Merge branch 'features' into staging

griffithlab · Mar 29, 2024 · 685c756 · 685c756
2 parents 88c73ce + 513667f
commit 685c756
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Showing 21 changed files with 235 additions and 160 deletions.
diff --git a/client/src/app/components/features/feature-popover/feature-popover.component.html b/client/src/app/components/features/feature-popover/feature-popover.component.html
@@ -17,6 +17,12 @@
         nzSize="small"
         [nzColumn]="2"
         nzBordered="true">
+        <nz-descriptions-item
+          *ngIf="feature.fullName"
+          nzSpan="2"
+          nzTitle="Full Name">
+          {{ feature.fullName }}
+        </nz-descriptions-item>
         <!-- aliases -->
         <nz-descriptions-item
           nzTitle="Aliases"

diff --git a/client/src/app/components/features/feature-popover/feature-popover.query.gql b/client/src/app/components/features/feature-popover/feature-popover.query.gql
@@ -7,6 +7,7 @@ query FeaturePopover($featureId: Int!) {
 fragment featurePopover on Feature {
   id
   name
+  fullName
   featureInstance {
     __typename
   }

diff --git a/...olecular-profile-factor-variant-card/molecular-profile-factor-variant-card.component.html b/...olecular-profile-factor-variant-card/molecular-profile-factor-variant-card.component.html
@@ -1,109 +1,116 @@
-@if(variant.__typename == "FactorVariant") {
-<nz-card
-  [nzTitle]="cardTitle"
-  nzType="inner"
-  nzSize="small">
-  <ng-template #cardTitle>
-    <i
-      nz-icon
-      nzType="civic-variant"
-      nzTheme="twotone"
-      [nzTwotoneColor]="'Variant' | entityColor"></i>
-    {{ variant.name }}
-  </ng-template>
-  <nz-row [nzGutter]="[8, 16]">
-    <nz-col [nzSpan]="24">
-      <nz-row [nzGutter]="[8, 8]">
-        <!-- gene attributes block -->
-        <nz-col nzSpan="24">
-          <nz-descriptions
-            nzLayout="horizontal"
-            nzSize="small"
-            [nzColumn]="4"
-            nzBordered="true">
-            <nz-descriptions-item
-              [nzSpan]="4"
-              nzTitle="Factor Variant">
-              <cvc-feature-variant-tag
-                [variant]="variant"></cvc-feature-variant-tag>
-            </nz-descriptions-item>
-            <!-- aliases -->
-            <nz-descriptions-item
-              [nzSpan]="2"
-              nzTitle="Aliases">
-              <ng-container
-                *ngIf="variant.variantAliases.length > 0; else noAliases">
-                <cvc-tag-list>
-                  <nz-tag *ngFor="let alias of variant.variantAliases">{{
-                    alias
-                  }}</nz-tag>
-                </cvc-tag-list>
-              </ng-container>
-              <ng-template #noAliases>
-                <span
-                  nz-typography
-                  nzType="secondary"
-                  >None specified</span
-                >
-              </ng-template>
-            </nz-descriptions-item>
-
-            <!-- variant type(s) -->
-            <nz-descriptions-item
-              [nzSpan]="2"
-              [nzTitle]="
-                variant.variantTypes.length > 1
-                  ? 'Variant Types'
-                  : 'Variant Type'
-              ">
-              <ng-container
-                *ngIf="variant.variantTypes.length > 0; else noTypes">
-                <cvc-tag-list>
-                  <cvc-variant-type-tag
-                    [variantType]="type"
-                    *ngFor="let type of variant.variantTypes">
-                  </cvc-variant-type-tag>
-                </cvc-tag-list>
-              </ng-container>
-              <ng-template #noTypes>
-                <span
-                  nz-typography
-                  nzType="secondary"
-                  >None specified</span
-                >
-              </ng-template>
-            </nz-descriptions-item>
-
-            <nz-descriptions-item
-              [nzSpan]="4"
-              *ngIf="this.displayMps.length > 0"
-              nzTitle="Other Molecular Profiles">
-              <cvc-tag-list>
-                <ng-container *ngFor="let mp of this.displayMps">
-                  <cvc-molecular-profile-tag
-                    [molecularProfile]="mp"
-                    [truncateLongName]="true"></cvc-molecular-profile-tag>
+@if (variant.__typename == 'FactorVariant') {
+  <nz-card
+    [nzTitle]="cardTitle"
+    nzType="inner"
+    nzSize="small">
+    <ng-template #cardTitle>
+      <i
+        nz-icon
+        nzType="civic-variant"
+        nzTheme="twotone"
+        [nzTwotoneColor]="'Variant' | entityColor"></i>
+      <span
+        nz-typography
+        nzType="secondary">
+        {{ variant.feature.name }}
+      </span>
+      <span nz-typography>
+        {{ variant.name }}
+      </span>
+    </ng-template>
+    <nz-row [nzGutter]="[8, 16]">
+      <nz-col [nzSpan]="24">
+        <nz-row [nzGutter]="[8, 8]">
+          <!-- gene attributes block -->
+          <nz-col nzSpan="24">
+            <nz-descriptions
+              nzLayout="horizontal"
+              nzSize="small"
+              [nzColumn]="4"
+              nzBordered="true">
+              <nz-descriptions-item
+                [nzSpan]="4"
+                nzTitle="Factor Variant">
+                <cvc-feature-variant-tag
+                  [variant]="variant"></cvc-feature-variant-tag>
+              </nz-descriptions-item>
+              <!-- aliases -->
+              <nz-descriptions-item
+                [nzSpan]="2"
+                nzTitle="Aliases">
+                <ng-container
+                  *ngIf="variant.variantAliases.length > 0; else noAliases">
+                  <cvc-tag-list>
+                    <nz-tag *ngFor="let alias of variant.variantAliases">{{
+                      alias
+                    }}</nz-tag>
+                  </cvc-tag-list>
                 </ng-container>
+                <ng-template #noAliases>
+                  <span
+                    nz-typography
+                    nzType="secondary"
+                    >None specified</span
+                  >
+                </ng-template>
+              </nz-descriptions-item>
+
+              <!-- variant type(s) -->
+              <nz-descriptions-item
+                [nzSpan]="2"
+                [nzTitle]="
+                  variant.variantTypes.length > 1
+                    ? 'Variant Types'
+                    : 'Variant Type'
+                ">
                 <ng-container
-                  *ngIf="
-                    variant.molecularProfiles.totalCount >
-                    this.displayMps.length + 1
-                  ">
-                  <a routerLink="/variants/{{ variant.id }}/summary">
-                    + view
-                    {{
-                      variant.molecularProfiles.totalCount -
-                        this.displayMps.length
-                    }}
-                    more
-                  </a>
+                  *ngIf="variant.variantTypes.length > 0; else noTypes">
+                  <cvc-tag-list>
+                    <cvc-variant-type-tag
+                      [variantType]="type"
+                      *ngFor="let type of variant.variantTypes">
+                    </cvc-variant-type-tag>
+                  </cvc-tag-list>
                 </ng-container>
-              </cvc-tag-list>
-            </nz-descriptions-item>
-          </nz-descriptions>
-        </nz-col>
-      </nz-row>
-    </nz-col>
-  </nz-row>
-</nz-card>
+                <ng-template #noTypes>
+                  <span
+                    nz-typography
+                    nzType="secondary"
+                    >None specified</span
+                  >
+                </ng-template>
+              </nz-descriptions-item>
+
+              <nz-descriptions-item
+                [nzSpan]="4"
+                *ngIf="this.displayMps.length > 0"
+                nzTitle="Other Molecular Profiles">
+                <cvc-tag-list>
+                  <ng-container *ngFor="let mp of this.displayMps">
+                    <cvc-molecular-profile-tag
+                      [molecularProfile]="mp"
+                      [truncateLongName]="true"></cvc-molecular-profile-tag>
+                  </ng-container>
+                  <ng-container
+                    *ngIf="
+                      variant.molecularProfiles.totalCount >
+                      this.displayMps.length + 1
+                    ">
+                    <a routerLink="/variants/{{ variant.id }}/summary">
+                      + view
+                      {{
+                        variant.molecularProfiles.totalCount -
+                          this.displayMps.length
+                      }}
+                      more
+                    </a>
+                  </ng-container>
+                </cvc-tag-list>
+              </nz-descriptions-item>
+            </nz-descriptions>
+          </nz-col>
+        </nz-row>
+      </nz-col>
+    </nz-row>
+  </nz-card>
 }
diff --git a/client/src/app/components/variants/factor-variant-summary/factor-variant-summary.page.html b/client/src/app/components/variants/factor-variant-summary/factor-variant-summary.page.html
@@ -158,7 +158,7 @@
       <cvc-molecular-profiles-table
         [variantId]="variant.id"
         cvcHeight="300px"
-        cvcTitle="{{ variant.name }} Molecular Profiles">
+        cvcTitle="Molecular Profiles">
       </cvc-molecular-profiles-table>
     </nz-col>
   </nz-row>

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
@@ -55,8 +55,13 @@
         </th>
         <th
           nzLeft
-          nzWidth="70px">
-          Category
+          nzWidth="70px"
+          nz-tooltip
+          nzTooltipTitle="Feature Type">
+          <i
+            nz-icon
+            nzType="civic-feature"></i>
+          Type
         </th>
         <th
           nzWidth="100px"

diff --git a/client/src/app/forms/components/entity-tag/entity-tag.component.ts b/client/src/app/forms/components/entity-tag/entity-tag.component.ts
@@ -145,6 +145,7 @@ export class CvcEntityTagComponent implements OnChanges {
       )
       return
     }
+    console.log(typename)
     // get linkable entity
     let fragment = undefined
     if (!this.cvcDisableLink) {

diff --git a/client/src/app/forms/config/variantgroup-revise/variantgroup-revise.form.config.ts b/client/src/app/forms/config/variantgroup-revise/variantgroup-revise.form.config.ts
@@ -53,7 +53,7 @@ const formFieldConfig: FormlyFieldConfig[] = [
             props: {
               label: 'Variants',
               required: true,
-              requireGene: false,
+              requireFeature: false,
               showManagerBtn: true,
             },
           },

diff --git a/client/src/app/forms/config/variantgroup-submit/variantgroup-submit.form.config.ts b/client/src/app/forms/config/variantgroup-submit/variantgroup-submit.form.config.ts
@@ -56,7 +56,7 @@ const formFieldConfig: FormlyFieldConfig[] = [
               label: 'Variants',
               required: true,
               colSpan: 24,
-              requireGene: false,
+              requireFeature: false,
               showManagerBtn: true,
             },
           },

diff --git a/client/src/app/forms/types/feature-select/feature-select.type.ts b/client/src/app/forms/types/feature-select/feature-select.type.ts
@@ -32,8 +32,8 @@ import { FormlyFieldProps } from '@ngx-formly/ng-zorro-antd/form-field'
 import { NzSelectOptionInterface } from 'ng-zorro-antd/select'
 import mixin from 'ts-mixin-extended'
 import { FeatureIdWithCreationStatus } from './feature-quick-add/feature-quick-add.form'
-import { BehaviorSubject, Subscription } from 'rxjs'
-import { UntilDestroy, untilDestroyed } from '@ngneat/until-destroy'
+import { BehaviorSubject } from 'rxjs'
+import { UntilDestroy } from '@ngneat/until-destroy'
 
 export type CvcFeatureSelectFieldOption = Partial<
   FieldTypeConfig<Partial<CvcFeatureSelectFieldProps>>
@@ -109,12 +109,6 @@ export class CvcFeatureSelectField
 
   ngAfterViewInit(): void {
     this.selectedFeatureType = this.props.featureType
-    if (this.props.featureTypeCallback) {
-      this.onFeatureType$
-        .pipe(untilDestroyed(this))
-        .subscribe((ft) => this.props.featureTypeCallback(ft))
-      this.onFeatureType$.next(this.selectedFeatureType)
-    }
     this.configureBaseField() // mixin fn
     this.configureEntitySelectField({
       // mixin fn

diff --git a/client/src/app/forms/types/molecular-profile-select/mp-finder/mp-finder.component.ts b/client/src/app/forms/types/molecular-profile-select/mp-finder/mp-finder.component.ts
@@ -17,9 +17,7 @@ import { Apollo, gql } from 'apollo-angular'
 import { Maybe } from 'graphql/jsutils/Maybe'
 import { NzFormLayoutType } from 'ng-zorro-antd/form'
 import { BehaviorSubject } from 'rxjs'
-import { tag } from 'rxjs-spy/operators'
 import { CvcVariantSelectFieldOption } from '../../variant-select/variant-select.type'
-import { EnumToTitlePipe } from '@app/core/pipes/enum-to-title-pipe'
 
 type MpFinderModel = {
   featureId?: number
@@ -45,7 +43,6 @@ export class MpFinderComponent {
   model: MpFinderModel
   form: UntypedFormGroup
   config: FormlyFieldConfig[]
-  featureType?: CreateableFeatureTypes
 
   finderState: MpFinderState = {
     formLayout: 'horizontal',
@@ -82,9 +79,6 @@ export class MpFinderComponent {
               showExtra: false,
               showErrorTip: false,
               required: true,
-              featureTypeCallback: (ft: CreateableFeatureTypes) => {
-                this.featureType = ft
-              },
             },
           },
           <CvcVariantSelectFieldOption>{
@@ -119,11 +113,10 @@ export class MpFinderComponent {
 
   getSelectedVariant(variantId: Maybe<number>): Maybe<Variant> {
     if (!variantId) return
-    const feature = new EnumToTitlePipe().transform(this.featureType)
     const fragment = {
-      id: `${feature}Variant:${variantId}`,
+      id: `Variant:${variantId}`,
       fragment: gql`
-        fragment VariantSelectQuery on ${feature}Variant {
+        fragment VariantSelectQuery on Variant {
           id
           name
           link

diff --git a/client/src/app/forms/types/variant-select/variant-select.query.gql b/client/src/app/forms/types/variant-select/variant-select.query.gql
@@ -1,14 +1,6 @@
 query VariantSelectTypeahead($name: String!, $featureId: Int) {
-  variants(name: $name, featureId: $featureId, first: 50) {
-    totalCount
-    edges {
-      node {
-        ...VariantSelectTypeaheadFields
-      }
-    }
-    nodes {
-      ...VariantSelectTypeaheadFields
-    }
+  variantsTypeahead(queryTerm: $name, featureId: $featureId) {
+    ...VariantSelectTypeaheadFields
   }
 }