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Fix error while calculating profiled samples count #3041

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merged 1 commit into from
Feb 6, 2020
Merged

Fix error while calculating profiled samples count #3041

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33 changes: 22 additions & 11 deletions src/pages/resultsView/ResultsViewPageStore.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -194,6 +194,8 @@ import {
getUniqueKey,
StudyWithSamples,
UniqueKey,
getUniqueKeyFromMolecularProfileIds,
ChartMetaDataTypeEnum,
} from 'pages/studyView/StudyViewUtils';
import {
FRACTION_GENOME_ALTERED,
Expand All @@ -206,6 +208,7 @@ import {
fetchTreatmentByMolecularProfileIds,
Treatment,
} from 'shared/lib/GenericAssayUtils/TreatmentUtils';
import { ChartTypeEnum } from 'pages/studyView/StudyViewConfig';

type Optional<T> =
| { isApplicable: true; value: T }
Expand Down Expand Up @@ -2378,28 +2381,38 @@ export class ResultsViewPageStore {
);

if (!_.isEmpty(this.mutationProfiles.result!)) {
_chartMetaSet[UniqueKey.MUTATED_GENES_TABLE] = {
uniqueKey: UniqueKey.MUTATED_GENES_TABLE,
dataType: getChartMetaDataType(UniqueKey.MUTATED_GENES_TABLE),
const uniqueKey = getUniqueKeyFromMolecularProfileIds(
this.mutationProfiles.result.map(
profile => profile.molecularProfileId
)
);
_chartMetaSet[uniqueKey] = {
uniqueKey: uniqueKey,
dataType: ChartMetaDataTypeEnum.GENOMIC,
patientAttribute: false,
displayName: 'Mutated Genes',
priority: getDefaultPriorityByUniqueKey(
UniqueKey.MUTATED_GENES_TABLE
ChartTypeEnum.MUTATED_GENES_TABLE
),
renderWhenDataChange: false,
description: '',
};
}

if (!_.isEmpty(this.cnaProfiles.result)) {
_chartMetaSet[UniqueKey.CNA_GENES_TABLE] = {
uniqueKey: UniqueKey.CNA_GENES_TABLE,
dataType: getChartMetaDataType(UniqueKey.CNA_GENES_TABLE),
const uniqueKey = getUniqueKeyFromMolecularProfileIds(
this.cnaProfiles.result.map(
profile => profile.molecularProfileId
)
);
_chartMetaSet[uniqueKey] = {
uniqueKey: uniqueKey,
dataType: ChartMetaDataTypeEnum.GENOMIC,
patientAttribute: false,
displayName: 'CNA Genes',
renderWhenDataChange: false,
priority: getDefaultPriorityByUniqueKey(
UniqueKey.CNA_GENES_TABLE
ChartTypeEnum.CNA_GENES_TABLE
),
description: '',
};
Expand All @@ -2424,9 +2437,7 @@ export class ResultsViewPageStore {
scatterRequiredParams[FRACTION_GENOME_ALTERED]
) {
_chartMetaSet[UniqueKey.MUTATION_COUNT_CNA_FRACTION] = {
dataType: getChartMetaDataType(
UniqueKey.MUTATION_COUNT_CNA_FRACTION
),
dataType: ChartMetaDataTypeEnum.GENOMIC,
patientAttribute: false,
uniqueKey: UniqueKey.MUTATION_COUNT_CNA_FRACTION,
displayName: 'Mutation Count vs Fraction of Genome Altered',
Expand Down
56 changes: 35 additions & 21 deletions src/pages/studyView/StudyViewPageStore.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -90,6 +90,7 @@ import {
getMolecularProfileIdsFromUniqueKey,
getClinicalDataBySamples,
updateSavedUserPreferenceChartIds,
ChartMetaDataTypeEnum,
} from './StudyViewUtils';
import MobxPromise from 'mobxpromise';
import { SingleGeneQuery } from 'shared/lib/oql/oql-parser';
Expand Down Expand Up @@ -2936,11 +2937,11 @@ export class StudyViewPageStore {
);
_chartMetaSet[uniqueKey] = {
uniqueKey: uniqueKey,
dataType: getChartMetaDataType(UniqueKey.MUTATED_GENES_TABLE),
dataType: ChartMetaDataTypeEnum.GENOMIC,
patientAttribute: false,
displayName: 'Mutated Genes',
priority: getDefaultPriorityByUniqueKey(
UniqueKey.MUTATED_GENES_TABLE
ChartTypeEnum.MUTATED_GENES_TABLE
),
renderWhenDataChange: false,
description: '',
Expand All @@ -2955,11 +2956,11 @@ export class StudyViewPageStore {
);
_chartMetaSet[uniqueKey] = {
uniqueKey: uniqueKey,
dataType: getChartMetaDataType(UniqueKey.FUSION_GENES_TABLE),
dataType: ChartMetaDataTypeEnum.GENOMIC,
patientAttribute: false,
displayName: 'Fusion Genes',
priority: getDefaultPriorityByUniqueKey(
UniqueKey.FUSION_GENES_TABLE
ChartTypeEnum.FUSION_GENES_TABLE
),
renderWhenDataChange: true,
description: '',
Expand All @@ -2974,12 +2975,12 @@ export class StudyViewPageStore {
);
_chartMetaSet[uniqueKey] = {
uniqueKey: uniqueKey,
dataType: getChartMetaDataType(UniqueKey.CNA_GENES_TABLE),
dataType: ChartMetaDataTypeEnum.GENOMIC,
patientAttribute: false,
displayName: 'CNA Genes',
renderWhenDataChange: false,
priority: getDefaultPriorityByUniqueKey(
UniqueKey.CNA_GENES_TABLE
ChartTypeEnum.CNA_GENES_TABLE
),
description: '',
};
Expand All @@ -3004,9 +3005,7 @@ export class StudyViewPageStore {
scatterRequiredParams[FRACTION_GENOME_ALTERED]
) {
_chartMetaSet[UniqueKey.MUTATION_COUNT_CNA_FRACTION] = {
dataType: getChartMetaDataType(
UniqueKey.MUTATION_COUNT_CNA_FRACTION
),
dataType: ChartMetaDataTypeEnum.GENOMIC,
patientAttribute: false,
uniqueKey: UniqueKey.MUTATION_COUNT_CNA_FRACTION,
displayName: 'Mutation Count vs Fraction of Genome Altered',
Expand Down Expand Up @@ -3273,19 +3272,19 @@ export class StudyViewPageStore {
}

switch (chartUserSettings.chartType) {
case UniqueKey.MUTATED_GENES_TABLE:
case ChartTypeEnum.MUTATED_GENES_TABLE:
this._filterMutatedGenesTableByCancerGenes =
chartUserSettings.filterByCancerGenes === undefined
? true
: chartUserSettings.filterByCancerGenes;
break;
case UniqueKey.FUSION_GENES_TABLE:
case ChartTypeEnum.FUSION_GENES_TABLE:
this._filterFusionGenesTableByCancerGenes =
chartUserSettings.filterByCancerGenes === undefined
? true
: chartUserSettings.filterByCancerGenes;
break;
case UniqueKey.CNA_GENES_TABLE:
case ChartTypeEnum.CNA_GENES_TABLE:
this._filterCNAGenesTableByCancerGenes =
chartUserSettings.filterByCancerGenes === undefined
? true
Expand Down Expand Up @@ -4843,9 +4842,14 @@ export class StudyViewPageStore {
{}
);

if (UniqueKey.MUTATED_GENES_TABLE in this.chartMetaSet) {
ret[UniqueKey.MUTATED_GENES_TABLE] = this
.molecularProfileSampleCounts.result
if (!_.isEmpty(this.mutationProfiles.result)) {
const uniqueKey = getUniqueKeyFromMolecularProfileIds(
this.mutationProfiles.result.map(
profile => profile.molecularProfileId
)
);

ret[uniqueKey] = this.molecularProfileSampleCounts.result
? this.molecularProfileSampleCounts.result
.numberOfMutationProfiledSamples
: 0;
Expand All @@ -4856,9 +4860,14 @@ export class StudyViewPageStore {
: 0;
}

if (UniqueKey.FUSION_GENES_TABLE in this.chartMetaSet) {
ret[UniqueKey.FUSION_GENES_TABLE] = this
.molecularProfileSampleCounts.result
if (!_.isEmpty(this.structuralVariantProfiles.result)) {
const uniqueKey = getUniqueKeyFromMolecularProfileIds(
this.structuralVariantProfiles.result.map(
profile => profile.molecularProfileId
)
);

ret[uniqueKey] = this.molecularProfileSampleCounts.result
? this.molecularProfileSampleCounts.result
.numberOfFusionProfiledSamples
: 0;
Expand All @@ -4869,9 +4878,14 @@ export class StudyViewPageStore {
: 0;
}

if (UniqueKey.CNA_GENES_TABLE in this.chartMetaSet) {
ret[UniqueKey.CNA_GENES_TABLE] = this
.molecularProfileSampleCounts.result
if (!_.isEmpty(this.cnaProfiles.result)) {
const uniqueKey = getUniqueKeyFromMolecularProfileIds(
this.cnaProfiles.result.map(
profile => profile.molecularProfileId
)
);

ret[uniqueKey] = this.molecularProfileSampleCounts.result
? this.molecularProfileSampleCounts.result
.numberOfCNAProfiledSamples
: 0;
Expand Down
12 changes: 3 additions & 9 deletions src/pages/studyView/StudyViewUtils.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -86,9 +86,6 @@ export type ChartType =
| 'NONE';

export enum UniqueKey {
MUTATED_GENES_TABLE = 'MUTATED_GENES_TABLE',
FUSION_GENES_TABLE = 'FUSION_GENES_TABLE',
CNA_GENES_TABLE = 'CNA_GENES_TABLE',
CUSTOM_SELECT = 'CUSTOM_SELECT',
SELECTED_COMPARISON_GROUPS = 'SELECTED_COMPARISON_GROUPS',
MUTATION_COUNT_CNA_FRACTION = 'MUTATION_COUNT_CNA_FRACTION',
Expand Down Expand Up @@ -1258,14 +1255,11 @@ export function toFixedDigit(value: number, fractionDigits: number = 2) {
export function getChartMetaDataType(uniqueKey: string): ChartMetaDataType {
const GENOMIC_DATA_TYPES = [
UniqueKey.MUTATION_COUNT_CNA_FRACTION,
UniqueKey.CNA_GENES_TABLE,
UniqueKey.MUTATED_GENES_TABLE,
UniqueKey.MUTATION_COUNT,
UniqueKey.FRACTION_GENOME_ALTERED,
UniqueKey.WITH_MUTATION_DATA,
UniqueKey.WITH_CNA_DATA,
UniqueKey.WITH_FUSION_DATA,
UniqueKey.FUSION_GENES_TABLE,
];
return _.includes(GENOMIC_DATA_TYPES, uniqueKey)
? ChartMetaDataTypeEnum.GENOMIC
Expand Down Expand Up @@ -2193,15 +2187,15 @@ export function getChartSettingsMap(
chartType,
patientAttribute: attribute.patientAttribute, // add chart attribute type
};
if (chartType === UniqueKey.MUTATED_GENES_TABLE) {
if (chartType === ChartTypeEnum.MUTATED_GENES_TABLE) {
chartSettingsMap[
attribute.uniqueKey
].filterByCancerGenes = filterMutatedGenesTableByCancerGenes;
} else if (chartType === UniqueKey.FUSION_GENES_TABLE) {
} else if (chartType === ChartTypeEnum.FUSION_GENES_TABLE) {
chartSettingsMap[
attribute.uniqueKey
].filterByCancerGenes = filterFusionGenesTableByCancerGenes;
} else if (chartType === UniqueKey.CNA_GENES_TABLE) {
} else if (chartType === ChartTypeEnum.CNA_GENES_TABLE) {
chartSettingsMap[
attribute.uniqueKey
].filterByCancerGenes = filterCNAGenesTableByCancerGenes;
Expand Down
8 changes: 4 additions & 4 deletions src/pages/studyView/UserSelections.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@ import {
import { PillTag } from '../../shared/components/PillTag/PillTag';
import { GroupLogic } from './filters/groupLogic/GroupLogic';
import classnames from 'classnames';
import { STUDY_VIEW_CONFIG } from './StudyViewConfig';
import { STUDY_VIEW_CONFIG, ChartTypeEnum } from './StudyViewConfig';
import {
DEFAULT_NA_COLOR,
MUT_COLOR_FUSION,
Expand Down Expand Up @@ -319,13 +319,13 @@ export default class UserSelections extends React.Component<
switch (
chartMeta.chartType
) {
case UniqueKey.MUTATED_GENES_TABLE:
case ChartTypeEnum.MUTATED_GENES_TABLE:
color = MUT_COLOR_MISSENSE;
break;
case UniqueKey.FUSION_GENES_TABLE:
case ChartTypeEnum.FUSION_GENES_TABLE:
color = MUT_COLOR_FUSION;
break;
case UniqueKey.CNA_GENES_TABLE: {
case ChartTypeEnum.CNA_GENES_TABLE: {
const oqlParts = oql
.trim()
.split(':');
Expand Down