetails?: { __typename: 'NcitDetails', synonyms: Array<{ __typename: 'NcitSynonym', name: string, source: string }>, definitions: Array<{ __typename: 'NcitDefinition', definition: string, source: string }> } | undefined } | { __typename: 'FusionVariant', id: number, name: string, variantAliases: Array, viccCompliantName: string, feature: { __typename: 'Feature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean }, variantTypes: Array<{ __typename: 'VariantType', id: number, link: string, soid: string, name: string }>, flags: { __typename: 'FlagConnection', totalCount: number }, revisions: { __typename: 'RevisionConnection', totalCount: number }, comments: { __typename: 'CommentConnection', totalCount: number }, lastSubmittedRevisionEvent?: { __typename: 'Event', originatingUser: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, lastAcceptedRevisionEvent?: { __typename: 'Event', originatingUser: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, creationActivity?: { __typename: 'CreateVariantActivity', createdAt: any, user: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, deprecationActivity?: { __typename: 'DeprecateVariantActivity', createdAt: any, user: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined }, parsedNote: Array<{ __typename: 'CommentTagSegment', entityId: number, displayName: string, tagType: TaggableEntity, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlagged', entityId: number, displayName: string, tagType: TaggableEntity, flagged: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlaggedAndDeprecated', entityId: number, displayName: string, tagType: TaggableEntity, flagged: boolean, deprecated: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlaggedAndWithStatus', entityId: number, displayName: string, tagType: TaggableEntity, status: EvidenceStatus, flagged: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTextSegment', text: string } | { __typename: 'User', id: number, username: string, displayName: string, name?: string | undefined, role: UserRole, profileImagePath?: string | undefined, organizations: Array<{ __typename: 'Organization', id: number, name: string, profileImagePath?: string | undefined }> }> } | undefined, fusion: { __typename: 'Fusion', fivePrimePartnerStatus: FusionPartnerStatus, threePrimePartnerStatus: FusionPartnerStatus, fivePrimeGene?: { __typename: 'Gene', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined, threePrimeGene?: { __typename: 'Gene', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined }, fivePrimeCoordinates?: { __typename: 'VariantCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, referenceBases?: string | undefined, variantBases?: string | undefined, coordinateType: VariantCoordinateType } | undefined, threePrimeCoordinates?: { __typename: 'VariantCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, referenceBases?: string | undefined, variantBases?: string | undefined, coordinateType: VariantCoordinateType } | undefined, fivePrimeStartExonCoordinates?: { __typename: 'ExonCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, exon?: number | undefined, exonOffset?: number | undefined, exonOffsetDirection?: Direction | undefined, ensemblId?: string | undefined, strand?: Direction | undefined, coordinateType: ExonCoordinateType } | undefined, fivePrimeEndExonCoordinates?: { __typename: 'ExonCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, exon?: number | undefined, exonOffset?: number | undefined, exonOffsetDirection?: Direction | undefined, ensemblId?: string | undefined, strand?: Direction | undefined, coordinateType: ExonCoordinateType } | undefined, threePrimeStartExonCoordinates?: { __typename: 'ExonCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, exon?: number | undefined, exonOffset?: number | undefined, exonOffsetDirection?: Direction | undefined, ensemblId?: string | undefined, strand?: Direction | undefined, coordinateType: ExonCoordinateType } | undefined, threePrimeEndExonCoordinates?: { __typename: 'ExonCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, exon?: number | undefined, exonOffset?: number | undefined, exonOffsetDirection?: Direction | undefined, ensemblId?: string | undefined, strand?: Direction | undefined, coordinateType: ExonCoordinateType } | undefined } | { __typename: 'GeneVariant', id: number, name: string, variantAliases: Array, alleleRegistryId?: string | undefined, openCravatUrl?: string | undefined, maneSelectTranscript?: string | undefined, hgvsDescriptions: Array, clinvarIds: Array, openCravatAnnotations?: any | undefined, feature: { __typename: 'Feature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean }, variantTypes: Array<{ __typename: 'VariantType', id: number, link: string, soid: string, name: string }>, flags: { __typename: 'FlagConnection', totalCount: number }, revisions: { __typename: 'RevisionConnection', totalCount: number }, comments: { __typename: 'CommentConnection', totalCount: number }, lastSubmittedRevisionEvent?: { __typename: 'Event', originatingUser: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, lastAcceptedRevisionEvent?: { __typename: 'Event', originatingUser: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, creationActivity?: { __typename: 'CreateVariantActivity', createdAt: any, user: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, deprecationActivity?: { __typename: 'DeprecateVariantActivity', createdAt: any, user: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined }, parsedNote: Array<{ __typename: 'CommentTagSegment', entityId: number, displayName: string, tagType: TaggableEntity, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlagged', entityId: number, displayName: string, tagType: TaggableEntity, flagged: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlaggedAndDeprecated', entityId: number, displayName: string, tagType: TaggableEntity, flagged: boolean, deprecated: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlaggedAndWithStatus', entityId: number, displayName: string, tagType: TaggableEntity, status: EvidenceStatus, flagged: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTextSegment', text: string } | { __typename: 'User', id: number, username: string, displayName: string, name?: string | undefined, role: UserRole, profileImagePath?: string | undefined, organizations: Array<{ __typename: 'Organization', id: number, name: string, profileImagePath?: string | undefined }> }> } | undefined, coordinates?: { __typename: 'VariantCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, referenceBases?: string | undefined, variantBases?: string | undefined, coordinateType: VariantCoordinateType } | undefined, myVariantInfo?: { __typename: 'MyVariantInfo', myVariantInfoId: string, caddConsequence: Array, caddDetail: Array, caddScore?: number | undefined, caddPhred?: number | undefined, clinvarClinicalSignificance: Array, clinvarHgvsCoding: Array, clinvarHgvsGenomic: Array, clinvarHgvsNonCoding: Array, clinvarHgvsProtein: Array, clinvarId?: number | undefined, clinvarOmim?: string | undefined, cosmicId?: string | undefined, dbnsfpInterproDomain: Array, dbsnpRsid?: string | undefined, eglClass?: string | undefined, eglHgvs: Array, eglProtein?: string | undefined, eglTranscript?: string | undefined, exacAlleleCount?: number | undefined, exacAlleleFrequency?: number | undefined, exacAlleleNumber?: number | undefined, fathmmMklPrediction?: string | undefined, fathmmMklScore?: number | undefined, fathmmPrediction: Array, fathmmScore: Array, fitconsScore?: number | undefined, gerp?: number | undefined, gnomadExomeAlleleCount?: number | undefined, gnomadExomeAlleleFrequency?: number | undefined, gnomadExomeAlleleNumber?: number | undefined, gnomadExomeFilter?: string | undefined, gnomadGenomeAlleleCount?: number | undefined, gnomadGenomeAlleleFrequency?: number | undefined, gnomadGenomeAlleleNumber?: number | undefined, gnomadGenomeFilter?: string | undefined, lrtPrediction?: string | undefined, lrtScore?: number | undefined, metalrPrediction?: string | undefined, metalrScore?: number | undefined, metasvmPrediction?: string | undefined, metasvmScore?: number | undefined, mutationassessorPrediction: Array, mutationassessorScore: Array, mutationtasterPrediction: Array, mutationtasterScore: Array, phastcons100way?: number | undefined, phastcons30way?: number | undefined, phyloP100way?: number | undefined, phyloP30way?: number | undefined, polyphen2HdivPrediction: Array, polyphen2HdivScore: Array, polyphen2HvarPrediction: Array, polyphen2HvarScore: Array, proveanPrediction: Array, proveanScore: Array, revelScore?: Array | undefined, siftPrediction: Array, siftScore: Array, siphy?: number | undefined, snpeffSnpEffect: Array, snpeffSnpImpact: Array } | undefined } | { __typename: 'Variant', id: number, name: string, variantAliases: Array, feature: { __typename: 'Feature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean }, variantTypes: Array<{ __typename: 'VariantType', id: number, link: string, soid: string, name: string }>, flags: { __typename: 'FlagConnection', totalCount: number }, revisions: { __typename: 'RevisionConnection', totalCount: number }, comments: { __typename: 'CommentConnection', totalCount: number }, lastSubmittedRevisionEvent?: { __typename: 'Event', originatingUser: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, lastAcceptedRevisionEvent?: { __typename: 'Event', originatingUser: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, creationActivity?: { __typename: 'CreateVariantActivity', createdAt: any, user: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, deprecationActivity?: { __typename: 'DeprecateVariantActivity', createdAt: any, user: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined }, parsedNote: Array<{ __typename: 'CommentTagSegment', entityId: number, displayName: string, tagType: TaggableEntity, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlagged', entityId: number, displayName: string, tagType: TaggableEntity, flagged: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlaggedAndDeprecated', entityId: number, displayName: string, tagType: TaggableEntity, flagged: boolean, deprecated: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlaggedAndWithStatus', entityId: number, displayName: string, tagType: TaggableEntity, status: EvidenceStatus, flagged: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTextSegment', text: string } | { __typename: 'User', id: number, username: string, displayName: string, name?: string | undefined, role: UserRole, profileImagePath?: string | undefined, organizations: Array<{ __typename: 'Organization', id: number, name: string, profileImagePath?: string | undefined }> }> } | undefined } | undefined }; type VariantSummaryFields_FactorVariant_Fragment = { __typename: 'FactorVariant', id: number, name: string, variantAliases: Array, ncitId?: string | undefined, feature: { __typename: 'Feature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean }, variantTypes: Array<{ __typename: 'VariantType', id: number, link: string, soid: string, name: string }>, flags: { __typename: 'FlagConnection', totalCount: number }, revisions: { __typename: 'RevisionConnection', totalCount: number }, comments: { __typename: 'CommentConnection', totalCount: number }, lastSubmittedRevisionEvent?: { __typename: 'Event', originatingUser: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, lastAcceptedRevisionEvent?: { __typename: 'Event', originatingUser: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, creationActivity?: { __typename: 'CreateVariantActivity', createdAt: any, user: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, deprecationActivity?: { __typename: 'DeprecateVariantActivity', createdAt: any, user: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined }, parsedNote: Array<{ __typename: 'CommentTagSegment', entityId: number, displayName: string, tagType: TaggableEntity, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlagged', entityId: number, displayName: string, tagType: TaggableEntity, flagged: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlaggedAndDeprecated', entityId: number, displayName: string, tagType: TaggableEntity, flagged: boolean, deprecated: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlaggedAndWithStatus', entityId: number, displayName: string, tagType: TaggableEntity, status: EvidenceStatus, flagged: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTextSegment', text: string } | { __typename: 'User', id: number, username: string, displayName: string, name?: string | undefined, role: UserRole, profileImagePath?: string | undefined, organizations: Array<{ __typename: 'Organization', id: number, name: string, profileImagePath?: string | undefined }> }> } | undefined, ncitDetails?: { __typename: 'NcitDetails', synonyms: Array<{ __typename: 'NcitSynonym', name: string, source: string }>, definitions: Array<{ __typename: 'NcitDefinition', definition: string, source: string }> } | undefined }; type VariantSummaryFields_FusionVariant_Fragment = { __typename: 'FusionVariant', id: number, name: string, variantAliases: Array, viccCompliantName: string, feature: { __typename: 'Feature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean }, variantTypes: Array<{ __typename: 'VariantType', id: number, link: string, soid: string, name: string }>, flags: { __typename: 'FlagConnection', totalCount: number }, revisions: { __typename: 'RevisionConnection', totalCount: number }, comments: { __typename: 'CommentConnection', totalCount: number }, lastSubmittedRevisionEvent?: { __typename: 'Event', originatingUser: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, lastAcceptedRevisionEvent?: { __typename: 'Event', originatingUser: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, creationActivity?: { __typename: 'CreateVariantActivity', createdAt: any, user: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, deprecationActivity?: { __typename: 'DeprecateVariantActivity', createdAt: any, user: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined }, parsedNote: Array<{ __typename: 'CommentTagSegment', entityId: number, displayName: string, tagType: TaggableEntity, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlagged', entityId: number, displayName: string, tagType: TaggableEntity, flagged: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlaggedAndDeprecated', entityId: number, displayName: string, tagType: TaggableEntity, flagged: boolean, deprecated: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlaggedAndWithStatus', entityId: number, displayName: string, tagType: TaggableEntity, status: EvidenceStatus, flagged: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTextSegment', text: string } | { __typename: 'User', id: number, username: string, displayName: string, name?: string | undefined, role: UserRole, profileImagePath?: string | undefined, organizations: Array<{ __typename: 'Organization', id: number, name: string, profileImagePath?: string | undefined }> }> } | undefined, fusion: { __typename: 'Fusion', fivePrimePartnerStatus: FusionPartnerStatus, threePrimePartnerStatus: FusionPartnerStatus, fivePrimeGene?: { __typename: 'Gene', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined, threePrimeGene?: { __typename: 'Gene', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined }, fivePrimeCoordinates?: { __typename: 'VariantCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, referenceBases?: string | undefined, variantBases?: string | undefined, coordinateType: VariantCoordinateType } | undefined, threePrimeCoordinates?: { __typename: 'VariantCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, referenceBases?: string | undefined, variantBases?: string | undefined, coordinateType: VariantCoordinateType } | undefined, fivePrimeStartExonCoordinates?: { __typename: 'ExonCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, exon?: number | undefined, exonOffset?: number | undefined, exonOffsetDirection?: Direction | undefined, ensemblId?: string | undefined, strand?: Direction | undefined, coordinateType: ExonCoordinateType } | undefined, fivePrimeEndExonCoordinates?: { __typename: 'ExonCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, exon?: number | undefined, exonOffset?: number | undefined, exonOffsetDirection?: Direction | undefined, ensemblId?: string | undefined, strand?: Direction | undefined, coordinateType: ExonCoordinateType } | undefined, threePrimeStartExonCoordinates?: { __typename: 'ExonCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, exon?: number | undefined, exonOffset?: number | undefined, exonOffsetDirection?: Direction | undefined, ensemblId?: string | undefined, strand?: Direction | undefined, coordinateType: ExonCoordinateType } | undefined, threePrimeEndExonCoordinates?: { __typename: 'ExonCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, exon?: number | undefined, exonOffset?: number | undefined, exonOffsetDirection?: Direction | undefined, ensemblId?: string | undefined, strand?: Direction | undefined, coordinateType: ExonCoordinateType } | undefined }; -type VariantSummaryFields_GeneVariant_Fragment = { __typename: 'GeneVariant', id: number, name: string, variantAliases: Array, alleleRegistryId?: string | undefined, openCravatUrl?: string | undefined, maneSelectTranscript?: string | undefined, hgvsDescriptions: Array, clinvarIds: Array, feature: { __typename: 'Feature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean }, variantTypes: Array<{ __typename: 'VariantType', id: number, link: string, soid: string, name: string }>, flags: { __typename: 'FlagConnection', totalCount: number }, revisions: { __typename: 'RevisionConnection', totalCount: number }, comments: { __typename: 'CommentConnection', totalCount: number }, lastSubmittedRevisionEvent?: { __typename: 'Event', originatingUser: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, lastAcceptedRevisionEvent?: { __typename: 'Event', originatingUser: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, creationActivity?: { __typename: 'CreateVariantActivity', createdAt: any, user: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, deprecationActivity?: { __typename: 'DeprecateVariantActivity', createdAt: any, user: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined }, parsedNote: Array<{ __typename: 'CommentTagSegment', entityId: number, displayName: string, tagType: TaggableEntity, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlagged', entityId: number, displayName: string, tagType: TaggableEntity, flagged: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlaggedAndDeprecated', entityId: number, displayName: string, tagType: TaggableEntity, flagged: boolean, deprecated: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlaggedAndWithStatus', entityId: number, displayName: string, tagType: TaggableEntity, status: EvidenceStatus, flagged: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTextSegment', text: string } | { __typename: 'User', id: number, username: string, displayName: string, name?: string | undefined, role: UserRole, profileImagePath?: string | undefined, organizations: Array<{ __typename: 'Organization', id: number, name: string, profileImagePath?: string | undefined }> }> } | undefined, coordinates?: { __typename: 'VariantCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, referenceBases?: string | undefined, variantBases?: string | undefined, coordinateType: VariantCoordinateType } | undefined, myVariantInfo?: { __typename: 'MyVariantInfo', myVariantInfoId: string, caddConsequence: Array, caddDetail: Array, caddScore?: number | undefined, caddPhred?: number | undefined, clinvarClinicalSignificance: Array, clinvarHgvsCoding: Array, clinvarHgvsGenomic: Array, clinvarHgvsNonCoding: Array, clinvarHgvsProtein: Array, clinvarId?: number | undefined, clinvarOmim?: string | undefined, cosmicId?: string | undefined, dbnsfpInterproDomain: Array, dbsnpRsid?: string | undefined, eglClass?: string | undefined, eglHgvs: Array, eglProtein?: string | undefined, eglTranscript?: string | undefined, exacAlleleCount?: number | undefined, exacAlleleFrequency?: number | undefined, exacAlleleNumber?: number | undefined, fathmmMklPrediction?: string | undefined, fathmmMklScore?: number | undefined, fathmmPrediction: Array, fathmmScore: Array, fitconsScore?: number | undefined, gerp?: number | undefined, gnomadExomeAlleleCount?: number | undefined, gnomadExomeAlleleFrequency?: number | undefined, gnomadExomeAlleleNumber?: number | undefined, gnomadExomeFilter?: string | undefined, gnomadGenomeAlleleCount?: number | undefined, gnomadGenomeAlleleFrequency?: number | undefined, gnomadGenomeAlleleNumber?: number | undefined, gnomadGenomeFilter?: string | undefined, lrtPrediction?: string | undefined, lrtScore?: number | undefined, metalrPrediction?: string | undefined, metalrScore?: number | undefined, metasvmPrediction?: string | undefined, metasvmScore?: number | undefined, mutationassessorPrediction: Array, mutationassessorScore: Array, mutationtasterPrediction: Array, mutationtasterScore: Array, phastcons100way?: number | undefined, phastcons30way?: number | undefined, phyloP100way?: number | undefined, phyloP30way?: number | undefined, polyphen2HdivPrediction: Array, polyphen2HdivScore: Array, polyphen2HvarPrediction: Array, polyphen2HvarScore: Array, proveanPrediction: Array, proveanScore: Array, revelScore?: Array | undefined, siftPrediction: Array, siftScore: Array, siphy?: number | undefined, snpeffSnpEffect: Array, snpeffSnpImpact: Array } | undefined }; +type VariantSummaryFields_GeneVariant_Fragment = { __typename: 'GeneVariant', id: number, name: string, variantAliases: Array, alleleRegistryId?: string | undefined, openCravatUrl?: string | undefined, maneSelectTranscript?: string | undefined, hgvsDescriptions: Array, clinvarIds: Array, openCravatAnnotations?: any | undefined, feature: { __typename: 'Feature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean }, variantTypes: Array<{ __typename: 'VariantType', id: number, link: string, soid: string, name: string }>, flags: { __typename: 'FlagConnection', totalCount: number }, revisions: { __typename: 'RevisionConnection', totalCount: number }, comments: { __typename: 'CommentConnection', totalCount: number }, lastSubmittedRevisionEvent?: { __typename: 'Event', originatingUser: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, lastAcceptedRevisionEvent?: { __typename: 'Event', originatingUser: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, creationActivity?: { __typename: 'CreateVariantActivity', createdAt: any, user: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, deprecationActivity?: { __typename: 'DeprecateVariantActivity', createdAt: any, user: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined }, parsedNote: Array<{ __typename: 'CommentTagSegment', entityId: number, displayName: string, tagType: TaggableEntity, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlagged', entityId: number, displayName: string, tagType: TaggableEntity, flagged: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlaggedAndDeprecated', entityId: number, displayName: string, tagType: TaggableEntity, flagged: boolean, deprecated: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlaggedAndWithStatus', entityId: number, displayName: string, tagType: TaggableEntity, status: EvidenceStatus, flagged: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTextSegment', text: string } | { __typename: 'User', id: number, username: string, displayName: string, name?: string | undefined, role: UserRole, profileImagePath?: string | undefined, organizations: Array<{ __typename: 'Organization', id: number, name: string, profileImagePath?: string | undefined }> }> } | undefined, coordinates?: { __typename: 'VariantCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, referenceBases?: string | undefined, variantBases?: string | undefined, coordinateType: VariantCoordinateType } | undefined, myVariantInfo?: { __typename: 'MyVariantInfo', myVariantInfoId: string, caddConsequence: Array, caddDetail: Array, caddScore?: number | undefined, caddPhred?: number | undefined, clinvarClinicalSignificance: Array, clinvarHgvsCoding: Array, clinvarHgvsGenomic: Array, clinvarHgvsNonCoding: Array, clinvarHgvsProtein: Array, clinvarId?: number | undefined, clinvarOmim?: string | undefined, cosmicId?: string | undefined, dbnsfpInterproDomain: Array, dbsnpRsid?: string | undefined, eglClass?: string | undefined, eglHgvs: Array, eglProtein?: string | undefined, eglTranscript?: string | undefined, exacAlleleCount?: number | undefined, exacAlleleFrequency?: number | undefined, exacAlleleNumber?: number | undefined, fathmmMklPrediction?: string | undefined, fathmmMklScore?: number | undefined, fathmmPrediction: Array, fathmmScore: Array, fitconsScore?: number | undefined, gerp?: number | undefined, gnomadExomeAlleleCount?: number | undefined, gnomadExomeAlleleFrequency?: number | undefined, gnomadExomeAlleleNumber?: number | undefined, gnomadExomeFilter?: string | undefined, gnomadGenomeAlleleCount?: number | undefined, gnomadGenomeAlleleFrequency?: number | undefined, gnomadGenomeAlleleNumber?: number | undefined, gnomadGenomeFilter?: string | undefined, lrtPrediction?: string | undefined, lrtScore?: number | undefined, metalrPrediction?: string | undefined, metalrScore?: number | undefined, metasvmPrediction?: string | undefined, metasvmScore?: number | undefined, mutationassessorPrediction: Array, mutationassessorScore: Array, mutationtasterPrediction: Array, mutationtasterScore: Array, phastcons100way?: number | undefined, phastcons30way?: number | undefined, phyloP100way?: number | undefined, phyloP30way?: number | undefined, polyphen2HdivPrediction: Array, polyphen2HdivScore: Array, polyphen2HvarPrediction: Array, polyphen2HvarScore: Array, proveanPrediction: Array, proveanScore: Array, revelScore?: Array | undefined, siftPrediction: Array, siftScore: Array, siphy?: number | undefined, snpeffSnpEffect: Array, snpeffSnpImpact: Array } | undefined }; type VariantSummaryFields_Variant_Fragment = { __typename: 'Variant', id: number, name: string, variantAliases: Array, feature: { __typename: 'Feature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean }, variantTypes: Array<{ __typename: 'VariantType', id: number, link: string, soid: string, name: string }>, flags: { __typename: 'FlagConnection', totalCount: number }, revisions: { __typename: 'RevisionConnection', totalCount: number }, comments: { __typename: 'CommentConnection', totalCount: number }, lastSubmittedRevisionEvent?: { __typename: 'Event', originatingUser: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, lastAcceptedRevisionEvent?: { __typename: 'Event', originatingUser: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, creationActivity?: { __typename: 'CreateVariantActivity', createdAt: any, user: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined } } | undefined, deprecationActivity?: { __typename: 'DeprecateVariantActivity', createdAt: any, user: { __typename: 'User', id: number, displayName: string, role: UserRole, profileImagePath?: string | undefined }, parsedNote: Array<{ __typename: 'CommentTagSegment', entityId: number, displayName: string, tagType: TaggableEntity, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlagged', entityId: number, displayName: string, tagType: TaggableEntity, flagged: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlaggedAndDeprecated', entityId: number, displayName: string, tagType: TaggableEntity, flagged: boolean, deprecated: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTagSegmentFlaggedAndWithStatus', entityId: number, displayName: string, tagType: TaggableEntity, status: EvidenceStatus, flagged: boolean, link: string, revisionSetId?: number | undefined, feature?: { __typename: 'LinkableFeature', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined } | { __typename: 'CommentTextSegment', text: string } | { __typename: 'User', id: number, username: string, displayName: string, name?: string | undefined, role: UserRole, profileImagePath?: string | undefined, organizations: Array<{ __typename: 'Organization', id: number, name: string, profileImagePath?: string | undefined }> }> } | undefined }; @@ -9903,7 +9904,7 @@ export type VariantSummaryFieldsFragment = VariantSummaryFields_FactorVariant_Fr export type FactorVariantSummaryFieldsFragment = { __typename: 'FactorVariant', ncitId?: string | undefined, ncitDetails?: { __typename: 'NcitDetails', synonyms: Array<{ __typename: 'NcitSynonym', name: string, source: string }>, definitions: Array<{ __typename: 'NcitDefinition', definition: string, source: string }> } | undefined }; -export type GeneVariantSummaryFieldsFragment = { __typename: 'GeneVariant', alleleRegistryId?: string | undefined, openCravatUrl?: string | undefined, maneSelectTranscript?: string | undefined, hgvsDescriptions: Array, clinvarIds: Array, coordinates?: { __typename: 'VariantCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, referenceBases?: string | undefined, variantBases?: string | undefined, coordinateType: VariantCoordinateType } | undefined, myVariantInfo?: { __typename: 'MyVariantInfo', myVariantInfoId: string, caddConsequence: Array, caddDetail: Array, caddScore?: number | undefined, caddPhred?: number | undefined, clinvarClinicalSignificance: Array, clinvarHgvsCoding: Array, clinvarHgvsGenomic: Array, clinvarHgvsNonCoding: Array, clinvarHgvsProtein: Array, clinvarId?: number | undefined, clinvarOmim?: string | undefined, cosmicId?: string | undefined, dbnsfpInterproDomain: Array, dbsnpRsid?: string | undefined, eglClass?: string | undefined, eglHgvs: Array, eglProtein?: string | undefined, eglTranscript?: string | undefined, exacAlleleCount?: number | undefined, exacAlleleFrequency?: number | undefined, exacAlleleNumber?: number | undefined, fathmmMklPrediction?: string | undefined, fathmmMklScore?: number | undefined, fathmmPrediction: Array, fathmmScore: Array, fitconsScore?: number | undefined, gerp?: number | undefined, gnomadExomeAlleleCount?: number | undefined, gnomadExomeAlleleFrequency?: number | undefined, gnomadExomeAlleleNumber?: number | undefined, gnomadExomeFilter?: string | undefined, gnomadGenomeAlleleCount?: number | undefined, gnomadGenomeAlleleFrequency?: number | undefined, gnomadGenomeAlleleNumber?: number | undefined, gnomadGenomeFilter?: string | undefined, lrtPrediction?: string | undefined, lrtScore?: number | undefined, metalrPrediction?: string | undefined, metalrScore?: number | undefined, metasvmPrediction?: string | undefined, metasvmScore?: number | undefined, mutationassessorPrediction: Array, mutationassessorScore: Array, mutationtasterPrediction: Array, mutationtasterScore: Array, phastcons100way?: number | undefined, phastcons30way?: number | undefined, phyloP100way?: number | undefined, phyloP30way?: number | undefined, polyphen2HdivPrediction: Array, polyphen2HdivScore: Array, polyphen2HvarPrediction: Array, polyphen2HvarScore: Array, proveanPrediction: Array, proveanScore: Array, revelScore?: Array | undefined, siftPrediction: Array, siftScore: Array, siphy?: number | undefined, snpeffSnpEffect: Array, snpeffSnpImpact: Array } | undefined }; +export type GeneVariantSummaryFieldsFragment = { __typename: 'GeneVariant', alleleRegistryId?: string | undefined, openCravatUrl?: string | undefined, maneSelectTranscript?: string | undefined, hgvsDescriptions: Array, clinvarIds: Array, openCravatAnnotations?: any | undefined, coordinates?: { __typename: 'VariantCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, referenceBases?: string | undefined, variantBases?: string | undefined, coordinateType: VariantCoordinateType } | undefined, myVariantInfo?: { __typename: 'MyVariantInfo', myVariantInfoId: string, caddConsequence: Array, caddDetail: Array, caddScore?: number | undefined, caddPhred?: number | undefined, clinvarClinicalSignificance: Array, clinvarHgvsCoding: Array, clinvarHgvsGenomic: Array, clinvarHgvsNonCoding: Array, clinvarHgvsProtein: Array, clinvarId?: number | undefined, clinvarOmim?: string | undefined, cosmicId?: string | undefined, dbnsfpInterproDomain: Array, dbsnpRsid?: string | undefined, eglClass?: string | undefined, eglHgvs: Array, eglProtein?: string | undefined, eglTranscript?: string | undefined, exacAlleleCount?: number | undefined, exacAlleleFrequency?: number | undefined, exacAlleleNumber?: number | undefined, fathmmMklPrediction?: string | undefined, fathmmMklScore?: number | undefined, fathmmPrediction: Array, fathmmScore: Array, fitconsScore?: number | undefined, gerp?: number | undefined, gnomadExomeAlleleCount?: number | undefined, gnomadExomeAlleleFrequency?: number | undefined, gnomadExomeAlleleNumber?: number | undefined, gnomadExomeFilter?: string | undefined, gnomadGenomeAlleleCount?: number | undefined, gnomadGenomeAlleleFrequency?: number | undefined, gnomadGenomeAlleleNumber?: number | undefined, gnomadGenomeFilter?: string | undefined, lrtPrediction?: string | undefined, lrtScore?: number | undefined, metalrPrediction?: string | undefined, metalrScore?: number | undefined, metasvmPrediction?: string | undefined, metasvmScore?: number | undefined, mutationassessorPrediction: Array, mutationassessorScore: Array, mutationtasterPrediction: Array, mutationtasterScore: Array, phastcons100way?: number | undefined, phastcons30way?: number | undefined, phyloP100way?: number | undefined, phyloP30way?: number | undefined, polyphen2HdivPrediction: Array, polyphen2HdivScore: Array, polyphen2HvarPrediction: Array, polyphen2HvarScore: Array, proveanPrediction: Array, proveanScore: Array, revelScore?: Array | undefined, siftPrediction: Array, siftScore: Array, siphy?: number | undefined, snpeffSnpEffect: Array, snpeffSnpImpact: Array } | undefined }; export type FusionVariantSummaryFieldsFragment = { __typename: 'FusionVariant', viccCompliantName: string, fusion: { __typename: 'Fusion', fivePrimePartnerStatus: FusionPartnerStatus, threePrimePartnerStatus: FusionPartnerStatus, fivePrimeGene?: { __typename: 'Gene', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined, threePrimeGene?: { __typename: 'Gene', id: number, name: string, link: string, deprecated: boolean, flagged: boolean } | undefined }, fivePrimeCoordinates?: { __typename: 'VariantCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, referenceBases?: string | undefined, variantBases?: string | undefined, coordinateType: VariantCoordinateType } | undefined, threePrimeCoordinates?: { __typename: 'VariantCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, referenceBases?: string | undefined, variantBases?: string | undefined, coordinateType: VariantCoordinateType } | undefined, fivePrimeStartExonCoordinates?: { __typename: 'ExonCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, exon?: number | undefined, exonOffset?: number | undefined, exonOffsetDirection?: Direction | undefined, ensemblId?: string | undefined, strand?: Direction | undefined, coordinateType: ExonCoordinateType } | undefined, fivePrimeEndExonCoordinates?: { __typename: 'ExonCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, exon?: number | undefined, exonOffset?: number | undefined, exonOffsetDirection?: Direction | undefined, ensemblId?: string | undefined, strand?: Direction | undefined, coordinateType: ExonCoordinateType } | undefined, threePrimeStartExonCoordinates?: { __typename: 'ExonCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, exon?: number | undefined, exonOffset?: number | undefined, exonOffsetDirection?: Direction | undefined, ensemblId?: string | undefined, strand?: Direction | undefined, coordinateType: ExonCoordinateType } | undefined, threePrimeEndExonCoordinates?: { __typename: 'ExonCoordinate', referenceBuild?: ReferenceBuild | undefined, ensemblVersion?: number | undefined, chromosome?: string | undefined, representativeTranscript?: string | undefined, start?: number | undefined, stop?: number | undefined, exon?: number | undefined, exonOffset?: number | undefined, exonOffsetDirection?: Direction | undefined, ensemblId?: string | undefined, strand?: Direction | undefined, coordinateType: ExonCoordinateType } | undefined }; @@ -13006,6 +13007,7 @@ export const GeneVariantSummaryFieldsFragmentDoc = gql` myVariantInfo { ...MyVariantInfoFields } + openCravatAnnotations } ${CoordinateFieldsFragmentDoc} ${MyVariantInfoFieldsFragmentDoc}`; diff --git a/client/src/app/generated/server.model.graphql b/client/src/app/generated/server.model.graphql index 250c9002d..783d026f2 100644 --- a/client/src/app/generated/server.model.graphql +++ b/client/src/app/generated/server.model.graphql @@ -6000,6 +6000,7 @@ type GeneVariant implements Commentable & EventOriginObject & EventSubject & Fla ): MolecularProfileConnection! myVariantInfo: MyVariantInfo name: String! + openCravatAnnotations: JSON openCravatUrl: String openRevisionCount: Int! primaryCoordinates: VariantCoordinate @deprecated(reason: "The new Fusion variant type means Gene variants no longer have primary and secondary coordinates. Use 'coordinates' instead.") diff --git a/client/src/app/generated/server.schema.json b/client/src/app/generated/server.schema.json index e3f2fc52e..683b6461a 100644 --- a/client/src/app/generated/server.schema.json +++ b/client/src/app/generated/server.schema.json @@ -27725,6 +27725,18 @@ "isDeprecated": false, "deprecationReason": null }, + { + "name": "openCravatAnnotations", + "description": null, + "args": [], + "type": { + "kind": "SCALAR", + "name": "JSON", + "ofType": null + }, + "isDeprecated": false, + "deprecationReason": null + }, { "name": "openCravatUrl", "description": null, diff --git a/client/src/app/views/variants/variants-detail/variants-summary/variants-summary.query.gql b/client/src/app/views/variants/variants-detail/variants-summary/variants-summary.query.gql index 051e281f8..bf261d73e 100644 --- a/client/src/app/views/variants/variants-detail/variants-summary/variants-summary.query.gql +++ b/client/src/app/views/variants/variants-detail/variants-summary/variants-summary.query.gql @@ -99,6 +99,7 @@ fragment GeneVariantSummaryFields on GeneVariant { myVariantInfo { ...MyVariantInfoFields } + openCravatAnnotations } fragment FusionVariantSummaryFields on FusionVariant { diff --git a/server/app/graphql/types/variants/gene_variant_type.rb b/server/app/graphql/types/variants/gene_variant_type.rb index 742f27af2..cc2552215 100644 --- a/server/app/graphql/types/variants/gene_variant_type.rb +++ b/server/app/graphql/types/variants/gene_variant_type.rb @@ -10,6 +10,7 @@ class GeneVariantType < Types::Entities::VariantType field :my_variant_info, Types::Entities::MyVariantInfoType, null: true field :mane_select_transcript, String, null: true field :open_cravat_url, String, null: true + field :open_cravat_annotations, GraphQL::Types::JSON, null: true def coordinates Loaders::AssociationLoader.for(Variants::GeneVariant, :coordinates).load(object) @@ -48,5 +49,15 @@ def open_revision_count end end end + + def open_cravat_url + if object.open_cravat_url_parameters.present? + "https://run.opencravat.org/webapps/variantreport/index.html?" + object.open_cravat_url_parameters + end + end + + def open_cravat_annotations + OpenCravat.new(object).response + end end end diff --git a/server/app/jobs/generate_open_cravat_link.rb b/server/app/jobs/generate_open_cravat_link.rb index b12663b17..a90755b0b 100644 --- a/server/app/jobs/generate_open_cravat_link.rb +++ b/server/app/jobs/generate_open_cravat_link.rb @@ -6,10 +6,10 @@ def perform(variant) return unless coords - open_cravat_url = make_open_cravat_url(coords) + open_cravat_url_parameters = make_open_cravat_url_parameters(coords) - variant.open_cravat_url = open_cravat_url - variant.save! + variant.open_cravat_url_parameters = open_cravat_url_parameters + variant.save(validate: false) end @@ -36,9 +36,7 @@ def make_allele_registry_url(variant) "https://reg.genome.network/allele/#{variant.allele_registry_id}" end - def make_open_cravat_url(coords) - base_url = "https://run.opencravat.org/webapps/variantreport/index.html?" - + def make_open_cravat_url_parameters(coords) start = coords["coordinates"].first["start"] ref = coords["coordinates"].first["referenceAllele"] alt = coords["coordinates"].first["allele"] @@ -60,7 +58,7 @@ def make_open_cravat_url(coords) alt_base: alt, }.to_query - base_url + query_params + query_params end #https://www.biostars.org/p/84686/ diff --git a/server/app/models/open_cravat.rb b/server/app/models/open_cravat.rb new file mode 100644 index 000000000..a1aeb4d97 --- /dev/null +++ b/server/app/models/open_cravat.rb @@ -0,0 +1,93 @@ +class OpenCravat + attr_reader :variant + + def initialize(variant) + @variant = variant + end + + def response + Rails.cache.fetch(cache_key(variant), expires_in: 24.hours) do + if variant.open_cravat_url_parameters.present? + response = make_request(variant.open_cravat_url_parameters) + parse_response(response) + else + nil + end + end + rescue StandardError => e + nil + end + + def parse_response(response) + p = JSON.parse(response) + benignity = { + 'cadd_exome': p.dig("cadd_exome", "benign"), + 'cadd': p.dig("cadd", "benign"), + 'revel': p.dig("revel", "benign"), + 'sift': p.dig("sift", "benign"), + 'gerp': p.dig("gerp", "benign"), + 'phylop': p.dig("phylop", "benign"), + 'vest': p.dig("vest", "benign"), + 'bayesdel': p.dig("bayesdel", "benign"), + } + pathogenicity = { + 'cadd_exome': p.dig("cadd_exome", "pathogenic"), + 'cadd': p.dig("cadd", "pathogenic"), + 'revel': p.dig("revel", "pathogenic"), + 'sift': p.dig("sift", "pathogenic"), + 'fathmm': p.dig("fathmm", "fathmm_pathogenicity")&.sub("PP3 ", ""), + 'phylop': p.dig("phylop", "pathogenic"), + 'vest': p.dig("vest", "pathogenic"), + 'bayesdel': p.dig("bayesdel", "pathogenic"), + } + { + 'benignity': benignity, + 'benignity_counts': benignity.values.compact.tally, + 'benignity_counts_details': benignity.group_by{|k,v| v}.map { |k, v| [k, v.map(&:first)] }.to_h, + 'pathogenicity': pathogenicity, + 'pathogenicity_counts': pathogenicity.values.compact.tally, + 'pathogenicity_counts_details': pathogenicity.group_by{|k,v| v}.map { |k, v| [k, v.map(&:first)] }.to_h, + } + rescue StandardError => e + end + + def extract_value(p, position, final_key) + raw_value = p.dig(*position) + if raw_value.nil? + [] + elsif raw_value.is_a?(Hash) + [raw_value[final_key]] + else + raw_value.map{|v| v[final_key]}.uniq + end + end + + def annotators + [ + 'bayesdel', + 'cadd', + 'cadd_exome', + 'fathmm', + 'gerp', + 'phylop', + 'primateai', + 'revel', + 'sift', + 'vest', + ] + end + + private + def make_request(open_cravat_url_parameters) + Scrapers::Util.make_get_request(open_cravat_url(open_cravat_url_parameters)) + end + + def open_cravat_url(open_cravat_url_parameters) + annotator_list = annotators.join(',') + "https://run.opencravat.org/submit/annotate?#{open_cravat_url_parameters}&annotators=#{annotator_list}" + end + + def cache_key(variant) + "open_cravat_#{variant.id}_#{variant.updated_at}" + end +end diff --git a/server/db/migrate/20250128191951_rename_open_cravat_url_to_open_cravat_url_parameters.rb b/server/db/migrate/20250128191951_rename_open_cravat_url_to_open_cravat_url_parameters.rb new file mode 100644 index 000000000..4d74ad7a0 --- /dev/null +++ b/server/db/migrate/20250128191951_rename_open_cravat_url_to_open_cravat_url_parameters.rb @@ -0,0 +1,5 @@ +class RenameOpenCravatUrlToOpenCravatUrlParameters < ActiveRecord::Migration[7.1] + def change + rename_column :variants, :open_cravat_url, :open_cravat_url_parameters + end +end diff --git a/server/db/schema.rb b/server/db/schema.rb index 761d1e078..8c52ae78f 100644 --- a/server/db/schema.rb +++ b/server/db/schema.rb @@ -10,7 +10,7 @@ # # It's strongly recommended that you check this file into your version control system. -ActiveRecord::Schema[7.1].define(version: 2024_09_14_154057) do +ActiveRecord::Schema[7.1].define(version: 2025_01_28_191951) do # These are extensions that must be enabled in order to support this database enable_extension "plpgsql" @@ -1003,7 +1003,7 @@ t.boolean "deprecated", default: false, null: false t.integer "deprecation_reason" t.integer "deprecation_comment_id" - t.text "open_cravat_url" + t.text "open_cravat_url_parameters" t.bigint "feature_id" t.string "type", null: false t.string "ncit_id" From 75c3a62d9883309ae03b934e8e0f6a532edb12e3 Mon Sep 17 00:00:00 2001 From: Joshua McMichael Date: Thu, 6 Feb 2025 04:33:41 -0600 Subject: [PATCH 2/9] moved gene to left col, removed border from tags containing simple strings (e.g. aliases) --- .../gene-variant-summary.page.html | 490 +++++++++--------- 1 file changed, 251 insertions(+), 239 deletions(-) diff --git a/client/src/app/components/variants/gene-variant-summary/gene-variant-summary.page.html b/client/src/app/components/variants/gene-variant-summary/gene-variant-summary.page.html index 62ec8c925..264181661 100644 --- a/client/src/app/components/variants/gene-variant-summary/gene-variant-summary.page.html +++ b/client/src/app/components/variants/gene-variant-summary/gene-variant-summary.page.html @@ -1,282 +1,294 @@ @if (variant.__typename == 'GeneVariant') { - - - - - - - - - - - - - - {{ - alias - }} - - - - None specified - - + + + + + + + + + + + + + + + {{ alias }} + + + + + + None specified + + + + + + + - - 1 ? 'Variant Types' : 'Variant Type' - "> - - - + + + - - - - None specified - - + + + + None specified + + - - 1 ? 'HGVS Descriptions' : 'HGVS Description' - "> - + - - {{ - desc - }} - - - - None specified - - + + + {{ desc }} + + + - - - - - {{ variant.maneSelectTranscript }} - - - - None found - - - - - - - - - - + + + None specified + + + - - - - - - - - - - - by - - - - Created - - ({{ variant.creationActivity.createdAt | timeAgo }}) - - + + + + + + {{ variant.maneSelectTranscript }} + + - - - by - - - - Deprecated - - ({{ variant.deprecationActivity.createdAt | timeAgo }}) - - - - - + + None found + + + + + + + + + + - - - - - - + + + + + + + + + + + by + + + + Created + + ({{ variant.creationActivity.createdAt | timeAgo }}) + + + + + + by + + + Deprecated + + ({{ variant.deprecationActivity.createdAt | timeAgo }}) + + + + + - - - + + + + - {{ variant.alleleRegistryId }} - - - Unregistered - - + tooltip="View on ClinGen Allele Registry"> + {{ variant.alleleRegistryId }} + + + Unregistered + + - - 1 ? 'ClinVar IDs' : 'ClinVar ID' "> - - 0; else noClinvarIds"> + - - + - {{ id }} - - - - + tooltip="View on ClinVar"> + {{ id }} + + + + - - {{ variant.clinvarIds[0] }} - + + {{ variant.clinvarIds[0] }} + - - None provided - - - - + + None provided + + + + - - - - - - - - - - - - + + + + + + + + + + + + - - - @if (variant.openCravatAnnotations && variant.openCravatUrl) { - - - } @else { - - - - - } - - - - + + + @if (variant.openCravatAnnotations && variant.openCravatUrl) { + + + } @else { + + + + + } + + + + - - - - - - + + + + + + } From 67b6ba2d5c58e5d441ebb7058c7debba986b3058 Mon Sep 17 00:00:00 2001 From: Joshua McMichael Date: Thu, 6 Feb 2025 09:30:40 -0600 Subject: [PATCH 3/9] added tinycolor to fix ng-zorro dependency issue --- client/package.json | 3 +- client/yarn.lock | 6860 +++++++++++++++++-------------------------- 2 files changed, 2773 insertions(+), 4090 deletions(-) diff --git a/client/package.json b/client/package.json index 89f3bae1b..42320f7ab 100644 --- a/client/package.json +++ b/client/package.json @@ -33,6 +33,7 @@ "@angular/platform-browser-dynamic": "^18.1.2", "@angular/router": "^18.1.2", "@apollo/client": "^3.11.1", + "@ctrl/tinycolor": "^4.1.0", "@ngneat/until-destroy": "^10.0.0", "@ngrx/component": "^18.0.1", "@ngx-formly/core": "^6.3.6", @@ -40,13 +41,13 @@ "apollo-angular": "^7.0.2", "ng-zorro-antd": "18.0.1", "ngx-cookie-service": "^18.0.0", + "ngx-ui-scroll": "3.2.0", "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", "vscroll": "1.6.1", - "ngx-ui-scroll": "3.2.0", "zone.js": "0.14.3" }, "devDependencies": { diff --git a/client/yarn.lock b/client/yarn.lock index 966297b92..5e2fba1eb 100644 --- a/client/yarn.lock +++ b/client/yarn.lock @@ -2,7 +2,7 @@ # yarn lockfile v1 -"@ampproject/remapping@2.3.0": +"@ampproject/remapping@2.3.0", "@ampproject/remapping@^2.2.0": version "2.3.0" resolved "https://registry.yarnpkg.com/@ampproject/remapping/-/remapping-2.3.0.tgz#ed441b6fa600072520ce18b43d2c8cc8caecc7f4" integrity sha512-30iZtAPgz+LTIYoeivqYo853f02jBYSd5uGnGpkFV0M3xOt9aN73erkgYAmZU43x4VfqcnLxW9Kpg3R5LC4YYw== @@ -10,71 +10,55 @@ "@jridgewell/gen-mapping" "^0.3.5" "@jridgewell/trace-mapping" "^0.3.24" -"@ampproject/remapping@^2.1.0": - version "2.2.0" - resolved "https://registry.yarnpkg.com/@ampproject/remapping/-/remapping-2.2.0.tgz#56c133824780de3174aed5ab6834f3026790154d" - integrity sha512-qRmjj8nj9qmLTQXXmaR1cck3UXSRMPrbsLJAasZpF+t3riI71BXed5ebIOYwQntykeZuhjsdweEc9BxH5Jc26w== - dependencies: - "@jridgewell/gen-mapping" "^0.1.0" - "@jridgewell/trace-mapping" "^0.3.9" - -"@ampproject/remapping@^2.2.0": - version "2.2.1" - resolved "https://registry.yarnpkg.com/@ampproject/remapping/-/remapping-2.2.1.tgz#99e8e11851128b8702cd57c33684f1d0f260b630" - integrity sha512-lFMjJTrFL3j7L9yBxwYfCq2k6qqwHyzuUl/XBnif78PWTJYyL/dfowQHWE3sp6U6ZzqWiiIZnpTMO96zhkjwtg== +"@angular-devkit/architect@0.1802.14": + version "0.1802.14" + resolved "https://registry.yarnpkg.com/@angular-devkit/architect/-/architect-0.1802.14.tgz#da0bca3fc42844ae7b251593495d912d10b90ed4" + integrity sha512-eplaGCXSlPwf1f4XwyzsYTd8/lJ0/Adm6XsODsBxvkZlIpLcps80/h2lH5MVJpoDREzIFu1BweDpYCoNK5yYZg== dependencies: - "@jridgewell/gen-mapping" "^0.3.0" - "@jridgewell/trace-mapping" "^0.3.9" - -"@angular-devkit/architect@0.1801.2": - version "0.1801.2" - resolved "https://registry.yarnpkg.com/@angular-devkit/architect/-/architect-0.1801.2.tgz#36bcd91ba6c696a200330ae8735c55ec2ca28383" - integrity sha512-y2rV8wRwTnmCH/dUo632wHi6r41Gs9XucyGm/ybzB/5tN3x6dS+O3c3zajRpdqTUr8YcD6os6sT+Ay6zS31tOw== - dependencies: - "@angular-devkit/core" "18.1.2" + "@angular-devkit/core" "18.2.14" rxjs "7.8.1" "@angular-devkit/build-angular@^18.1.2": - version "18.1.2" - resolved "https://registry.yarnpkg.com/@angular-devkit/build-angular/-/build-angular-18.1.2.tgz#5801c6e7ed62432b7885f9ddb23604878c88f0d9" - 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-ansi-colors@4.1.3, ansi-colors@^4.1.1: +ansi-colors@4.1.3: version "4.1.3" resolved "https://registry.yarnpkg.com/ansi-colors/-/ansi-colors-4.1.3.tgz#37611340eb2243e70cc604cad35d63270d48781b" integrity sha512-/6w/C21Pm1A7aZitlI5Ni/2J6FFQN8i1Cvz3kHABAAbw93v/NlvKdVOqz7CCWz/3iv/JplRSEEZ83XION15ovw== @@ -4373,10 +3741,12 @@ ansi-escapes@^4.2.1, ansi-escapes@^4.3.0, ansi-escapes@^4.3.2: dependencies: type-fest "^0.21.3" -ansi-escapes@^6.2.0: - version "6.2.1" - resolved "https://registry.yarnpkg.com/ansi-escapes/-/ansi-escapes-6.2.1.tgz#76c54ce9b081dad39acec4b5d53377913825fb0f" - integrity sha512-4nJ3yixlEthEJ9Rk4vPcdBRkZvQZlYyu8j4/Mqz5sgIkddmEnH2Yj2ZrnP9S3tQOvSNRUIgVNF/1yPpRAGNRig== +ansi-escapes@^7.0.0: + version "7.0.0" + resolved "https://registry.yarnpkg.com/ansi-escapes/-/ansi-escapes-7.0.0.tgz#00fc19f491bbb18e1d481b97868204f92109bfe7" + integrity sha512-GdYO7a61mR0fOlAsvC9/rIHf7L96sBc6dEWzeOu+KAea5bZyQRPIpojrVoI4AXGJS/ycu/fBTdLrUkA4ODrvjw== + dependencies: + environment "^1.0.0" 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integrity sha512-Cxwpt2SfTzTtXcfOlzGEee8O+c+MmUgGrNiBcXnuWxuFJHe6a5Hz7qwhwe5OgaSYI0IJvkLqWX1ASG+cJOkEiA== - ansi-styles@^6.0.0, ansi-styles@^6.1.0, ansi-styles@^6.2.1: version "6.2.1" resolved "https://registry.yarnpkg.com/ansi-styles/-/ansi-styles-6.2.1.tgz#0e62320cf99c21afff3b3012192546aacbfb05c5" @@ -4426,9 +3791,9 @@ anymatch@~3.1.2: picomatch "^2.0.4" apollo-angular@^7.0.2: - version "7.0.2" - resolved "https://registry.yarnpkg.com/apollo-angular/-/apollo-angular-7.0.2.tgz#35f4d396aedbc905acd0d40402802666ec6449ce" - integrity sha512-OBj+KnVfGsJ1wdsOj5CENyjBnd85vseAlgqW1kG4tvgz0QPgPlUHx5KBKhwlf2hWZceNQQcXoWQmnXxzdZbWDg== + version "7.2.1" + resolved "https://registry.yarnpkg.com/apollo-angular/-/apollo-angular-7.2.1.tgz#ebcff99eaa93fba3c305b108d8c18e2d1ca5b90b" + integrity sha512-kUztS6VPI4IMOT6i1f2U+Ps9DOMoGXLfOURiEN2LApek7ajOSsz1pmWmItg6lZ/5om3sO+cbuaNCwb2M1sy26Q== dependencies: tslib "^2.6.2" @@ -4449,12 +3814,10 @@ argparse@^2.0.1: resolved 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+axobject-query@4.1.0: + version "4.1.0" + resolved "https://registry.yarnpkg.com/axobject-query/-/axobject-query-4.1.0.tgz#28768c76d0e3cff21bc62a9e2d0b6ac30042a1ee" + integrity sha512-qIj0G9wZbMGNLjLmg1PT6v2mE9AH2zlnADJD/2tC6E00hgmhUOfEB6greHPAfLRSufHqROIUTkw6E+M3lH0PTQ== babel-loader@9.1.3: version "9.1.3" @@ -4547,28 +3880,28 @@ babel-loader@9.1.3: schema-utils "^4.0.0" babel-plugin-polyfill-corejs2@^0.4.10: - version "0.4.11" - resolved "https://registry.yarnpkg.com/babel-plugin-polyfill-corejs2/-/babel-plugin-polyfill-corejs2-0.4.11.tgz#30320dfe3ffe1a336c15afdcdafd6fd615b25e33" - integrity sha512-sMEJ27L0gRHShOh5G54uAAPaiCOygY/5ratXuiyb2G46FmlSpc9eFCzYVyDiPxfNbwzA7mYahmjQc5q+CZQ09Q== + version "0.4.12" + resolved "https://registry.yarnpkg.com/babel-plugin-polyfill-corejs2/-/babel-plugin-polyfill-corejs2-0.4.12.tgz#ca55bbec8ab0edeeef3d7b8ffd75322e210879a9" + integrity sha512-CPWT6BwvhrTO2d8QVorhTCQw9Y43zOu7G9HigcfxvepOU6b8o3tcWad6oVgZIsZCTt42FFv97aA7ZJsbM4+8og== dependencies: 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delayed-stream "~1.0.0" - command-line-args@^5.2.0: version "5.2.1" resolved "https://registry.yarnpkg.com/command-line-args/-/command-line-args-5.2.1.tgz#c44c32e437a57d7c51157696893c5909e9cec42e" @@ -5189,7 +4433,7 @@ common-tags@1.8.2: resolved "https://registry.yarnpkg.com/common-tags/-/common-tags-1.8.2.tgz#94ebb3c076d26032745fd54face7f688ef5ac9c6" integrity sha512-gk/Z852D2Wtb//0I+kRFNKKE9dIIVirjoqPoA1wJU+XePVXZfGeBpk45+A1rKO4Q43prqWBNY/MiIeRLbPWUaA== -compressible@~2.0.16: +compressible@~2.0.18: version "2.0.18" resolved "https://registry.yarnpkg.com/compressible/-/compressible-2.0.18.tgz#af53cca6b070d4c3c0750fbd77286a6d7cc46fba" integrity sha512-AF3r7P5dWxL8MxyITRMlORQNaOA2IkAFaTr4k7BUumjPtRpGDTZpl0Pb1XCO6JeDCBdp126Cgs9sMxqSjgYyRg== @@ -5197,16 +4441,16 @@ compressible@~2.0.16: mime-db ">= 1.43.0 < 2" compression@^1.7.4: - version "1.7.4" - resolved "https://registry.yarnpkg.com/compression/-/compression-1.7.4.tgz#95523eff170ca57c29a0ca41e6fe131f41e5bb8f" - integrity 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content-type@~1.0.5: version "1.0.5" resolved "https://registry.yarnpkg.com/content-type/-/content-type-1.0.5.tgz#8b773162656d1d1086784c8f23a54ce6d73d7918" integrity sha512-nTjqfcBFEipKdXCv4YDQWCfmcLZKm81ldF0pAopTvyrFGVbcR6P/VAAd5G7N+0tTr8QqiU0tFadD6FK4NtJwOA== @@ -5284,19 +4523,12 @@ copy-webpack-plugin@12.0.2: schema-utils "^4.2.0" serialize-javascript "^6.0.2" -core-js-compat@^3.31.0: - version "3.31.1" - resolved "https://registry.yarnpkg.com/core-js-compat/-/core-js-compat-3.31.1.tgz#5084ad1a46858df50ff89ace152441a63ba7aae0" - integrity sha512-wIDWd2s5/5aJSdpOJHfSibxNODxoGoWOBHt8JSPB41NOE94M7kuTPZCYLOlTtuoXTsBPKobpJ6T+y0SSy5L9SA== - dependencies: - browserslist "^4.21.9" - -core-js-compat@^3.36.1: - version "3.37.1" - resolved "https://registry.yarnpkg.com/core-js-compat/-/core-js-compat-3.37.1.tgz#c844310c7852f4bdf49b8d339730b97e17ff09ee" - integrity sha512-9TNiImhKvQqSUkOvk/mMRZzOANTiEVC7WaBNhHcKM7x+/5E1l5NvsysR19zuDQScE8k+kfQXWRN3AtS/eOSHpg== +core-js-compat@^3.37.1, core-js-compat@^3.38.0: + version "3.40.0" + resolved "https://registry.yarnpkg.com/core-js-compat/-/core-js-compat-3.40.0.tgz#7485912a5a4a4315c2fdb2cbdc623e6881c88b38" + integrity sha512-0XEDpr5y5mijvw8Lbc6E5AkjrHfp7eEoPlu36SWeAbcL8fn1G1ANe8DBlo2XoNN89oVpxWwOjYIPVzR4ZvsKCQ== dependencies: - browserslist "^4.23.0" + browserslist "^4.24.3" core-util-is@~1.0.0: version "1.0.3" @@ -5353,16 +4585,16 @@ critters@0.0.24: postcss-media-query-parser "^0.2.3" cross-fetch@^3.1.5: - version "3.1.5" - resolved "https://registry.yarnpkg.com/cross-fetch/-/cross-fetch-3.1.5.tgz#e1389f44d9e7ba767907f7af8454787952ab534f" - integrity sha512-lvb1SBsI0Z7GDwmuid+mU3kWVBwTVUbe7S0H52yaaAdQOXq2YktTCZdlAcNKFzE6QtRz0snpw9bNiPeOIkkQvw== + version "3.2.0" + resolved "https://registry.yarnpkg.com/cross-fetch/-/cross-fetch-3.2.0.tgz#34e9192f53bc757d6614304d9e5e6fb4edb782e3" + integrity sha512-Q+xVJLoGOeIMXZmbUK4HYk+69cQH6LudR0Vu/pRm2YlU/hDV9CiS0gKUMaWY5f2NeUH9C1nV3bsTlCo0FsTV1Q== dependencies: - node-fetch "2.6.7" + node-fetch "^2.7.0" -cross-inspect@1.0.0: - version "1.0.0" - resolved "https://registry.yarnpkg.com/cross-inspect/-/cross-inspect-1.0.0.tgz#5fda1af759a148594d2d58394a9e21364f6849af" - integrity sha512-4PFfn4b5ZN6FMNGSZlyb7wUhuN8wvj8t/VQHZdM4JsDcruGJ8L2kf9zao98QIrBPFCpdk27qst/AGTl7pL3ypQ== +cross-inspect@1.0.1: + version "1.0.1" + resolved "https://registry.yarnpkg.com/cross-inspect/-/cross-inspect-1.0.1.tgz#15f6f65e4ca963cf4cc1a2b5fef18f6ca328712b" + integrity sha512-Pcw1JTvZLSJH83iiGWt6fRcT+BjZlCDRVwYLbUcHzv/CRpB7r0MlSrGbIyQvVSNyGnbt7G4AXuyCiDR3POvZ1A== dependencies: tslib "^2.4.0" @@ -5433,10 +4665,15 @@ csso@^5.0.5: dependencies: css-tree "~2.2.0" -dataloader@^2.2.2: - version "2.2.2" - resolved "https://registry.yarnpkg.com/dataloader/-/dataloader-2.2.2.tgz#216dc509b5abe39d43a9b9d97e6e5e473dfbe3e0" - integrity sha512-8YnDaaf7N3k/q5HnTJVuzSyLETjoZjVmHc4AeKAzOvKHEFQKcn64OKBfzHYtE9zGjctNM7V9I0MfnUVLpi7M5g== +data-uri-to-buffer@^4.0.0: + version "4.0.1" + resolved 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- version "1.1.4" - resolved "https://registry.yarnpkg.com/define-data-property/-/define-data-property-1.1.4.tgz#894dc141bb7d3060ae4366f6a0107e68fbe48c5e" - integrity sha512-rBMvIzlpA8v6E+SJZoo++HAYqsLrkg7MSfIinMPFhmkorw7X+dOXVJQs+QT69zGkzMyfDnIMN2Wid1+NbL3T+A== - dependencies: - es-define-property "^1.0.0" - es-errors "^1.3.0" - gopd "^1.0.1" - -define-lazy-prop@^2.0.0: - version "2.0.0" - resolved "https://registry.yarnpkg.com/define-lazy-prop/-/define-lazy-prop-2.0.0.tgz#3f7ae421129bcaaac9bc74905c98a0009ec9ee7f" - integrity sha512-Ds09qNh8yw3khSjiJjiUInaGX9xlqZDY7JVryGxdxV7NPeuqQfplOpQ66yJFZut3jLa5zOwkXw1g9EI2uKh4Og== - define-lazy-prop@^3.0.0: version "3.0.0" resolved "https://registry.yarnpkg.com/define-lazy-prop/-/define-lazy-prop-3.0.0.tgz#dbb19adfb746d7fc6d734a06b72f4a00d021255f" integrity sha512-N+MeXYoqr3pOgn8xfyRPREN7gHakLYjhsHhWGT3fWAiL4IkAt0iDw14QiiEm2bE30c5XX5q0FtAA3CK5f9/BUg== -delayed-stream@~1.0.0: - version "1.0.0" - resolved 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fast-json-stable-stringify@^2.0.0: version "2.1.0" @@ -6147,29 +5327,15 @@ fast-levenshtein@^2.0.6: resolved "https://registry.yarnpkg.com/fast-levenshtein/-/fast-levenshtein-2.0.6.tgz#3d8a5c66883a16a30ca8643e851f19baa7797917" integrity sha512-DCXu6Ifhqcks7TZKY3Hxp3y6qphY5SJZmrWMDrKcERSOXWQdMhU9Ig/PYrzyw/ul9jOIyh0N4M0tbC5hodg8dw== -fast-querystring@^1.1.1: - version "1.1.2" - resolved "https://registry.yarnpkg.com/fast-querystring/-/fast-querystring-1.1.2.tgz#a6d24937b4fc6f791b4ee31dcb6f53aeafb89f53" - integrity sha512-g6KuKWmFXc0fID8WWH0jit4g0AGBoJhCkJMb1RmbsSEUNvQ+ZC8D6CUZ+GtF8nMzSPXnhiePyyqqipzNNEnHjg== - dependencies: - fast-decode-uri-component "^1.0.1" - fast-uri@^3.0.1: - version "3.0.1" - resolved "https://registry.yarnpkg.com/fast-uri/-/fast-uri-3.0.1.tgz#cddd2eecfc83a71c1be2cc2ef2061331be8a7134" - integrity sha512-MWipKbbYiYI0UC7cl8m/i/IWTqfC8YXsqjzybjddLsFjStroQzsHXkc73JutMvBiXmOvapk+axIl79ig5t55Bw== - -fast-url-parser@^1.1.3: - version "1.1.3" - resolved 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reusify "^1.0.4" @@ -6193,9 +5359,9 @@ fbjs-css-vars@^1.0.0: integrity sha512-b2XGFAFdWZWg0phtAWLHCk836A1Xann+I+Dgd3Gk64MHKZO44FfoD1KxyvbSh0qZsIoXQGGlVztIY+oitJPpRQ== fbjs@^3.0.0: - version "3.0.4" - resolved "https://registry.yarnpkg.com/fbjs/-/fbjs-3.0.4.tgz#e1871c6bd3083bac71ff2da868ad5067d37716c6" - integrity sha512-ucV0tDODnGV3JCnnkmoszb5lf4bNpzjv80K41wd4k798Etq+UYD0y0TIfalLjZoKgjive6/adkRnszwapiDgBQ== + version "3.0.5" + resolved "https://registry.yarnpkg.com/fbjs/-/fbjs-3.0.5.tgz#aa0edb7d5caa6340011790bd9249dbef8a81128d" + integrity sha512-ztsSx77JBtkuMrEypfhgc3cI0+0h+svqeie7xHbh1k/IKdcydnvadp/mUaGgjAOXQmQSxsqgaRhS3q9fy+1kxg== dependencies: cross-fetch "^3.1.5" fbjs-css-vars "^1.0.0" @@ -6203,9 +5369,17 @@ fbjs@^3.0.0: object-assign "^4.1.0" promise "^7.1.1" setimmediate "^1.0.5" - ua-parser-js "^0.7.30" + ua-parser-js "^1.0.35" + +fetch-blob@^3.1.2, fetch-blob@^3.1.4: + version "3.2.0" + resolved "https://registry.yarnpkg.com/fetch-blob/-/fetch-blob-3.2.0.tgz#f09b8d4bbd45adc6f0c20b7e787e793e309dcce9" + integrity sha512-7yAQpD2UMJzLi1Dqv7qFYnPbaPx7ZfFK6PiIxQ4PfkGPyNyl2Ugx+a/umUonmKqjhM4DnfbMvdX6otXq83soQQ== + dependencies: + node-domexception "^1.0.0" + web-streams-polyfill "^3.0.3" -figures@3.2.0, figures@^3.0.0: +figures@^3.0.0: version "3.2.0" resolved "https://registry.yarnpkg.com/figures/-/figures-3.2.0.tgz#625c18bd293c604dc4a8ddb2febf0c88341746af" integrity sha512-yaduQFRKLXYOGgEn6AZau90j3ggSOyiqXU0F9JZfeXYhNa+Jk4X+s45A2zg5jns87GAFa34BBm2kXw4XpNcbdg== @@ -6219,13 +5393,6 @@ file-entry-cache@^6.0.1: dependencies: flat-cache "^3.0.4" -filelist@^1.0.4: - version "1.0.4" - resolved "https://registry.yarnpkg.com/filelist/-/filelist-1.0.4.tgz#f78978a1e944775ff9e62e744424f215e58352b5" - integrity sha512-w1cEuf3S+DrLCQL7ET6kz+gmlJdbq9J7yXCSjK/OZCPA+qEN1WyF4ZAf0YYJa4/shHJra2t/d/r8SV4Ji+x+8Q== - dependencies: - minimatch "^5.0.1" - fill-range@^7.1.1: version "7.1.1" resolved 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-7073,6 +6163,11 @@ is-plain-object@^2.0.4: dependencies: isobject "^3.0.1" +is-plain-object@^5.0.0: + version "5.0.0" + resolved "https://registry.yarnpkg.com/is-plain-object/-/is-plain-object-5.0.0.tgz#4427f50ab3429e9025ea7d52e9043a9ef4159344" + integrity sha512-VRSzKkbMm5jMDoKLbltAkFQ5Qr7VDiTFGXxYFXXowVj387GeGNOCsOH6Msy00SGZ3Fp84b1Naa1psqgcCIEP5Q== + is-relative@^1.0.0: version "1.0.0" resolved "https://registry.yarnpkg.com/is-relative/-/is-relative-1.0.0.tgz#a1bb6935ce8c5dba1e8b9754b9b2dcc020e2260d" @@ -7114,13 +6209,6 @@ is-windows@^1.0.1: resolved "https://registry.yarnpkg.com/is-windows/-/is-windows-1.0.2.tgz#d1850eb9791ecd18e6182ce12a30f396634bb19d" integrity sha512-eXK1UInq2bPmjyX6e3VHIzMLobc4J94i4AWn+Hpq3OU5KkrRC96OAcR3PRJ/pGu6m8TRnBHP9dkXQVsT/COVIA== -is-wsl@^2.2.0: - version "2.2.0" - resolved "https://registry.yarnpkg.com/is-wsl/-/is-wsl-2.2.0.tgz#74a4c76e77ca9fd3f932f290c17ea326cd157271" - integrity 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"https://registry.yarnpkg.com/jsesc/-/jsesc-3.1.0.tgz#74d335a234f67ed19907fdadfac7ccf9d409825d" + integrity sha512-/sM3dO2FOzXjKQhJuo0Q173wf2KOo8t4I8vHy6lF9poUp7bKT0/NHE8fPX23PwfhnykfqnC2xRxOnVw5XuGIaA== + +jsesc@~3.0.2: + version "3.0.2" + resolved "https://registry.yarnpkg.com/jsesc/-/jsesc-3.0.2.tgz#bb8b09a6597ba426425f2e4a07245c3d00b9343e" + integrity sha512-xKqzzWXDttJuOcawBt4KnKHHIf5oQ/Cxax+0PWFG+DFDgHNAdi+TXECADI+RYiFUMmx8792xsMbbgXj4CwnP4g== json-buffer@3.0.1: version "3.0.1" @@ -7281,9 +6341,9 @@ json-parse-even-better-errors@^2.3.0, json-parse-even-better-errors@^2.3.1: integrity sha512-xyFwyhro/JEof6Ghe2iz2NcXoj2sloNsWr/XsERDK/oiPCfaNhl5ONfp+jQdAZRQQ0IJWNzH9zIZF7li91kh2w== json-parse-even-better-errors@^3.0.0: - version "3.0.0" - resolved "https://registry.yarnpkg.com/json-parse-even-better-errors/-/json-parse-even-better-errors-3.0.0.tgz#2cb2ee33069a78870a0c7e3da560026b89669cf7" - integrity sha512-iZbGHafX/59r39gPwVPRBGw0QQKnA7tte5pSMrhWOW7swGsVvVTjmfyAV9pNqk8YGT7tRCdxRu8uzcgZwoDooA== + version "3.0.2" + resolved "https://registry.yarnpkg.com/json-parse-even-better-errors/-/json-parse-even-better-errors-3.0.2.tgz#b43d35e89c0f3be6b5fbbe9dc6c82467b30c28da" + integrity sha512-fi0NG4bPjCHunUJffmLd0gxssIgkNmArMvis4iNah6Owg1MCJjWhEcDLmsK6iGkJq3tHwbDkTlce70/tmXN4cQ== json-schema-traverse@^0.4.1: version "0.4.1" @@ -7308,30 +6368,16 @@ json-to-pretty-yaml@^1.2.2: remedial "^1.0.7" remove-trailing-spaces "^1.0.6" -json5@^2.1.2, json5@^2.2.2, json5@^2.2.3: +json5@^2.1.2, json5@^2.2.3: version "2.2.3" resolved "https://registry.yarnpkg.com/json5/-/json5-2.2.3.tgz#78cd6f1a19bdc12b73db5ad0c61efd66c1e29283" integrity sha512-XmOWe7eyHYH14cLdVPoyg+GOH3rYX++KpzrylJwSW98t3Nk+U8XOl8FWKOgwtzdb8lXGf6zYwDUzeHMWfxasyg== -jsonc-parser@3.2.0: - version "3.2.0" - resolved "https://registry.yarnpkg.com/jsonc-parser/-/jsonc-parser-3.2.0.tgz#31ff3f4c2b9793f89c67212627c51c6394f88e76" - integrity 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launch-editor@^2.6.1: - version "2.8.0" - resolved "https://registry.yarnpkg.com/launch-editor/-/launch-editor-2.8.0.tgz#7255d90bdba414448e2138faa770a74f28451305" - integrity sha512-vJranOAJrI/llyWGRQqiDM+adrw+k83fvmmx3+nV47g3+36xM15jE+zyZ6Ffel02+xSvuM0b2GDRosXZkbb6wA== + version "2.9.1" + resolved "https://registry.yarnpkg.com/launch-editor/-/launch-editor-2.9.1.tgz#253f173bd441e342d4344b4dae58291abb425047" + integrity sha512-Gcnl4Bd+hRO9P9icCP/RVVT2o8SFlPXofuCxvA2SaZuH45whSvf5p8x5oih5ftLiVhEI4sp5xDY+R+b3zJBh5w== dependencies: picocolors "^1.0.0" shell-quote "^1.8.1" @@ -7411,20 +6457,15 @@ lines-and-columns@^1.1.6: resolved "https://registry.yarnpkg.com/lines-and-columns/-/lines-and-columns-1.2.4.tgz#eca284f75d2965079309dc0ad9255abb2ebc1632" integrity sha512-7ylylesZQ/PV29jhEDl3Ufjo6ZX7gCqJr5F7PKrqc93v7fzSymt1BpwEU8nAUXs8qzzvqhbjhK5QZg6Mt/HkBg== -lines-and-columns@~2.0.3: - version "2.0.3" - resolved 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resolved "https://registry.yarnpkg.com/lmdb/-/lmdb-3.0.12.tgz#24dd824f9e50b3a7873d1ebe32f70d0e52befab1" - integrity sha512-JnoEulTgveoC64vlYJ9sufGLuNkk6TcxSYpKxSC9aM42I61jIv3pQH0fgb6qW7HV0+FNqA3g1WCQQYfhfawGoQ== +lmdb@3.0.13: + version "3.0.13" + resolved "https://registry.yarnpkg.com/lmdb/-/lmdb-3.0.13.tgz#5f326ac13cd60c239c481c42b601ebae39935026" + integrity sha512-UGe+BbaSUQtAMZobTb4nHvFMrmvuAQKSeaqAX2meTEQjfsbpl5sxdHD8T72OnwD4GU9uwNhYXIVe4QGs8N9Zyw== dependencies: msgpackr "^1.10.2" node-addon-api "^6.1.0" @@ -7453,12 +6494,12 @@ lmdb@3.0.12: ordered-binary "^1.4.1" weak-lru-cache "^1.2.2" optionalDependencies: - "@lmdb/lmdb-darwin-arm64" "3.0.12" - "@lmdb/lmdb-darwin-x64" "3.0.12" - "@lmdb/lmdb-linux-arm" "3.0.12" - "@lmdb/lmdb-linux-arm64" "3.0.12" - "@lmdb/lmdb-linux-x64" "3.0.12" - "@lmdb/lmdb-win32-x64" "3.0.12" + "@lmdb/lmdb-darwin-arm64" "3.0.13" + "@lmdb/lmdb-darwin-x64" "3.0.13" + "@lmdb/lmdb-linux-arm" "3.0.13" + "@lmdb/lmdb-linux-arm64" "3.0.13" + "@lmdb/lmdb-linux-x64" "3.0.13" + "@lmdb/lmdb-win32-x64" "3.0.13" loader-runner@^4.2.0: version "4.3.0" @@ -7553,14 +6594,14 @@ log-update@^4.0.0: slice-ansi "^4.0.0" wrap-ansi "^6.2.0" -log-update@^6.0.0: - version "6.0.0" - resolved "https://registry.yarnpkg.com/log-update/-/log-update-6.0.0.tgz#0ddeb7ac6ad658c944c1de902993fce7c33f5e59" - integrity sha512-niTvB4gqvtof056rRIrTZvjNYE4rCUzO6X/X+kYjd7WFxXeJ0NwEFnRxX6ehkvv3jTwrXnNdtAak5XYZuIyPFw== +log-update@^6.1.0: + version "6.1.0" + resolved "https://registry.yarnpkg.com/log-update/-/log-update-6.1.0.tgz#1a04ff38166f94647ae1af562f4bd6a15b1b7cd4" + integrity sha512-9ie8ItPR6tjY5uYJh8K/Zrv/RMZ5VOlOWvtZdEHYSTFKZfIBPQa9tOAEeAWhd+AnIneLJ22w5fjOYtoutpWq5w== dependencies: - ansi-escapes "^6.2.0" - cli-cursor "^4.0.0" - slice-ansi "^7.0.0" + ansi-escapes "^7.0.0" + cli-cursor "^5.0.0" + slice-ansi "^7.1.0" strip-ansi "^7.1.0" wrap-ansi "^9.0.0" @@ -7585,12 +6626,7 @@ lower-case@^2.0.2: dependencies: tslib "^2.0.3" -lru-cache@^10.0.1: - version "10.1.0" - resolved 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"https://registry.yarnpkg.com/lru-cache/-/lru-cache-10.0.0.tgz#b9e2a6a72a129d81ab317202d93c7691df727e61" - integrity sha512-svTf/fzsKHffP42sujkO/Rjs37BCIsQVRCeNYIm9WN8rgT7ffoUnRtZCqU+6BqcSBdv8gwJeTz8knJpgACeQMw== - magic-string@0.30.10: version "0.30.10" resolved "https://registry.yarnpkg.com/magic-string/-/magic-string-0.30.10.tgz#123d9c41a0cb5640c892b041d4cfb3bd0aa4b39e" @@ -7621,6 +6645,13 @@ magic-string@0.30.10: dependencies: "@jridgewell/sourcemap-codec" "^1.4.15" +magic-string@0.30.11: + version "0.30.11" + resolved "https://registry.yarnpkg.com/magic-string/-/magic-string-0.30.11.tgz#301a6f93b3e8c2cb13ac1a7a673492c0dfd12954" + integrity sha512-+Wri9p0QHMy+545hKww7YAu5NyzF8iomPL/RQazugQ9+Ez4Ic3mERMd8ZTX5rfK944j+560ZJi8iAwgak1Ac7A== + dependencies: + "@jridgewell/sourcemap-codec" "^1.5.0" + make-dir@^2.1.0: version "2.1.0" resolved "https://registry.yarnpkg.com/make-dir/-/make-dir-2.1.0.tgz#5f0310e18b8be898cc07009295a30ae41e91e6f5" @@ -7634,24 +6665,7 @@ make-error@^1.1.1: resolved "https://registry.yarnpkg.com/make-error/-/make-error-1.3.6.tgz#2eb2e37ea9b67c4891f684a1394799af484cf7a2" integrity sha512-s8UhlNe7vPKomQhC1qFelMokr/Sc3AgNbso3n74mVPA5LTZwkB9NlXf4XPamLxJE8h0gh73rM94xvwRT2CVInw== -make-fetch-happen@^13.0.0: - version "13.0.0" - resolved "https://registry.yarnpkg.com/make-fetch-happen/-/make-fetch-happen-13.0.0.tgz#705d6f6cbd7faecb8eac2432f551e49475bfedf0" - integrity sha512-7ThobcL8brtGo9CavByQrQi+23aIfgYU++wg4B87AIS8Rb2ZBt/MEaDqzA00Xwv/jUjAjYkLHjVolYuTLKda2A== - dependencies: - "@npmcli/agent" "^2.0.0" - cacache "^18.0.0" - http-cache-semantics "^4.1.1" - is-lambda "^1.0.1" - minipass "^7.0.2" - minipass-fetch "^3.0.0" - minipass-flush "^1.0.5" - minipass-pipeline "^1.2.4" - negotiator "^0.6.3" - promise-retry "^2.0.1" - ssri "^10.0.0" - -make-fetch-happen@^13.0.1: +make-fetch-happen@^13.0.0, make-fetch-happen@^13.0.1: version "13.0.1" resolved 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micromatch@^4.0.4, micromatch@^4.0.5: +micromatch@^4.0.2, micromatch@^4.0.4, micromatch@^4.0.5, micromatch@^4.0.8: version "4.0.8" resolved "https://registry.yarnpkg.com/micromatch/-/micromatch-4.0.8.tgz#d66fa18f3a47076789320b9b1af32bd86d9fa202" integrity sha512-PXwfBhYu0hBCPw8Dn0E+WDYb7af3dSLVWKi3HGv84IdF4TyFoC0ysxFd0Goxw7nSv4T/PzEJQxsYsEiFCKo2BA== @@ -7737,12 +6756,17 @@ micromatch@^4.0.2, micromatch@^4.0.4, micromatch@^4.0.5: braces "^3.0.3" picomatch "^2.3.1" -mime-db@1.52.0, "mime-db@>= 1.43.0 < 2": +mime-db@1.52.0: version "1.52.0" resolved "https://registry.yarnpkg.com/mime-db/-/mime-db-1.52.0.tgz#bbabcdc02859f4987301c856e3387ce5ec43bf70" integrity sha512-sPU4uV7dYlvtWJxwwxHD0PuihVNiE7TyAbQ5SWxDCB9mUYvOgroQOwYQQOKPJ8CIbE+1ETVlOoK1UC2nU3gYvg== -mime-types@^2.1.12, mime-types@^2.1.27, mime-types@^2.1.31, mime-types@~2.1.17, mime-types@~2.1.24, mime-types@~2.1.34: +"mime-db@>= 1.43.0 < 2": + version "1.53.0" + resolved "https://registry.yarnpkg.com/mime-db/-/mime-db-1.53.0.tgz#3cb63cd820fc29896d9d4e8c32ab4fcd74ccb447" + integrity sha512-oHlN/w+3MQ3rba9rqFr6V/ypF10LSkdwUysQL7GkXoTgIWeV+tcXGA852TBxH+gsh8UWoyhR1hKcoMJTuWflpg== + +mime-types@^2.1.27, mime-types@^2.1.31, mime-types@~2.1.17, mime-types@~2.1.24, mime-types@~2.1.34: version "2.1.35" resolved "https://registry.yarnpkg.com/mime-types/-/mime-types-2.1.35.tgz#381a871b62a734450660ae3deee44813f70d959a" integrity sha512-ZDY+bPm5zTTF+YpCrAU9nK0UgICYPT0QtT1NZWFv4s++TNkcgVaT0g6+4R2uI4MjQjzysHB1zxuWL50hzaeXiw== @@ -7759,6 +6783,11 @@ mimic-fn@^2.1.0: resolved "https://registry.yarnpkg.com/mimic-fn/-/mimic-fn-2.1.0.tgz#7ed2c2ccccaf84d3ffcb7a69b57711fc2083401b" integrity sha512-OqbOk5oEQeAZ8WXWydlu9HJjz9WVdEIvamMCcXmuqUYjTknH/sqsWvhQ3vgwKFRR1HpjvNBKQ37nbJgYzGqGcg== +mimic-function@^5.0.0: + version "5.0.1" + resolved "https://registry.yarnpkg.com/mimic-function/-/mimic-function-5.0.1.tgz#acbe2b3349f99b9deaca7fb70e48b83e94e67076" + integrity sha512-VP79XUPxV2CigYP3jWwAUFSku2aKqBH7uTAapFWCBqutsbmDo96KY5o8uh6U+/YSIn5OxJnXp73beVkpqMIGhA== + mini-css-extract-plugin@2.9.0: version "2.9.0" resolved "https://registry.yarnpkg.com/mini-css-extract-plugin/-/mini-css-extract-plugin-2.9.0.tgz#c73a1327ccf466f69026ac22a8e8fd707b78a235" @@ -7772,13 +6801,6 @@ minimalistic-assert@^1.0.0: resolved "https://registry.yarnpkg.com/minimalistic-assert/-/minimalistic-assert-1.0.1.tgz#2e194de044626d4a10e7f7fbc00ce73e83e4d5c7" integrity sha512-UtJcAD4yEaGtjPezWuO9wC4nwUnVH/8/Im3yEHQP4b67cXlD/Qr9hdITCU1xDbSEXg2XKNaP8jsReV7vQd00/A== -minimatch@9.0.3, minimatch@^9.0.0, minimatch@^9.0.1: - version "9.0.3" - resolved "https://registry.yarnpkg.com/minimatch/-/minimatch-9.0.3.tgz#a6e00c3de44c3a542bfaae70abfc22420a6da825" - integrity sha512-RHiac9mvaRw0x3AYRgDC1CxAP7HTcNrrECeA8YYJeWnpo+2Q5CegtZjaotWTWxDG3UeGA1coE05iH1mPjT/2mg== - dependencies: - brace-expansion "^2.0.1" - minimatch@^3.0.4, minimatch@^3.0.5, minimatch@^3.1.1, minimatch@^3.1.2: version "3.1.2" resolved "https://registry.yarnpkg.com/minimatch/-/minimatch-3.1.2.tgz#19cd194bfd3e428f049a70817c038d89ab4be35b" @@ -7786,37 +6808,18 @@ minimatch@^3.0.4, minimatch@^3.0.5, minimatch@^3.1.1, minimatch@^3.1.2: dependencies: brace-expansion "^1.1.7" -minimatch@^4.2.3: - version "4.2.3" - resolved "https://registry.yarnpkg.com/minimatch/-/minimatch-4.2.3.tgz#b4dcece1d674dee104bb0fb833ebb85a78cbbca6" - integrity sha512-lIUdtK5hdofgCTu3aT0sOaHsYR37viUuIc0rwnnDXImbwFRcumyLMeZaM0t0I/fgxS6s6JMfu0rLD1Wz9pv1ng== - dependencies: - brace-expansion "^1.1.7" - -minimatch@^5.0.1: - version "5.1.4" - resolved "https://registry.yarnpkg.com/minimatch/-/minimatch-5.1.4.tgz#4e2d39d872684e97b309a9104251c3f1aa4e9d1c" - integrity sha512-U0iNYXt9wALljzfnGkhFSy5sAC6/SCR3JrHrlsdJz4kF8MvhTRQNiC59iUi1iqsitV7abrNAJWElVL9pdnoUgw== - dependencies: - brace-expansion "^2.0.1" - -minimatch@^9.0.4: +minimatch@^9.0.0, minimatch@^9.0.4, minimatch@^9.0.5: version "9.0.5" resolved 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minipass "^7.0.3" minipass-fetch@^3.0.0: - version "3.0.1" - resolved "https://registry.yarnpkg.com/minipass-fetch/-/minipass-fetch-3.0.1.tgz#bae3789f668d82ffae3ea47edc6b78b8283b3656" - integrity sha512-t9/wowtf7DYkwz8cfMSt0rMwiyNIBXf5CKZ3S5ZMqRqMYT0oLTp0x1WorMI9WTwvaPg21r1JbFxJMum8JrLGfw== + version "3.0.5" + resolved "https://registry.yarnpkg.com/minipass-fetch/-/minipass-fetch-3.0.5.tgz#f0f97e40580affc4a35cc4a1349f05ae36cb1e4c" + integrity sha512-2N8elDQAtSnFV0Dk7gt15KHsS0Fyz6CbYZ360h0WTYV1Ty46li3rAXVOQj1THMNLdmrD9Vt5pBPtWtVkpwGBqg== dependencies: - minipass "^4.0.0" + minipass "^7.0.3" minipass-sized "^1.0.3" minizlib "^2.1.2" optionalDependencies: @@ -7863,29 +6866,12 @@ minipass@^3.0.0: dependencies: yallist "^4.0.0" -minipass@^4.0.0: - version "4.0.0" - resolved "https://registry.yarnpkg.com/minipass/-/minipass-4.0.0.tgz#7cebb0f9fa7d56f0c5b17853cbe28838a8dbbd3b" - integrity sha512-g2Uuh2jEKoht+zvO6vJqXmYpflPqzRBT+Th2h01DKh5z7wbY/AZ2gCQ78cP70YoHPyFdY30YBV5WxgLOEwOykw== - dependencies: - yallist "^4.0.0" - minipass@^5.0.0: version "5.0.0" resolved "https://registry.yarnpkg.com/minipass/-/minipass-5.0.0.tgz#3e9788ffb90b694a5d0ec94479a45b5d8738133d" integrity sha512-3FnjYuehv9k6ovOEbyOswadCDPX1piCfhV8ncmYtHOjuPwylVWsghTLo7rabjC3Rx5xD4HDx8Wm1xnMF7S5qFQ== -"minipass@^5.0.0 || ^6.0.2 || ^7.0.0": - version "7.0.2" - resolved "https://registry.yarnpkg.com/minipass/-/minipass-7.0.2.tgz#58a82b7d81c7010da5bd4b2c0c85ac4b4ec5131e" - integrity sha512-eL79dXrE1q9dBbDCLg7xfn/vl7MS4F1gvJAgjJrQli/jbQWdUttuVawphqpffoIYfRdq78LHx6GP4bU/EQ2ATA== - -minipass@^7.0.2, minipass@^7.0.3: - version "7.0.4" - resolved "https://registry.yarnpkg.com/minipass/-/minipass-7.0.4.tgz#dbce03740f50a4786ba994c1fb908844d27b038c" - integrity sha512-jYofLM5Dam9279rdkWzqHozUo4ybjdZmCsDHePy5V/PbBcVMiSZR97gmAy45aqi8CK1lG2ECd356FU86avfwUQ== - -minipass@^7.1.2: +"minipass@^5.0.0 || ^6.0.2 || ^7.0.0", minipass@^7.0.2, minipass@^7.0.3, minipass@^7.1.2: version "7.1.2" resolved "https://registry.yarnpkg.com/minipass/-/minipass-7.1.2.tgz#93a9626ce5e5e66bd4db86849e7515e92340a707" integrity sha512-qOOzS1cBTWYF4BH8fVePDBOO9iptMnGUEZwNc/cMWnTV2nVLZ7VoNWEPHkYczZA0pdoA7dl6e7FL659nX9S2aw== @@ -7920,12 +6906,7 @@ ms@2.0.0: resolved "https://registry.yarnpkg.com/ms/-/ms-2.0.0.tgz#5608aeadfc00be6c2901df5f9861788de0d597c8" integrity sha512-Tpp60P6IUJDTuOq/5Z8cdskzJujfwqfOTkrwIwj7IRISpnkJnT6SyJ4PCPnGMoFjC9ddhal5KVIYtAt97ix05A== -ms@2.1.2: - version "2.1.2" - resolved "https://registry.yarnpkg.com/ms/-/ms-2.1.2.tgz#d09d1f357b443f493382a8eb3ccd183872ae6009" - integrity sha512-sGkPx+VjMtmA6MX27oA4FBFELFCZZ4S4XqeGOXCv68tT+jb3vk/RyaKWP0PTKyWtmLSM0b+adUTEvbs1PEaH2w== - -ms@2.1.3, ms@^2.1.1: +ms@2.1.3, ms@^2.1.3: version "2.1.3" resolved "https://registry.yarnpkg.com/ms/-/ms-2.1.3.tgz#574c8138ce1d2b5861f0b44579dbadd60c6615b2" integrity sha512-6FlzubTLZG3J2a/NVCAleEhjzq5oxgHyaCU9yYXvcLsvoVaHJq/s5xXI6/XXP6tz7R9xAOtHnSO/tXtF3WRTlA== @@ -7945,9 +6926,9 @@ msgpackr-extract@^3.0.2: "@msgpackr-extract/msgpackr-extract-win32-x64" "3.0.3" msgpackr@^1.10.2: - version "1.11.0" - resolved "https://registry.yarnpkg.com/msgpackr/-/msgpackr-1.11.0.tgz#8321d52333048cadc749f56385e3231e65337091" - integrity sha512-I8qXuuALqJe5laEBYoFykChhSXLikZmUhccjGsPuSJ/7uPip2TJ7lwdIQwWSAi0jGZDXv4WOP8Qg65QZRuXxXw== + version "1.11.2" + resolved "https://registry.yarnpkg.com/msgpackr/-/msgpackr-1.11.2.tgz#4463b7f7d68f2e24865c395664973562ad24473d" + integrity sha512-F9UngXRlPyWCDEASDpTf6c9uNhGPTqnTeLVt7bN+bU1eajoR/8V9ys2BRaV5C/e5ihE6sJ9uPIKaYt6bFuO32g== optionalDependencies: msgpackr-extract "^3.0.2" @@ -7974,7 +6955,7 @@ mute-stream@^1.0.0: resolved "https://registry.yarnpkg.com/mute-stream/-/mute-stream-1.0.0.tgz#e31bd9fe62f0aed23520aa4324ea6671531e013e" integrity sha512-avsJQhyd+680gKXyG/sQc0nXaC6rBkPOfyHYcFb9+hdkqQkR9bdnkJ0AMZhke0oesPqIO+mFFJ+IdBc7mst4IA== -nanoid@^3.3.7: +nanoid@^3.3.7, nanoid@^3.3.8: version "3.3.8" resolved 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postcss-selector-parser "^7.0.0" postcss-value-parser "^4.1.0" postcss-modules-scope@^3.2.0: - version "3.2.0" - resolved "https://registry.yarnpkg.com/postcss-modules-scope/-/postcss-modules-scope-3.2.0.tgz#a43d28289a169ce2c15c00c4e64c0858e43457d5" - integrity sha512-oq+g1ssrsZOsx9M96c5w8laRmvEu9C3adDSjI8oTcbfkrTE8hx/zfyobUoWIxaKPO8bt6S62kxpw5GqypEw1QQ== + version "3.2.1" + resolved "https://registry.yarnpkg.com/postcss-modules-scope/-/postcss-modules-scope-3.2.1.tgz#1bbccddcb398f1d7a511e0a2d1d047718af4078c" + integrity sha512-m9jZstCVaqGjTAuny8MdgE88scJnCiQSlSrOWcTQgM2t32UBe+MUmFSO5t7VMSfAf/FJKImAxBav8ooCHJXCJA== dependencies: - postcss-selector-parser "^6.0.4" + postcss-selector-parser "^7.0.0" postcss-modules-values@^4.0.0: version "4.0.0" @@ -8766,10 +7646,10 @@ postcss-modules-values@^4.0.0: dependencies: icss-utils "^5.0.0" -postcss-selector-parser@^6.0.2, postcss-selector-parser@^6.0.4: - version "6.0.11" - resolved 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unique-slug@^4.0.0: dependencies: imurmurhash "^0.1.4" -universalify@^2.0.0: - version "2.0.0" - resolved "https://registry.yarnpkg.com/universalify/-/universalify-2.0.0.tgz#75a4984efedc4b08975c5aeb73f530d02df25717" - integrity sha512-hAZsKq7Yy11Zu1DE0OzWjw7nnLZmJZYTDZZyEFHZdUhV8FkH5MCfoU1XMaxXovpyW5nq5scPqq0ZDP9Zyl04oQ== - unixify@^1.0.0: version "1.0.0" resolved "https://registry.yarnpkg.com/unixify/-/unixify-1.0.0.tgz#3a641c8c2ffbce4da683a5c70f03a462940c2090" @@ -10407,37 +9144,13 @@ unpipe@1.0.0, unpipe@~1.0.0: resolved "https://registry.yarnpkg.com/unpipe/-/unpipe-1.0.0.tgz#b2bf4ee8514aae6165b4817829d21b2ef49904ec" integrity sha512-pjy2bYhSsufwWlKwPc+l3cN7+wuJlK6uz0YdJEOlQDbl6jo/YlPi4mb8agUkVC8BF7V8NuzeyPNqRksA3hztKQ== -update-browserslist-db@^1.0.11: - version "1.0.11" - resolved "https://registry.yarnpkg.com/update-browserslist-db/-/update-browserslist-db-1.0.11.tgz#9a2a641ad2907ae7b3616506f4b977851db5b940" - integrity 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+webpack-merge@6.0.1: + version "6.0.1" + resolved "https://registry.yarnpkg.com/webpack-merge/-/webpack-merge-6.0.1.tgz#50c776868e080574725abc5869bd6e4ef0a16c6a" + integrity sha512-hXXvrjtx2PLYx4qruKl+kyRSLc52V+cCvMxRjmKwoA+CBbbF5GfIBtR6kCvl0fYGqTUPKB+1ktVmTHqMOzgCBg== dependencies: clone-deep "^4.0.1" flat "^5.0.2" - wildcard "^2.0.0" + wildcard "^2.0.1" webpack-sources@^3.0.0, webpack-sources@^3.2.3: version "3.2.3" @@ -10680,12 +9371,11 @@ webpack-subresource-integrity@5.1.0: dependencies: typed-assert "^1.0.8" -webpack@5.92.1: - version "5.92.1" - resolved "https://registry.yarnpkg.com/webpack/-/webpack-5.92.1.tgz#eca5c1725b9e189cffbd86e8b6c3c7400efc5788" - integrity sha512-JECQ7IwJb+7fgUFBlrJzbyu3GEuNBcdqr1LD7IbSzwkSmIevTm8PF+wej3Oxuz/JFBUZ6O1o43zsPkwm1C4TmA== +webpack@5.94.0: + version "5.94.0" + resolved "https://registry.yarnpkg.com/webpack/-/webpack-5.94.0.tgz#77a6089c716e7ab90c1c67574a28da518a20970f" + integrity 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"https://registry.yarnpkg.com/ws/-/ws-7.5.10.tgz#58b5c20dc281633f6c19113f39b349bd8bd558d9" integrity sha512-+dbF1tHwZpXcbOJdVOkzLDxZP1ailvSxM6ZweXTegylPny803bFhA+vqBYw4s31NSAk4S2Qz+AKXK9a4wkdjcQ== -ws@^8.12.0, ws@^8.16.0, ws@^8.17.1: +ws@^8.16.0, ws@^8.17.1: version "8.18.0" resolved "https://registry.yarnpkg.com/ws/-/ws-8.18.0.tgz#0d7505a6eafe2b0e712d232b42279f53bc289bbc" integrity sha512-8VbfWfHLbbwu3+N6OKsOMpBdT4kXPDDB9cJk2bJ6mh9ucxdlnNvH1e+roYkKmN9Nxw2yjz7VzeO9oOz2zJ04Pw== @@ -10860,14 +9555,9 @@ yaml@^1.7.2: integrity sha512-r3vXyErRCYJ7wg28yvBY5VSoAF8ZvlcW9/BwUzEtUsjvX/DKs24dIkuwjtuprwJJHsbyUbLApepYTR1BN4uHrg== yaml@^2.3.1: - version "2.5.0" - resolved "https://registry.yarnpkg.com/yaml/-/yaml-2.5.0.tgz#c6165a721cf8000e91c36490a41d7be25176cf5d" - integrity sha512-2wWLbGbYDiSqqIKoPjar3MPgB94ErzCtrNE1FdqGuaO0pi2JGjmE8aW8TDZwzU7vuxcGRdL/4gPQwQ7hD5AMSw== - -yargs-parser@21.1.1, yargs-parser@^21.1.1: - version "21.1.1" - resolved "https://registry.yarnpkg.com/yargs-parser/-/yargs-parser-21.1.1.tgz#9096bceebf990d21bb31fa9516e0ede294a77d35" - integrity sha512-tVpsJW7DdjecAiFpbIB1e3qxIQsE6NoPc5/eTdrbbIC4h0LVsWhnoa3g+m2HclBIujHzsxZ4VJVA+GUuc2/LBw== + version "2.7.0" + resolved "https://registry.yarnpkg.com/yaml/-/yaml-2.7.0.tgz#aef9bb617a64c937a9a748803786ad8d3ffe1e98" + integrity sha512-+hSoy/QHluxmC9kCIJyL/uyFmLmc+e5CFR5Wa+bpIhIj85LVb9ZH2nVnqrHoSvKogwODv0ClqZkmiSSaIH5LTA== yargs-parser@^18.1.2: version "18.1.3" @@ -10877,7 +9567,12 @@ yargs-parser@^18.1.2: camelcase "^5.0.0" decamelize "^1.2.0" -yargs@17.7.2, yargs@^17.6.2: +yargs-parser@^21.1.1: + version "21.1.1" + resolved "https://registry.yarnpkg.com/yargs-parser/-/yargs-parser-21.1.1.tgz#9096bceebf990d21bb31fa9516e0ede294a77d35" + integrity sha512-tVpsJW7DdjecAiFpbIB1e3qxIQsE6NoPc5/eTdrbbIC4h0LVsWhnoa3g+m2HclBIujHzsxZ4VJVA+GUuc2/LBw== + +yargs@17.7.2, yargs@^17.0.0, yargs@^17.2.1: version "17.7.2" resolved "https://registry.yarnpkg.com/yargs/-/yargs-17.7.2.tgz#991df39aca675a192b816e1e0363f9d75d2aa269" integrity sha512-7dSzzRQ++CKnNI/krKnYRV7JKKPUXMEh61soaHKg9mrWEhzFWhFnxPxGl+69cD1Ou63C13NUPCnmIcrvqCuM6w== @@ -10907,19 +9602,6 @@ yargs@^15.3.1: y18n "^4.0.0" yargs-parser "^18.1.2" -yargs@^17.0.0, yargs@^17.2.1: - version "17.6.2" - resolved "https://registry.yarnpkg.com/yargs/-/yargs-17.6.2.tgz#2e23f2944e976339a1ee00f18c77fedee8332541" - integrity sha512-1/9UrdHjDZc0eOU0HxOHoS78C69UD3JRMvzlJ7S79S2nTaWRA/whGCTV8o9e/N/1Va9YIV7Q4sOxD8VV4pCWOw== - dependencies: - cliui "^8.0.1" - escalade "^3.1.1" - get-caller-file "^2.0.5" - require-directory "^2.1.1" - string-width "^4.2.3" - y18n "^5.0.5" - yargs-parser "^21.1.1" - yn@3.1.1: version "3.1.1" resolved "https://registry.yarnpkg.com/yn/-/yn-3.1.1.tgz#1e87401a09d767c1d5eab26a6e4c185182d2eb50" @@ -10931,9 +9613,9 @@ yocto-queue@^0.1.0: integrity sha512-rVksvsnNCdJ/ohGc6xgPwyN8eheCxsiLM8mxuE/t/mOVqJewPuO1miLpTHQiRgTKCLexL4MeAFVagts7HmNZ2Q== yocto-queue@^1.0.0: - version "1.0.0" - resolved "https://registry.yarnpkg.com/yocto-queue/-/yocto-queue-1.0.0.tgz#7f816433fb2cbc511ec8bf7d263c3b58a1a3c251" - integrity sha512-9bnSc/HEW2uRy67wc+T8UwauLuPJVn28jb+GtJY16iiKWyvmYJRXVT4UamsAEGQfPohgr2q4Tq0sQbQlxTfi1g== + version "1.1.1" + resolved "https://registry.yarnpkg.com/yocto-queue/-/yocto-queue-1.1.1.tgz#fef65ce3ac9f8a32ceac5a634f74e17e5b232110" + integrity sha512-b4JR1PFR10y1mKjhHY9LaGo6tmrgjit7hxVIeAmyMw3jegXR4dhYqLaQF5zMXZxY7tLpMyJeLjr1C4rLmkVe8g== yoctocolors-cjs@^2.1.2: version "2.1.2" From 640c9a1dc91e4796d3d9d18b45d1bd45893c0aed Mon Sep 17 00:00:00 2001 From: Joshua McMichael Date: Thu, 6 Feb 2025 10:10:40 -0600 Subject: [PATCH 4/9] created variant-info tab-card containing myvariantinfo and opencravat annotations --- .../gene-variant-summary.page.html | 25 +++++++++----- .../gene-variant-summary.page.ts | 2 ++ .../variant-info/variant-info.component.html | 34 +++++++++++++++++++ .../variant-info/variant-info.component.less | 0 .../variant-info/variant-info.component.ts | 29 ++++++++++++++++ .../variant-info/variant-info.types.ts | 7 ++++ client/src/app/generated/civic.apollo.ts | 2 -- 7 files changed, 89 insertions(+), 10 deletions(-) create mode 100644 client/src/app/components/variants/variant-info/variant-info.component.html create mode 100644 client/src/app/components/variants/variant-info/variant-info.component.less create mode 100644 client/src/app/components/variants/variant-info/variant-info.component.ts create mode 100644 client/src/app/components/variants/variant-info/variant-info.types.ts diff --git a/client/src/app/components/variants/gene-variant-summary/gene-variant-summary.page.html b/client/src/app/components/variants/gene-variant-summary/gene-variant-summary.page.html index 264181661..38cda9f25 100644 --- a/client/src/app/components/variants/gene-variant-summary/gene-variant-summary.page.html +++ b/client/src/app/components/variants/gene-variant-summary/gene-variant-summary.page.html @@ -131,13 +131,14 @@ - + + nzBordered="true"> @@ -247,9 +248,17 @@ - - + + + + + - + diff --git a/client/src/app/components/variants/gene-variant-summary/gene-variant-summary.page.ts b/client/src/app/components/variants/gene-variant-summary/gene-variant-summary.page.ts index 7512e4e7f..53f2be435 100644 --- a/client/src/app/components/variants/gene-variant-summary/gene-variant-summary.page.ts +++ b/client/src/app/components/variants/gene-variant-summary/gene-variant-summary.page.ts @@ -18,6 +18,7 @@ import { CvcUserTagModule } from '@app/components/users/user-tag/user-tag.module import { CvcFeatureTagModule } from '@app/components/features/feature-tag/feature-tag.module' import { CvcPipesModule } from '@app/core/pipes/pipes.module' import { CvcOpenCravatAnnotationsModule } from '../open-cravat-annotations/open-cravat-annotations.module' +import { CvcVariantInfo } from '../variant-info/variant-info.component' @Component({ standalone: true, @@ -42,6 +43,7 @@ import { CvcOpenCravatAnnotationsModule } from '../open-cravat-annotations/open- CvcMyVariantInfoModule, CvcOpenCravatAnnotationsModule, CvcPipesModule, + CvcVariantInfo, ], }) export class CvcGeneVariantSummaryComponent implements OnInit { diff --git a/client/src/app/components/variants/variant-info/variant-info.component.html b/client/src/app/components/variants/variant-info/variant-info.component.html new file mode 100644 index 000000000..26b631277 --- /dev/null +++ b/client/src/app/components/variants/variant-info/variant-info.component.html @@ -0,0 +1,34 @@ + + + + + + + + @if (selectedTab() === 0) { + @if (variantInfo().myVariantInfo) { + + } @else { + + + } + } + @if (selectedTab() === 1) { + @if (variantInfo().openCravatAnnotations && variantInfo().openCravatUrl) { + + + } @else { + + + } + } + diff --git a/client/src/app/components/variants/variant-info/variant-info.component.less b/client/src/app/components/variants/variant-info/variant-info.component.less new file mode 100644 index 000000000..e69de29bb diff --git a/client/src/app/components/variants/variant-info/variant-info.component.ts b/client/src/app/components/variants/variant-info/variant-info.component.ts new file mode 100644 index 000000000..633f6b01a --- /dev/null +++ b/client/src/app/components/variants/variant-info/variant-info.component.ts @@ -0,0 +1,29 @@ +import { Component, input, model } from '@angular/core' +import { VariantInfo } from './variant-info.types' +import { NzCardModule } from 'ng-zorro-antd/card' +import { NzTabsModule } from 'ng-zorro-antd/tabs' +import { NzDescriptionsModule } from 'ng-zorro-antd/descriptions' +import { NzTagModule } from 'ng-zorro-antd/tag' +import { CvcMyVariantInfoModule } from '../my-variant-info/my-variant-info.module' +import { CvcEmptyRevisableModule } from '@app/components/shared/empty-revisable/empty-revisable.module' +import { CvcOpenCravatAnnotationsModule } from '../open-cravat-annotations/open-cravat-annotations.module' + +@Component({ + selector: 'cvc-variant-info', + standalone: true, + imports: [ + NzCardModule, + NzTabsModule, + NzDescriptionsModule, + NzTagModule, + CvcMyVariantInfoModule, + CvcEmptyRevisableModule, + CvcOpenCravatAnnotationsModule, + ], + templateUrl: './variant-info.component.html', + styleUrl: './variant-info.component.less', +}) +export class CvcVariantInfo { + variantInfo = input.required() + selectedTab = model(0) +} diff --git a/client/src/app/components/variants/variant-info/variant-info.types.ts b/client/src/app/components/variants/variant-info/variant-info.types.ts new file mode 100644 index 000000000..8cf83b5fa --- /dev/null +++ b/client/src/app/components/variants/variant-info/variant-info.types.ts @@ -0,0 +1,7 @@ +import { Maybe, MyVariantInfoFieldsFragment } from '@app/generated/civic.apollo' + +export type VariantInfo = { + myVariantInfo: Maybe + openCravatAnnotations: Maybe + openCravatUrl: Maybe +} diff --git a/client/src/app/generated/civic.apollo.ts b/client/src/app/generated/civic.apollo.ts index 001b27dd2..9bb570ee2 100644 --- a/client/src/app/generated/civic.apollo.ts +++ b/client/src/app/generated/civic.apollo.ts @@ -129,7 +129,6 @@ export enum ActivitySubjectInput { Assertion = 'ASSERTION', Comment = 'COMMENT', EvidenceItem = 'EVIDENCE_ITEM', - ExonCoordinate = 'EXON_COORDINATE', Feature = 'FEATURE', Flag = 'FLAG', MolecularProfile = 'MOLECULAR_PROFILE', @@ -138,7 +137,6 @@ export enum ActivitySubjectInput { Source = 'SOURCE', SourceSuggestion = 'SOURCE_SUGGESTION', Variant = 'VARIANT', - VariantCoordinate = 'VARIANT_COORDINATE', VariantGroup = 'VARIANT_GROUP' } From 872b0d8ea771b8b0eb8987346f15babf95693172 Mon Sep 17 00:00:00 2001 From: Joshua McMichael Date: Thu, 6 Feb 2025 11:11:40 -0600 Subject: [PATCH 5/9] updated my-variant-info component to fix in variant-info tab-card --- .../my-gene-info/my-gene-info.component.html | 4 +- .../my-variant-info.component.html | 1550 ++++++++--------- .../my-variant-info.component.less | 7 + .../my-variant-info.component.ts | 15 +- .../variant-info/variant-info.component.html | 4 +- 5 files changed, 776 insertions(+), 804 deletions(-) diff --git a/client/src/app/components/genes/my-gene-info/my-gene-info.component.html b/client/src/app/components/genes/my-gene-info/my-gene-info.component.html index b4000728f..bcf6347ef 100644 --- a/client/src/app/components/genes/my-gene-info/my-gene-info.component.html +++ b/client/src/app/components/genes/my-gene-info/my-gene-info.component.html @@ -17,7 +17,7 @@ -
+
@@ -91,7 +91,7 @@ -
+

- - - - - - - - - - - - - - - - - -

-
-
- MyVariant.info ID: -
-
- {{ variantInfo.myVariantInfoId }} - ClinVar ID:  - - - {{ variantInfo.clinvarId }} - - -
-
-
-
- dbSNP RSID: -
-
- - - {{ variantInfo.dbsnpRsid }} - - - COSMIC ID (v68):  - - - {{ variantInfo.cosmicId }} - - -
-
-
-
- SNPEff Effect: -
-
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+
+
+ MyVariant.info ID: +
+
+ {{ variantInfo.myVariantInfoId }} + ClinVar ID:  + + + {{ variantInfo.clinvarId }} + + +
+
+
+
+ dbSNP RSID: +
+
+ + + {{ variantInfo.dbsnpRsid }} + + + COSMIC ID (v68):  + + + {{ variantInfo.cosmicId }} + + +
+
+
+
+ SNPEff Effect: +
+
+ + + {{ e }}, + + +
+
+
+
+ SNPEff Impact: +
+
+ + + {{ i }}, + + +
+
+
+ + + +
+
+
+ ClinVar ID: +
+
+ + + {{ variantInfo.clinvarId }} + + + OMIM:  + + + {{ variantInfo.clinvarOmim }} + + +
+
+
+
+ ClinVar Clinical Significance: +
+
+ + + {{ cs }}, + + +
+
+
+
+ HGVS Coding: +
+
+ + + {{ hgvs }}
 + + +
+
+
+
+ HGVS Genomic: +
+
+ + + {{ hgvs }}
 + + +
+
+
+
+ HGVS Non-Coding: +
+
+ + + {{ hgvs }}
 + + +
+
+
+
+ HGVS Protein: +
+
+ + + {{ hgvs }}
 + + +
+
+
+ + + + + View this variant in the gnomAD browser + + + + + Type + Allele Frequency + Allele Count + Allele Number + Filter + + + + + Total Exome + + {{ variantInfo.gnomadExomeAlleleFrequency | ifEmpty: '--' }} + + {{ variantInfo.gnomadExomeAlleleCount | ifEmpty: '--' }} + + {{ variantInfo.gnomadExomeAlleleNumber | ifEmpty: '--' }} + + {{ variantInfo.gnomadExomeFilter | ifEmpty: '--' }} + + + Total Genome + + {{ variantInfo.gnomadGenomeAlleleFrequency | ifEmpty: '--' }} + + + {{ variantInfo.gnomadGenomeAlleleCount | ifEmpty: '--' }} + + + {{ variantInfo.gnomadGenomeAlleleNumber | ifEmpty: '--' }} + + {{ variantInfo.gnomadGenomeFilter | ifEmpty: '--' }} + + + + + + +
+
+
+ Allele Count: +
+
+ {{ variantInfo.exacAlleleCount | ifEmpty: '--' }} +
+
+
+
+ Allele Number: +
+
+ {{ variantInfo.exacAlleleNumber | ifEmpty: '--' }} +
+
+
+
+ Adjusted Allele Frequency: +
+
+ {{ variantInfo.exacAlleleFrequency | ifEmpty: '--' }} +
+
+
+ + + +
+
+
+ phyloP100way: +
+
+ {{ variantInfo.phyloP100way | ifEmpty: '--' }} +
+
+
+
+ phyloP30way: +
+
+ {{ variantInfo.phyloP30way | ifEmpty: '--' }} +
+
+
+
+ phastCons100way: +
+
+ {{ variantInfo.phastcons100way | ifEmpty: '--' }} +
+
+
+
+ phastCons30way: +
+
+ {{ variantInfo.phastcons30way | ifEmpty: '--' }} +
+
+
+
+ GERP++: +
+
+ {{ variantInfo.gerp | ifEmpty: '--' }} +
+
+
+
+ SiPhy: +
+
+ {{ variantInfo.siphy | ifEmpty: '--' }} +
+
+
+ + + +
+
+
+ EGL Class: +
+
+ {{ variantInfo.eglClass | ifEmpty: '--' }} +
+
+
+
+ Protein Variant Name: +
+
+ {{ variantInfo.eglProtein | ifEmpty: '--' }} +
+
+
+
+ Transcript Variant Name: +
+
+ {{ variantInfo.eglTranscript | ifEmpty: '--' }} +
+
+
+
+ HGVS: +
+
+ + + {{ hgvs }}
 + + +
+
+
+ + + +
+ + + + Predictor + Prediction + Score + + + + + REVEL + N/A + + {{ variantInfo.revelScore.join(', ') | ifEmpty: '--' }} + + + + SIFT + + *ngIf="variantInfo.siftPrediction.length > 0; else noValue"> - {{ e }}, + *ngFor="let p of variantInfo.siftPrediction; last as isLast"> + {{ p }}, -
-
-
-
- SNPEff Impact: -
-
+ + + *ngIf="variantInfo.siftScore.length > 0; else noValue"> - {{ i }}, + *ngFor="let s of variantInfo.siftScore; last as isLast"> + {{ s }}, -
-
-
- - - -
-
-
- ClinVar ID: -
-
- - - {{ variantInfo.clinvarId }} - - - OMIM:  - - - {{ variantInfo.clinvarOmim }} - - -
-
-
-
- ClinVar Clinical Significance: -
-
+ + + + Polyphen2 HDIV + - {{ cs }}, + {{ p }}, -
-
-
-
- HGVS Coding: -
-
+ + + *ngIf="variantInfo.polyphen2HdivScore.length > 0; else noValue"> - {{ hgvs }}
 + {{ s }}, -
-
-
-
- HGVS Genomic: -
-
+ + + + Polyphen2 HVAR + + *ngIf=" + variantInfo.polyphen2HvarPrediction.length > 0; + else noValue + "> - {{ hgvs }}
 + {{ p }}, -
-
-
-
- HGVS Non-Coding: -
-
+ + + *ngIf="variantInfo.polyphen2HvarScore.length > 0; else noValue"> - {{ hgvs }}
 + {{ s }}, -
-
-
-
- HGVS Protein: -
-
+ + + + LRT + {{ variantInfo.lrtPrediction | ifEmpty: '--' }} + {{ variantInfo.lrtScore | ifEmpty: '--' }} + + + MutationTaster + + *ngIf=" + variantInfo.mutationtasterPrediction.length > 0; + else noValue + "> - {{ hgvs }}
 + {{ p }}, -
-
-
- - - - - View this variant in the gnomAD browser - - - - - Type - Allele Frequency - Allele Count - Allele Number - Filter - - - - - Total Exome - - {{ variantInfo.gnomadExomeAlleleFrequency | ifEmpty : '--' }} - - {{ variantInfo.gnomadExomeAlleleCount | ifEmpty : '--' }} - - {{ variantInfo.gnomadExomeAlleleNumber | ifEmpty : '--' }} - - {{ variantInfo.gnomadExomeFilter | ifEmpty : '--' }} - - - Total Genome - - {{ variantInfo.gnomadGenomeAlleleFrequency | ifEmpty : '--' }} - - - {{ variantInfo.gnomadGenomeAlleleCount | ifEmpty : '--' }} - - - {{ variantInfo.gnomadGenomeAlleleNumber | ifEmpty : '--' }} - - {{ variantInfo.gnomadGenomeFilter | ifEmpty : '--' }} - - - - - - -
-
-
- Allele Count: -
-
- {{ variantInfo.exacAlleleCount | ifEmpty : '--' }} -
-
-
-
- Allele Number: -
-
- {{ variantInfo.exacAlleleNumber | ifEmpty : '--' }} -
-
-
-
- Adjusted Allele Frequency: -
-
- {{ variantInfo.exacAlleleFrequency | ifEmpty : '--' }} -
-
-
- - - -
-
-
- phyloP100way: -
-
- {{ variantInfo.phyloP100way | ifEmpty : '--' }} -
-
-
-
- phyloP30way: -
-
- {{ variantInfo.phyloP30way | ifEmpty : '--' }} -
-
-
-
- phastCons100way: -
-
- {{ variantInfo.phastcons100way | ifEmpty : '--' }} -
-
-
-
- phastCons30way: -
-
- {{ variantInfo.phastcons30way | ifEmpty : '--' }} -
-
-
-
- GERP++: -
-
- {{ variantInfo.gerp | ifEmpty : '--' }} -
-
-
-
- SiPhy: -
-
- {{ variantInfo.siphy | ifEmpty : '--' }} -
-
-
- - - -
-
-
- EGL Class: -
-
- {{ variantInfo.eglClass | ifEmpty : '--' }} -
-
-
-
- Protein Variant Name: -
-
- {{ variantInfo.eglProtein | ifEmpty : '--' }} -
-
-
-
- Transcript Variant Name: -
-
- {{ variantInfo.eglTranscript | ifEmpty : '--' }} -
-
-
-
- HGVS: -
-
+ + - - {{ hgvs }}
 - - -
-
-
- - - - - - - Predictor - Prediction - Score - - - - - REVEL - N/A - {{ variantInfo.revelScore.join(', ') | ifEmpty : '--' }} - - - SIFT - - - - {{ p }}, - - - - - - - {{ s }}, - - - - - - Polyphen2 HDIV - - - - {{ p }}, - - - - - - - {{ s }}, - - - - - - Polyphen2 HVAR - - - - {{ p }}, - - - - - - - {{ s }}, - - - - - - LRT - {{ variantInfo.lrtPrediction | ifEmpty : '--' }} - {{ variantInfo.lrtScore | ifEmpty : '--' }} - - - MutationTaster - + *ngIf=" + variantInfo.mutationtasterScore.length > 0; + else noValue + "> - - {{ p }}, - + {{ s }}, - - + + + + + MutationAssessor + + - - {{ s }}, - + {{ p }}, - - - - MutationAssessor - + + + + - - {{ p }}, - + {{ s }}, - - + + + + + FATHMM + + - - {{ s }}, - + {{ p }}, - - - - FATHMM - - - - {{ p }}, - - - - + + + + - - {{ s }}, - + *ngFor="let s of variantInfo.fathmmScore; last as isLast"> + {{ s }}, - - - - PROVEAN - + + + + + PROVEAN + + - - {{ p }}, - + {{ p }}, - - + + + + - - {{ s }}, - + *ngFor="let s of variantInfo.proveanScore; last as isLast"> + {{ s }}, - - - - MetaSVM - {{ variantInfo.metasvmPrediction | ifEmpty : '--' }} - {{ variantInfo.metasvmScore | ifEmpty : '--' }} - - - MetaLR - {{ variantInfo.metalrPrediction | ifEmpty : '--' }} - {{ variantInfo.metalrScore | ifEmpty : '--' }} - - - CADD - - Consequence: + + + + + MetaSVM + {{ variantInfo.metasvmPrediction | ifEmpty: '--' }} + {{ variantInfo.metasvmScore | ifEmpty: '--' }} + + + MetaLR + {{ variantInfo.metalrPrediction | ifEmpty: '--' }} + {{ variantInfo.metalrScore | ifEmpty: '--' }} + + + CADD + + Consequence: + - - {{ c }}, - + *ngFor="let c of variantInfo.caddConsequence; last as isLast"> + {{ c }}, -
- Consequence Detail: + +
+ Consequence Detail: + - - {{ d }}, - + *ngFor="let d of variantInfo.caddDetail; last as isLast"> + {{ d }}, - - - {{ variantInfo.caddScore | ifEmpty : '--' }} (raw) -
- {{ variantInfo.caddPhred | ifEmpty : '--' }} (PHRED) - - - - FATHMM-MKL - {{ variantInfo.fathmmMklPrediction | ifEmpty : '--' }} - {{ variantInfo.fathmmMklScore | ifEmpty : '--' }} - - - fitCons - N/A - {{ variantInfo.fitconsScore | ifEmpty : '--' }} - - - - - - + + + + {{ variantInfo.caddScore | ifEmpty: '--' }} (raw) +
+ {{ variantInfo.caddPhred | ifEmpty: '--' }} (PHRED) + + + + FATHMM-MKL + {{ variantInfo.fathmmMklPrediction | ifEmpty: '--' }} + {{ variantInfo.fathmmMklScore | ifEmpty: '--' }} + + + fitCons + N/A + {{ variantInfo.fitconsScore | ifEmpty: '--' }} + + + +
+ -- diff --git a/client/src/app/components/variants/my-variant-info/my-variant-info.component.less b/client/src/app/components/variants/my-variant-info/my-variant-info.component.less index 30681b7cc..dea8f5c57 100644 --- a/client/src/app/components/variants/my-variant-info/my-variant-info.component.less +++ b/client/src/app/components/variants/my-variant-info/my-variant-info.component.less @@ -1,5 +1,6 @@ :host { display: block; + margin: -8px; } nz-card { @@ -13,3 +14,9 @@ nz-card { .button-col { text-align: right; } + +.tab-content { + margin: 12px; + max-height: 260px; + overflow-y: auto; +} diff --git a/client/src/app/components/variants/my-variant-info/my-variant-info.component.ts b/client/src/app/components/variants/my-variant-info/my-variant-info.component.ts index 64cae1900..6cc9cec54 100644 --- a/client/src/app/components/variants/my-variant-info/my-variant-info.component.ts +++ b/client/src/app/components/variants/my-variant-info/my-variant-info.component.ts @@ -1,25 +1,12 @@ import { Component, Input, OnDestroy } from '@angular/core' import { Maybe } from '@app/generated/civic.apollo' import { MyVariantInfoFieldsFragment } from '@app/generated/civic.apollo' -import { BehaviorSubject } from 'rxjs' @Component({ selector: 'cvc-my-variant-info', templateUrl: './my-variant-info.component.html', styleUrls: ['./my-variant-info.component.less'], }) -export class CvcMyVariantInfoComponent implements OnDestroy { +export class CvcMyVariantInfoComponent { @Input() variantInfo: Maybe - - tabIndex = new BehaviorSubject(0) - - constructor() {} - - tabChange(index: number): void { - this.tabIndex.next(index) - } - - ngOnDestroy(): void { - this.tabIndex.unsubscribe() - } } diff --git a/client/src/app/components/variants/variant-info/variant-info.component.html b/client/src/app/components/variants/variant-info/variant-info.component.html index 26b631277..b5aaabbc1 100644 --- a/client/src/app/components/variants/variant-info/variant-info.component.html +++ b/client/src/app/components/variants/variant-info/variant-info.component.html @@ -1,9 +1,9 @@ + nzSize="default"> From 6a6254d81ac7e021263260c9e6508f2c61db037e Mon Sep 17 00:00:00 2001 From: Joshua McMichael Date: Thu, 6 Feb 2025 11:55:16 -0600 Subject: [PATCH 6/9] integtated open-cravat-annotations component to fit in variant-info tab-card --- .../gene-variant-summary.page.html | 30 -- .../gene-variant-summary.page.ts | 2 - .../my-variant-info.component.less | 6 +- .../open-cravat-annotations.component.html | 263 ++++++++++-------- .../open-cravat-annotations.component.less | 12 +- 5 files changed, 162 insertions(+), 151 deletions(-) diff --git a/client/src/app/components/variants/gene-variant-summary/gene-variant-summary.page.html b/client/src/app/components/variants/gene-variant-summary/gene-variant-summary.page.html index 38cda9f25..e702961f1 100644 --- a/client/src/app/components/variants/gene-variant-summary/gene-variant-summary.page.html +++ b/client/src/app/components/variants/gene-variant-summary/gene-variant-summary.page.html @@ -257,36 +257,6 @@ openCravatUrl: variant.openCravatUrl }"> - - - - - diff --git a/client/src/app/components/variants/gene-variant-summary/gene-variant-summary.page.ts b/client/src/app/components/variants/gene-variant-summary/gene-variant-summary.page.ts index 53f2be435..83913a9ce 100644 --- a/client/src/app/components/variants/gene-variant-summary/gene-variant-summary.page.ts +++ b/client/src/app/components/variants/gene-variant-summary/gene-variant-summary.page.ts @@ -40,8 +40,6 @@ import { CvcVariantInfo } from '../variant-info/variant-info.component' CvcUserTagModule, CvcFeatureTagModule, CvcMolecularProfilesTableModule, - CvcMyVariantInfoModule, - CvcOpenCravatAnnotationsModule, CvcPipesModule, CvcVariantInfo, ], diff --git a/client/src/app/components/variants/my-variant-info/my-variant-info.component.less b/client/src/app/components/variants/my-variant-info/my-variant-info.component.less index dea8f5c57..4bda475f6 100644 --- a/client/src/app/components/variants/my-variant-info/my-variant-info.component.less +++ b/client/src/app/components/variants/my-variant-info/my-variant-info.component.less @@ -3,10 +3,6 @@ margin: -8px; } -nz-card { - width: 100%; -} - .key-col { text-align: right; font-weight: bold; @@ -16,7 +12,7 @@ nz-card { } .tab-content { - margin: 12px; + // margin: 12px; max-height: 260px; overflow-y: auto; } diff --git a/client/src/app/components/variants/open-cravat-annotations/open-cravat-annotations.component.html b/client/src/app/components/variants/open-cravat-annotations/open-cravat-annotations.component.html index 56844440a..fc2f345c6 100644 --- a/client/src/app/components/variants/open-cravat-annotations/open-cravat-annotations.component.html +++ b/client/src/app/components/variants/open-cravat-annotations/open-cravat-annotations.component.html @@ -1,121 +1,164 @@ - - + + + + + + + + + + + + +
Variant Report - - - - - - - - - - - - - -
-
- - @if ((openCravatAnnotations.benignity_counts|keyvalue).length === 0) { -
- No Annotations -
- } - @for (keypar of openCravatAnnotations.benignity_counts|keyvalue; track keypar.key) { -
- {{ keypar.key }} ({{ keypar.value }}) -
- } - -
-
- - @if ((openCravatAnnotations.pathogenicity_counts|keyvalue).length === 0) { -
- None -
- } - @for (keypar of openCravatAnnotations.pathogenicity_counts|keyvalue; track keypar.key) { -
- {{ keypar.key }} ({{ keypar.value }}) -
- } - -
+
+ + + +
+
+
+ + @if ( + (openCravatAnnotations.benignity_counts | keyvalue).length === 0 + ) { +
+ No Annotations +
+ } + @for ( + keypar of openCravatAnnotations.benignity_counts | keyvalue; + track keypar.key + ) { +
+ {{ keypar.key }} ({{ keypar.value }}) +
+ } +
- - - - - +
+ + @if ( + (openCravatAnnotations.pathogenicity_counts | keyvalue).length === + 0 + ) { +
None
+ } + @for ( + keypar of openCravatAnnotations.pathogenicity_counts | keyvalue; + track keypar.key + ) { +
+ {{ keypar.key }} ({{ keypar.value }}) +
+ } + +
+
+
+ + + +
+ + + + Predictor + Annotation + + + + @for ( + keypar of openCravatAnnotations.benignity | keyvalue; + track keypar.key + ) { - Predictor - Annotation + {{ keypar.key }} + + {{ keypar.value | ifEmpty: '--' }} + - - - @for (keypar of openCravatAnnotations.benignity|keyvalue; track keypar.key) { - - {{ keypar.key }} - - {{ keypar.value | ifEmpty : '--' }} - - - } - - - - - - - + } + + +
+ + + +
+ + + + Predictor + Annotation + + + + @for ( + keypar of openCravatAnnotations.pathogenicity | keyvalue; + track keypar.key + ) { - Predictor - Annotation + {{ keypar.key }} + + {{ keypar.value | ifEmpty: '--' }} + - - - @for (keypar of openCravatAnnotations.pathogenicity|keyvalue; track keypar.key) { - - {{ keypar.key }} - - {{ keypar.value | ifEmpty : '--' }} - - - } - - - - - - \ No newline at end of file + } + + +
+ + diff --git a/client/src/app/components/variants/open-cravat-annotations/open-cravat-annotations.component.less b/client/src/app/components/variants/open-cravat-annotations/open-cravat-annotations.component.less index 30681b7cc..8a5fab3bf 100644 --- a/client/src/app/components/variants/open-cravat-annotations/open-cravat-annotations.component.less +++ b/client/src/app/components/variants/open-cravat-annotations/open-cravat-annotations.component.less @@ -1,9 +1,7 @@ :host { display: block; -} - -nz-card { - width: 100%; + margin: -8px; + // border: 1px solid red; } .key-col { @@ -13,3 +11,9 @@ nz-card { .button-col { text-align: right; } + +.tab-content { + // margin: 12px; + max-height: 260px; + overflow-y: auto; +} From ce78501bdebdc8fd4e907d24190c0728198a0d53 Mon Sep 17 00:00:00 2001 From: Joshua McMichael Date: Thu, 6 Feb 2025 14:33:43 -0600 Subject: [PATCH 7/9] fixed spelling --- .../app/forms/types/evidence-select/evidence-select.type.ts | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/client/src/app/forms/types/evidence-select/evidence-select.type.ts b/client/src/app/forms/types/evidence-select/evidence-select.type.ts index 7999d8805..658f81f67 100644 --- a/client/src/app/forms/types/evidence-select/evidence-select.type.ts +++ b/client/src/app/forms/types/evidence-select/evidence-select.type.ts @@ -261,7 +261,7 @@ export class CvcEvidenceSelectField ) }) - // combine all synchronized requireds updates, emit table filter changes array + // combine all synchronized required updates, emit table filter changes array this.onFieldsChange$ = combineLatest(this.synchronizedFields$).pipe( map((fields) => { const newFilters: CvcFilterChange[] = [] @@ -279,7 +279,7 @@ export class CvcEvidenceSelectField // tag('onFieldsChange$') ) - // combine all synchronized requireds updates, emit table prefs array + // combine all synchronized required updates, emit table prefs array this.onRequiredChange$ = combineLatest(this.synchronizedRequired$).pipe( map((fields) => { const newPrefs: Partial[] = [] From 77233a0ae6f5a25d05e652884720cbfcbd21b5fd Mon Sep 17 00:00:00 2001 From: Joshua McMichael Date: Fri, 7 Feb 2025 11:44:02 -0600 Subject: [PATCH 8/9] moved clinvar ids to curated attributes section, allele reg. id & var report above coordinates section --- .../gene-variant-summary.page.html | 179 ++++++++++-------- .../my-variant-info.component.less | 3 +- .../open-cravat-annotations.component.html | 12 +- .../open-cravat-annotations.component.less | 3 +- 4 files changed, 101 insertions(+), 96 deletions(-) diff --git a/client/src/app/components/variants/gene-variant-summary/gene-variant-summary.page.html b/client/src/app/components/variants/gene-variant-summary/gene-variant-summary.page.html index e702961f1..14dc95bb3 100644 --- a/client/src/app/components/variants/gene-variant-summary/gene-variant-summary.page.html +++ b/client/src/app/components/variants/gene-variant-summary/gene-variant-summary.page.html @@ -61,9 +61,9 @@ None specified + nzType="secondary"> + None specified + @@ -112,13 +112,105 @@ None found + nzType="secondary"> + None found + + + + + + + + + + {{ id }} + + + + + + + + {{ variant.clinvarIds[0] }} + + + + + + None provided + + + + + + + + + {{ variant.alleleRegistryId }} + + + + Unregistered + + + + + + + @if (variant.openCravatUrl) { + + Variant Report + + } @else { + + Not available + + } + + + @@ -173,81 +265,6 @@ - - - - - - - {{ variant.alleleRegistryId }} - - - Unregistered - - - - - - - - - - {{ id }} - - - - - - - {{ variant.clinvarIds[0] }} - - - - None provided - - - - + nzTabPosition="left"> @@ -14,15 +13,6 @@ - -
- - Variant Report - -
-
diff --git a/client/src/app/components/variants/open-cravat-annotations/open-cravat-annotations.component.less b/client/src/app/components/variants/open-cravat-annotations/open-cravat-annotations.component.less index 8a5fab3bf..8d8945071 100644 --- a/client/src/app/components/variants/open-cravat-annotations/open-cravat-annotations.component.less +++ b/client/src/app/components/variants/open-cravat-annotations/open-cravat-annotations.component.less @@ -13,7 +13,6 @@ } .tab-content { - // margin: 12px; - max-height: 260px; + max-height: 350px; overflow-y: auto; } From 173328be25e1bd2fe1fe047f04a4a7084e97c0a8 Mon Sep 17 00:00:00 2001 From: Joshua McMichael Date: Fri, 7 Feb 2025 13:57:22 -0600 Subject: [PATCH 9/9] added organization icons to variant-info tabs --- .../variant-info/variant-info.component.html | 46 ++++++++++++++++++- .../variant-info/variant-info.component.ts | 5 +- 2 files changed, 48 insertions(+), 3 deletions(-) diff --git a/client/src/app/components/variants/variant-info/variant-info.component.html b/client/src/app/components/variants/variant-info/variant-info.component.html index b5aaabbc1..7ea81f848 100644 --- a/client/src/app/components/variants/variant-info/variant-info.component.html +++ b/client/src/app/components/variants/variant-info/variant-info.component.html @@ -5,8 +5,50 @@ - - + + + + + + + + + My Variant Info + + + + + + + + + + + OpenCravat Annotations + @if (selectedTab() === 0) { diff --git a/client/src/app/components/variants/variant-info/variant-info.component.ts b/client/src/app/components/variants/variant-info/variant-info.component.ts index 633f6b01a..1bfed889f 100644 --- a/client/src/app/components/variants/variant-info/variant-info.component.ts +++ b/client/src/app/components/variants/variant-info/variant-info.component.ts @@ -7,15 +7,18 @@ import { NzTagModule } from 'ng-zorro-antd/tag' import { CvcMyVariantInfoModule } from '../my-variant-info/my-variant-info.module' import { CvcEmptyRevisableModule } from '@app/components/shared/empty-revisable/empty-revisable.module' import { CvcOpenCravatAnnotationsModule } from '../open-cravat-annotations/open-cravat-annotations.module' - +import { NzIconModule } from 'ng-zorro-antd/icon' +import { CommonModule } from '@angular/common' @Component({ selector: 'cvc-variant-info', standalone: true, imports: [ + CommonModule, NzCardModule, NzTabsModule, NzDescriptionsModule, NzTagModule, + NzIconModule, CvcMyVariantInfoModule, CvcEmptyRevisableModule, CvcOpenCravatAnnotationsModule,