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Add OpenCRAVAT predictor annotations
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121 changes: 121 additions & 0 deletions
121
...rc/app/components/variants/open-cravat-annotations/open-cravat-annotations.component.html
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,121 @@ | ||
| <ng-container *ngIf="openCravatAnnotations && openCravatUrl"> | ||
| <nz-card | ||
| nzTitle="OpenCRAVAT Annotations" | ||
| [nzExtra]="openCravatUrlTemplate"> | ||
| <ng-template #openCravatUrlTemplate> | ||
| <cvc-link-tag | ||
| [href]="openCravatUrl" | ||
| tooltip="View on OpenCRAVAT"> | ||
| Variant Report | ||
| </cvc-link-tag> | ||
| </ng-template> | ||
| <nz-card-tab> | ||
| <nz-tabset | ||
| nzSize="small" | ||
| [nzAnimated]="true"> | ||
| <nz-tab | ||
| (nzClick)="tabIndex.next(0)" | ||
| nzTitle="Overview"> | ||
| </nz-tab> | ||
| <nz-tab | ||
| (nzClick)="tabIndex.next(1)" | ||
| nzTitle="Benignity Details"> | ||
| </nz-tab> | ||
| <nz-tab | ||
| (nzClick)="tabIndex.next(2)" | ||
| nzTitle="Pathogenicity Details"></nz-tab> | ||
| </nz-tabset> | ||
| </nz-card-tab> | ||
| <ng-container [ngSwitch]="tabIndex | async"> | ||
| <!-- Overview tab --> | ||
| <ng-container *ngSwitchCase="0"> | ||
| <div nz-row [nzGutter]="8"> | ||
| <div nz-col nzXs="24" nzSm="24" nzMd="24" nzLg="12" nzXl="12"> | ||
| <nz-card nzTitle="ACMG/AMP Benign (BP4)" nzSize="small"> | ||
| @if ((openCravatAnnotations.benignity_counts|keyvalue).length === 0) { | ||
| <div nz-typography nzType="secondary"> | ||
| No Annotations | ||
| </div> | ||
| } | ||
| @for (keypar of openCravatAnnotations.benignity_counts|keyvalue; track keypar.key) { | ||
| <div | ||
| nz-tooltip | ||
| nzTooltipPlacement="topLeft" | ||
| [nzTooltipTitle]="openCravatAnnotations.benignity_counts_details[keypar.key+''].join(', ')"> | ||
| {{ keypar.key }} ({{ keypar.value }}) | ||
| </div> | ||
| } | ||
| </nz-card> | ||
| </div> | ||
| <div nz-col nzXs="24" nzSm="24" nzMd="24" nzLg="12" nzXl="12"> | ||
| <nz-card nzTitle="ACMG/AMP Pathogenic (PP3)" nzSize="small"> | ||
| @if ((openCravatAnnotations.pathogenicity_counts|keyvalue).length === 0) { | ||
| <div> | ||
| None | ||
| </div> | ||
| } | ||
| @for (keypar of openCravatAnnotations.pathogenicity_counts|keyvalue; track keypar.key) { | ||
| <div | ||
| nz-tooltip | ||
| nzTooltipPlacement="topLeft" | ||
| [nzTooltipTitle]="openCravatAnnotations.pathogenicity_counts_details[keypar.key+''].join(', ')"> | ||
| {{ keypar.key }} ({{ keypar.value }}) | ||
| </div> | ||
| } | ||
| </nz-card> | ||
| </div> | ||
| </div> | ||
| </ng-container> | ||
| <!-- Benignity tab --> | ||
| <ng-container *ngSwitchCase="1"> | ||
| <nz-table | ||
| [nzData]="['.']" | ||
| [nzFrontPagination]="false" | ||
| [nzShowPagination]="false" | ||
| nzSize="small"> | ||
| <thead> | ||
| <tr> | ||
| <th>Predictor</th> | ||
| <th>Annotation</th> | ||
| </tr> | ||
| </thead> | ||
| <tbody> | ||
| @for (keypar of openCravatAnnotations.benignity|keyvalue; track keypar.key) { | ||
| <tr> | ||
| <td>{{ keypar.key }}</td> | ||
| <td> | ||
| {{ keypar.value | ifEmpty : '--' }} | ||
| </td> | ||
| </tr> | ||
| } | ||
| </tbody> | ||
| </nz-table> | ||
| </ng-container> | ||
| <!-- Pathogenicity tab --> | ||
| <ng-container *ngSwitchCase="2"> | ||
| <nz-table | ||
| [nzData]="['.']" | ||
| [nzFrontPagination]="false" | ||
| [nzShowPagination]="false" | ||
| nzSize="small"> | ||
| <thead> | ||
| <tr> | ||
| <th>Predictor</th> | ||
| <th>Annotation</th> | ||
| </tr> | ||
| </thead> | ||
| <tbody> | ||
| @for (keypar of openCravatAnnotations.pathogenicity|keyvalue; track keypar.key) { | ||
| <tr> | ||
| <td>{{ keypar.key }}</td> | ||
| <td> | ||
| {{ keypar.value | ifEmpty : '--' }} | ||
| </td> | ||
| </tr> | ||
| } | ||
| </tbody> | ||
| </nz-table> | ||
| </ng-container> | ||
| </ng-container> | ||
| </nz-card> | ||
| </ng-container> |
15 changes: 15 additions & 0 deletions
15
...rc/app/components/variants/open-cravat-annotations/open-cravat-annotations.component.less
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,15 @@ | ||
| :host { | ||
| display: block; | ||
| } | ||
|
|
||
| nz-card { | ||
| width: 100%; | ||
| } | ||
|
|
||
| .key-col { | ||
| text-align: right; | ||
| font-weight: bold; | ||
| } | ||
| .button-col { | ||
| text-align: right; | ||
| } |
26 changes: 26 additions & 0 deletions
26
.../src/app/components/variants/open-cravat-annotations/open-cravat-annotations.component.ts
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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<string> | ||
|
|
||
| tabIndex = new BehaviorSubject<number>(0) | ||
|
|
||
| constructor() { | ||
| } | ||
|
|
||
| tabChange(index: number): void { | ||
| this.tabIndex.next(index) | ||
| } | ||
|
|
||
| ngOnDestroy(): void { | ||
| this.tabIndex.unsubscribe() | ||
| } | ||
| } |
29 changes: 29 additions & 0 deletions
29
client/src/app/components/variants/open-cravat-annotations/open-cravat-annotations.module.ts
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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 {} |
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