add oncokb patient report tab to patient view page

src/pages/patientView/PatientViewPage.tsx

@@ -816,7 +816,8 @@ export class PatientViewPageInner extends React.Component<
                     {patientViewTabs(
                         this,
                         this.urlWrapper,
-                        this.pageStore.sampleManager.result!
+                        this.pageStore.sampleManager.result!,
+                        this.props.appStore
                     )}
                 </>
             );

src/pages/patientView/PatientViewPageTabs.tsx

@@ -37,6 +37,9 @@ import { HelpWidget } from 'shared/components/HelpWidget/HelpWidget';
 import MutationTableWrapper from './mutation/MutationTableWrapper';
 import { PatientViewPageInner } from 'pages/patientView/PatientViewPage';
 import { Else, If } from 'react-if';
+import PatientReportTab from './oncokb/PatientReportTab';
+import { AppStore } from 'AppStore';
+import { FeatureFlagEnum } from 'shared/featureFlags';
 
 export enum PatientViewPageTabs {
     Summary = 'summary',
@@ -49,6 +52,7 @@ export enum PatientViewPageTabs {
     TrialMatchTab = 'trialMatchTab',
     MutationalSignatures = 'mutationalSignatures',
     PathwayMapper = 'pathways',
+    OncoKBPatientReport = 'oncokbKBPatientReport',
 }
 
 export const PatientViewResourceTabPrefix = 'openResource_';
@@ -69,7 +73,8 @@ export function extractResourceIdFromTabId(tabId: string) {
 export function patientViewTabs(
     pageInstance: PatientViewPageInner,
     urlWrapper: PatientViewUrlWrapper,
-    sampleManager: SampleManager | null
+    sampleManager: SampleManager | null,
+    appStore: AppStore
 ) {
     return (
         <MSKTabs
@@ -84,15 +89,15 @@ export function patientViewTabs(
                 <HelpWidget path={urlWrapper.routing.location.pathname} />
             }
         >
-            {tabs(pageInstance, sampleManager, urlWrapper)}
+            {tabs(pageInstance, sampleManager, appStore)}
         </MSKTabs>
     );
 }
 
 export function tabs(
     pageComponent: PatientViewPageInner,
     sampleManager: SampleManager | null,
-    urlWrapper: PatientViewUrlWrapper
+    appStore: AppStore
 ) {
     const tabs: JSX.Element[] = [];
     tabs.push(
@@ -702,6 +707,20 @@ export function tabs(
             </MSKTab>
         );
 
+    if (appStore.featureFlagStore.has(FeatureFlagEnum.ONCOKB_PATIENT_REPORT)) {
+        tabs.push(
+            <MSKTab
+                key={9}
+                id={PatientViewPageTabs.OncoKBPatientReport}
+                linkText="OncoKB Patient Report"
+            >
+                <PatientReportTab
+                    patientViewPageStore={pageComponent.patientViewPageStore}
+                />
+            </MSKTab>
+        );
+    }
+
     pageComponent.resourceTabs.component &&
         /* @ts-ignore */
         tabs.push(...pageComponent.resourceTabs.component);

src/pages/patientView/oncokb/PatientReportTab.tsx

@@ -0,0 +1,90 @@
+import { observer } from 'mobx-react';
+import React, { useEffect } from 'react';
+import IFrameLoader from 'shared/components/iframeLoader/IFrameLoader';
+import WindowStore from 'shared/components/window/WindowStore';
+import { CLINICAL_ATTRIBUTE_ID_ENUM } from 'shared/constants';
+import { PatientViewPageStore } from '../clinicalInformation/PatientViewPageStore';
+import { getAnnotatedSamples } from './PatientReportUtils';
+
+interface IPatientReportTabProps {
+    patientViewPageStore: PatientViewPageStore;
+}
+
+class PatientMetadata {
+    id = '';
+    name = '';
+    age = '';
+    sex = '';
+}
+
+const IFRAME_NAME = 'patient-report-iframe';
+
+const PatientReportTab = observer(
+    ({ patientViewPageStore }: IPatientReportTabProps) => {
+        const isDataComplete =
+            patientViewPageStore.clinicalDataGroupedBySample.isComplete &&
+            patientViewPageStore.patientViewData.isComplete &&
+            patientViewPageStore.mutationData.isComplete &&
+            patientViewPageStore.oncoKbData.isComplete &&
+            patientViewPageStore.discreteCNAData.isComplete &&
+            patientViewPageStore.cnaOncoKbData.isComplete &&
+            patientViewPageStore.structuralVariantData.isComplete &&
+            patientViewPageStore.structuralVariantOncoKbData.isComplete;
+
+        useEffect(() => {
+            if (isDataComplete) {
+                const patientMetadata = new PatientMetadata();
+                patientMetadata.id = patientViewPageStore.patientId;
+                patientMetadata.sex =
+                    patientViewPageStore.patientViewData.result.patient?.clinicalData.find(
+                        data =>
+                            data.clinicalAttributeId ===
+                            CLINICAL_ATTRIBUTE_ID_ENUM.SEX
+                    )?.value ?? '';
+
+                const samples = getAnnotatedSamples(
+                    patientViewPageStore.clinicalDataGroupedBySample.result,
+                    patientViewPageStore.uniqueSampleKeyToTumorType,
+                    patientViewPageStore.mutationData.result,
+                    patientViewPageStore.oncoKbData.result,
+                    patientViewPageStore.discreteCNAData.result,
+                    patientViewPageStore.cnaOncoKbData.result,
+                    patientViewPageStore.structuralVariantData.result,
+                    patientViewPageStore.structuralVariantOncoKbData.result
+                );
+
+                const form = document.createElement('form');
+                form.method = 'POST';
+                form.action =
+                    'https://beta.report.oncokb.org/report/cbioportal';
+                form.target = IFRAME_NAME;
+
+                let input = document.createElement('input');
+                input.type = 'hidden';
+                input.name = 'annotatedSamples';
+                input.value = JSON.stringify(samples);
+                form.appendChild(input);
+
+                input = document.createElement('input');
+                input.type = 'hidden';
+                input.name = 'patientMetadata';
+                input.value = JSON.stringify(patientMetadata);
+                form.appendChild(input);
+
+                document.body.appendChild(form);
+                form.submit();
+                document.body.removeChild(form);
+            }
+        }, [isDataComplete]);
+
+        return (
+            <div>
+                <IFrameLoader
+                    height={WindowStore.size.height - 220}
+                    name={IFRAME_NAME}
+                />
+            </div>
+        );
+    }
+);
+export default PatientReportTab;

src/pages/patientView/oncokb/PatientReportUtils.spec.ts

@@ -0,0 +1,101 @@
+import { IOncoKbData } from 'cbioportal-utils';
+import { getAnnotatedSamples } from './PatientReportUtils';
+import {
+    ClinicalData,
+    DiscreteCopyNumberData,
+    Mutation,
+    StructuralVariant,
+} from 'cbioportal-ts-api-client';
+import { assert } from 'chai';
+
+describe('Patient Report Utils', () => {
+    const clinicalDataGroupedBySample: {
+        id: string;
+        clinicalData: ClinicalData[];
+    }[] = [
+        { id: '1', clinicalData: [] },
+        { id: '2', clinicalData: [] },
+    ];
+    const uniqueSampleKeyToTumorType: { [sampleId: string]: string } = {
+        '1': 'Melanoma',
+        '2': 'Breast Cancer',
+    };
+    const mutations: Partial<Mutation>[] = [
+        {
+            entrezGeneId: 673,
+            gene: {
+                entrezGeneId: 673,
+                geneticEntityId: 0,
+                hugoGeneSymbol: 'BRAF',
+                type: '',
+            },
+            mutationType: 'Missense_Mutation',
+            proteinChange: 'V600E',
+            sampleId: '1',
+            uniqueSampleKey: '1',
+        },
+    ];
+    const mutationsOncoKBData: IOncoKbData = {
+        indicatorMap: { '673_Melanoma_V600E_Missense_Mutation': {} as any },
+    };
+    const copyNumberAlterations: Partial<DiscreteCopyNumberData>[] = [
+        {
+            alteration: 2, // Amplification
+            entrezGeneId: 2064,
+            gene: {
+                entrezGeneId: 2064,
+                geneticEntityId: 0,
+                hugoGeneSymbol: 'ERBB2',
+                type: '',
+            },
+            molecularProfileId: '',
+            sampleId: '1',
+            uniqueSampleKey: '1',
+        },
+    ];
+    const copyNumberAlterationsOncoKBData: IOncoKbData = {
+        indicatorMap: { '2064_Melanoma_Amplification': {} as any },
+    };
+    const structuralVariants: Partial<StructuralVariant>[] = [
+        {
+            sampleId: '2',
+            site1EntrezGeneId: 613,
+            site1HugoSymbol: 'BCR',
+            site2EntrezGeneId: 25,
+            site2HugoSymbol: 'ABL1',
+            uniqueSampleKey: '2',
+        },
+    ];
+    const structuralVariantsOncoKBData: IOncoKbData = { indicatorMap: {} };
+
+    it('should construct samples from alteration data', () => {
+        const annotatedSamples = getAnnotatedSamples(
+            clinicalDataGroupedBySample,
+            uniqueSampleKeyToTumorType,
+            mutations as Mutation[],
+            mutationsOncoKBData,
+            copyNumberAlterations as DiscreteCopyNumberData[],
+            copyNumberAlterationsOncoKBData,
+            structuralVariants as StructuralVariant[],
+            structuralVariantsOncoKBData
+        );
+
+        const sample1 = annotatedSamples.find(sample => sample.id === '1');
+        assert(sample1 !== undefined);
+        const sample2 = annotatedSamples.find(sample => sample.id === '2');
+        assert(sample2 !== undefined);
+
+        assert(sample1!.mutations.length === 1);
+        assert(sample1!.copyNumberAlterations.length === 1);
+        assert(sample1!.structuralVariants.length === 0);
+
+        assert(sample2!.mutations.length === 0);
+        assert(sample2!.copyNumberAlterations.length === 0);
+        assert(sample2!.structuralVariants.length === 1);
+
+        const structuralVariant = sample2!.structuralVariants[0];
+        assert(structuralVariant.query.hugoSymbol === 'BCR');
+        assert(structuralVariant.query.alteration === 'BCR-ABL1 Fusion');
+        assert(structuralVariant.query.consequence === 'fusion');
+    });
+});