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Download tab fetch Non-Select profiles data individually #3725

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merged 2 commits into from
Apr 30, 2021
Merged

Download tab fetch Non-Select profiles data individually #3725

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fdd30fe
change text for Generic Assay in download tab
Apr 28, 2021
96de201
Download tab fetch Non-Select profiles data individually
Apr 28, 2021
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1 change: 0 additions & 1 deletion src/pages/resultsView/ResultsViewPageStore.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -1411,7 +1411,6 @@ export class ResultsViewPageStore {
NumericGeneMolecularData[]
>({
await: () => [
this.studyToDataQueryFilter,
this.genes,
this.nonSelectedDownloadableMolecularProfiles,
this.samples,
Expand Down
204 changes: 56 additions & 148 deletions src/pages/resultsView/download/DownloadTab.tsx
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
import * as React from 'react';
import * as _ from 'lodash';
import { computed, observable, action, makeObservable } from 'mobx';
import { action, makeObservable } from 'mobx';
import { observer } from 'mobx-react';
import fileDownload from 'react-file-download';
import {
Expand All @@ -15,10 +15,8 @@ import {
getSingleGeneResultKey,
getMultipleGeneResultKey,
} from '../ResultsViewPageStoreUtils';
import { CoverageInformation } from 'shared/lib/GenePanelUtils';
import {
OQLLineFilterOutput,
UnflattenedOQLLineFilterOutput,
MergedTrackLineFilterOutput,
} from 'shared/lib/oql/oqlfilter';
import FeatureTitle from 'shared/components/featureTitle/FeatureTitle';
Expand All @@ -44,13 +42,16 @@ import {
hasValidStructuralVariantData,
hasValidMutationData,
stringify2DArray,
generateOtherMolecularProfileData,
generateOtherMolecularProfileDownloadData,
generateGenericAssayProfileData,
generateGenericAssayProfileDownloadData,
generateStructuralVariantData,
generateStructuralDownloadData,
makeIsSampleProfiledFunction,
downloadOtherMolecularProfileData,
downloadDataText,
unzipDownloadData,
downloadDataTextGroupByKey,
unzipDownloadDataGroupByKey,
} from './DownloadUtils';

import styles from './styles.module.scss';
Expand All @@ -64,7 +65,6 @@ import onMobxPromise from 'shared/lib/onMobxPromise';
import {
MolecularProfile,
Sample,
CancerStudy,
GenericAssayData,
} from 'cbioportal-ts-api-client';
import ErrorMessage from '../../../shared/components/ErrorMessage';
Expand Down Expand Up @@ -202,87 +202,6 @@ export default class DownloadTab extends React.Component<
),
});

readonly allOtherMolecularProfileDataGroupByProfileName = remoteData<{
[profileName: string]: { [key: string]: ExtendedAlteration[] };
}>({
await: () => [
this.props.store.nonSelectedDownloadableMolecularData,
this.props.store
.nonSelectedDownloadableMolecularProfilesGroupByName,
],
invoke: () => {
const profileNames = _.keys(
this.props.store
.nonSelectedDownloadableMolecularProfilesGroupByName.result
);
if (
this.props.store.doNonSelectedDownloadableMolecularProfilesExist
) {
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[];
};
}
);
return Promise.resolve(
allOtherMolecularProfileDataGroupByProfileName
);
}
return Promise.resolve({});
},
});

readonly allOtherMolecularProfileDownloadDataGroupByProfileName = remoteData<{
[key: string]: string[][];
}>({
await: () => [
this.allOtherMolecularProfileDataGroupByProfileName,
this.props.store.samples,
this.props.store.genes,
this.props.store.coverageInformation,
],
invoke: () =>
Promise.resolve(
_.mapValues(
this.allOtherMolecularProfileDataGroupByProfileName.result,
otherMolecularProfileData => {
return generateOtherMolecularProfileDownloadData(
otherMolecularProfileData,
this.props.store.samples.result!,
this.props.store.genes.result!
);
}
)
),
});

readonly genericAssayProfileDownloadDataGroupByProfileIdSuffix = remoteData<{
[key: string]: string[][];
}>({
Expand Down Expand Up @@ -996,7 +915,7 @@ export default class DownloadTab extends React.Component<
<div>
<a
onClick={() =>
this.handleOtherMolecularProfileDownload(
this.handleNonSelectedMolecularProfileDownload(
option.name
)
}
Expand All @@ -1010,7 +929,7 @@ export default class DownloadTab extends React.Component<
<span style={{ margin: '0px 10px' }}>|</span>
<a
onClick={() =>
this.handleTransposedOtherMolecularProfileDownload(
this.handleTransposedNonSelectedMolecularProfileDownload(
option.name
)
}
Expand Down Expand Up @@ -1109,7 +1028,7 @@ export default class DownloadTab extends React.Component<
</a>
</Then>
<Else>
Heatmap tracks added in the&nbsp;
Tracks added in the&nbsp;
<a
onClick={() =>
this.props.store.handleTabChange(
Expand Down Expand Up @@ -1256,102 +1175,118 @@ export default class DownloadTab extends React.Component<

private handleMutationDownload() {
onMobxPromise(this.mutationDownloadData, data => {
const text = this.downloadDataText(data);
const text = downloadDataText(data);
fileDownload(text, 'mutations.txt');
});
}

private handleTransposedMutationDownload() {
onMobxPromise(this.mutationDownloadData, data => {
const text = this.downloadDataText(this.unzipDownloadData(data));
const text = downloadDataText(unzipDownloadData(data));
fileDownload(text, 'mutations_transposed.txt');
});
}

@autobind
private handleStructuralVariantDownload() {
onMobxPromise(this.structuralVariantDownloadData, data => {
const text = this.downloadDataText(data);
const text = downloadDataText(data);
fileDownload(text, 'structural_variants.txt');
});
}

@autobind
private handleTransposedStructuralVariantDownload() {
onMobxPromise(this.structuralVariantDownloadData, data => {
const text = this.downloadDataText(this.unzipDownloadData(data));
const text = downloadDataText(unzipDownloadData(data));
fileDownload(text, 'structural_variants_transposed.txt');
});
}

private handleMrnaDownload(profileName: string) {
onMobxPromise(this.mrnaDownloadData, data => {
const text = this.downloadDataText(data);
const text = downloadDataText(data);
fileDownload(text, `${profileName}.txt`);
});
}

private handleTransposedMrnaDownload(profileName: string) {
onMobxPromise(this.mrnaDownloadData, data => {
const text = this.downloadDataText(this.unzipDownloadData(data));
const text = downloadDataText(unzipDownloadData(data));
fileDownload(text, `${profileName}.txt`);
});
}

private handleProteinDownload(profileName: string) {
onMobxPromise(this.proteinDownloadData, data => {
const text = this.downloadDataText(data);
const text = downloadDataText(data);
fileDownload(text, `${profileName}.txt`);
});
}

private handleTransposedProteinDownload(profileName: string) {
onMobxPromise(this.proteinDownloadData, data => {
const text = this.downloadDataText(this.unzipDownloadData(data));
const text = downloadDataText(unzipDownloadData(data));
fileDownload(text, `${profileName}.txt`);
});
}

private handleCnaDownload() {
onMobxPromise(this.cnaDownloadData, data => {
const text = this.downloadDataText(data);
const text = downloadDataText(data);
fileDownload(text, 'cna.txt');
});
}

private handleTransposedCnaDownload() {
onMobxPromise(this.cnaDownloadData, data => {
const text = this.downloadDataText(this.unzipDownloadData(data));
const text = downloadDataText(unzipDownloadData(data));
fileDownload(text, 'cna_transposed.txt');
});
}

@autobind
private handleOtherMolecularProfileDownload(profileName: string) {
onMobxPromise(
this.allOtherMolecularProfileDownloadDataGroupByProfileName,
downloadDataGroupByProfileName => {
const textMap = this.downloadDataTextGroupByKey(
downloadDataGroupByProfileName
private handleNonSelectedMolecularProfileDownload(profileName: string) {
onMobxPromise<any>(
[
this.props.store.nonSelectedDownloadableMolecularProfiles,
this.props.store.samples,
this.props.store.genes,
],
(nonSelectedDownloadableMolecularProfiles, samples, genes) => {
const profiles: MolecularProfile[] = nonSelectedDownloadableMolecularProfiles.filter(
(profile: MolecularProfile) => profile.name === profileName
);
downloadOtherMolecularProfileData(
profileName,
profiles,
samples,
genes
);
fileDownload(textMap[profileName], `${profileName}.txt`);
}
);
}

@autobind
private handleTransposedOtherMolecularProfileDownload(profileName: string) {
onMobxPromise(
this.allOtherMolecularProfileDownloadDataGroupByProfileName,
downloadDataGroupByProfileName => {
const transposedTextMap = this.downloadDataTextGroupByKey(
this.unzipDownloadDataGroupByKey(
downloadDataGroupByProfileName
)
private handleTransposedNonSelectedMolecularProfileDownload(
profileName: string
) {
onMobxPromise<any>(
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maybe put a comment above this explaining what "other" means. i think it means non-selected, right?

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I changed those Other to NonSelected

[
this.props.store.nonSelectedDownloadableMolecularProfiles,
this.props.store.samples,
this.props.store.genes,
],
(nonSelectedDownloadableMolecularProfiles, samples, genes) => {
const profiles: MolecularProfile[] = nonSelectedDownloadableMolecularProfiles.filter(
(profile: MolecularProfile) => profile.name === profileName
);
fileDownload(
transposedTextMap[profileName],
`${profileName}.txt`
downloadOtherMolecularProfileData(
profileName,
profiles,
samples,
genes,
true
);
}
);
Expand All @@ -1365,7 +1300,7 @@ export default class DownloadTab extends React.Component<
onMobxPromise(
this.genericAssayProfileDownloadDataGroupByProfileIdSuffix,
downloadDataGroupByProfileIdSuffix => {
const textMap = this.downloadDataTextGroupByKey(
const textMap = downloadDataTextGroupByKey(
downloadDataGroupByProfileIdSuffix
);
fileDownload(textMap[profileIdSuffix], `${profileName}.txt`);
Expand All @@ -1381,8 +1316,8 @@ export default class DownloadTab extends React.Component<
onMobxPromise(
this.genericAssayProfileDownloadDataGroupByProfileIdSuffix,
downloadDataGroupByProfileIdSuffix => {
const transposedTextMap = this.downloadDataTextGroupByKey(
this.unzipDownloadDataGroupByKey(
const transposedTextMap = downloadDataTextGroupByKey(
unzipDownloadDataGroupByKey(
downloadDataGroupByProfileIdSuffix
)
);
Expand All @@ -1404,31 +1339,4 @@ export default class DownloadTab extends React.Component<
this.props.store.modifyQueryParams = modifyQueryParams;
this.props.store.queryFormVisible = true;
}

private unzipDownloadDataGroupByKey(downloadDataGroupByKey: {
[key: string]: string[][];
}): { [key: string]: string[][] } {
return _.mapValues(
downloadDataGroupByKey,
otherMolecularProfileDownloadData => {
return _.unzip(otherMolecularProfileDownloadData);
}
);
}

private downloadDataTextGroupByKey(downloadDataGroupByKey: {
[key: string]: string[][];
}): { [x: string]: string } {
return _.mapValues(downloadDataGroupByKey, downloadData => {
return stringify2DArray(downloadData);
});
}

private unzipDownloadData(downloadData: string[][]): string[][] {
return _.unzip(downloadData);
}

private downloadDataText(downloadData: string[][]): string {
return stringify2DArray(downloadData);
}
}