RFC83: Make virtual study available for all users on their landing pa…

…ges (#4923) * Render public virtual studies as a separate section * Use public virtual study metadata to blend it in regular studies
cBioPortal · Jul 18, 2024 · 9ca3198 · 9ca3198
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diff --git a/end-to-end-test/local/runtime-config/portal.properties b/end-to-end-test/local/runtime-config/portal.properties
@@ -181,6 +181,8 @@ session.service.url=
 # session.service.user=user
 # session.service.password=pass
 
+session.endpoint.publisher-api-key=SECRETKEY
+
 # disabled tabs, | delimited
 # possible values: cancer_types_summary, mutual_exclusivity, plots, mutations, co_expression, enrichments, survival, network, download, bookmark, IGV
 disabled_tabs=

diff --git a/end-to-end-test/local/specs/virtual-study.spec.js b/end-to-end-test/local/specs/virtual-study.spec.js
@@ -0,0 +1,171 @@
+var assert = require('assert');
+var goToUrlAndSetLocalStorage = require('../../shared/specUtils')
+    .goToUrlAndSetLocalStorage;
+
+const CBIOPORTAL_URL = process.env.CBIOPORTAL_URL.replace(/\/$/, '');
+const studyEs0Summary = CBIOPORTAL_URL + '/study/summary?id=study_es_0';
+
+describe('Virtual Study life cycle', function() {
+    const vsTitle = 'Test VS ' + Date.now();
+    let link;
+    let vsId;
+    const X_PUBLISHER_API_KEY = 'SECRETKEY';
+
+    it('Login and navigate to the study_es_0 study summary page', function() {
+        goToUrlAndSetLocalStorage(studyEs0Summary, true);
+    });
+    it('Click Share Virtual Study button', function() {
+        const studyView = $('.studyView');
+        const shareVSBtn = studyView.$(
+            'button[data-tour="action-button-bookmark"]'
+        );
+        shareVSBtn.waitForClickable();
+        shareVSBtn.click();
+    });
+    it('Provide the title and save', function() {
+        const modalDialog = $('.modal-dialog');
+        modalDialog.waitForDisplayed();
+        const titleInput = modalDialog.$('input#sniglet');
+        titleInput.setValue(vsTitle);
+        const saveBtn = modalDialog.$(
+            '[data-tour="virtual-study-summary-save-btn"]'
+        );
+        saveBtn.click();
+        modalDialog.$('.text-success').waitForDisplayed();
+        const linkInput = modalDialog.$('input[type="text"]');
+        link = linkInput.getValue();
+        assert.ok(
+            link.startsWith('http'),
+            'The value should be link, but was ' + link
+        );
+        vsId = link
+            .split('?')[1]
+            .split('&')
+            .map(paramEqValue => paramEqValue.split('='))
+            .find(([key, value]) => key === 'id')[1];
+        assert.ok(vsId, 'Virtual Study ID has not to be empty');
+    });
+    it('See the VS in My Virtual Studies section on the landing page', function() {
+        goToUrlAndSetLocalStorage(CBIOPORTAL_URL, true);
+        const vsSection = $(`//*[text()="${vsTitle}"]/ancestor::ul[1]`);
+        vsSection.waitForDisplayed();
+        const sectionTitle = vsSection.$('li label span');
+        assert.equal(sectionTitle.getText(), 'My Virtual Studies');
+    });
+    it('Publish the VS', function() {
+        const result = browser.executeAsync(
+            function(cbioUrl, vsId, key, done) {
+                const url = cbioUrl + '/api/public_virtual_studies/' + vsId;
+                const headers = new Headers();
+                headers.append('X-PUBLISHER-API-KEY', key);
+                fetch(url, {
+                    method: 'POST',
+                    headers: headers,
+                })
+                    .then(response => {
+                        done({
+                            success: response.ok,
+                            message: 'HTTP Status: ' + response.status,
+                        });
+                    })
+                    .catch(error => {
+                        done({ success: false, message: error.message });
+                    });
+            },
+            CBIOPORTAL_URL,
+            vsId,
+            X_PUBLISHER_API_KEY
+        );
+        assert.ok(result.success, result.message);
+    });
+    it('See the VS in Public Virtual Studies section on the landing page', function() {
+        goToUrlAndSetLocalStorage(CBIOPORTAL_URL, true);
+        const vsSection = $(`//*[text()="${vsTitle}"]/ancestor::ul[1]`);
+        vsSection.waitForDisplayed();
+        const sectionTitle = vsSection.$('li label span');
+        assert.equal(sectionTitle.getText(), 'Public Virtual Studies');
+    });
+    it('Re-publish the VS specifying PubMed ID and type of cancer', function() {
+        const result = browser.executeAsync(
+            function(cbioUrl, vsId, key, done) {
+                const headers = new Headers();
+                headers.append('X-PUBLISHER-API-KEY', key);
+                fetch(
+                    cbioUrl +
+                        '/api/public_virtual_studies/' +
+                        vsId +
+                        '?pmid=28783718&typeOfCancerId=aca',
+                    {
+                        method: 'POST',
+                        headers: headers,
+                    }
+                )
+                    .then(response => {
+                        done({
+                            success: response.ok,
+                            message: 'HTTP Status: ' + response.status,
+                        });
+                    })
+                    .catch(error => {
+                        done({ success: false, message: error.message });
+                    });
+            },
+            CBIOPORTAL_URL,
+            vsId,
+            X_PUBLISHER_API_KEY
+        );
+        assert.ok(result.success, result.message);
+    });
+    it('See the VS in the Adrenocortical Adenoma section with PubMed link', function() {
+        goToUrlAndSetLocalStorage(CBIOPORTAL_URL, true);
+        const vsRow = $(`//*[text()="${vsTitle}"]/ancestor::li[1]`);
+        const vsSection = vsRow.parentElement();
+        vsSection.waitForDisplayed();
+        const sectionTitle = vsSection.$('li label span');
+        assert.equal(sectionTitle.getText(), 'Adrenocortical Adenoma');
+        //has PubMed link
+        assert.ok(vsRow.$('.fa-book').isExisting());
+    });
+    it('Un-publish the VS', function() {
+        const result = browser.executeAsync(
+            function(cbioUrl, vsId, key, done) {
+                const headers = new Headers();
+                headers.append('X-PUBLISHER-API-KEY', key);
+                fetch(cbioUrl + '/api/public_virtual_studies/' + vsId, {
+                    method: 'DELETE',
+                    headers: headers,
+                })
+                    .then(response => {
+                        done({
+                            success: response.ok,
+                            message: 'HTTP Status: ' + response.status,
+                        });
+                    })
+                    .catch(error => {
+                        done({ success: false, message: error.message });
+                    });
+            },
+            CBIOPORTAL_URL,
+            vsId,
+            X_PUBLISHER_API_KEY
+        );
+        assert.ok(result.success, result.message);
+    });
+
+    it('Removing the VS', function() {
+        goToUrlAndSetLocalStorage(CBIOPORTAL_URL, true);
+        const vsRow = $(`//*[text()="${vsTitle}"]/ancestor::li[1]`);
+        vsRow.waitForDisplayed();
+
+        const removeBtn = vsRow.$('.fa-trash');
+        removeBtn.click();
+    });
+
+    it('The VS disappears from the landing page', function() {
+        goToUrlAndSetLocalStorage(CBIOPORTAL_URL, true);
+        $('[data-test="cancerTypeListContainer"]').waitForDisplayed();
+        const vsRowTitle = $(`//*[text()="${vsTitle}"]`);
+        browser.pause(100);
+        assert.ok(!vsRowTitle.isExisting());
+    });
+});
diff --git a/src/shared/api/session-service/sessionServiceAPI.ts b/src/shared/api/session-service/sessionServiceAPI.ts
@@ -17,6 +17,10 @@ export default class sessionServiceAPI {
         return `${getSessionUrl()}/virtual_study`;
     }
 
+    getPublicVirtualStudyServiceUrl() {
+        return getSessionUrl('api/public_virtual_studies');
+    }
+
     getSessionServiceUrl() {
         return `${getSessionUrl()}/main_session`;
     }
@@ -44,6 +48,18 @@ export default class sessionServiceAPI {
         );
     }
 
+    getPublicVirtualStudies(): Promise<Array<VirtualStudy>> {
+        return (
+            request
+                .get(this.getPublicVirtualStudyServiceUrl())
+                // @ts-ignore: this method comes from caching plugin and isn't in typing
+                .forceUpdate(true)
+                .then((res: any) => {
+                    return res.body;
+                })
+        );
+    }
+
     getVirtualStudy(id: string): Promise<VirtualStudy> {
         return (
             request

diff --git a/src/shared/api/session-service/sessionServiceModels.ts b/src/shared/api/session-service/sessionServiceModels.ts
@@ -33,6 +33,8 @@ export interface VirtualStudyData {
     studies: { id: string; samples: string[] }[];
     origin: string[];
     studyViewFilter: StudyViewFilter;
+    typeOfCancerId?: string;
+    pmid?: string;
 }
 
 export type GroupData = Omit<VirtualStudyData, 'studyViewFilter'>;

diff --git a/src/shared/api/urls.ts b/src/shared/api/urls.ts
@@ -245,14 +245,14 @@ export function getGenomeNexusHgvsgUrl(
         : `${getServerConfig().genomenexus_website_url}/variant/${hgvsg}`;
 }
 
-export function getSessionUrl() {
+export function getSessionUrl(path = 'api/session') {
     if (getServerConfig() && getServerConfig().hasOwnProperty('apiRoot')) {
         // TODO: remove this after switch to AWS. This is a hack to use proxy
         // session-service from non apiRoot. We'll have to come up with a better
         // solution for auth portals
-        return buildCBioPortalPageUrl('api/session');
+        return buildCBioPortalPageUrl(path);
     } else {
-        return buildCBioPortalAPIUrl('api/session');
+        return buildCBioPortalAPIUrl(path);
     }
 }
 

diff --git a/src/shared/components/query/CancerStudyTreeData.ts b/src/shared/components/query/CancerStudyTreeData.ts
@@ -8,6 +8,7 @@ import { VirtualStudy } from 'shared/api/session-service/sessionServiceModels';
 
 export const CANCER_TYPE_ROOT = 'tissue';
 export const VIRTUAL_STUDY_NAME = 'My Virtual Studies';
+export const PUBLIC_VIRTUAL_STUDY_NAME = 'Public Virtual Studies';
 export const PHYSICAL_STUDY_NAME = 'Studies';
 
 export type CancerTypeWithVisibility = CancerType & {
@@ -63,6 +64,16 @@ export default class CancerStudyTreeData {
         alwaysVisible: true,
     };
 
+    publicVirtualStudyCategory: CancerTypeWithVisibility = {
+        id: 'public_virtual_studies_list',
+        dedicatedColor: '',
+        name: PUBLIC_VIRTUAL_STUDY_NAME,
+        parent: CANCER_TYPE_ROOT,
+        shortName: PUBLIC_VIRTUAL_STUDY_NAME,
+        cancerTypeId: PUBLIC_VIRTUAL_STUDY_NAME,
+        alwaysVisible: true,
+    };
+
     physicalStudyCategory: CancerTypeWithVisibility = {
         dedicatedColor: '',
         name: PHYSICAL_STUDY_NAME,
@@ -83,13 +94,15 @@ export default class CancerStudyTreeData {
         allStudyTags = [],
         priorityStudies = {},
         virtualStudies = [],
+        publicVirtualStudies = [],
         maxTreeDepth = 0,
     }: {
         cancerTypes: CancerTypeWithVisibility[];
         studies: CancerStudy[];
         allStudyTags: StudyTags[];
         priorityStudies?: CategorizedConfigItems;
         virtualStudies?: VirtualStudy[];
+        publicVirtualStudies?: VirtualStudy[];
         maxTreeDepth: number;
     }) {
         let nodes: CancerTreeNode[];
@@ -99,6 +112,25 @@ export default class CancerStudyTreeData {
         // sort by name
         cancerTypes = CancerStudyTreeData.sortNodes(cancerTypes);
 
+        //map public virtual study to cancer study
+        const _publicVirtualStudies = publicVirtualStudies.map(
+            publicVirtualStudy => {
+                return {
+                    allSampleCount: _.sumBy(
+                        publicVirtualStudy.data.studies,
+                        study => study.samples.length
+                    ),
+                    studyId: publicVirtualStudy.id,
+                    name: publicVirtualStudy.data.name,
+                    description: publicVirtualStudy.data.description,
+                    cancerTypeId:
+                        publicVirtualStudy.data.typeOfCancerId ||
+                        PUBLIC_VIRTUAL_STUDY_NAME,
+                    pmid: publicVirtualStudy.data.pmid,
+                } as CancerStudy;
+            }
+        );
+
         //map virtual study to cancer study
         const _virtualStudies = virtualStudies
             .map(virtualstudy => {
@@ -140,13 +172,15 @@ export default class CancerStudyTreeData {
         }
         // add virtual study category, and studies
         cancerTypes = [
+            this.publicVirtualStudyCategory,
             this.virtualStudyCategory,
             this.physicalStudyCategory,
             ...this.priorityCategories,
             this.rootCancerType,
             ...cancerTypes,
         ];
         studies = CancerStudyTreeData.sortNodes([
+            ..._publicVirtualStudies,
             ..._virtualStudies,
             ...studies,
         ]);