Merge commit '6a59ec325f82c207fbb69020b342b02a2ae7839d' into release

griffithlab · Mar 23, 2023 · c11d476 · c11d476
2 parents 52f635a + 6a59ec3
commit c11d476
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Showing 31 changed files with 1,325 additions and 48 deletions.
diff --git a/client/src/app/components/diseases/my-disease-info/my-disease-info.component.html b/client/src/app/components/diseases/my-disease-info/my-disease-info.component.html
@@ -0,0 +1,94 @@
+<ng-container *ngIf="diseaseInfo">
+  <nz-card nzTitle="MyDiseaseInfo">
+    <nz-card-tab>
+      <nz-tabset nzSize="small" [nzAnimated]="true">
+        <nz-tab (nzClick)="tabIndex.next(0)" nzTitle="Disease Ontology"> </nz-tab>
+        <nz-tab (nzClick)="tabIndex.next(1)" nzTitle="Mondo"> </nz-tab>
+      </nz-tabset>
+    </nz-card-tab>
+    <ng-container [ngSwitch]="tabIndex | async">
+      <!-- DO tab -->
+      <ng-container *ngSwitchCase="0">
+        <div class="tab-padding">
+          <nz-row [nzGutter]="8">
+            <nz-col [nzSpan]="12">
+              <nz-descriptions nzSize="small" [nzBordered]="true" [nzColumn]="1">
+                <nz-descriptions-item nzTitle="Definition">
+                  <ng-container *ngIf="diseaseInfo.doDef; else noValue">
+                    {{diseaseInfo.doDef}}
+                  </ng-container>
+                </nz-descriptions-item>
+                <nz-descriptions-item nzTitle="Citations">
+                  <ng-container *ngIf="diseaseInfo.doDefCitations.length > 0; else noValue">
+                    <cvc-tag-list>
+                      <cvc-link-tag *ngFor="let url of diseaseInfo.doDefCitations; let i = index" [href]="url">Source {{ i + 1 }}</cvc-link-tag>
+                    </cvc-tag-list>
+                  </ng-container>
+                </nz-descriptions-item>
+              </nz-descriptions>
+            </nz-col>
+            <nz-col [nzSpan]="12">
+              <nz-descriptions nzSize="small" [nzBordered]="true" [nzColumn]="2">
+                <nz-descriptions-item nzTitle="Exact Synonyms" *ngIf="diseaseInfo.diseaseOntologyExactSynonyms.length > 0"
+                  [nzSpan]="2">
+                  <cvc-tag-list>
+                    <nz-tag *ngFor="let a of diseaseInfo.diseaseOntologyExactSynonyms">
+                      {{ a }}
+                    </nz-tag>
+                  </cvc-tag-list>
+                </nz-descriptions-item>
+                <nz-descriptions-item nzTitle="Related Synonyms" *ngIf="diseaseInfo.diseaseOntologyRelatedSynonyms.length > 0"
+                  [nzSpan]="2">
+                  <cvc-tag-list>
+                    <nz-tag *ngFor="let a of diseaseInfo.diseaseOntologyRelatedSynonyms">
+                      {{ a }}
+                    </nz-tag>
+                  </cvc-tag-list>
+                </nz-descriptions-item>
+                <nz-descriptions-item nzTitle="External Identifiers" [nzSpan]="2">
+                  <cvc-tag-list>
+                    <cvc-link-tag *ngIf="diseaseInfo.mesh" [href]="'https://meshb.nlm.nih.gov/record/ui?ui=' + diseaseInfo.mesh"
+                      tooltip="View in MeSH">
+                      MeSH:{{diseaseInfo.mesh}}
+                    </cvc-link-tag>
+                    <cvc-link-tag *ngFor="let ncit of diseaseInfo.ncit"
+                      [href]="'https://ncithesaurus.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&ns=ncit&code=' + ncit"
+                      tooltip="View in NCI Thesaurus">
+                      NCIt:{{ncit}}
+                    </cvc-link-tag>
+                    <cvc-link-tag *ngIf="diseaseInfo.omim" [href]="'https://www.omim.org/entry/' + diseaseInfo.omim"
+                      tooltip="View on OMIM">
+                      OMIM:{{diseaseInfo.omim}}
+                    </cvc-link-tag>
+                  </cvc-tag-list>
+                </nz-descriptions-item>
+                <nz-descriptions-item *ngIf="diseaseInfo.icd10" nzTitle="ICD - 10">
+                  {{diseaseInfo.icd10}}
+                </nz-descriptions-item>
+                <nz-descriptions-item *ngIf="diseaseInfo.icdo" nzTitle="ICD - O">
+                  {{diseaseInfo.icdo}}
+                </nz-descriptions-item>
+              </nz-descriptions>
+            </nz-col>
+          </nz-row>
+        </div>
+      </ng-container>
+      <ng-container *ngSwitchCase="1">
+        <div class="tab-padding">
+          <nz-row [nzGutter]="8">
+            <nz-col [nzSpan]="12">
+              <nz-descriptions nzSize="small" [nzBordered]="true" [nzColumn]="2">
+                <nz-descriptions-item nzTitle="Definition">
+                  <ng-container *ngIf="diseaseInfo.mondoDef; else noValue">
+                    {{diseaseInfo.mondoDef}}
+                  </ng-container>
+                </nz-descriptions-item>
+              </nz-descriptions>
+            </nz-col>
+          </nz-row>
+        </div>
+      </ng-container>
+    </ng-container>
+  </nz-card>
+</ng-container>
+<ng-template #noValue><span nz-typography nzType="secondary">Not Found</span></ng-template>
diff --git a/client/src/app/components/diseases/my-disease-info/my-disease-info.component.less b/client/src/app/components/diseases/my-disease-info/my-disease-info.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/diseases/my-disease-info/my-disease-info.component.ts b/client/src/app/components/diseases/my-disease-info/my-disease-info.component.ts
@@ -0,0 +1,25 @@
+import { Component, Input, OnDestroy } from "@angular/core";
+import { Maybe } from "@app/generated/civic.apollo";
+import { MyDiseaseInfoFieldsFragment } from "@app/generated/civic.apollo";
+import { BehaviorSubject } from "rxjs";
+
+@Component({
+    selector: 'cvc-my-disease-info',
+    templateUrl: './my-disease-info.component.html',
+    styleUrls: ['./my-disease-info.component.less']
+})
+export class CvcMyDiseaseInfoComponent implements OnDestroy {
+  @Input() diseaseInfo: Maybe<MyDiseaseInfoFieldsFragment>;
+
+  tabIndex = new BehaviorSubject<number>(0);
+
+  constructor() { }
+
+  tabChange(index: number): void {
+    this.tabIndex.next(index);
+  }
+
+  ngOnDestroy(): void {
+    this.tabIndex.unsubscribe();
+  }
+}
diff --git a/client/src/app/components/diseases/my-disease-info/my-disease-info.module.ts b/client/src/app/components/diseases/my-disease-info/my-disease-info.module.ts
@@ -0,0 +1,32 @@
+import { NgModule } from '@angular/core';
+import { CommonModule } from '@angular/common';
+import { CvcMyDiseaseInfoComponent } from './my-disease-info.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 { NzDescriptionsModule } from 'ng-zorro-antd/descriptions';
+import { CvcTagListModule } from '@app/components/shared/tag-list/tag-list.module';
+import { NzTagModule } from 'ng-zorro-antd/tag';
+import { NzTypographyModule } from 'ng-zorro-antd/typography';
+
+@NgModule({
+  declarations: [CvcMyDiseaseInfoComponent],
+  imports: [
+    CommonModule,
+    NzTabsModule,
+    NzTableModule,
+    NzCardModule,
+    NzDescriptionsModule,
+    NzGridModule,
+    NzTagModule,
+    NzTypographyModule,
+    CvcPipesModule,
+    CvcLinkTagModule,
+    CvcTagListModule
+  ],
+  exports: [CvcMyDiseaseInfoComponent],
+})
+export class CvcMyDiseaseInfoModule { }
diff --git a/client/src/app/components/therapies/my-chem-info/my-chem-info.component.html b/client/src/app/components/therapies/my-chem-info/my-chem-info.component.html
@@ -0,0 +1,82 @@
+<ng-container *ngIf="chemInfo">
+  <nz-card nzTitle="MyChemInfo">
+    <div class="tab-padding">
+      <nz-row [nzGutter]="8">
+        <nz-col [nzSpan]="12">
+          <nz-descriptions nzSize="small" [nzBordered]="true" [nzColumn]="2">
+            <nz-descriptions-item nzTitle="ChEBI Definition" [nzSpan]="2">
+              <ng-container *ngIf="chemInfo.chebiDefinition; else noValue">
+                {{chemInfo.chebiDefinition}}
+              </ng-container>
+            </nz-descriptions-item>
+            <nz-descriptions-item nzTitle="Inidications" [nzSpan]="2">
+              <ng-container *ngIf="chemInfo.indications.length > 0; else noValue">
+                <cvc-tag-list>
+                  <nz-tag *ngFor="let i of chemInfo.indications">{{i}}</nz-tag>
+                </cvc-tag-list>
+              </ng-container>
+            </nz-descriptions-item>
+            <nz-descriptions-item *ngIf="chemInfo.inchikey" nzTitle="InChIKey" [nzSpan]="2">
+              {{chemInfo.inchikey}}
+            </nz-descriptions-item>
+          </nz-descriptions>
+        </nz-col>
+        <nz-col [nzSpan]="12">
+          <nz-descriptions nzSize="small" [nzBordered]="true" [nzColumn]="2">
+            <nz-descriptions-item *ngIf="chemInfo.firstApproval" nzTitle="First Approval">
+              {{chemInfo.firstApproval}}
+            </nz-descriptions-item>
+            <nz-descriptions-item *ngIf="chemInfo.chemblMoleculeType" nzTitle="Molecule Type">
+              {{chemInfo.chemblMoleculeType}}
+            </nz-descriptions-item>
+            <ng-container *ngFor="let epc of chemInfo.fdaEpcCodes">
+              <nz-descriptions-item  nzTitle="FDA EPC Code">
+                {{epc.code}}
+              </nz-descriptions-item>
+              <nz-descriptions-item nzTitle="FDA EPC Description">
+                {{epc.description}}
+              </nz-descriptions-item>
+            </ng-container>
+            <ng-container *ngFor="let moa of chemInfo.fdaMoaCodes">
+              <nz-descriptions-item  nzTitle="FDA MOA Code">
+                {{moa.code}}
+              </nz-descriptions-item>
+              <nz-descriptions-item nzTitle="FDA MOA Description">
+                {{moa.description}}
+              </nz-descriptions-item>
+            </ng-container>
+            <nz-descriptions-item nzTitle="External Identifiers" [nzSpan]="2">
+              <cvc-tag-list>
+                <cvc-link-tag *ngIf="chemInfo.chebiId" [href]="'https://www.ebi.ac.uk/chebi/searchId.do?chebiId=' + chemInfo.chebiId"
+                  tooltip="View in ChEBI">
+                  {{chemInfo.chebiId}}
+                </cvc-link-tag>
+                <cvc-link-tag *ngIf="chemInfo.chemblId" [href]="'https://www.ebi.ac.uk/chembl/compound_report_card/' + chemInfo.chemblId"
+                  tooltip="View in ChEMBL">
+                  {{chemInfo.chemblId}}
+                </cvc-link-tag>
+                <cvc-link-tag *ngIf="chemInfo.pubchemCid" [href]="'https://pubchem.ncbi.nlm.nih.gov/compound/' + chemInfo.pubchemCid"
+                  tooltip="View in PubChem">
+                  PubChem {{chemInfo.pubchemCid}}
+                </cvc-link-tag>
+                <cvc-link-tag *ngIf="chemInfo.pharmgkbId" [href]="'https://www.pharmgkb.org/chemical/' + chemInfo.pharmgkbId"
+                  tooltip="View in PHARMGKB">
+                  PHARMGKB {{chemInfo.pharmgkbId}}
+                </cvc-link-tag>
+                <cvc-link-tag *ngIf="chemInfo.rxnorm" [href]="'https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm=' + chemInfo.rxnorm"
+                  tooltip="View in RxNav">
+                  RxNav {{chemInfo.rxnorm}}
+                </cvc-link-tag>
+                <cvc-link-tag *ngIf="chemInfo.drugbankId" [href]="'https://go.drugbank.com/drugs/' + chemInfo.drugbankId"
+                  tooltip="View in DrugBank">
+                  DrugBank {{chemInfo.drugbankId}}
+                </cvc-link-tag>
+              </cvc-tag-list>
+            </nz-descriptions-item>
+          </nz-descriptions>
+        </nz-col>
+      </nz-row>
+    </div>
+  </nz-card>
+</ng-container>
+<ng-template #noValue><span nz-typography nzType="secondary">Not Found</span></ng-template>
diff --git a/client/src/app/components/therapies/my-chem-info/my-chem-info.component.less b/client/src/app/components/therapies/my-chem-info/my-chem-info.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/therapies/my-chem-info/my-chem-info.component.ts b/client/src/app/components/therapies/my-chem-info/my-chem-info.component.ts
@@ -0,0 +1,24 @@
+import { Component, Input, OnDestroy } from "@angular/core";
+import { Maybe, MyChemInfoFieldsFragment } from "@app/generated/civic.apollo";
+import { BehaviorSubject } from "rxjs";
+
+@Component({
+    selector: 'cvc-my-chem-info',
+    templateUrl: './my-chem-info.component.html',
+    styleUrls: ['./my-chem-info.component.less']
+})
+export class CvcMyChemInfoComponent implements OnDestroy {
+  @Input() chemInfo: Maybe<MyChemInfoFieldsFragment>;
+
+  tabIndex = new BehaviorSubject<number>(0);
+
+  constructor() { }
+
+  tabChange(index: number): void {
+    this.tabIndex.next(index);
+  }
+
+  ngOnDestroy(): void {
+    this.tabIndex.unsubscribe();
+  }
+}
diff --git a/client/src/app/components/therapies/my-chem-info/my-chem-info.module.ts b/client/src/app/components/therapies/my-chem-info/my-chem-info.module.ts
@@ -0,0 +1,32 @@
+import { NgModule } from '@angular/core';
+import { CommonModule } from '@angular/common';
+import { CvcMyChemInfoComponent } from './my-chem-info.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 { NzDescriptionsModule } from 'ng-zorro-antd/descriptions';
+import { CvcTagListModule } from '@app/components/shared/tag-list/tag-list.module';
+import { NzTagModule } from 'ng-zorro-antd/tag';
+import { NzTypographyModule } from 'ng-zorro-antd/typography';
+
+@NgModule({
+  declarations: [CvcMyChemInfoComponent],
+  imports: [
+    CommonModule,
+    NzTabsModule,
+    NzTableModule,
+    NzCardModule,
+    NzDescriptionsModule,
+    NzGridModule,
+    NzTagModule,
+    NzTypographyModule,
+    CvcPipesModule,
+    CvcLinkTagModule,
+    CvcTagListModule
+  ],
+  exports: [CvcMyChemInfoComponent],
+})
+export class CvcMyChemInfoModule { }
diff --git a/client/src/app/components/variants/coordinates-card/coordinates-card.component.html b/client/src/app/components/variants/coordinates-card/coordinates-card.component.html
@@ -71,10 +71,13 @@
           <!-- representative transcript -->
           <nz-descriptions-item nzTitle="Transcript"
             nzColumn="5">
-            <cvc-link-tag tooltip="View on Ensembl"
+            <cvc-link-tag *ngIf="coords.representativeTranscript" tooltip="View on Ensembl"
               [href]="'http://www.ensembl.org/Homo_sapiens/transview?transcript=' + coords.representativeTranscript">
               {{ coords.representativeTranscript }}
             </cvc-link-tag>
+            <ng-container *ngIf="!coords.representativeTranscript">
+              --
+            </ng-container>
           </nz-descriptions-item>
 
         </nz-descriptions>
@@ -110,10 +113,13 @@
           <!-- representative transcript -->
           <nz-descriptions-item nzTitle="Transcript"
             nzColumn="5">
-            <cvc-link-tag tooltip="View on Ensembl"
+            <cvc-link-tag *ngIf="coords.representativeTranscript" tooltip="View on Ensembl"
               [href]="'http://www.ensembl.org/Homo_sapiens/transview?transcript=' + coords.representativeTranscript">
               {{ coords.representativeTranscript }}
             </cvc-link-tag>
+            <ng-container *ngIf="!coords.representativeTranscript">
+              --
+            </ng-container>
           </nz-descriptions-item>
 
         </nz-descriptions>