Feature/ch/10184 support patient filters sent via postdata (#4635)

* refactor StudyId extractor * 🔨 Refactor Extraction code of StudyViewURL Query * Update StudyViewPage to accept filterJson from PostData * Remove debug statement * Update localdb test * Update postedQuery.spec.js * Update to use correct json format of patientIdentifiers * Remove only from test, and small clean up * Update StudyViewPage to use lodash unescape to convert html entity * Remove localdist from getUrl fn
cBioPortal · Jun 7, 2023 · e9a08df · e9a08df
1 parent bf23302
commit e9a08df
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Showing 5 changed files with 289 additions and 135 deletions.
diff --git a/end-to-end-test/local/specs/core/postedquery.spec.js b/end-to-end-test/local/specs/core/postedquery.spec.js
@@ -7,6 +7,7 @@ var _ = require('lodash');
 var {
     useExternalFrontend,
     waitForOncoprint,
+    getElementByTestHandle,
 } = require('../../../shared/specUtils');
 
 const CBIOPORTAL_URL = process.env.CBIOPORTAL_URL.replace(/\/$/, '');
@@ -56,3 +57,30 @@ describe('posting query parameters (instead of GET) to query page', function() {
         waitForOncoprint();
     });
 });
+
+describe('Post Data for StudyView Filtering with filterJson via HTTP Post', () => {
+    it('Verify PatientIdentifier Filter via postData', () => {
+        const filterJsonQuery = {
+            filterJson:
+                '{"patientIdentifiers":[{"studyId":"lgg_ucsf_2014_test_generic_assay","patientId":"P01"}]}',
+        };
+
+        const NUMBER_OF_PATIENTS_AFTER_FILTER = 1;
+
+        goToUrlAndSetLocalStorage(`${CBIOPORTAL_URL}`, true);
+
+        postDataToUrl(
+            `${CBIOPORTAL_URL}/study/summary?id=lgg_ucsf_2014_test_generic_assay`,
+            filterJsonQuery
+        );
+
+        getElementByTestHandle('selected-patients').waitForExist({
+            timeout: 20000,
+        });
+
+        assert.equal(
+            getElementByTestHandle('selected-patients').getText(),
+            NUMBER_OF_PATIENTS_AFTER_FILTER
+        );
+    });
+});
diff --git a/end-to-end-test/shared/specUtils.js b/end-to-end-test/shared/specUtils.js
@@ -189,6 +189,22 @@ function setDropdownOpen(
     );
 }
 
+/**
+ * @param {string} url
+ * @returns {string} modifiedUrl
+ */
+function getUrl(url) {
+    if (!useExternalFrontend) {
+        console.log('Connecting to: ' + url);
+    } else {
+        const urlparam = 'localdev';
+        const prefix = url.indexOf('?') > 0 ? '&' : '?';
+        console.log('Connecting to: ' + `${url}${prefix}${urlparam}=true`);
+        url = `${url}${prefix}${urlparam}=true`;
+    }
+    return url;
+}
+
 function goToUrlAndSetLocalStorage(url, authenticated = false) {
     const currentUrl = browser.getUrl();
     const needToLogin =
@@ -554,12 +570,20 @@ function getOncoprintGroupHeaderOptionsElements(trackGroupIndex) {
     };
 }
 
+/**
+ *
+ * @param {string} url
+ * @param {any} data
+ * @param {boolean} authenticated
+ */
 function postDataToUrl(url, data, authenticated = true) {
     const currentUrl = browser.getUrl();
     const needToLogin =
         authenticated && (!currentUrl || !currentUrl.includes('http'));
+
+    url = getUrl(url);
     browser.execute(
-        (url, data) => {
+        (/** @type {string} */ url, /** @type {any} */ data) => {
             function formSubmit(url, params) {
                 // method="smart" means submit with GET iff the URL wouldn't be too long
 

diff --git a/src/pages/studyView/StudyViewPage.tsx b/src/pages/studyView/StudyViewPage.tsx
@@ -76,6 +76,7 @@ import { CustomChartData } from 'shared/api/session-service/sessionServiceModels
 import { HelpWidget } from 'shared/components/HelpWidget/HelpWidget';
 import { buildCBioPortalPageUrl } from 'shared/api/urls';
 import StudyViewPageSettingsMenu from 'pages/studyView/menu/StudyViewPageSettingsMenu';
+import QueryString from 'qs';
 
 export interface IStudyViewPageProps {
     routing: any;
@@ -191,6 +192,12 @@ export default class StudyViewPage extends React.Component<
             }
         }
 
+        // Overrite filterJson from URL with what is defined in postData
+        const postDataFilterJson = this.getFilterJsonFromPostData();
+        if (postDataFilterJson) {
+            newStudyViewFilter.filterJson = postDataFilterJson;
+        }
+
         let updateStoreFromURLPromise = remoteData(() => Promise.resolve([]));
         if (!_.isEqual(newStudyViewFilter, this.store.studyViewQueryFilter)) {
             this.store.studyViewQueryFilter = newStudyViewFilter;
@@ -234,6 +241,26 @@ export default class StudyViewPage extends React.Component<
         }, 500);
     }
 
+    private getFilterJsonFromPostData(): string | undefined {
+        let filterJson: string | undefined;
+
+        const parsedFilterJson = _.unescape(
+            getBrowserWindow()?.postData?.filterJson
+        );
+
+        if (parsedFilterJson) {
+            try {
+                JSON.parse(parsedFilterJson);
+                filterJson = parsedFilterJson;
+            } catch (error) {
+                console.error(
+                    `PostData.filterJson does not have valid JSON, error: ${error}`
+                );
+            }
+        }
+        return filterJson;
+    }
+
     @autobind
     private toolbarRef(ref: any) {
         this.toolbar = ref;

diff --git a/src/pages/studyView/StudyViewPageStore.ts b/src/pages/studyView/StudyViewPageStore.ts
@@ -273,6 +273,13 @@ import {
     PatientIdentifier,
     PatientIdentifierFilter,
 } from 'shared/model/PatientIdentifierFilter';
+import {
+    ClinicalAttributeQueryExtractor,
+    SharedGroupsAndCustomDataQueryExtractor,
+    StudyIdQueryExtractor,
+    StudyViewFilterQueryExtractor,
+    StudyViewQueryExtractor,
+} from './StudyViewQueryExtractor';
 
 export const STUDY_VIEW_FILTER_AUTOSUBMIT = 'study_view_filter_autosubmit';
 
@@ -2136,114 +2143,27 @@ export class StudyViewPageStore
 
     @action
     async updateStoreFromURL(query: StudyViewURLQuery): Promise<void> {
-        let studyIdsString: string = '';
-        let studyIds: string[] = [];
-        if (query.studyId) {
-            studyIdsString = query.studyId;
-        }
-        if (query.cancer_study_id) {
-            studyIdsString = query.cancer_study_id;
-        }
-        if (query.id) {
-            studyIdsString = query.id;
-        }
-        if (studyIdsString) {
-            studyIds = studyIdsString.trim().split(',');
-            if (!_.isEqual(studyIds, toJS(this.studyIds))) {
-                // update if different
-                this.studyIds = studyIds;
-            }
-        }
-        if (query.sharedGroups) {
-            this.sharedGroupSet = stringListToSet(
-                query.sharedGroups.trim().split(',')
-            );
-            // Open group comparison manager if there are shared groups in the url
-            this.showComparisonGroupUI = true;
-        }
-        if (query.sharedCustomData) {
-            this.sharedCustomChartSet = stringListToSet(
-                query.sharedCustomData.trim().split(',')
-            );
-            this.showCustomDataSelectionUI = true;
-        }
+        const queryExtractors: Array<StudyViewQueryExtractor<void>> = [
+            new StudyIdQueryExtractor(),
+            new SharedGroupsAndCustomDataQueryExtractor(),
+        ];
 
-        // We do not support studyIds in the query filters
-        let filters: Partial<StudyViewFilter> = {};
+        const asyncQueryExtractors: Array<StudyViewQueryExtractor<
+            Promise<void>
+        >> = [];
         if (query.filterJson) {
-            const parsedFilterJson = this.parseRawFilterJson(query.filterJson);
-            if (query.filterJson.includes('patientIdentifiers')) {
-                const sampleListIds = studyIds.map(s => s.concat('', '_all'));
-                const samples = await this.fetchSamplesWithSampleListIds(
-                    sampleListIds
-                );
-                filters = this.getStudyViewFilterFromPatientIdentifierFilter(
-                    parsedFilterJson as PatientIdentifierFilter,
-                    samples
-                );
-            } else {
-                filters = parsedFilterJson as Partial<StudyViewFilter>;
-            }
-            this.updateStoreByFilters(filters);
+            asyncQueryExtractors.push(new StudyViewFilterQueryExtractor());
         } else if (query.filterAttributeId && query.filterValues) {
-            const clinicalAttributes = _.uniqBy(
-                await defaultClient.fetchClinicalAttributesUsingPOST({
-                    studyIds: studyIds,
-                }),
-                clinicalAttribute =>
-                    `${clinicalAttribute.patientAttribute}-${clinicalAttribute.clinicalAttributeId}`
-            );
-
-            const matchedAttr = _.find(
-                clinicalAttributes,
-                (attr: ClinicalAttribute) =>
-                    attr.clinicalAttributeId.toUpperCase() ===
-                    query.filterAttributeId!.toUpperCase()
-            );
-            if (matchedAttr !== undefined) {
-                if (matchedAttr.datatype == DataType.NUMBER) {
-                    filters.clinicalDataFilters = [
-                        {
-                            attributeId: matchedAttr.clinicalAttributeId,
-                            values: query
-                                .filterValues!.split(',')
-                                .map(range => {
-                                    const convertResult = range.split('-');
-                                    return {
-                                        start: Number(convertResult[0]),
-                                        end: Number(convertResult[1]),
-                                    } as DataFilterValue;
-                                }),
-                        } as ClinicalDataFilter,
-                    ];
-                } else {
-                    filters.clinicalDataFilters = [
-                        {
-                            attributeId: matchedAttr.clinicalAttributeId,
-                            values: getClinicalEqualityFilterValuesByString(
-                                query.filterValues
-                            ).map(value => ({ value })),
-                        } as ClinicalDataFilter,
-                    ];
-                }
-                this.updateStoreByFilters(filters);
-            } else {
-                this.pageStatusMessages['unknownClinicalAttribute'] = {
-                    message: `The clinical attribute ${query.filterAttributeId} is not available for this study`,
-                    status: 'danger',
-                };
-            }
+            asyncQueryExtractors.push(new ClinicalAttributeQueryExtractor());
         }
-    }
 
-    parseRawFilterJson(filterJson: string): any {
-        let rawJson;
-        try {
-            rawJson = JSON.parse(decodeURIComponent(filterJson));
-        } catch (e) {
-            console.error('FilterJson invalid Json: error: ', e);
+        for (const extractor of queryExtractors) {
+            extractor.accept(query, this);
         }
-        return rawJson;
+
+        await Promise.all(
+            asyncQueryExtractors.map(ex => ex.accept(query, this))
+        );
     }
 
     fetchSamplesWithSampleListIds(sampleListIds: string[]) {
@@ -2255,38 +2175,6 @@ export class StudyViewPageStore
         });
     }
 
-    getStudyViewFilterFromPatientIdentifierFilter(
-        patientIdentifierFilter: PatientIdentifierFilter,
-        samples: Sample[]
-    ): Partial<StudyViewFilter> {
-        const filters: Partial<StudyViewFilter> = {};
-        const sampleIdentifiers = this.convertPatientIdentifiersToSampleIdentifiers(
-            patientIdentifierFilter.patientIdentifiers,
-            samples
-        );
-        if (sampleIdentifiers.length > 0) {
-            filters.sampleIdentifiers = sampleIdentifiers;
-        }
-        return filters;
-    }
-
-    convertPatientIdentifiersToSampleIdentifiers(
-        patientIdentifiers: Array<PatientIdentifier>,
-        samples: Sample[]
-    ): SampleIdentifier[] {
-        const patientIdentifiersMap = new Map<string, PatientIdentifier>(
-            patientIdentifiers.map(p => [p.studyId.concat('_', p.patientId), p])
-        );
-        return samples
-            .filter(s =>
-                patientIdentifiersMap.has(s.studyId.concat('_', s.patientId))
-            )
-            .map(s => ({
-                sampleId: s.sampleId,
-                studyId: s.studyId,
-            }));
-    }
-
     @computed
     get initialFilters(): StudyViewFilter {
         let initialFilter = {} as StudyViewFilter;