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On Study View handle larger number of resource files #5034

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merged 10 commits into from
Nov 1, 2024
Merged

On Study View handle larger number of resource files #5034

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4c2f184
Modify FilesAndLinks table to use the new resource-data-all endpoint.
hweej Oct 27, 2024
e6da0c7
Add filtering logic based off studyview sample selection
hweej Oct 28, 2024
cf69080
Merge branch 'master' into reduce-api-calls-files-and-links-tab
hweej Oct 28, 2024
4ef97bf
Add missing typescript types
hweej Oct 28, 2024
a417dac
Merge branch 'reduce-api-calls-files-and-links-tab' of github.com:hwe…
hweej Oct 28, 2024
e029bb0
Remove clinicalData request, rename variables, add relevant comments on
hweej Oct 29, 2024
c4f1df8
Update linear array lookup to a key Map lookup for optimization. Replace
hweej Oct 30, 2024
f8aff81
Exchange string for actual property for typesafety.
hweej Oct 30, 2024
07f04bb
Remove unnecessary Map instantiation
hweej Oct 31, 2024
42ea827
Add latest typescript api definition files
hweej Nov 1, 2024
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70 changes: 61 additions & 9 deletions src/pages/studyView/resources/FilesAndLinks.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,19 @@ class FilesLinksTableComponent extends LazyMobXTable<{

const RECORD_LIMIT = 500;

function getResourceDataOfEntireStudy(studyIds: string[]) {
// Only handle the first studyId for now. Can be expanded to make a call per
// studyId.
const studyId = studyIds[0];
const allResources = internalClient.getAllStudyResourceDataInStudyPatientSampleUsingGET(
{
studyId: studyId,
projection: 'DETAILED',
}
);
return allResources;
}

function getResourceDataOfPatients(studyClinicalData: {
[uniqueSampleKey: string]: ClinicalData[];
}) {
Expand Down Expand Up @@ -97,7 +110,7 @@ function buildItemsAndResources(resourceData: {

async function fetchFilesLinksData(
filters: StudyViewFilter,
sampleIdResourceData: { [sampleId: string]: ResourceData[] },
selectedSamples: Array<any>,
searchTerm: string | undefined,
sortAttributeId: string | undefined,
sortDirection: 'asc' | 'desc' | undefined,
Expand All @@ -112,13 +125,52 @@ async function fetchFilesLinksData(
0
);

const resourcesForPatients = await getResourceDataOfPatients(
studyClinicalDataResponse.data
const selectedStudyIds = [
...new Set(selectedSamples.map(item => item.studyId)),
];
const selectedSampleIds = selectedSamples.map(item => item.sampleId);
const selectedPatientIds = [
...new Set(selectedSamples.map(item => item.patientId)),
];

const resourcesForEntireStudy = await getResourceDataOfEntireStudy(
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selectedStudyIds
);
const resourcesForPatientsAndSamples: { [key: string]: ResourceData[] } = {
...sampleIdResourceData,
...resourcesForPatients,
};

const resourcesForPatientsAndSamples = resourcesForEntireStudy
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// Filter the resources to consist of only studyView selected samples
// Also keep patient level resources (e.g. Those don't have a sampleId)
.filter(
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one more thing here: this is operation is Rsamples+Rpatients. could easily get to billion. easily optimized by putting selectedSamples in a map so you can use IN operator.

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I have replaced this with Maps instead of arrays to remove the linear lookup. I don't think you can use the IN operator with Maps so we're opting for the .has('key') expression instead.

(resource: ResourceData) =>
selectedSampleIds.includes(resource.sampleId) ||
selectedPatientIds.includes(resource.patientId)
)
.reduce(
(
idMap: { [key: string]: ResourceData[] },
resource: ResourceData
) => {
const { resourceType } = resource.resourceDefinition;
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this whole operation would be more clearly handled by lodash's keyBy function. we like to use these kind of named helpers because they make the operation more explicit.

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Hm, I couldn't make lodash keyBy function to work the way I wanted it to for this use case. In python this would be a case for collections.defaultDict. But I couldn't make this work where I could create new arrays and append to them.

LMK if you want me to work on this part some more.

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@hweej sorry, i mean _.groupBy

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I have replaced these lines with a single lodash groupBy('patientId'). Thanks @alisman !

const { patientId, sampleId } = resource;

if (resourceType == 'PATIENT') {
if (idMap.hasOwnProperty(patientId)) {
idMap[patientId].push(resource);
} else {
idMap[patientId] = [resource];
}
} else if (resourceType == 'SAMPLE') {
if (idMap.hasOwnProperty(sampleId)) {
idMap[sampleId].push(resource);
} else {
idMap[sampleId] = [resource];
}
}

return idMap;
},
{}
);

// we create objects with the necessary properties for each resource
// calculate the total number of resources per patient.
Expand Down Expand Up @@ -197,7 +249,6 @@ export class FilesAndLinks extends React.Component<IFilesLinksTable, {}> {
await: () => [
this.props.store.selectedSamples,
this.props.store.resourceDefinitions,
this.props.store.sampleResourceData,
],
onError: () => {},
invoke: async () => {
Expand All @@ -207,12 +258,13 @@ export class FilesAndLinks extends React.Component<IFilesLinksTable, {}> {

const resources = await fetchFilesLinksData(
this.props.store.filters,
this.props.store.sampleResourceData.result!,
this.props.store.selectedSamples.result,
this.searchTerm,
'patientId',
'asc',
RECORD_LIMIT
);

return Promise.resolve(resources);
},
});
Expand Down
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