Hyperlink Analysis Protocol to corresponding Pipelines page in the portal. Resolves #950.

Author: Fran McDade

spa/src/app/files/analysis-protocol-pipeline-linker/analysis-protocol-pipeline-linker.component.html

@@ -0,0 +1,6 @@
+<ng-container *ngFor="let analysisProtocol of getAnalysisProtocols(); last as lastAnalysisProtocol">
+    <ng-container [ngSwitch]="isAnalysisProtocolLinked(analysisProtocol)">
+        <a href="{{getPipelineLink(analysisProtocol)}}" rel="noopener noreferrer" target="_blank" *ngSwitchDefault>{{analysisProtocol}}<span class="comma" *ngIf="!lastAnalysisProtocol">, </span></a>
+        <span *ngSwitchCase="false">{{analysisProtocol}}<span class="comma" *ngIf="!lastAnalysisProtocol">, </span></span>
+    </ng-container>
+</ng-container>

spa/src/app/files/analysis-protocol-pipeline-linker/analysis-protocol-pipeline-linker.component.scss

@@ -0,0 +1,27 @@
+/*
+ * Human Cell Atlas
+ * https://www.humancellatlas.org/
+ *
+ * Styles for analysis protocol pipeline linker.
+ */
+@import "../../site/theme/cgl.vars";
+
+/* Tables */
+/* HCATableFilesComponent */
+/* HCATableProjectsComponent */
+/* HCATableSamplesComponent */
+:host-context(.hca-table) {
+
+    .comma {
+        color: $hca-gray-dark;
+    }
+}
+
+/* Project detail page */
+/* HCAProjectComponent */
+:host-context(.explore-project) {
+
+    .comma {
+        color: black;
+    }
+}

spa/src/app/files/analysis-protocol-pipeline-linker/analysis-protocol-pipeline-linker.component.spec.ts

@@ -0,0 +1,344 @@
+/*
+ * Human Cell Atlas
+ * https://www.humancellatlas.org/
+ *
+ * Test suite for AnalysisProtocolPipelineLinker.
+ */
+
+// Core dependencies
+import { DebugElement } from "@angular/core";
+import { async, ComponentFixture, TestBed } from "@angular/core/testing";
+import { By } from "@angular/platform-browser";
+
+// App dependencies
+import { ConfigService } from "../../config/config.service";
+import { AnalysisProtocolPipelineLinkerComponent } from "./analysis-protocol-pipeline-linker.component";
+
+describe("AnalysisProtocolPipelineLinkerComponent", () => {
+
+    let component: AnalysisProtocolPipelineLinkerComponent;
+    let fixture: ComponentFixture<AnalysisProtocolPipelineLinkerComponent>;
+
+    const testConfig = jasmine.createSpyObj("ConfigService", ["getPortalURL"]);
+
+    // Create response for testConfig.getPortalUrl()
+    testConfig.getPortalURL.and.returnValue("https://test.com");
+
+    // Template values
+    const TEMPLATE_VALUE_DATA_PORTAL_LINK_SMARTSEQ2 = "/pipelines/smart-seq2-workflow";
+    const TEMPLATE_VALUE_DATA_PORTAL_LINK_OPTIMUS = "/pipelines/optimus-workflow";
+
+    // Test values
+    const TEST_VALUE_CELL_RANGER = "cellranger_v1.0.1";
+    const TEST_VALUE_OPTIMUS = "optimus_v1.3.2";
+    const TEST_VALUE_SMARTSEQ2 = "smartseq2_v2.4.0";
+    const TEST_VALUE_ANALYSIS_PROTOCOLS_MULTIPLE_MIXED_VALUES = [TEST_VALUE_CELL_RANGER, TEST_VALUE_OPTIMUS, TEST_VALUE_SMARTSEQ2];
+
+    // Input values
+    const INPUT_VALUE_WORKFLOW_MULTIPLE_LINKED_VALUES = "optimus_v2.0.2, optimus_v1.3.2, smartseq2_v2.4.0";
+    const INPUT_VALUE_WORKFLOW_MULTIPLE_MIXED_VALUES = "cellranger_v1.0.1, optimus_v1.3.2, smartseq2_v2.4.0";
+    const INPUT_VALUE_WORKFLOW_MULTIPLE_UNLINKED_VALUES = "cellranger_v1.0.1, cellranger_v1.0.4, se-rm-pipeline-version-output";
+    const INPUT_VALUE_WORKFLOW_SINGLE_OPTIMUS_VALUE = TEST_VALUE_OPTIMUS;
+    const INPUT_VALUE_WORKFLOW_SINGLE_SMARTSEQ2_VALUE = TEST_VALUE_SMARTSEQ2;
+
+    beforeEach(async(() => {
+
+        TestBed.configureTestingModule({
+            declarations: [
+                AnalysisProtocolPipelineLinkerComponent
+            ],
+            imports: [],
+            providers: [{
+                provide: ConfigService,
+                useValue: testConfig
+            }]
+        }).compileComponents();
+
+        fixture = TestBed.createComponent(AnalysisProtocolPipelineLinkerComponent);
+        component = fixture.componentInstance;
+    }));
+
+    /**
+     * Smoke test
+     */
+    it("should create an instance", () => {
+
+        expect(component).toBeTruthy();
+    });
+
+    /**
+     * Confirm get analysis protocols returns a concatenated string array when multiple workflow values.
+     */
+    it("should get analysis protocols returns a concatenated string array when multiple workflow values", () => {
+
+        component.workflow = INPUT_VALUE_WORKFLOW_MULTIPLE_MIXED_VALUES;
+        fixture.detectChanges();
+
+        // Confirm get analysis protocols returns a concatenated string array
+        const getAnalysisProtocols = component.getAnalysisProtocols();
+        expect(getAnalysisProtocols).toEqual(TEST_VALUE_ANALYSIS_PROTOCOLS_MULTIPLE_MIXED_VALUES);
+    });
+
+    /**
+     * Confirm get analysis protocols returns a string array when single workflow values.
+     */
+    it("should get analysis protocols returns a string array when single workflow values", () => {
+
+        component.workflow = INPUT_VALUE_WORKFLOW_SINGLE_OPTIMUS_VALUE;
+        fixture.detectChanges();
+
+        // Confirm get analysis protocols returns a string array
+        const getAnalysisProtocols = component.getAnalysisProtocols();
+        expect(getAnalysisProtocols).toEqual([TEST_VALUE_OPTIMUS]);
+    });
+
+    /**
+     * Confirm get analysis protocols returns an empty array when empty workflow values.
+     */
+    it("should get analysis protocols returns an empty array when empty workflow values", () => {
+
+        component.workflow = "";
+        fixture.detectChanges();
+
+        // Confirm get analysis protocols returns a concatenated string array
+        const getAnalysisProtocols = component.getAnalysisProtocols();
+        expect(getAnalysisProtocols).toEqual([]);
+    });
+    /**
+     * Confirm get analysis protocols returns a string array when single workflow values.
+     */
+    it("should get analysis protocols returns a string array when single workflow values", () => {
+
+        component.workflow = INPUT_VALUE_WORKFLOW_SINGLE_OPTIMUS_VALUE;
+        fixture.detectChanges();
+
+        // Confirm get analysis protocols returns a string array
+        const getAnalysisProtocols = component.getAnalysisProtocols();
+        expect(getAnalysisProtocols).toEqual([TEST_VALUE_OPTIMUS]);
+    });
+
+    /**
+     * Confirm get pipeline link returns corresponding data portal optimus link when analysis protocol includes "optimus".
+     */
+    it(`should get pipeline link returns corresponding data portal optimus link when analysis protocol includes "optimus"`, () => {
+
+        // Confirm link is for data portal optimus
+        const getPipelineLink = component.getPipelineLink(TEST_VALUE_OPTIMUS);
+        expect(getPipelineLink).toEqual(testConfig.getPortalURL() + TEMPLATE_VALUE_DATA_PORTAL_LINK_OPTIMUS);
+    });
+
+    /**
+     * Confirm get pipeline link returns corresponding data portal smartseq2 link when analysis protocol includes "smartseq2".
+     */
+    it(`should get pipeline link returns corresponding data portal smartseq2 link when analysis protocol includes "smartseq2"`, () => {
+
+        // Confirm link is for data portal smartseq2
+        const getPipelineLink = component.getPipelineLink(TEST_VALUE_SMARTSEQ2);
+        expect(getPipelineLink).toEqual(testConfig.getPortalURL() + TEMPLATE_VALUE_DATA_PORTAL_LINK_SMARTSEQ2);
+    });
+
+    /**
+     * Confirm get pipeline link returns the root base path when there is no corresponding pipeline.
+     */
+    it("should get pipeline link returns the root base path when there is no corresponding pipeline", () => {
+
+        // Confirm no link is returned
+        const getPipelineLink = component.getPipelineLink(TEST_VALUE_CELL_RANGER);
+        expect(getPipelineLink).toEqual("/");
+    });
+
+    /**
+     * Confirm is analysis protocol linked returns true when analysis protocol includes "optimus".
+     */
+    it(`should is analysis protocol linked returns true when analysis protocol includes "optimus"`, () => {
+
+        // Confirm true is returned
+        const isAnalysisProtocolLinked = component.isAnalysisProtocolLinked(TEST_VALUE_OPTIMUS);
+        expect(isAnalysisProtocolLinked).toEqual(true);
+    });
+
+    /**
+     * Confirm is analysis protocol linked returns true when analysis protocol includes "smartseq2".
+     */
+    it(`should is analysis protocol linked returns true when analysis protocol includes "smartseq2"`, () => {
+
+        // Confirm true is returned
+        const isAnalysisProtocolLinked = component.isAnalysisProtocolLinked(TEST_VALUE_SMARTSEQ2);
+        expect(isAnalysisProtocolLinked).toEqual(true);
+    });
+
+    /**
+     * Confirm is analysis protocol linked returns false when analysis protocol neither includes "smartseq2" nor "optimus".
+     */
+    it(`should is analysis protocol linked returns true when analysis protocol neither includes "smartseq2" nor "optimus"`, () => {
+
+        // Confirm true is returned
+        const isAnalysisProtocolLinked = component.isAnalysisProtocolLinked(TEST_VALUE_CELL_RANGER);
+        expect(isAnalysisProtocolLinked).toEqual(false);
+    });
+
+    /**
+     * Confirm all unlinked analysis protocols are displayed, when multiple unlinked workflow.
+     */
+    it("should display all unlinked analysis protocols when multiple unlinked workflow", () => {
+
+        // Set up initial component state
+        component.workflow = INPUT_VALUE_WORKFLOW_MULTIPLE_UNLINKED_VALUES;
+
+        fixture.detectChanges();
+
+        // Confirm all protocols are displayed
+        expect(getAnalysisProtocolsDisplayed("span").length).toEqual(3);
+    });
+
+    /**
+     * Confirm all linked analysis protocols are displayed, when multiple linked workflow.
+     */
+    it("should display all linked analysis protocols when multiple linked workflow", () => {
+
+        // Set up initial component state
+        component.workflow = INPUT_VALUE_WORKFLOW_MULTIPLE_LINKED_VALUES;
+
+        fixture.detectChanges();
+
+        // Confirm all protocols are displayed
+        expect(getAnalysisProtocolsDisplayed("a").length).toEqual(3);
+    });
+
+    /**
+     * Confirm all linked analysis protocols are displayed, when multiple mixed workflow.
+     */
+    it("should display all linked analysis protocols when multiple mixed workflow", () => {
+
+        // Set up initial component state
+        component.workflow = INPUT_VALUE_WORKFLOW_MULTIPLE_MIXED_VALUES;
+
+        fixture.detectChanges();
+
+        // Confirm linked protocols are displayed
+        expect(getAnalysisProtocolsDisplayed("a").length).toEqual(2);
+    });
+
+    /**
+     * Confirm all unlinked analysis protocols are displayed, when multiple mixed workflow.
+     */
+    it("should display all unlinked analysis protocols when multiple mixed workflow", () => {
+
+        // Set up initial component state
+        component.workflow = INPUT_VALUE_WORKFLOW_MULTIPLE_MIXED_VALUES;
+
+        fixture.detectChanges();
+
+        // Confirm unlinked protocols are displayed
+        expect(getAnalysisProtocolsDisplayed("span").length).toEqual(1);
+    });
+
+    /**
+     * Confirm no analysis protocols are displayed, when workflow is empty.
+     */
+    it("should display no analysis protocols when workflow is empty", () => {
+
+        // Set up initial component state
+        component.workflow = "";
+
+        fixture.detectChanges();
+
+        // Confirm no protocols are displayed
+        expect(getAnalysisProtocolsDisplayed("span").length).toEqual(0);
+        expect(getAnalysisProtocolsDisplayed("a").length).toEqual(0);
+    });
+
+    /**
+     * Confirm data portal optimus pipeline link is added to href attribute when workflow includes "optimus".
+     */
+    it(`should data portal optimus pipeline link is added to href attribute when workflow includes "optimus"`, () => {
+
+        // Set up initial component state
+        component.workflow = INPUT_VALUE_WORKFLOW_SINGLE_OPTIMUS_VALUE;
+
+        fixture.detectChanges();
+
+        const analysisPortalDEs = getAnalysisProtocolsDisplayed("a");
+
+        // Confirm href link
+        expect(getHrefValue(analysisPortalDEs[0])).toEqual(testConfig.getPortalURL() + TEMPLATE_VALUE_DATA_PORTAL_LINK_OPTIMUS);
+    });
+
+    /**
+     * Confirm data portal smartseq2 pipeline link is added to href attribute when workflow includes "smartseq2".
+     */
+    it(`should data portal smartseq2 pipeline link is added to href attribute when workflow includes "smartseq2"`, () => {
+
+        // Set up initial component state
+        component.workflow = INPUT_VALUE_WORKFLOW_SINGLE_SMARTSEQ2_VALUE;
+
+        fixture.detectChanges();
+
+        const analysisPortalDEs = getAnalysisProtocolsDisplayed("a");
+
+        // Confirm href link
+        expect(getHrefValue(analysisPortalDEs[0])).toEqual(testConfig.getPortalURL() + TEMPLATE_VALUE_DATA_PORTAL_LINK_SMARTSEQ2);
+    });
+
+    /**
+     * Confirm comma is not displayed last when multiple workflow.
+     */
+    it("should not display comma last when multiple workflow", () => {
+
+        // Set up initial component state
+        component.workflow = INPUT_VALUE_WORKFLOW_MULTIPLE_MIXED_VALUES;
+
+        fixture.detectChanges();
+
+        const componentChildren = fixture.debugElement.children;
+        const componentChildLast = componentChildren[componentChildren.length - 1];
+
+        // Confirm comma is not displayed last
+        expect(componentChildLast.children.length).toEqual(0);
+    });
+
+    /**
+     * Returns all analysis protocols displayed, specified by class name.
+     *
+     * @param {string} className
+     * @returns {DebugElement[]}
+     */
+    function getAnalysisProtocolsDisplayed(className: string): DebugElement[] {
+
+        const debugElements = getDebugElements(className);
+
+        if ( !debugElements ) {
+
+            return;
+        }
+
+        return debugElements.filter(spanDE => spanDE.nativeElement.innerHTML !== ", ");
+    }
+
+    /**
+     * Returns the href attribute value for the specified debug element.
+     *
+     * @param {DebugElement} de
+     * @returns {string}
+     */
+    function getHrefValue(de: DebugElement): string {
+
+        if ( !de ) {
+
+            return;
+        }
+
+        return de.properties.href;
+    }
+
+    /**
+     * Returns all debug elements specified by class name.
+     *
+     * @param {string} className
+     * @returns {DebugElement[]}
+     */
+    function getDebugElements(className: string): DebugElement[] {
+
+        return fixture.debugElement.queryAll(By.css(className));
+    }
+});