Added species selection to get matrix journey. Resolves #891. (#972)

* Added species selection to get matrix journey. Resolves #891.

* Updated partial query match calculation to exclude mouse. Resolves #891.

Author: MillenniumFalconMechanic

spa/src/app/files/files.module.ts

@@ -55,6 +55,7 @@ import { HCAGetDataFileSummaryComponent } from "./hca-get-data/hca-get-data-file
 import { HCAGetDataSummaryComponent } from "./hca-get-data/hca-get-data-summary/hca-get-data-summary.component";
 import { HCAGetManifestComponent } from "./hca-get-data/hca-get-manifest/hca-get-manifest.component";
 import { HCAGetMatrixComponent } from "./hca-get-data/hca-get-matrix/hca-get-matrix.component";
+import { HCAGetMatrixSpeciesSelectionComponent } from "./hca-get-data/hca-get-matrix-species-selection/hca-get-matrix-species-selection.component";
 import { MatrixPartialQueryMatchWarningComponent } from "./hca-get-data/matrix-partial-query-match-warning/matrix-partial-query-match-warning.component";
 import { MatrixUrlRequestFormComponent } from "./hca-get-data/matrix-url-request-form/matrix-url-request-form.component";
 import { MatrixUrlRequestCompletedComponent } from "./hca-get-data/matrix-url-request-completed/matrix-url-request-completed.component";
@@ -160,6 +161,7 @@ import { TableScroll } from "./table-scroll/table-scroll.component";
         HCAGetDataSummaryComponent,
         HCAGetManifestComponent,
         HCAGetMatrixComponent,
+        HCAGetMatrixSpeciesSelectionComponent,
         HCAProjectComponent,
         HCASearchComponent,
         HCATableCellComponent,

spa/src/app/files/hca-get-data/download-view-state.model.ts

@@ -8,6 +8,7 @@
 export enum DownloadViewState {
     "MANIFEST" = "MANIFEST",
     "MATRIX" = "MATRIX",
+    "MATRIX_SPECIES_SELECTION" = "MATRIX_SPECIES_SELECTION",
     "NONE" = "NONE",
     "TERRA" = "TERRA"
 }

spa/src/app/files/hca-get-data/hca-get-data-downloads/hca-get-data-downloads.component.html

@@ -22,7 +22,7 @@ <h4 class="fontsize-m semi-bold">Create Concatenated Expression Matrix</h4>
         <div class="start">
             <button class="button secondary"
                     type="button"
-                    (click)="onStartGetData('MATRIX')"
+                    (click)="onStartGetData(getMatrixDownloadAction())"
                     [disabled]="!matrixEnabled">Start
             </button>
             <!--<p class="fontsize-m delimiter">|</p><a><p class="fontsize-m">Help</p></a>-->

spa/src/app/files/hca-get-data/hca-get-data-downloads/hca-get-data-downloads.component.spec.ts

@@ -61,7 +61,7 @@ describe("HCAGetDataDownloadsComponent", () => {
     /**
      * Confirm is matrix supported loading returns false when matrix is supported.
      */
-    it("should is matrix supported loading return false when matrix is supported", () => {
+    it("detects matrix supported loading is false when matrix is supported", () => {
 
         // Confirm is matrix supported loading returns false, when matrix is supported - first execute the
         // method and then confirm the returned value is false.
@@ -72,7 +72,7 @@ describe("HCAGetDataDownloadsComponent", () => {
     /**
      * Confirm is matrix supported loading returns false when matrix is not supported.
      */
-    it("should is matrix supported loading return false when matrix is not supported", () => {
+    it("detects matrix supported loading is false when matrix is not supported", () => {
 
         // Confirm is matrix supported loading returns false, when matrix is not supported - first execute the
         // method and then confirm the returned value is false.
@@ -83,7 +83,7 @@ describe("HCAGetDataDownloadsComponent", () => {
     /**
      * Confirm is matrix supported loading returns true when matrix is not yet determined.
      */
-    it("should is matrix supported loading return true when matrix is not yet determined", () => {
+    it("detects matrix supported as loading when matrix is not yet determined", () => {
 
         // Confirm is matrix supported loading returns true, when matrix is not yet determined - first execute the
         // method and then confirm the returned value is true.
@@ -94,7 +94,7 @@ describe("HCAGetDataDownloadsComponent", () => {
     /**
      * Confirm "Create Concatenated Expression Matrix" is displayed.
      */
-    it(`should display "Create Concatenated Expression Matrix"`, () => {
+    it(`displays "Create Concatenated Expression Matrix"`, () => {
 
         // Confirm "Create Concatenated Expression Matrix" is displayed
         expect(isPanelHeaderDisplayed("Create Concatenated Expression Matrix")).toEqual(true);
@@ -103,7 +103,7 @@ describe("HCAGetDataDownloadsComponent", () => {
     /**
      * Confirm "Request an expression matrix for the selected data from the HCA Matrix service." is displayed when matrix enabled is true.
      */
-    it(`should display "Request an expression matrix for the selected data from the HCA Matrix service." when matrix enabled is true`, () => {
+    it(`displays "Request an expression matrix for the selected data from the HCA Matrix service." when matrix enabled is true`, () => {
 
         component.matrixEnabled = true;
         fixture.detectChanges();
@@ -115,7 +115,7 @@ describe("HCAGetDataDownloadsComponent", () => {
     /**
      * Confirm <warning> is not displayed when matrix enabled is true.
      */
-    it("should not display component warning when matrix enabled is true", () => {
+    it("hides component warning when matrix enabled is true", () => {
 
         component.matrixEnabled = true;
         fixture.detectChanges();
@@ -129,7 +129,7 @@ describe("HCAGetDataDownloadsComponent", () => {
     /**
      * Confirm matrix start button is not disabled when matrix enabled is true.
      */
-    it("should matrix start button is not disabled when matrix enabled is true", () => {
+    it("enables matrix start button when matrix enabled is true", () => {
 
         component.matrixEnabled = true;
         fixture.detectChanges();
@@ -144,7 +144,7 @@ describe("HCAGetDataDownloadsComponent", () => {
     /**
      * Confirm "Request an expression matrix for the selected data from the HCA Matrix service." is not displayed when matrix enabled is false.
      */
-    it(`should not display "Request an expression matrix for the selected data from the HCA Matrix service." when matrix enabled is false`, () => {
+    it(`hides "Request an expression matrix for the selected data from the HCA Matrix service." when matrix enabled is false`, () => {
 
         component.matrixEnabled = false;
         fixture.detectChanges();
@@ -156,7 +156,7 @@ describe("HCAGetDataDownloadsComponent", () => {
     /**
      * Confirm <warning> is displayed when matrix enabled is false.
      */
-    it("should display component warning when matrix enabled is false", () => {
+    it("displays component warning when matrix enabled is false", () => {
 
         component.matrixEnabled = false;
         fixture.detectChanges();
@@ -170,7 +170,7 @@ describe("HCAGetDataDownloadsComponent", () => {
     /**
      * Confirm matrix start button is disabled when matrix enabled is false.
      */
-    it("should matrix start button is not disabled when matrix enabled is false", () => {
+    it("disables matrix start button when matrix enabled is false", () => {
 
         component.matrixEnabled = false;
         fixture.detectChanges();
@@ -185,7 +185,7 @@ describe("HCAGetDataDownloadsComponent", () => {
     /**
      * Confirm "Request a File Manifest (for downloading files via the HCA CLI)" is displayed.
      */
-    it(`should display "Request a File Manifest (for downloading files via the HCA CLI)"`, () => {
+    it(`displays "Request a File Manifest (for downloading files via the HCA CLI)"`, () => {
 
         // Confirm "Request a File Manifest (for downloading files via the HCA CLI)" is displayed
         expect(isPanelHeaderDisplayed("Request a File Manifest (for downloading files via the HCA CLI)")).toEqual(true);
@@ -194,7 +194,7 @@ describe("HCAGetDataDownloadsComponent", () => {
     /**
      * Confirm "Export to Terra" is displayed 
      */
-    it(`should display "Export to Terra"`, () => {
+    it(`displays "Export to Terra"`, () => {
 
         fixture.detectChanges();
 
@@ -205,7 +205,7 @@ describe("HCAGetDataDownloadsComponent", () => {
     /**
      * Confirm emit "MATRIX" on click of matrix start button.
      */
-    it(`should emit "MATRIX" on click of matrix start button`, () => {
+    it(`emits "MATRIX" on click of matrix start button`, () => {
 
         component.matrixEnabled = true;
         fixture.detectChanges();
@@ -225,7 +225,7 @@ describe("HCAGetDataDownloadsComponent", () => {
     /**
      * Confirm emit "MANIFEST" on click of manifest start button.
      */
-    it(`should emit "MANIFEST" on click of manifest start button`, () => {
+    it(`emits "MANIFEST" on click of manifest start button`, () => {
 
         component.matrixEnabled = true;
         fixture.detectChanges();
@@ -245,7 +245,7 @@ describe("HCAGetDataDownloadsComponent", () => {
     /**
      * Confirm emit "TERRA" on click of terra start button.
      */
-    it(`should emit "TERRA" on click of terra start button`, () => {
+    it(`emits "TERRA" on click of terra start button`, () => {
 
         component.matrixEnabled = true;
         fixture.detectChanges();
@@ -262,6 +262,48 @@ describe("HCAGetDataDownloadsComponent", () => {
         expect(selectedDownload).toBe(DownloadViewState.TERRA);
     });
 
+    /**
+     * Confirm emit "MATRIX_SPECIES_SELECTION" if matrix species selection is required.
+     */
+    it(`emits "MATRIX_SPECIES_SELECTION" on click of matrix start button when species selection is required`, () => {
+
+        component.matrixEnabled = true;
+        component.matrixSpeciesSelectionRequired = true;
+        fixture.detectChanges();
+
+        let selectedDownload: string;
+        component.downloadSelected.subscribe((download: string) => selectedDownload = download);
+
+        const matrixStartButton = getButtonEl("MATRIX");
+
+        // Execute click on terra start button
+        matrixStartButton.triggerEventHandler("click", null);
+
+        // Confirm emit "TERRA"
+        expect(selectedDownload).toBe(DownloadViewState.MATRIX_SPECIES_SELECTION);
+    });
+
+    /**
+     * Confirm emit "MATRIX" if matrix species selection is not required.
+     */
+    it(`emits "MATRIX" on click of matrix start button when species selection is not required`, () => {
+
+        component.matrixEnabled = true;
+        component.matrixSpeciesSelectionRequired = false;
+        fixture.detectChanges();
+
+        let selectedDownload: string;
+        component.downloadSelected.subscribe((download: string) => selectedDownload = download);
+
+        const matrixStartButton = getButtonEl("MATRIX");
+
+        // Execute click on terra start button
+        matrixStartButton.triggerEventHandler("click", null);
+
+        // Confirm emit "TERRA"
+        expect(selectedDownload).toBe(DownloadViewState.MATRIX);
+    });
+
     /**
      * Returns button element for specified panel download type.
      *

spa/src/app/files/hca-get-data/hca-get-data-downloads/hca-get-data-downloads.component.ts

@@ -10,6 +10,7 @@ import { Component, ChangeDetectionStrategy, EventEmitter, Output, Input } from
 
 // App dependencies
 import { ConfigService } from "../../../config/config.service";
+import { DownloadViewState } from "../download-view-state.model";
 
 @Component({
     selector: "hca-get-data-downloads",
@@ -25,6 +26,7 @@ export class HCAGetDataDownloadsComponent {
 
     // Inputs
     @Input() matrixEnabled: boolean;
+    @Input() matrixSpeciesSelectionRequired: boolean;
 
     // Outputs
     @Output() downloadSelected = new EventEmitter<string>();
@@ -36,6 +38,24 @@ export class HCAGetDataDownloadsComponent {
         this.portalURL = this.configService.getPortalURL();
     }
 
+    /**
+     * Returns the download action for matrix - either MATRIX_SPECIES_SELECTION if species selection is required for
+     * the current data, or MATRIX if species selection is not required.
+     * 
+     * Note, this functionality will no longer be required once deep-linking to download related modes (matrix,
+     * manifest, terra) is added.
+     * 
+     * @returns {string}
+     */
+    public getMatrixDownloadAction(): string {
+
+        if ( this.matrixSpeciesSelectionRequired ) {
+            return DownloadViewState.MATRIX_SPECIES_SELECTION;
+        }
+
+        return DownloadViewState.MATRIX;
+    }
+
     /**
      * Returns true if whether matrix is supported or not, is not yet determined.
      *

spa/src/app/files/hca-get-data/hca-get-data.component.html

@@ -11,14 +11,18 @@
                     <ng-container *ngSwitchDefault>
                         <div *ngIf="state.matrixSupportedLoaded" [@fadeIn]>
                             <hca-get-data-downloads [matrixEnabled]="state.matrixSupported"
-                                                    (downloadSelected)="onDownloadSelected($event)"></hca-get-data-downloads>
+                                                    [matrixSpeciesSelectionRequired]="state.matrixSpeciesSelectionRequired"
+                                                    (downloadSelected)="onDownloadSelected($event, state.fileFacets)"></hca-get-data-downloads>
                         </div>
                         <div class="spinner-container" *ngIf="!state.matrixSupportedLoaded">
                             <mat-spinner *ngIf="true"
                                          class="hca-spinner hca-spinner-grey"
                                          diameter="32"></mat-spinner>
                         </div>
                     </ng-container>
+                    <hca-get-matrix-species-selection *ngSwitchCase="'MATRIX_SPECIES_SELECTION'"
+                                                      [speciesFileFacet]="getSpeciesFileFacet(state.fileFacets)"
+                                                      (speciesSelected)="onDownloadSelected('MATRIX')"></hca-get-matrix-species-selection>
                     <hca-get-matrix *ngSwitchCase="'MATRIX'"></hca-get-matrix>
                     <hca-get-manifest *ngSwitchCase="'MANIFEST'"></hca-get-manifest>
                     <hca-export-to-terra *ngSwitchCase="'TERRA'"></hca-export-to-terra>

spa/src/app/files/hca-get-data/hca-get-data.component.ts

@@ -62,10 +62,6 @@ export class HCAGetDataComponent implements OnInit {
                        private store: Store<AppState>) {
     }
 
-    /**
-     * Public API
-     */
-
     /**
      * Returns null value for EntitySpec, no need for an active tab.
      *
@@ -88,16 +84,37 @@ export class HCAGetDataComponent implements OnInit {
         return [{key: selectedEntity.key, displayName: displayName}];
     }
 
+    /**
+     * Find and return the species facet from the species set of facets.
+     * 
+     * @param {FileFacet[]} fileFacets
+     * @returns {FileFacet}
+     */
+    public getSpeciesFileFacet(fileFacets: FileFacet[]): FileFacet {
+
+        return fileFacets.find(facet => facet.name === FileFacetName.GENUS_SPECIES);
+    }
+
+    /**
+     * Returns the page title.
+     *
+     * @returns {string}
+     */
     public getTitle(): string {
+        
+        if ( this.viewState === DownloadViewState.MANIFEST ) {
+            return "Request File Manifest";
+        }
+        
+        if ( this.viewState === DownloadViewState.TERRA ) {
+            return "Export to Terra";
+        }
+        
+        if ( this.viewState === DownloadViewState.MATRIX || DownloadViewState.MATRIX_SPECIES_SELECTION ) {
+            return "Request Expression Matrix";
+        }
 
-        let downloadTitle = this.viewState === DownloadViewState.MANIFEST ?
-            "Request File Manifest" :
-            this.viewState === DownloadViewState.TERRA ?
-                "Export to Terra" :
-                this.viewState === DownloadViewState.MATRIX ?
-                    "Request Expression Matrix" :
-                    null;
-        return this.viewState !== DownloadViewState.NONE ? downloadTitle : "Export Data";
+        return "Export Data";
     }
 
     /**
@@ -161,6 +178,40 @@ export class HCAGetDataComponent implements OnInit {
         }
     }
 
+    /**
+     * Returns true if user must select the set of species to be included in a matrix download.
+     * 
+     * For the set of species present in the current data:
+     * 
+     * - one species, human, not selected, species selection required
+     * - one species, non-human, not selected, species selection required
+     * - one species, either human or non-human, selected, species selection not required
+     * - more than one species, none selected, species selection required
+     * - more than one species, at least one selected (either human or non-human), species selection not required 
+     * 
+     * @returns {boolean}
+     */
+    private isMatrixSpeciesSelectionRequired(fileFacets: FileFacet[]): boolean {
+
+        const speciesFileFacet = this.getSpeciesFileFacet(fileFacets);
+        if ( !speciesFileFacet ) {
+            return false;
+        }
+
+        const effectiveTerms = speciesFileFacet.getEffectiveTerms();
+
+        // There's only one species in our data set, species selection is required if the species is not currently
+        // selected
+        if ( effectiveTerms.length === 1 ) {
+            return !effectiveTerms[0].selected;
+        }
+
+        // There's more than one species in our data set, species selection is required if non species is currently
+        // selected
+        const selectedTerms = effectiveTerms.filter(term => term.selected);
+        return selectedTerms.length === 0;
+    }
+
     /**
      * Returns true if whether matrix is supported or not, has been determined.
      *
@@ -225,10 +276,13 @@ export class HCAGetDataComponent implements OnInit {
         )
             .pipe(
                 map(([selectedEntity, fileFacets, matrixSupported]) => {
+                    
+                    const matrixSpeciesSelectionRequired = this.isMatrixSpeciesSelectionRequired(fileFacets);
 
                     return {
                         selectedEntity,
                         fileFacets,
+                        matrixSpeciesSelectionRequired,
                         matrixSupported,
                         matrixSupportedLoaded: this.isMatrixSupportedLoaded(matrixSupported)
                     };

spa/src/app/files/hca-get-data/hca-get-data.state.ts

@@ -13,6 +13,7 @@ import { FileFacet } from "../shared/file-facet.model";
 export interface HCAGetDataState {
 
     fileFacets: FileFacet[];
+    matrixSpeciesSelectionRequired: boolean;
     matrixSupported: boolean;
     matrixSupportedLoaded: boolean;
     selectedEntity: EntitySpec;