Merge remote-tracking branch 'origin/main' into release

griffithlab · Apr 15, 2022 · 9f2bc6c · 9f2bc6c
2 parents 701934e + 800a203
commit 9f2bc6c
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Showing 27 changed files with 94 additions and 22 deletions.
diff --git a/client/src/app/components/assertions/assertions-table/assertions-table.component.html b/client/src/app/components/assertions/assertions-table/assertions-table.component.html
@@ -73,6 +73,7 @@
         <th nzWidth="3%"
           [nzColumnKey]="sortColumns.EvidenceItemsCount"
           [nzSortFn]="true"
+          [nzSortDirections]="['descend', 'ascend', null]"
           nz-tooltip
           nzTooltipTitle="Evidence Count"><i nz-icon
             nzType="civic:evidence"></i>

diff --git a/...app/components/clinical-trials/clinical-trials-table/clinical-trials-table.component.html b/...app/components/clinical-trials/clinical-trials-table/clinical-trials-table.component.html
@@ -22,6 +22,7 @@
           nzRight
           [nzColumnKey]="sortColumns.SourceCount"
           [nzSortFn]="true"
+          [nzSortDirections]="['descend', 'ascend', null]"
           nz-tooltip
           nzTooltipTitle="Source Count">
           <i nz-icon nzType="civic:source"></i>
@@ -30,6 +31,7 @@
           nzRight
           [nzColumnKey]="sortColumns.EvidenceItemCount"
           [nzSortFn]="true"
+          [nzSortDirections]="['descend', 'ascend', null]"
           nz-tooltip
           nzTooltipTitle="Evidence Count">
           <i nz-icon nzType="civic:evidence"></i>

diff --git a/client/src/app/components/diseases/diseases-table/diseases-table.component.html b/client/src/app/components/diseases/diseases-table/diseases-table.component.html
@@ -23,27 +23,31 @@
         <th nzWidth="8%"
           [nzColumnKey]="sortColumns.GeneCount"
           [nzSortFn]="true"
+          [nzSortDirections]="['descend', 'ascend', null]"
           nz-tooltip
           nzTooltipTitle="Gene Count">
           <i nz-icon nzType="civic:gene"></i>
         </th>
         <th nzWidth="8%"
           [nzColumnKey]="sortColumns.VariantCount"
           [nzSortFn]="true"
+          [nzSortDirections]="['descend', 'ascend', null]"
           nz-tooltip
           nzTooltipTitle="Variant Count">
           <i nz-icon nzType="civic:variant"></i>
         </th>
         <th nzWidth="8%"
           [nzColumnKey]="sortColumns.EvidenceItemCount"
           [nzSortFn]="true"
+          [nzSortDirections]="['descend', 'ascend', null]"
           nz-tooltip
           nzTooltipTitle="Evidence Count">
           <i nz-icon nzType="civic:evidence"></i>
         </th>
         <th nzWidth="8%"
           [nzColumnKey]="sortColumns.AssertionCount"
           [nzSortFn]="true"
+          [nzSortDirections]="['descend', 'ascend', null]"
           nz-tooltip
           nzTooltipTitle="Assertion Count">
           <i nz-icon nzType="civic:assertion"></i>

diff --git a/client/src/app/components/drugs/drugs-table/drugs-table.component.html b/client/src/app/components/drugs/drugs-table/drugs-table.component.html
@@ -21,6 +21,7 @@
         <th nzWidth="10%"
           nzRight
           [nzColumnKey]="sortColumns.EvidenceItemCount"
+          [nzSortDirections]="['descend', 'ascend', null]"
           [nzSortFn]="true"
           nz-tooltip
           nzTooltipTitle="Evidence Count">
@@ -29,6 +30,7 @@
         <th nzWidth="10%"
           nzRight
           [nzColumnKey]="sortColumns.AssertionCount"
+          [nzSortDirections]="['descend', 'ascend', null]"
           [nzSortFn]="true"
           nz-tooltip
           nzTooltipTitle="Assertion Count">

diff --git a/client/src/app/components/evidence/evidence-table/evidence-table.component.html b/client/src/app/components/evidence/evidence-table/evidence-table.component.html
@@ -91,6 +91,7 @@
         </th>
         <th nzWidth="5%"
           [nzColumnKey]="sortColumns.EvidenceRating"
+          [nzSortDirections]="['descend', 'ascend', null]"
           [nzSortFn]="true"
           nzAlign="center"
           nz-tooltip

diff --git a/client/src/app/components/genes/genes-table/genes-table.component.html b/client/src/app/components/genes/genes-table/genes-table.component.html
@@ -26,6 +26,7 @@
             nzRight
             [nzColumnKey]="sortColumns.VariantCount"
             [nzSortFn]="true"
+            [nzSortDirections]="['descend', 'ascend', null]"
             nz-tooltip
             nzTooltipTitle="Variant Count">
             <i nz-icon nzType="civic:variant"></i>
@@ -34,6 +35,7 @@
             nzRight
             [nzColumnKey]="sortColumns.EvidenceItemCount"
             [nzSortFn]="true"
+            [nzSortDirections]="['descend', 'ascend', null]"
             nz-tooltip
             nzTooltipTitle="Evidence Count">
             <i nz-icon nzType="civic:evidence"></i>
@@ -42,6 +44,7 @@
             nzRight
             [nzColumnKey]="sortColumns.AssertionCount"
             [nzSortFn]="true"
+            [nzSortDirections]="['descend', 'ascend', null]"
             nz-tooltip
             nzTooltipTitle="Assertion Count">
             <i nz-icon nzType="civic:assertion"></i>

diff --git a/client/src/app/components/phenotypes/phenotypes-table/phenotypes-table.component.html b/client/src/app/components/phenotypes/phenotypes-table/phenotypes-table.component.html
@@ -22,6 +22,7 @@
           nzRight
           [nzColumnKey]="sortColumns.EvidenceItemCount"
           [nzSortFn]="true"
+          [nzSortDirections]="['descend', 'ascend', null]"
           nz-tooltip
           nzTooltipTitle="Evidence Count">
           <i nz-icon nzType="civic:evidence"></i>
@@ -30,6 +31,7 @@
           nzRight
           [nzColumnKey]="sortColumns.AssertionCount"
           [nzSortFn]="true"
+          [nzSortDirections]="['descend', 'ascend', null]"
           nz-tooltip
           nzTooltipTitle="Assertion Count">
           <i nz-icon nzType="civic:assertion"></i>

diff --git a/client/src/app/components/revisions/revision-list/revision-list.component.ts b/client/src/app/components/revisions/revision-list/revision-list.component.ts
@@ -1,11 +1,12 @@
 import { Component, Input, OnChanges, OnInit, SimpleChanges, Output, EventEmitter, OnDestroy} from '@angular/core';
-import { AcceptRevisionGQL, AcceptRevisionMutation, AcceptRevisionMutationVariables, Maybe, Organization, RejectRevisionGQL, RejectRevisionMutation, RejectRevisionMutationVariables, Revision, ValidateRevisionsForAcceptanceGQL, ValidateRevisionsForAcceptanceQuery, ValidateRevisionsForAcceptanceQueryVariables, ValidationErrorFragment } from '@app/generated/civic.apollo';
-import { Observable, Subject, Subscription } from 'rxjs';
+import { AcceptRevisionGQL, AcceptRevisionMutation, AcceptRevisionMutationVariables, Maybe, Organization, RejectRevisionGQL, RejectRevisionMutation, RejectRevisionMutationVariables, Revision, ValidateRevisionsForAcceptanceGQL, ValidateRevisionsForAcceptanceQuery, ValidateRevisionsForAcceptanceQueryVariables, ValidationErrorFragment, VariantDetailGQL } from '@app/generated/civic.apollo';
+import { Observable, Subject } from 'rxjs';
 import { Viewer, ViewerService } from '@app/core/services/viewer/viewer.service';
 import { MutationState, MutatorWithState } from '@app/core/utilities/mutation-state-wrapper';
 import { NetworkErrorsService } from '@app/core/services/network-errors.service';
 import { map, startWith, takeUntil } from 'rxjs/operators';
 import { QueryRef } from 'apollo-angular';
+import { InternalRefetchQueryDescriptor } from '@apollo/client/core/types';
 
 type SuccessType = false | 'accepted' | 'rejected'
 
@@ -16,6 +17,7 @@ type SuccessType = false | 'accepted' | 'rejected'
 })
 export class RevisionListComponent implements OnInit, OnChanges, OnDestroy {
   @Input() revisions?: Revision[];
+  @Input() refetchQuery!: InternalRefetchQueryDescriptor
 
   mostRecentOrg!: Maybe<Organization>;
 
@@ -54,7 +56,7 @@ export class RevisionListComponent implements OnInit, OnChanges, OnDestroy {
     private networkErrorService: NetworkErrorsService,
     private acceptRevisionsGql: AcceptRevisionGQL,
     private rejectRevisionsGql: RejectRevisionGQL,
-    private validationGql: ValidateRevisionsForAcceptanceGQL
+    private validationGql: ValidateRevisionsForAcceptanceGQL,
   ) {
     this.acceptRevisionsMutator= new MutatorWithState(networkErrorService)
     this.rejectRevisionsMutator = new MutatorWithState(networkErrorService)
@@ -143,7 +145,10 @@ export class RevisionListComponent implements OnInit, OnChanges, OnDestroy {
           ids: this.selectedRevisionIds,
           organizationId: this.mostRecentOrg?.id,
           comment: this.revisionComment 
-        }
+        },
+      },
+      {
+        refetchQueries: [this.refetchQuery]
       })
       this.setupMutationResultHandlers(state, 'rejected')
     }
@@ -157,6 +162,9 @@ export class RevisionListComponent implements OnInit, OnChanges, OnDestroy {
         organizationId: this.mostRecentOrg?.id,
         comment: this.revisionComment === "" ? undefined : this.revisionComment
       }
+    },
+    {
+      refetchQueries: [this.refetchQuery]
     })
     this.setupMutationResultHandlers(state, 'accepted')
   }

diff --git a/...p/components/revisions/revisions-list-and-filter/revisions-list-and-filter.component.html b/...p/components/revisions/revisions-list-and-filter/revisions-list-and-filter.component.html
@@ -2,7 +2,8 @@
   <nz-row [nzGutter]="16">
     <nz-col nzSpan="18">
       <nz-space nzDirection="vertical">
-        <cvc-revision-list [revisions]="revisions$ | ngrxPush" (revisionSetSelectedEvent)="onRevisionSetSelected($event)" (revisionMutationCompleted)="refresh()" *nzSpaceItem></cvc-revision-list>
+        <cvc-revision-list [revisions]="revisions$ | ngrxPush" (revisionSetSelectedEvent)="onRevisionSetSelected($event)" (revisionMutationCompleted)="refresh()" 
+        [refetchQuery]="this.refetchQuery" *nzSpaceItem></cvc-revision-list>
         <ng-container *ngrxLet="pageInfo$ as pageInfo">
           <ng-container  *ngIf="pageInfo?.hasNextPage">
             <button nz-button nzBlock nzType="default" (click)="loadMore(pageInfo?.endCursor)" *nzSpaceItem>Load More</button>

diff --git a/...app/components/revisions/revisions-list-and-filter/revisions-list-and-filter.component.ts b/...app/components/revisions/revisions-list-and-filter/revisions-list-and-filter.component.ts
@@ -1,9 +1,10 @@
 import { Component, Input, OnDestroy, OnInit } from '@angular/core';
 import { ActivatedRoute } from '@angular/router';
-import { RevisionsGQL, RevisionsQuery, RevisionsQueryVariables, Maybe, Organization, RevisionFragment, ModeratedEntities, RevisionStatus, PageInfo } from '@app/generated/civic.apollo';
+import { RevisionsGQL, RevisionsQuery, RevisionsQueryVariables, Maybe, RevisionFragment, ModeratedEntities, RevisionStatus, PageInfo, VariantDetailGQL, AssertionDetailGQL, GeneDetailGQL, EvidenceDetailGQL, VariantGroupDetailGQL} from '@app/generated/civic.apollo';
 import { Observable, Subscription } from 'rxjs';
 import { QueryRef } from 'apollo-angular';
 import { map, pluck, startWith } from 'rxjs/operators';
+import { InternalRefetchQueryDescriptor } from '@apollo/client/core/types';
 
 export interface SelectableFieldName {
   id: number
@@ -55,9 +56,16 @@ export class RevisionsListAndFilterComponent implements OnDestroy, OnInit {
 
   private defaultPageSize = 10
 
+  refetchQuery!: InternalRefetchQueryDescriptor
+
   constructor(
     private gql: RevisionsGQL,
-    private route: ActivatedRoute
+    private route: ActivatedRoute,
+    private variantDetailGql: VariantDetailGQL,
+    private variantGroupDetailGql: VariantGroupDetailGQL,
+    private assertionDetailGql: AssertionDetailGQL,
+    private geneDetailGql: GeneDetailGQL,
+    private evidenceDetailGql: EvidenceDetailGQL,
   ) {
   }
 
@@ -109,6 +117,39 @@ export class RevisionsListAndFilterComponent implements OnDestroy, OnInit {
         pluck('data', 'revisions', 'unfilteredCountForSubject')
       )
     });
+
+    switch (this.entityType) {
+      case ModeratedEntities.Variant: 
+        this.refetchQuery = {
+          query: this.variantDetailGql.document,
+          variables: { variantId: this.id }
+        }
+        return
+      case ModeratedEntities.Assertion:
+        this.refetchQuery = {
+          query: this.assertionDetailGql.document,
+          variables: { assertionId: this.id }
+        }
+        return
+      case ModeratedEntities.EvidenceItem:
+        this.refetchQuery = {
+          query: this.evidenceDetailGql.document,
+          variables: { evidenceId: this.id }
+        }
+        return
+      case ModeratedEntities.Gene:
+        this.refetchQuery = {
+          query: this.geneDetailGql.document,
+          variables: { geneId: this.id }
+        }
+        return
+      case ModeratedEntities.VariantGroup:
+        this.refetchQuery = {
+          query: this.variantGroupDetailGql.document,
+          variables: { variantGroupId: this.id }
+        }
+        return
+    }
   }
 
   ngOnDestroy() {

diff --git a/client/src/app/components/sources/sources-table/sources-table.component.html b/client/src/app/components/sources/sources-table/sources-table.component.html
@@ -37,6 +37,7 @@
         <th nzRight
           [nzColumnKey]="sortColumns.EvidenceCount"
           [nzSortFn]="true"
+          [nzSortDirections]="['descend', 'ascend', null]"
           nz-tooltip
           nzTooltipTitle="Evidence Count">
           <i nz-icon nzType="civic:evidence"></i>

diff --git a/...rc/app/components/variant-groups/variant-groups-table/variant-groups-table.component.html b/...rc/app/components/variant-groups/variant-groups-table/variant-groups-table.component.html
@@ -22,13 +22,15 @@
           <th nzWidth="10%"
             [nzColumnKey]="sortColumns.VariantCount"
             [nzSortFn]="true"
+            [nzSortDirections]="['descend', 'ascend', null]"
             nz-tooltip
             nzTooltipTitle="Variant Count">
             <i nz-icon nzType="civic:variant"></i>
           </th>
           <th nzWidth="10%"
             [nzColumnKey]="sortColumns.EvidenceItemCount"
             [nzSortFn]="true"
+            [nzSortDirections]="['descend', 'ascend', null]"
             nz-tooltip
             nzTooltipTitle="Evidence Count">
             <i nz-icon nzType="civic:evidence"></i>

diff --git a/...t/src/app/components/variant-types/variant-types-table/variant-types-table.component.html b/...t/src/app/components/variant-types/variant-types-table/variant-types-table.component.html
@@ -22,6 +22,7 @@
           nzRight
           [nzColumnKey]="sortColumns.VariantCount"
           [nzSortFn]="true"
+          [nzSortDirections]="['descend', 'ascend', null]"
           nz-tooltip
           nzTooltipTitle="Variant Count">
           <i nz-icon nzType="civic:variant"></i>

diff --git a/client/src/app/components/variants/variants-table/variants-table.component.html b/client/src/app/components/variants/variants-table/variants-table.component.html
@@ -31,19 +31,22 @@
             nzRight
             [nzSortFn]="true"
             [nzColumnKey]="sortColumns.EvidenceScore"
+            [nzSortDirections]="['descend', 'ascend', null]"
             nz-tooltip
             nzTooltipTitle="Evidence Score"><div style="min-width: 60px; text-align: right;">
             <i nz-icon nzType="civic:evidence"></i>&nbsp;Score
             </div></th>
           <th nzWidth="3%"
             nzRight
             [nzColumnKey]="sortColumns.EvidenceItemCount"
+            [nzSortDirections]="['descend', 'ascend', null]"
             [nzSortFn]="true"
             nz-tooltip
             nzTooltipTitle="Evidence Count"><i nz-icon nzType="civic:evidence"></i></th>
           <th nzWidth="3%"
             nzRight
             [nzColumnKey]="sortColumns.AssertionCount"
+            [nzSortDirections]="['descend', 'ascend', null]"
             [nzSortFn]="true"
             nz-tooltip
             nzTooltipTitle="Assertion Count"><i nz-icon nzType="civic:assertion"></i></th>

diff --git a/client/src/app/core/pipes/color-name-for-status-pipe.ts b/client/src/app/core/pipes/color-name-for-status-pipe.ts
@@ -10,7 +10,7 @@ export class ColorNameForStatusPipe implements PipeTransform {
   transform(status: Maybe<EvidenceStatus>): string {
     switch(status) {
       case(EvidenceStatus.Accepted):
-        return 'default'
+        return 'green'
       case(EvidenceStatus.Rejected):
         return 'red'
       case(EvidenceStatus.Submitted):

diff --git a/client/src/app/core/pipes/icon-name-for-subscribable-entity.ts b/client/src/app/core/pipes/icon-name-for-subscribable-entity.ts
@@ -30,7 +30,7 @@ export class IconNameForSubscribableEntity implements PipeTransform {
         return 'civic:variant';
       case SubscribableEntities.VariantGroup:
       case 'VARIANT_GROUP':
-      case 'VariantGrou':
+      case 'VariantGroup':
         return 'civic:variant-group';
       default:
         console.log('String No icon name found for ' + e);

diff --git a/client/src/app/core/utilities/mutation-state-wrapper.ts b/client/src/app/core/utilities/mutation-state-wrapper.ts
@@ -1,6 +1,6 @@
 import { BehaviorSubject, Subject } from "rxjs";
 import { Mutation} from 'apollo-angular'
-import { EmptyObject } from "apollo-angular/types";
+import { EmptyObject, MutationOptionsAlone } from "apollo-angular/types";
 import { NetworkErrorsService } from "../services/network-errors.service";
 import { finalize, takeUntil } from "rxjs/operators";
 import { ApolloError, FetchResult } from '@apollo/client/core';
@@ -16,7 +16,7 @@ export class MutatorWithState<M extends Mutation<T, V>, T extends {}, V extends
   constructor(private networkErrorService: NetworkErrorsService) { }
 
   //TODO - define the data callback in terms of M, not any
-  mutate(mutation: M, vars: V, dataCallback?: (data: any) => void): MutationState {
+  mutate(mutation: M, vars: V, options?: MutationOptionsAlone<T, V>, dataCallback?: (data: any) => void): MutationState {
     let destroy$ = new Subject();
 
     let stateVals = {
@@ -28,7 +28,7 @@ export class MutatorWithState<M extends Mutation<T, V>, T extends {}, V extends
 
   stateVals.isSubmitting$.next(true)
 
-   mutation.mutate(vars)
+   mutation.mutate(vars, options)
       .pipe(
         takeUntil(destroy$),
         finalize(() => { stateVals.isSubmitting$.next(false)})

diff --git a/client/src/app/forms/assertion-submit/assertion-submit.form.ts b/client/src/app/forms/assertion-submit/assertion-submit.form.ts
@@ -318,7 +318,7 @@ export class AssertionSubmitForm implements OnDestroy {
 
       let state = this.submitAssertionMutator.mutate(this.submitAssertionGQL, {
         input: input
-      },
+      }, {},
         (data) => {
           this.newId = data.submitAssertion.assertion.id;
         })

diff --git a/client/src/app/forms/config/types/disease-input/disease-input.type.ts b/client/src/app/forms/config/types/disease-input/disease-input.type.ts
@@ -112,7 +112,7 @@ export class DiseaseInputType extends FieldType implements AfterViewInit, OnInit
   addDisease(diseaseName: string): void  {
     if(diseaseName && diseaseName != '') {
       let doid = +this.enteredDoid ? +this.enteredDoid : undefined
-      let state = this.addDiseaseMutator.mutate(this.addDiseaseGQL, { name: diseaseName, doid: doid },
+      let state = this.addDiseaseMutator.mutate(this.addDiseaseGQL, { name: diseaseName, doid: doid }, {},
         (data) => {
           this.field.formControl?.setValue( {id: data.addDisease.disease.id, name: data.addDisease.disease.name} )
           this.to.searchString = '';

diff --git a/client/src/app/forms/config/types/drug-input/drug-input.type.ts b/client/src/app/forms/config/types/drug-input/drug-input.type.ts
@@ -112,7 +112,7 @@ export class DrugInputType extends FieldType implements AfterViewInit, OnInit, O
 
   addDrug(drugName: string): void  {
     if(drugName && drugName != '') {
-      let state = this.addDrugMutator.mutate(this.addDrugGQL, { name: drugName },
+      let state = this.addDrugMutator.mutate(this.addDrugGQL, { name: drugName }, {},
 
         (data) => {
           this.field.formControl?.setValue( {id: data.addDrug.drug.id, name: data.addDrug.drug.name} )

diff --git a/client/src/app/forms/config/types/ensembl-input/ensembl-input.type.ts b/client/src/app/forms/config/types/ensembl-input/ensembl-input.type.ts
@@ -26,7 +26,7 @@ export class EnsemblInputType extends FieldType {
 export const ensemblVersionValidator: ValidatorOption = {
   name: 'ensembl-version',
   validation: (c: AbstractControl, f: FormlyFieldConfig): ValidationErrors | null => {
-    if (c.value === undefined) {
+    if (c.value === undefined || c.value === null) {
       return null;
     } else {
       let versionNum = +c.value;

diff --git a/client/src/app/forms/config/types/variant-input/variant-input.type.ts b/client/src/app/forms/config/types/variant-input/variant-input.type.ts
@@ -110,7 +110,7 @@ export class VariantInputType extends FieldType implements OnInit, AfterViewInit
 
   addVariant(variantName: string): void  {
     if(variantName && variantName != '' && this.to.geneId) {
-      let state = this.addVariantMutator.mutate(this.addVariantGQL, { name: variantName, geneId: this.to.geneId },
+      let state = this.addVariantMutator.mutate(this.addVariantGQL, { name: variantName, geneId: this.to.geneId }, {},
         (data) => {
           this.field.formControl?.setValue( {id: data.addVariant.variant.id, name: data.addVariant.variant.name})
           this.to.searchString = '';