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cancer study chart filter refactoring
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@dippindots
dippindots committed Oct 23, 2024
1 parent dcfd297 commit b03c0f2
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Showing 2 changed files with 221 additions and 38 deletions.
253 changes: 216 additions & 37 deletions src/pages/studyView/StudyViewPageStore.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -2073,6 +2073,7 @@ export class StudyViewPageStore
@observable private initialFiltersQuery: Partial<StudyViewFilter> = {};

@observable studyIds: string[] = [];
@observable unfilteredStudyIds: string[] = [];

private _clinicalDataFilterSet = observable.map<
AttributeId,
Expand Down Expand Up @@ -3084,15 +3085,7 @@ export class StudyViewPageStore
chartUniqueKey === SpecialChartsUniqueKeyEnum.CANCER_STUDIES
) {
// this is for pre-defined custom charts
let filteredSampleIdentifiers = getFilteredSampleIdentifiers(
this.samples.result.filter(sample =>
values.includes(sample.studyId)
)
);
this._chartSampleIdentifiersFilterSet.set(
chartUniqueKey,
filteredSampleIdentifiers
);
this.studyIds = values;
this.preDefinedCustomChartFilterSet.set(
chartUniqueKey,
clinicalDataFilter
Expand All @@ -3108,9 +3101,7 @@ export class StudyViewPageStore
chartUniqueKey === SpecialChartsUniqueKeyEnum.CANCER_STUDIES
) {
// this is for pre-defined custom charts
this._chartSampleIdentifiersFilterSet.delete(
chartUniqueKey
);
this.studyIds = this.unfilteredStudyIds;
this.preDefinedCustomChartFilterSet.delete(chartUniqueKey);
} else {
this._customDataFilterSet.delete(chartUniqueKey);
Expand Down Expand Up @@ -5504,6 +5495,113 @@ export class StudyViewPageStore
default: [],
});

// contains queried physical studies
readonly filteredPhysicalStudiesFromOriginalQuery = remoteData({
await: () => [this.everyStudyIdToStudy],
invoke: async () => {
const everyStudyIdToStudy = this.everyStudyIdToStudy.result!;
return _.reduce(
this.unfilteredStudyIds,
(acc: CancerStudy[], next) => {
if (
everyStudyIdToStudy[next] &&
isQueriedStudyAuthorized(everyStudyIdToStudy[next])
) {
acc.push(everyStudyIdToStudy[next]);
}
return acc;
},
[]
);
},
default: [],
});

// contains queried vaild virtual studies
readonly filteredVirtualStudiesFromOriginalQuery = remoteData({
await: () => [this.filteredPhysicalStudiesFromOriginalQuery],
invoke: async () => {
if (
this.filteredPhysicalStudiesFromOriginalQuery.result.length ===
this.unfilteredStudyIds.length
) {
return [];
}
let filteredVirtualStudies: VirtualStudy[] = [];
let validFilteredPhysicalStudyIds = this.filteredPhysicalStudiesFromOriginalQuery.result.map(
study => study.studyId
);
let virtualStudyIds = _.filter(
this.unfilteredStudyIds,
id => !_.includes(validFilteredPhysicalStudyIds, id)
);

await Promise.all(
virtualStudyIds.map(id =>
sessionServiceClient
.getVirtualStudy(id)
.then(res => {
filteredVirtualStudies.push(res);
})
.catch(() => {
/*do nothing*/
})
)
);
return filteredVirtualStudies;
},
default: [],
});

// includes all physical studies from queried virtual studies
readonly queriedPhysicalStudiesFromOriginalQuery = remoteData({
await: () => [
this.filteredPhysicalStudiesFromOriginalQuery,
this.filteredVirtualStudiesFromOriginalQuery,
],
invoke: async () => {
let everyStudyIdToStudy = this.everyStudyIdToStudy.result!;

let studies = _.reduce(
this.filteredPhysicalStudiesFromOriginalQuery.result,
(acc, next) => {
acc[next.studyId] = everyStudyIdToStudy[next.studyId];
return acc;
},
{} as { [id: string]: CancerStudy }
);

this.filteredVirtualStudiesFromOriginalQuery.result.forEach(
virtualStudy => {
virtualStudy.data.studies.forEach(study => {
if (
!studies[study.id] &&
everyStudyIdToStudy[study.id]
) {
studies[study.id] = everyStudyIdToStudy[study.id];
}
});
}
);
return _.values(studies);
},
default: [],
});

// includes all physical studies from queried virtual studies
readonly queriedPhysicalStudyIdsFromOriginalQuery = remoteData({
await: () => [this.queriedPhysicalStudiesFromOriginalQuery],
invoke: () => {
return Promise.resolve(
_.map(
this.queriedPhysicalStudiesFromOriginalQuery.result,
study => study.studyId
)
);
},
default: [],
});

readonly studyIdToStudy = remoteData(
{
await: () => [this.queriedPhysicalStudies],
Expand Down Expand Up @@ -5590,16 +5688,18 @@ export class StudyViewPageStore
// this is used in page header(name and description)
readonly displayedStudies = remoteData({
await: () => [
this.filteredVirtualStudies,
this.filteredPhysicalStudies,
this.queriedPhysicalStudies,
this.filteredVirtualStudiesFromOriginalQuery,
this.filteredPhysicalStudiesFromOriginalQuery,
this.queriedPhysicalStudiesFromOriginalQuery,
],
invoke: async () => {
if (
this.filteredPhysicalStudies.result.length === 0 &&
this.filteredVirtualStudies.result.length === 1
this.filteredPhysicalStudiesFromOriginalQuery.result.length ===
0 &&
this.filteredVirtualStudiesFromOriginalQuery.result.length === 1
) {
const virtualStudy = this.filteredVirtualStudies.result[0];
const virtualStudy = this
.filteredVirtualStudiesFromOriginalQuery.result[0];
return [
{
name: virtualStudy.data.name,
Expand All @@ -5608,7 +5708,7 @@ export class StudyViewPageStore
} as CancerStudy,
];
} else {
return this.queriedPhysicalStudies.result;
return this.queriedPhysicalStudiesFromOriginalQuery.result;
}
},
default: [],
Expand Down Expand Up @@ -9866,31 +9966,15 @@ export class StudyViewPageStore
}

readonly cancerStudiesData = remoteData<ClinicalDataCountSummary[]>({
await: () => [this.selectedSamples],
await: () => [this.selectedSamplesFromOriginalQuery],
invoke: async () => {
// return empty if there are no filtered samples
if (!this.hasFilteredSamples) {
return [];
}
let selectedSamples = [];
if (
this._chartSampleIdentifiersFilterSet.has(
SpecialChartsUniqueKeyEnum.CANCER_STUDIES
)
) {
selectedSamples = await getSamplesByExcludingFiltersOnChart(
SpecialChartsUniqueKeyEnum.CANCER_STUDIES,
this.filters,
_.fromPairs(this._chartSampleIdentifiersFilterSet.toJSON()),
this.queriedSampleIdentifiers.result,
this.queriedPhysicalStudyIds.result
);
} else {
selectedSamples = this.selectedSamples.result;
}
const counts = _.values(
_.reduce(
selectedSamples,
this.selectedSamplesFromOriginalQuery.result,
(acc, sample) => {
const studyId = sample.studyId;
if (acc[studyId]) {
Expand All @@ -9915,6 +9999,101 @@ export class StudyViewPageStore
default: [],
});

readonly samplesFromOriginalQuery = remoteData<Sample[]>({
await: () => [
// this.queriedSampleIdentifiers,
this.queriedPhysicalStudyIdsFromOriginalQuery,
],
invoke: () => {
let studyViewFilter: StudyViewFilter = {} as any;
//this logic is need since fetchFilteredSamplesUsingPOST api accepts sampleIdentifiers or studyIds not both
// if (this.queriedSampleIdentifiers.result.length > 0) {
// studyViewFilter.sampleIdentifiers = this.queriedSampleIdentifiers.result;
// } else {
studyViewFilter.studyIds = this.queriedPhysicalStudyIdsFromOriginalQuery.result;
// }

if (
// !_.isEmpty(studyViewFilter.sampleIdentifiers) ||
!_.isEmpty(studyViewFilter.studyIds)
) {
return this.internalClient.fetchFilteredSamplesUsingPOST({
studyViewFilter: studyViewFilter,
});
}
return Promise.resolve([]);
},
onError: () => {},
default: [],
});

readonly molecularProfilesFromOriginalQuery = remoteData<
MolecularProfile[]
>({
await: () => [this.queriedPhysicalStudyIdsFromOriginalQuery],
invoke: async () => {
if (
this.queriedPhysicalStudyIdsFromOriginalQuery.result.length > 0
) {
return await defaultClient.fetchMolecularProfilesUsingPOST({
molecularProfileFilter: {
studyIds: this.queriedPhysicalStudyIdsFromOriginalQuery
.result,
} as MolecularProfileFilter,
});
}
return [];
},
onError: () => {},
default: [],
});

readonly selectedSamplesFromOriginalQuery = remoteData<Sample[]>({
await: () => [
this.samplesFromOriginalQuery,
this.molecularProfilesFromOriginalQuery,
this.queriedPhysicalStudyIdsFromOriginalQuery,
],
invoke: () => {
//fetch samples when there are only filters applied
if (this.chartsAreFiltered) {
if (!this.hasSampleIdentifiersInFilter) {
return Promise.resolve([] as Sample[]);
}
// here we are validating only the molecular profile ids,
// but ideally we should validate the entire filters object
const invalidMolecularProfiles = findInvalidMolecularProfileIds(
this.filters,
this.molecularProfilesFromOriginalQuery.result
);
if (invalidMolecularProfiles.length > 0) {
this.appStore.addError(
`Invalid molecular profile id(s): ${invalidMolecularProfiles.join(
', '
)}`
);
}
return this.internalClient.fetchFilteredSamplesUsingPOST({
studyViewFilter: _.merge(_.clone(this.filters), {
studyIds: this.queriedPhysicalStudyIdsFromOriginalQuery
.result,
}),
});
} else {
return Promise.resolve(this.samplesFromOriginalQuery.result);
}
},
onError: () => {},
default: [],
onResult: samples => {
if (samples.length === 0) {
this.blockLoading = true;
} else {
this.blockLoading = false;
}
},
});

@action
showAsPieChart(uniqueKey: string, dataSize: number): void {
if (
Expand Down
6 changes: 5 additions & 1 deletion src/pages/studyView/StudyViewQueryExtractor.ts
View file
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
import { toJS } from 'mobx';
import { observable, toJS } from 'mobx';
import { StudyViewPageStore, StudyViewURLQuery } from './StudyViewPageStore';
import _ from 'lodash';
import {
Expand Down Expand Up @@ -36,6 +36,10 @@ export class StudyIdQueryExtractor implements StudyViewQueryExtractor<void> {
// update if different
store.studyIds = studyIds;
}
if (!_.isEqual(studyIds, toJS(store.unfilteredStudyIds))) {
// update if different
store.unfilteredStudyIds = studyIds;
}
}
}
}
Expand Down

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