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Merge pull request #4003 from adamabeshouse/8979-sv-opt
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Dont wait for selectedSamples to make several API calls in study view

Former-commit-id: 4ca0e4144ffe6249d88813805470355597a2093d
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@adamabeshouse
adamabeshouse authored Nov 29, 2021
2 parents 65cd9a0 + fc48e38 commit 8a858a4
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Showing 3 changed files with 57 additions and 90 deletions.
4 changes: 2 additions & 2 deletions end-to-end-test/shared/wdio/wdio.conf.js
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Original file line number Diff line number Diff line change
Expand Up @@ -300,13 +300,13 @@ exports.config = {
framework: 'mocha',
//
// The number of times to retry the entire specfile when it fails as a whole
specFileRetries: 2,
specFileRetries: 0,
//
// Delay in seconds between the spec file retry attempts
// specFileRetriesDelay: 0,
//
// Whether or not retried specfiles should be retried immediately or deferred to the end of the queue
specFileRetriesDeferred: true,
specFileRetriesDeferred: false,
//
// Test reporter for stdout.
// The only one supported by default is 'dot'
Expand Down
140 changes: 52 additions & 88 deletions src/pages/studyView/StudyViewPageStore.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -157,7 +157,7 @@ import {
getStudyDownloadListUrl,
redirectToComparisonPage,
} from '../../shared/api/urls';
import onMobxPromise from '../../shared/lib/onMobxPromise';
import onMobxPromise, { toPromise } from '../../shared/lib/onMobxPromise';
import request from 'superagent';
import { trackStudyViewFilterEvent } from '../../shared/lib/tracking';
import comparisonClient from '../../shared/api/comparisonGroupClientInstance';
Expand Down Expand Up @@ -3659,13 +3659,8 @@ export class StudyViewPageStore
}

readonly unfilteredClinicalDataCount = remoteData<ClinicalDataCountItem[]>({
await: () => [this.selectedSamples],
invoke: () => {
//only invoke if there are filtered samples
if (
this.hasFilteredSamples &&
!_.isEmpty(this.unfilteredAttrsForNonNumerical)
) {
if (!_.isEmpty(this.unfilteredAttrsForNonNumerical)) {
return internalClient.fetchClinicalDataCountsUsingPOST({
clinicalDataCountFilter: {
attributes: this.unfilteredAttrsForNonNumerical,
Expand Down Expand Up @@ -3718,13 +3713,8 @@ export class StudyViewPageStore
readonly newlyAddedUnfilteredClinicalDataCount = remoteData<
ClinicalDataCountItem[]
>({
await: () => [this.selectedSamples],
invoke: () => {
//only invoke if there are filtered samples
if (
this.hasFilteredSamples &&
!_.isEmpty(this.newlyAddedUnfilteredAttrsForNonNumerical)
) {
if (!_.isEmpty(this.newlyAddedUnfilteredAttrsForNonNumerical)) {
return internalClient.fetchClinicalDataCountsUsingPOST({
clinicalDataCountFilter: {
attributes: this
Expand Down Expand Up @@ -3829,7 +3819,6 @@ export class StudyViewPageStore
>({
await: () => {
return [
this.selectedSamples,
...getRequestedAwaitPromisesForClinicalData(
isDefaultAttr,
this.isInitialFilterState,
Expand Down Expand Up @@ -3860,10 +3849,6 @@ export class StudyViewPageStore
this._clinicalDataFilterSet.has(uniqueKey) ||
this.isInitialFilterState
) {
// return empty if there are no sample identifiers or study ids in the filter
if (!this.hasFilteredSamples) {
return [];
}
result = await internalClient.fetchClinicalDataCountsUsingPOST(
{
clinicalDataCountFilter: {
Expand Down Expand Up @@ -5028,7 +5013,8 @@ export class StudyViewPageStore
default: {},
});

@computed get oncokbCancerGeneFilterEnabled(): boolean {
@computed({ keepAlive: true })
get oncokbCancerGeneFilterEnabled(): boolean {
if (!getServerConfig().show_oncokb) {
return false;
}
Expand Down Expand Up @@ -5468,7 +5454,7 @@ export class StudyViewPageStore
_chartMetaSet
);

if (this.displaySampleTreatments.result) {
if (this.shouldDisplaySampleTreatments.result) {
_chartMetaSet['SAMPLE_TREATMENTS'] = {
uniqueKey: 'SAMPLE_TREATMENTS',
dataType: ChartMetaDataTypeEnum.CLINICAL,
Expand All @@ -5483,7 +5469,7 @@ export class StudyViewPageStore
};
}

if (this.displayPatientTreatments.result) {
if (this.shouldDisplayPatientTreatments.result) {
_chartMetaSet['PATIENT_TREATMENTS'] = {
uniqueKey: 'PATIENT_TREATMENTS',
dataType: ChartMetaDataTypeEnum.CLINICAL,
Expand All @@ -5498,7 +5484,7 @@ export class StudyViewPageStore
};
}

if (this.displaySampleTreatmentGroups.result) {
if (this.shouldDisplaySampleTreatmentGroups.result) {
_chartMetaSet['SAMPLE_TREATMENT_GROUPS'] = {
uniqueKey: 'SAMPLE_TREATMENT_GROUPS',
dataType: ChartMetaDataTypeEnum.CLINICAL,
Expand All @@ -5513,7 +5499,7 @@ export class StudyViewPageStore
};
}

if (this.displayPatientTreatmentGroups.result) {
if (this.shouldDisplayPatientTreatmentGroups.result) {
_chartMetaSet['PATIENT_TREATMENT_GROUPS'] = {
uniqueKey: 'PATIENT_TREATMENT_GROUPS',
dataType: ChartMetaDataTypeEnum.CLINICAL,
Expand Down Expand Up @@ -5677,7 +5663,7 @@ export class StudyViewPageStore
this.cnaProfiles.isPending ||
this.structuralVariantProfiles.isPending ||
this.survivalPlots.isPending ||
this.displayPatientTreatments.isPending ||
this.shouldDisplayPatientTreatments.isPending ||
this.sharedCustomData.isPending;

if (
Expand Down Expand Up @@ -6139,7 +6125,7 @@ export class StudyViewPageStore
}
}

if (this.displayPatientTreatments.result) {
if (this.shouldDisplayPatientTreatments.result) {
this.changeChartVisibility(
SpecialChartsUniqueKeyEnum.SAMPLE_TREATMENTS,
true
Expand All @@ -6160,7 +6146,7 @@ export class StudyViewPageStore
);
}

if (this.displaySampleTreatmentGroups.result) {
if (this.shouldDisplaySampleTreatmentGroups.result) {
this.changeChartVisibility(
SpecialChartsUniqueKeyEnum.SAMPLE_TREATMENT_GROUPS,
true
Expand Down Expand Up @@ -7037,14 +7023,10 @@ export class StudyViewPageStore
this.oncokbOncogeneEntrezGeneIds,
this.oncokbTumorSuppressorGeneEntrezGeneIds,
this.oncokbCancerGeneEntrezGeneIds,
this.selectedSamples,
]
: [this.mutationProfiles, this.selectedSamples],
: [this.mutationProfiles],
invoke: async () => {
if (
!_.isEmpty(this.mutationProfiles.result) &&
this.selectedSamples.result.length > 0
) {
if (!_.isEmpty(this.mutationProfiles.result)) {
let mutatedGenes = await internalClient.fetchMutatedGenesUsingPOST(
{
studyViewFilter: this.filters,
Expand Down Expand Up @@ -7097,14 +7079,10 @@ export class StudyViewPageStore
this.oncokbOncogeneEntrezGeneIds,
this.oncokbTumorSuppressorGeneEntrezGeneIds,
this.oncokbCancerGeneEntrezGeneIds,
this.selectedSamples,
]
: [this.mutationProfiles, this.selectedSamples],
: [this.structuralVariantProfiles],
invoke: async () => {
if (
!_.isEmpty(this.structuralVariantProfiles.result) &&
this.selectedSamples.result.length > 0
) {
if (!_.isEmpty(this.structuralVariantProfiles.result)) {
const structuralVariantGenes = await internalClient.fetchStructuralVariantGenesUsingPOST(
{
studyViewFilter: this.filters,
Expand Down Expand Up @@ -7155,14 +7133,10 @@ export class StudyViewPageStore
this.oncokbOncogeneEntrezGeneIds,
this.oncokbTumorSuppressorGeneEntrezGeneIds,
this.oncokbCancerGeneEntrezGeneIds,
this.selectedSamples,
]
: [this.mutationProfiles, this.selectedSamples],
: [this.cnaProfiles],
invoke: async () => {
if (
!_.isEmpty(this.cnaProfiles.result) &&
this.selectedSamples.result.length > 0
) {
if (!_.isEmpty(this.cnaProfiles.result)) {
let cnaGenes = await internalClient.fetchCNAGenesUsingPOST({
studyViewFilter: this.filters,
});
Expand Down Expand Up @@ -8008,47 +7982,50 @@ export class StudyViewPageStore
readonly molecularProfileSampleCounts = remoteData<
MultiSelectionTableRow[]
>({
await: () => [this.molecularProfiles, this.selectedSamples],
await: () => [this.molecularProfiles],
invoke: async () => {
// return empty if there are no filtered samples
if (!this.hasFilteredSamples) {
return [];
}
const counts = await internalClient.fetchMolecularProfileSampleCountsUsingPOST(
{
const [counts, selectedSamples] = await Promise.all([
internalClient.fetchMolecularProfileSampleCountsUsingPOST({
studyViewFilter: this.filters,
}
);
}),
toPromise(this.selectedSamples),
]);

return counts.map(caseListOption => {
return {
uniqueKey: caseListOption.value,
label: caseListOption.label,
// "Altered" and "Profiled" really just mean
// "numerator" and "denominator" in percent
// calculation of table. Here, they mean
// "# filtered samples in profile" and "# filtered samples overall"
numberOfAlteredCases: caseListOption.count,
numberOfProfiledCases: this.selectedSamples.result.length,
numberOfProfiledCases: selectedSamples.length,
} as any;
});
},
default: [],
});

readonly caseListSampleCounts = remoteData<MultiSelectionTableRow[]>({
await: () => [this.selectedSamples],
invoke: async () => {
// return empty if there are no filtered samples
if (!this.hasFilteredSamples) {
return [];
}
const counts = await internalClient.fetchCaseListCountsUsingPOST({
studyViewFilter: this.filters,
});
const [counts, selectedSamples] = await Promise.all([
internalClient.fetchCaseListCountsUsingPOST({
studyViewFilter: this.filters,
}),
toPromise(this.selectedSamples),
]);

return counts.map(caseListOption => {
return {
uniqueKey: caseListOption.value,
label: caseListOption.label,
// "Altered" and "Profiled" really just mean
// "numerator" and "denominator" in percent
// calculation of table. Here, they mean
// "# filtered samples in case list" and "# filtered samples overall"
numberOfAlteredCases: caseListOption.count,
numberOfProfiledCases: this.selectedSamples.result.length,
numberOfProfiledCases: selectedSamples.length,
} as any;
});
},
Expand All @@ -8073,7 +8050,6 @@ export class StudyViewPageStore
});

readonly initialMolecularProfileSampleCounts = remoteData({
await: () => [this.samples, this.molecularProfiles],
invoke: async () => {
return internalClient.fetchMolecularProfileSampleCountsUsingPOST({
studyViewFilter: this.initialFilters,
Expand Down Expand Up @@ -8938,12 +8914,9 @@ export class StudyViewPageStore
// a row represents a list of patients that either have or have not recieved
// a specific treatment
public readonly sampleTreatments = remoteData({
await: () => [this.selectedSamples, this.displaySampleTreatments],
await: () => [this.shouldDisplaySampleTreatments],
invoke: () => {
if (
this.hasFilteredSamples &&
this.displaySampleTreatments.result
) {
if (this.shouldDisplaySampleTreatments.result) {
return defaultClient.getAllSampleTreatmentsUsingPOST({
studyViewFilter: this.filters,
});
Expand All @@ -8952,7 +8925,7 @@ export class StudyViewPageStore
},
});

public readonly displayPatientTreatments = remoteData({
public readonly shouldDisplayPatientTreatments = remoteData({
await: () => [this.queriedPhysicalStudyIds],
invoke: () => {
return defaultClient.getContainsTreatmentDataUsingPOST({
Expand All @@ -8961,7 +8934,7 @@ export class StudyViewPageStore
},
});

public readonly displaySampleTreatments = remoteData({
public readonly shouldDisplaySampleTreatments = remoteData({
await: () => [this.queriedPhysicalStudyIds],
invoke: () => {
return defaultClient.getContainsSampleTreatmentDataUsingPOST({
Expand All @@ -8973,12 +8946,9 @@ export class StudyViewPageStore
// a row represents a list of samples that ether have or have not recieved
// a specific treatment
public readonly patientTreatments = remoteData({
await: () => [this.selectedSamples, this.displayPatientTreatments],
await: () => [this.shouldDisplayPatientTreatments],
invoke: () => {
if (
this.hasFilteredSamples &&
this.displayPatientTreatments.result
) {
if (this.shouldDisplayPatientTreatments.result) {
return defaultClient.getAllPatientTreatmentsUsingPOST({
studyViewFilter: this.filters,
});
Expand All @@ -8988,12 +8958,9 @@ export class StudyViewPageStore
});

public readonly sampleTreatmentGroups = remoteData({
await: () => [this.selectedSamples, this.displaySampleTreatmentGroups],
await: () => [this.shouldDisplaySampleTreatmentGroups],
invoke: () => {
if (
this.hasFilteredSamples &&
this.displaySampleTreatments.result
) {
if (this.shouldDisplaySampleTreatmentGroups.result) {
return defaultClient.getAllSampleTreatmentsUsingPOST({
studyViewFilter: this.filters,
tier: 'AgentClass',
Expand All @@ -9003,7 +8970,7 @@ export class StudyViewPageStore
},
});

public readonly displayPatientTreatmentGroups = remoteData({
public readonly shouldDisplayPatientTreatmentGroups = remoteData({
await: () => [this.queriedPhysicalStudyIds],
invoke: () => {
if (!getServerConfig().enable_treatment_groups) {
Expand All @@ -9016,7 +8983,7 @@ export class StudyViewPageStore
},
});

public readonly displaySampleTreatmentGroups = remoteData({
public readonly shouldDisplaySampleTreatmentGroups = remoteData({
await: () => [this.queriedPhysicalStudyIds],
invoke: () => {
if (!getServerConfig().enable_treatment_groups) {
Expand All @@ -9032,12 +8999,9 @@ export class StudyViewPageStore
// a row represents a list of samples that ether have or have not recieved
// a specific treatment
public readonly patientTreatmentGroups = remoteData({
await: () => [this.selectedSamples, this.displayPatientTreatments],
await: () => [this.shouldDisplayPatientTreatmentGroups],
invoke: () => {
if (
this.hasFilteredSamples &&
this.displayPatientTreatmentGroups.result
) {
if (this.shouldDisplayPatientTreatmentGroups.result) {
return defaultClient.getAllPatientTreatmentsUsingPOST({
studyViewFilter: this.filters,
tier: 'AgentClass',
Expand Down
3 changes: 3 additions & 0 deletions src/shared/lib/onMobxPromise.ts
View file
Original file line number Diff line number Diff line change
Expand Up @@ -30,6 +30,9 @@ export function onMobxPromise<T>(
}

export function toPromise<T>(promise: MobxPromise<T>): Promise<T> {
// Reference the `promise` result to trigger invoke if necessary, and
// to mobx-link the caller of `toPromise` to `promise`.
promise.result;
return new Promise(resolve => {
onMobxPromise(promise, resolve);
});
Expand Down

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