individual download

cBioPortal · Apr 28, 2021 · 96e922a · 96e922a
1 parent 054f43e
commit 96e922a
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Showing 2 changed files with 112 additions and 7 deletions.
diff --git a/src/pages/resultsView/ResultsViewPageStore.ts b/src/pages/resultsView/ResultsViewPageStore.ts
@@ -1411,7 +1411,6 @@ export class ResultsViewPageStore {
         NumericGeneMolecularData[]
     >({
         await: () => [
-            this.studyToDataQueryFilter,
             this.genes,
             this.nonSelectedDownloadableMolecularProfiles,
             this.samples,

diff --git a/src/pages/resultsView/download/DownloadTab.tsx b/src/pages/resultsView/download/DownloadTab.tsx
@@ -14,6 +14,7 @@ import {
 import {
     getSingleGeneResultKey,
     getMultipleGeneResultKey,
+    excludeSpecialMolecularProfiles,
 } from '../ResultsViewPageStoreUtils';
 import { CoverageInformation } from 'shared/lib/GenePanelUtils';
 import {
@@ -66,6 +67,9 @@ import {
     Sample,
     CancerStudy,
     GenericAssayData,
+    SampleMolecularIdentifier,
+    Gene,
+    MolecularDataMultipleStudyFilter,
 } from 'cbioportal-ts-api-client';
 import ErrorMessage from '../../../shared/components/ErrorMessage';
 import AlterationFilterWarning from '../../../shared/components/banners/AlterationFilterWarning';
@@ -77,6 +81,8 @@ import FontAwesome from 'react-fontawesome';
 import CaseFilterWarning from '../../../shared/components/banners/CaseFilterWarning';
 import { If, Then, Else } from 'react-if';
 import { ResultsViewTab } from '../ResultsViewPageHelpers';
+import client from 'shared/api/cbioportalClientInstance';
+import { REQUEST_ARG_ENUM } from 'shared/constants';
 
 export interface IDownloadTabProps {
     store: ResultsViewPageStore;
@@ -1328,13 +1334,113 @@ export default class DownloadTab extends React.Component<
 
     @autobind
     private handleOtherMolecularProfileDownload(profileName: string) {
-        onMobxPromise(
-            this.allOtherMolecularProfileDownloadDataGroupByProfileName,
-            downloadDataGroupByProfileName => {
-                const textMap = this.downloadDataTextGroupByKey(
-                    downloadDataGroupByProfileName
+        onMobxPromise<any>(
+            [
+                this.props.store.nonSelectedDownloadableMolecularProfiles,
+                this.props.store.samples,
+                this.props.store.genes,
+                this.props.store.coverageInformation,
+            ],
+            async (
+                nonSelectedDownloadableMolecularProfiles,
+                samples,
+                genes,
+                coverageInformation
+            ) => {
+                // STEP 1: fetch data
+                // we get mutations with mutations endpoint, structural variants and fusions with structural variant endpoint.
+                // filter out mutation genetic profile and structural variant profiles
+                const selectedProfiles: MolecularProfile[] = nonSelectedDownloadableMolecularProfiles.filter(
+                    (profile: MolecularProfile) => profile.name === profileName
                 );
-                fileDownload(textMap[profileName], `${profileName}.txt`);
+
+                if (
+                    selectedProfiles.length &&
+                    genes != undefined &&
+                    genes.length
+                ) {
+                    const selectedProfilesGroupByStudyId = _.groupBy(
+                        selectedProfiles,
+                        profile => profile.studyId
+                    );
+                    // find samples which share studyId with profile and add identifier
+                    const sampleIdentifiers: SampleMolecularIdentifier[] = (samples as Sample[])
+                        .filter(
+                            sample =>
+                                sample.studyId in selectedProfilesGroupByStudyId
+                        )
+                        .reduce((acc: SampleMolecularIdentifier[], sample) => {
+                            acc = acc.concat(
+                                selectedProfilesGroupByStudyId[
+                                    sample.studyId
+                                ].map(profile => {
+                                    return {
+                                        molecularProfileId:
+                                            profile.molecularProfileId,
+                                        sampleId: sample.sampleId,
+                                    } as SampleMolecularIdentifier;
+                                })
+                            );
+                            return acc;
+                        }, []);
+
+                    let molecularData: any[] = [];
+                    if (sampleIdentifiers.length) {
+                        molecularData = await client.fetchMolecularDataInMultipleMolecularProfilesUsingPOST(
+                            {
+                                projection:
+                                    REQUEST_ARG_ENUM.PROJECTION_DETAILED,
+                                molecularDataMultipleStudyFilter: {
+                                    entrezGeneIds: _.map(
+                                        genes,
+                                        (gene: Gene) => gene.entrezGeneId
+                                    ),
+                                    sampleMolecularIdentifiers: sampleIdentifiers,
+                                } as MolecularDataMultipleStudyFilter,
+                            }
+                        );
+                    }
+
+                    // STEP 2: fetch data
+                    // const data = {
+                    //     samples: _.groupBy(
+                    //         this.props.store.nonSelectedDownloadableMolecularData
+                    //             .result!,
+                    //         data => data.uniqueSampleKey
+                    //     ),
+                    // } as CaseAggregatedData<ExtendedAlteration>;
+                    // const allOtherMolecularProfileDataGroupByProfileName: {
+                    //     [profileName: string]: {
+                    //         [key: string]: ExtendedAlteration[];
+                    //     };
+                    // } = _.reduce(
+                    //     profileNames,
+                    //     (
+                    //         allOtherMolecularProfileDataGroupByProfileName,
+                    //         profileName
+                    //     ) => {
+                    //         allOtherMolecularProfileDataGroupByProfileName[
+                    //             profileName
+                    //         ] = generateOtherMolecularProfileData(
+                    //             this.props.store.nonSelectedDownloadableMolecularProfilesGroupByName.result[
+                    //                 profileName
+                    //             ].map(profile => profile.molecularProfileId),
+                    //             data
+                    //         );
+                    //         return allOtherMolecularProfileDataGroupByProfileName;
+                    //     },
+                    //     {} as {
+                    //         [profileName: string]: {
+                    //             [key: string]: ExtendedAlteration[];
+                    //         };
+                    //     }
+                    // );
+                }
+
+                // const textMap = this.downloadDataTextGroupByKey(
+                //     downloadDataGroupByProfileName
+                // );
+                // fileDownload(textMap[profileName], `${profileName}.txt`);
             }
         );
     }