Fix type issues after client update

cBioPortal · Jun 6, 2022 · 9f3a59a · 9f3a59a
1 parent 188b007
commit 9f3a59a
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Showing 15 changed files with 44 additions and 34 deletions.
diff --git a/end-to-end-test/remote/specs/core/results.spec.js b/end-to-end-test/remote/specs/core/results.spec.js
@@ -203,10 +203,7 @@ describe('Results Page', function() {
                 var url = `${CBIOPORTAL_URL}/results/mutations?tab_index=tab_visualize&cancer_study_list=ov_tcga_pub&cancer_study_id=ov_tcga_pub&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=ov_tcga_pub_mutations&Z_SCORE_THRESHOLD=2.0&case_set_id=ov_tcga_pub_3way_complete&gene_list=TP53+PTEN&gene_set_choice=user-defined-list&Action=Submit`;
                 browser.url(url);
                 $('[data-test=view3DStructure]').waitForExist({
-                    timeout: 10000,
-                });
-                $('[data-test=view3DStructure]').waitForEnabled({
-                    timeout: 10000,
+                    timeout: 20000,
                 });
                 $('[data-test=oncogenic-icon-image]').waitForDisplayed({
                     timeout: 10000,

diff --git a/src/AppStore.ts b/src/AppStore.ts
@@ -6,7 +6,7 @@ import {
 } from 'cbioportal-frontend-commons';
 import { getLoadConfig, getServerConfig } from './config/config';
 import _ from 'lodash';
-import internalClient from 'shared/api/cbioportalInternalClientInstance';
+import client from 'shared/api/cbioportalClientInstance';
 import { sendSentryMessage } from './shared/lib/tracking';
 
 export type SiteError = {
@@ -96,9 +96,7 @@ export class AppStore {
 
     readonly portalVersion = remoteData<string | undefined>({
         invoke: async () => {
-            const portalVersionResult = await internalClient.getInfoUsingGET(
-                {}
-            );
+            const portalVersionResult = await client.getInfoUsingGET({});
             if (portalVersionResult && portalVersionResult.portalVersion) {
                 let version = undefined;
 

diff --git a/src/pages/patientView/clinicalInformation/PatientViewPageStore.ts b/src/pages/patientView/clinicalInformation/PatientViewPageStore.ts
@@ -16,7 +16,6 @@ import {
     ResourceData,
     Sample,
     SampleMolecularIdentifier,
-    StructuralVariantFilter,
     GenericAssayData,
     GenericAssayMeta,
     GenericAssayDataMultipleStudyFilter,
@@ -200,6 +199,7 @@ import {
 } from 'shared/lib/GenericAssayUtils/MutationalSignaturesUtils';
 import { getServerConfig } from 'config/config';
 import { getOncoKbIconStyle } from 'shared/lib/AnnotationColumnUtils';
+import { StructuralVariantFilter } from 'cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal';
 
 type PageMode = 'patient' | 'sample';
 type ResourceId = string;
@@ -613,7 +613,7 @@ export class PatientViewPageStore {
                 .value();
 
             if (mutationalSignatureContributionStableIds.length > 0) {
-                return client.fetchGenericAssayMetaDataUsingPOST({
+                return client.fetchGenericAssayMetaUsingPOST({
                     genericAssayMetaFilter: {
                         genericAssayStableIds: mutationalSignatureContributionStableIds,
                     } as GenericAssayMetaFilter,
@@ -1615,7 +1615,7 @@ export class PatientViewPageStore {
                     }),
                 } as StructuralVariantFilter;
 
-                return client.fetchStructuralVariantsUsingPOST({
+                return internalClient.fetchStructuralVariantsUsingPOST({
                     structuralVariantFilter,
                 });
             }

diff --git a/src/pages/patientView/structuralVariant/PatientViewStructuralVariantTable.tsx b/src/pages/patientView/structuralVariant/PatientViewStructuralVariantTable.tsx
@@ -5,7 +5,6 @@ import { PatientViewPageStore } from '../clinicalInformation/PatientViewPageStor
 import LazyMobXTable, {
     Column,
 } from 'shared/components/lazyMobXTable/LazyMobXTable';
-import { StructuralVariant } from 'cbioportal-ts-api-client';
 import TumorColumnFormatter from '../mutation/column/TumorColumnFormatter';
 import HeaderIconMenu from '../mutation/HeaderIconMenu';
 import GeneFilterMenu from '../mutation/GeneFilterMenu';
@@ -26,6 +25,7 @@ import {
     DEFAULT_ONCOKB_CONTENT_WIDTH,
     updateOncoKbIconStyle,
 } from 'shared/lib/AnnotationColumnUtils';
+import { StructuralVariant } from 'cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal';
 
 export interface IPatientViewStructuralVariantTableProps {
     store: PatientViewPageStore;

diff --git a/src/pages/patientView/structuralVariant/column/AnnotationColumnFormatter.tsx b/src/pages/patientView/structuralVariant/column/AnnotationColumnFormatter.tsx
@@ -8,7 +8,7 @@ import {
     USE_DEFAULT_PUBLIC_INSTANCE_FOR_ONCOKB,
     oncoKbAnnotationSortValue,
 } from 'react-mutation-mapper';
-import { CancerStudy, StructuralVariant } from 'cbioportal-ts-api-client';
+import { CancerStudy } from 'cbioportal-ts-api-client';
 import { IAnnotationColumnProps } from 'shared/components/mutationTable/column/AnnotationColumnFormatter';
 import { CancerGene, IndicatorQueryResp } from 'oncokb-ts-api-client';
 import {
@@ -19,6 +19,7 @@ import {
     calculateOncoKbAvailableDataType,
 } from 'cbioportal-utils';
 import AnnotationHeader from 'shared/components/mutationTable/column/annotation/AnnotationHeader';
+import { StructuralVariant } from 'cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal';
 
 export default class AnnotationColumnFormatter {
     public static getData(

diff --git a/src/pages/resultsView/ResultsViewPageStore.ts b/src/pages/resultsView/ResultsViewPageStore.ts
@@ -33,9 +33,12 @@ import {
     SampleIdentifier,
     SampleList,
     SampleMolecularIdentifier,
+} from 'cbioportal-ts-api-client';
+import {
     StructuralVariant,
     StructuralVariantFilter,
-} from 'cbioportal-ts-api-client';
+} from 'cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal';
+
 import client from 'shared/api/cbioportalClientInstance';
 import {
     CanonicalMutationType,
@@ -3286,7 +3289,7 @@ export class ResultsViewPageStore
                     sampleMolecularIdentifiers: filters,
                 } as StructuralVariantFilter;
 
-                return await client.fetchStructuralVariantsUsingPOST({
+                return await internalClient.fetchStructuralVariantsUsingPOST({
                     structuralVariantFilter: data,
                 });
             }
@@ -5899,7 +5902,7 @@ export class ResultsViewPageStore
             if (_.isEmpty(filters)) {
                 return [];
             } else {
-                return client.fetchStructuralVariantsUsingPOST({
+                return internalClient.fetchStructuralVariantsUsingPOST({
                     structuralVariantFilter: {
                         entrezGeneIds: [q.entrezGeneId],
                         sampleMolecularIdentifiers: filters,

diff --git a/src/pages/resultsView/ResultsViewPageStoreUtils.ts b/src/pages/resultsView/ResultsViewPageStoreUtils.ts
@@ -9,9 +9,11 @@ import {
     PatientFilter,
     PatientIdentifier,
     ReferenceGenomeGene,
-    StructuralVariant,
     Sample,
 } from 'cbioportal-ts-api-client';
+
+import { StructuralVariant } from 'cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal';
+
 import { action, ObservableMap } from 'mobx';
 import AccessorsForOqlFilter, {
     getSimplifiedMutationType,

diff --git a/src/pages/resultsView/plots/PlotsTabUtils.tsx b/src/pages/resultsView/plots/PlotsTabUtils.tsx
@@ -22,8 +22,10 @@ import {
     Mutation,
     NumericGeneMolecularData,
     Sample,
-    StructuralVariant,
 } from 'cbioportal-ts-api-client';
+
+import { StructuralVariant } from 'cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal';
+
 import {
     capitalize,
     remoteData,

diff --git a/src/pages/studyView/StudyViewComparisonUtils.ts b/src/pages/studyView/StudyViewComparisonUtils.ts
@@ -10,9 +10,13 @@ import {
     Sample,
     SampleIdentifier,
     SampleMolecularIdentifier,
+} from 'cbioportal-ts-api-client';
+
+import {
     StructuralVariant,
     StructuralVariantFilter,
-} from 'cbioportal-ts-api-client';
+} from 'cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal';
+
 import { getGroupParameters } from 'pages/groupComparison/comparisonGroupManager/ComparisonGroupManagerUtils';
 import { LoadingPhase } from 'pages/groupComparison/GroupComparisonLoading';
 import comparisonClient from 'shared/api/comparisonGroupClientInstance';
@@ -21,6 +25,7 @@ import { ChartTypeEnum } from 'pages/studyView/StudyViewConfig';
 import { getGeneFromUniqueKey } from './TableUtils';
 import client from 'shared/api/cbioportalClientInstance';
 import { REQUEST_ARG_ENUM } from 'shared/constants';
+import internalClient from 'shared/api/cbioportalInternalClientInstance';
 
 export function doesChartHaveComparisonGroupsLimit(chartMeta: ChartMeta) {
     return chartMeta.uniqueKey !== SpecialChartsUniqueKeyEnum.CANCER_STUDIES;
@@ -145,7 +150,7 @@ export async function getSvData(
         geneIds: hugoGeneSymbols,
     });
 
-    return client.fetchStructuralVariantsUsingPOST({
+    return internalClient.fetchStructuralVariantsUsingPOST({
         structuralVariantFilter: {
             entrezGeneIds: genes.map(g => g.entrezGeneId),
             sampleMolecularIdentifiers,

diff --git a/src/shared/components/oncoprint/TooltipUtils.ts b/src/shared/components/oncoprint/TooltipUtils.ts
@@ -6,8 +6,10 @@ import {
     GenePanelData,
     MolecularProfile,
     Mutation,
-    StructuralVariant,
 } from 'cbioportal-ts-api-client';
+
+import { StructuralVariant } from 'cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal';
+
 import client from 'shared/api/cbioportalClientInstance';
 import {
     ClinicalTrackSpec,

diff --git a/src/shared/lib/GenericAssayUtils/GenericAssayCommonUtils.ts b/src/shared/lib/GenericAssayUtils/GenericAssayCommonUtils.ts
@@ -1,4 +1,5 @@
 import client from 'shared/api/cbioportalClientInstance';
+import internalClient from 'shared/api/cbioportalInternalClientInstance';
 import {
     GenericAssayMetaFilter,
     GenericAssayMeta,
@@ -112,7 +113,7 @@ export function fetchGenericAssayMetaByProfileIds(
     genericAssayProfileIds: string[]
 ) {
     if (genericAssayProfileIds.length > 0) {
-        return client.fetchGenericAssayMetaDataUsingPOST({
+        return client.fetchGenericAssayMetaUsingPOST({
             genericAssayMetaFilter: {
                 molecularProfileIds: genericAssayProfileIds,
                 // the Swagger-generated type expected by the client method below
@@ -126,7 +127,7 @@ export function fetchGenericAssayMetaByProfileIds(
 
 export function fetchGenericAssayMetaByEntityIds(entityIds: string[]) {
     if (entityIds.length > 0) {
-        return client.fetchGenericAssayMetaDataUsingPOST({
+        return client.fetchGenericAssayMetaUsingPOST({
             genericAssayMetaFilter: {
                 genericAssayStableIds: entityIds,
                 // the Swagger-generated type expected by the client method below

diff --git a/src/shared/lib/StoreUtils.ts b/src/shared/lib/StoreUtils.ts
@@ -33,7 +33,6 @@ import {
     ReferenceGenomeGene,
     Sample,
     SampleFilter,
-    StructuralVariant,
 } from 'cbioportal-ts-api-client';
 import defaultClient from 'shared/api/cbioportalClientInstance';
 import client from 'shared/api/cbioportalClientInstance';
@@ -109,6 +108,7 @@ import {
 } from 'shared/lib/MutationUtils';
 import { ObservableMap } from 'mobx';
 import { chunkCalls } from 'cbioportal-utils';
+import { StructuralVariant } from 'cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal';
 
 export const MolecularAlterationType_filenameSuffix: {
     [K in MolecularProfile['molecularAlterationType']]?: string;

diff --git a/src/shared/lib/oql/AccessorsForOqlFilter.ts b/src/shared/lib/oql/AccessorsForOqlFilter.ts
@@ -2,8 +2,9 @@ import {
     Mutation,
     MolecularProfile,
     NumericGeneMolecularData,
-    StructuralVariant,
 } from 'cbioportal-ts-api-client';
+import { StructuralVariant } from 'cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal';
+
 import _ from 'lodash';
 import {
     AlterationTypeConstants,

diff --git a/src/shared/lib/oql/annotateAlterationTypes.ts b/src/shared/lib/oql/annotateAlterationTypes.ts
@@ -1,8 +1,7 @@
 import AccessorsForOqlFilter from './AccessorsForOqlFilter';
-import {
-    NumericGeneMolecularData,
-    StructuralVariant,
-} from 'cbioportal-ts-api-client';
+import { NumericGeneMolecularData } from 'cbioportal-ts-api-client';
+import { StructuralVariant } from 'cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal';
+
 import {
     AlterationTypeConstants,
     AnnotatedMutation,

diff --git a/src/shared/lib/oql/oqlfilter.ts b/src/shared/lib/oql/oqlfilter.ts
@@ -18,11 +18,10 @@ import {
     ExtendedAlteration,
     AnnotatedStructuralVariant,
 } from '../../../pages/resultsView/ResultsViewPageStore';
-import {
-    NumericGeneMolecularData,
-    Mutation,
-    StructuralVariant,
-} from 'cbioportal-ts-api-client';
+import { NumericGeneMolecularData, Mutation } from 'cbioportal-ts-api-client';
+
+import { StructuralVariant } from 'cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal';
+
 import { Alteration } from 'shared/lib/oql/oql-parser';
 import AccessorsForOqlFilter, {
     Datum,