From 188b0078200711e8dd582cf146635d5be0cbe613 Mon Sep 17 00:00:00 2001 From: alisman Date: Fri, 3 Jun 2022 13:13:31 -0400 Subject: [PATCH] update API clients --- env/custom.sh | 4 +- env/master.sh | 2 +- .../src/generated/CBioPortalAPI-docs.json | 527 +++++++------- .../src/generated/CBioPortalAPI.ts | 661 ++++++++++++------ .../generated/CBioPortalAPIInternal-docs.json | 377 +++++++--- .../src/generated/CBioPortalAPIInternal.ts | 382 ++++++---- .../src/generated/GenomeNexusAPI-docs.json | 6 + .../src/generated/GenomeNexusAPI.ts | 2 + .../GenomeNexusAPIInternal-docs.json | 6 + .../src/generated/GenomeNexusAPIInternal.ts | 2 + yarn.lock | 20 +- 11 files changed, 1227 insertions(+), 762 deletions(-) diff --git a/env/custom.sh b/env/custom.sh index ef915d8ab0a..66cf05bfc9d 100644 --- a/env/custom.sh +++ b/env/custom.sh @@ -1,2 +1,2 @@ -export CBIOPORTAL_URL="http://localhost:8080" -export GENOME_NEXUS_URL="https://www.genomenexus.org" +#export CBIOPORTAL_URL="http://localhost:8080" +#export GENOME_NEXUS_URL="https://www.genomenexus.org" diff --git a/env/master.sh b/env/master.sh index d84e56dda80..fe9b4c528c8 100644 --- a/env/master.sh +++ b/env/master.sh @@ -1,2 +1,2 @@ -export CBIOPORTAL_URL="${CBIOPORTAL_URL:-https://www.cbioportal.org}" +export CBIOPORTAL_URL="${CBIOPORTAL_URL:-https://master.cbioportal.org}" export GENOME_NEXUS_URL="${GENOME_NEXUS_URL:-https://www.genomenexus.org}" diff --git a/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPI-docs.json b/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPI-docs.json index 78b6bb4c2a6..542f4bfc72a 100644 --- a/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPI-docs.json +++ b/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPI-docs.json @@ -61,7 +61,18 @@ "name": "Generic Assays" }, { - "name": "Structural Variants" + "name": "Generic Assay Data" + }, + { + "name": "Info" + }, + { + "name": "Gene Panel Data", + "description": " " + }, + { + "name": "Server running status", + "description": "This end point does not require authentication" }, { "name": "Treatments", @@ -480,7 +491,7 @@ "/gene-panel-data/fetch": { "post": { "tags": [ - "Gene Panels" + "Gene Panel Data" ], "summary": "Fetch gene panel data", "operationId": "fetchGenePanelDataInMultipleMolecularProfilesUsingPOST", @@ -693,10 +704,161 @@ "deprecated": false } }, + "/generic-assay-data/{molecularProfileId}/generic-assay/{genericAssayStableId}": { + "get": { + "tags": [ + "Generic Assay Data" + ], + "summary": "Get generic_assay_data in a molecular profile", + "operationId": "getGenericAssayDataInMolecularProfileUsingGET", + "produces": [ + "application/json" + ], + "parameters": [ + { + "name": "genericAssayStableId", + "in": "path", + "description": "Generic Assay stable ID", + "required": true, + "type": "string" + }, + { + "name": "molecularProfileId", + "in": "path", + "description": "Molecular Profile ID", + "required": true, + "type": "string" + }, + { + "name": "projection", + "in": "query", + "description": "Level of detail of the response", + "required": false, + "type": "string", + "default": "SUMMARY", + "allowEmptyValue": false, + "enum": [ + "ID", + "SUMMARY", + "DETAILED", + "META" + ] + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { + "$ref": "#/definitions/GenericAssayData" + } + } + } + }, + "deprecated": false + } + }, + "/generic-assay-meta/generic-assay/{genericAssayStableId}": { + "get": { + "tags": [ + "Generic Assays" + ], + "summary": "Fetch meta data for generic-assay by ID", + "operationId": "getGenericAssayMeta_gaUsingGET", + "produces": [ + "application/json" + ], + "parameters": [ + { + "name": "genericAssayStableId", + "in": "path", + "description": "Generic Assay stable ID", + "required": false, + "type": "string" + }, + { + "name": "projection", + "in": "query", + "description": "Level of detail of the response", + "required": false, + "type": "string", + "default": "SUMMARY", + "allowEmptyValue": false, + "enum": [ + "ID", + "SUMMARY", + "DETAILED", + "META" + ] + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { + "$ref": "#/definitions/GenericAssayMeta" + } + } + } + }, + "deprecated": false + } + }, + "/generic-assay-meta/{molecularProfileId}": { + "get": { + "tags": [ + "Generic Assays" + ], + "summary": "Fetch meta data for generic-assay by ID", + "operationId": "getGenericAssayMetaUsingGET", + "produces": [ + "application/json" + ], + "parameters": [ + { + "name": "molecularProfileId", + "in": "path", + "description": "Molecular Profile ID", + "required": true, + "type": "string" + }, + { + "name": "projection", + "in": "query", + "description": "Level of detail of the response", + "required": false, + "type": "string", + "default": "SUMMARY", + "allowEmptyValue": false, + "enum": [ + "ID", + "SUMMARY", + "DETAILED", + "META" + ] + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { + "$ref": "#/definitions/GenericAssayMeta" + } + } + } + }, + "deprecated": false + } + }, "/generic_assay_data/fetch": { "post": { "tags": [ - "Generic Assays" + "Generic Assay Data" ], "summary": "Fetch generic_assay_data", "operationId": "fetchGenericAssayDataInMultipleMolecularProfilesUsingPOST", @@ -749,7 +911,7 @@ "/generic_assay_data/{molecularProfileId}/fetch": { "post": { "tags": [ - "Generic Assays" + "Generic Assay Data" ], "summary": "fetch generic_assay_data in a molecular profile", "operationId": "fetchGenericAssayDataInMolecularProfileUsingPOST", @@ -812,7 +974,7 @@ "Generic Assays" ], "summary": "Fetch meta data for generic-assay by ID", - "operationId": "fetchGenericAssayMetaDataUsingPOST", + "operationId": "fetchGenericAssayMetaUsingPOST", "consumes": [ "application/json" ], @@ -1102,6 +1264,48 @@ "deprecated": false } }, + "/health": { + "get": { + "tags": [ + "Server running status" + ], + "summary": "Get the running status of the server", + "operationId": "getServerStatusUsingGET", + "produces": [ + "application/json" + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "$ref": "#/definitions/ServerStatusMessage" + } + } + }, + "deprecated": false + } + }, + "/info": { + "get": { + "tags": [ + "Info" + ], + "summary": "Get information about the running instance", + "operationId": "getInfoUsingGET", + "produces": [ + "application/json" + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "$ref": "#/definitions/Info" + } + } + }, + "deprecated": false + } + }, "/molecular-data/fetch": { "post": { "tags": [ @@ -1489,7 +1693,7 @@ "/molecular-profiles/{molecularProfileId}/gene-panel-data/fetch": { "post": { "tags": [ - "Gene Panels" + "Gene Panel Data" ], "summary": "Get gene panel data", "operationId": "getGenePanelDataUsingPOST", @@ -2563,81 +2767,6 @@ "deprecated": false } }, - "/structural-variant/fetch": { - "post": { - "tags": [ - "Structural Variants" - ], - "summary": "Fetch structural variants for entrezGeneIds and molecularProfileIds or sampleMolecularIdentifiers", - "operationId": "fetchStructuralVariantsUsingPOST", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "name": "entrezGeneIds", - "in": "query", - "required": false, - "type": "array", - "items": { - "type": "integer", - "format": "int32" - }, - "collectionFormat": "multi", - "maximum": 10000000, - "minimum": 0 - }, - { - "name": "molecularProfileIds", - "in": "query", - "required": false, - "type": "array", - "items": { - "type": "string" - }, - "collectionFormat": "multi", - "maximum": 10000000, - "minimum": 0 - }, - { - "name": "sampleMolecularIdentifiers[0].molecularProfileId", - "in": "query", - "required": false, - "type": "string" - }, - { - "name": "sampleMolecularIdentifiers[0].sampleId", - "in": "query", - "required": false, - "type": "string" - }, - { - "in": "body", - "name": "structuralVariantFilter", - "description": "List of entrezGeneIds and molecularProfileIds or sampleMolecularIdentifiers", - "required": true, - "schema": { - "$ref": "#/definitions/StructuralVariantFilter" - } - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "type": "array", - "items": { - "$ref": "#/definitions/StructuralVariant" - } - } - } - }, - "deprecated": false - } - }, "/studies": { "get": { "tags": [ @@ -5277,6 +5406,62 @@ }, "title": "GenomicDataFilter" }, + "Info": { + "type": "object", + "required": [ + "dbVersion", + "gitBranch", + "gitCommitId", + "gitCommitIdAbbrev", + "gitCommitIdDescribe", + "gitCommitIdDescribeShort", + "gitCommitMessageFull", + "gitCommitMessageShort", + "gitCommitMessageUserEmail", + "gitCommitMessageUserName", + "gitDirty", + "portalVersion" + ], + "properties": { + "dbVersion": { + "type": "string" + }, + "gitBranch": { + "type": "string" + }, + "gitCommitId": { + "type": "string" + }, + "gitCommitIdAbbrev": { + "type": "string" + }, + "gitCommitIdDescribe": { + "type": "string" + }, + "gitCommitIdDescribeShort": { + "type": "string" + }, + "gitCommitMessageFull": { + "type": "string" + }, + "gitCommitMessageShort": { + "type": "string" + }, + "gitCommitMessageUserEmail": { + "type": "string" + }, + "gitCommitMessageUserName": { + "type": "string" + }, + "gitDirty": { + "type": "boolean" + }, + "portalVersion": { + "type": "string" + } + }, + "title": "Info" + }, "MolecularDataFilter": { "type": "object", "properties": { @@ -5929,188 +6114,14 @@ }, "title": "SampleTreatmentRow" }, - "StructuralVariant": { + "ServerStatusMessage": { "type": "object", "properties": { - "annotation": { - "type": "string" - }, - "breakpointType": { - "type": "string" - }, - "center": { - "type": "string" - }, - "comments": { - "type": "string" - }, - "connectionType": { - "type": "string" - }, - "dnaSupport": { - "type": "string" - }, - "driverFilter": { - "type": "string" - }, - "driverFilterAnn": { - "type": "string" - }, - "driverTiersFilter": { - "type": "string" - }, - "driverTiersFilterAnn": { - "type": "string" - }, - "eventInfo": { - "type": "string" - }, - "externalAnnotation": { - "type": "string" - }, - "length": { - "type": "integer", - "format": "int32" - }, - "molecularProfileId": { - "type": "string" - }, - "ncbiBuild": { - "type": "string" - }, - "normalPairedEndReadCount": { - "type": "integer", - "format": "int32" - }, - "normalReadCount": { - "type": "integer", - "format": "int32" - }, - "normalSplitReadCount": { - "type": "integer", - "format": "int32" - }, - "normalVariantCount": { - "type": "integer", - "format": "int32" - }, - "patientId": { - "type": "string" - }, - "rnaSupport": { - "type": "string" - }, - "sampleId": { - "type": "string" - }, - "site1Chromosome": { - "type": "string" - }, - "site1Description": { - "type": "string" - }, - "site1EnsemblTranscriptId": { - "type": "string" - }, - "site1EntrezGeneId": { - "type": "integer", - "format": "int32" - }, - "site1Exon": { - "type": "integer", - "format": "int32" - }, - "site1HugoSymbol": { - "type": "string" - }, - "site1Position": { - "type": "integer", - "format": "int32" - }, - "site2Chromosome": { - "type": "string" - }, - "site2Description": { - "type": "string" - }, - "site2EffectOnFrame": { - "type": "string" - }, - "site2EnsemblTranscriptId": { - "type": "string" - }, - "site2EntrezGeneId": { - "type": "integer", - "format": "int32" - }, - "site2Exon": { - "type": "integer", - "format": "int32" - }, - "site2HugoSymbol": { - "type": "string" - }, - "site2Position": { - "type": "integer", - "format": "int32" - }, - "studyId": { - "type": "string" - }, - "tumorPairedEndReadCount": { - "type": "integer", - "format": "int32" - }, - "tumorReadCount": { - "type": "integer", - "format": "int32" - }, - "tumorSplitReadCount": { - "type": "integer", - "format": "int32" - }, - "tumorVariantCount": { - "type": "integer", - "format": "int32" - }, - "uniquePatientKey": { - "type": "string" - }, - "uniqueSampleKey": { - "type": "string" - }, - "variantClass": { + "status": { "type": "string" } }, - "title": "StructuralVariant" - }, - "StructuralVariantFilter": { - "type": "object", - "properties": { - "entrezGeneIds": { - "type": "array", - "items": { - "type": "integer", - "format": "int32", - "minimum": 0, - "maximum": 10000000 - } - }, - "molecularProfileIds": { - "type": "array", - "items": { - "type": "string" - } - }, - "sampleMolecularIdentifiers": { - "type": "array", - "items": { - "$ref": "#/definitions/SampleMolecularIdentifier" - } - } - }, - "title": "StructuralVariantFilter" + "title": "ServerStatusMessage" }, "StudyViewFilter": { "type": "object", diff --git a/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPI.ts b/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPI.ts index b0e40269bbc..ba4a6966c43 100644 --- a/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPI.ts +++ b/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPI.ts @@ -391,6 +391,32 @@ export type GenomicDataFilter = { 'values': Array < DataFilterValue > +}; +export type Info = { + 'dbVersion': string + + 'gitBranch': string + + 'gitCommitId': string + + 'gitCommitIdAbbrev': string + + 'gitCommitIdDescribe': string + + 'gitCommitIdDescribeShort': string + + 'gitCommitMessageFull': string + + 'gitCommitMessageShort': string + + 'gitCommitMessageUserEmail': string + + 'gitCommitMessageUserName': string + + 'gitDirty': boolean + + 'portalVersion': string + }; export type MolecularDataFilter = { 'entrezGeneIds': Array < number > @@ -674,104 +700,8 @@ export type SampleTreatmentRow = { 'treatment': string }; -export type StructuralVariant = { - 'annotation': string - - 'breakpointType': string - - 'center': string - - 'comments': string - - 'connectionType': string - - 'dnaSupport': string - - 'driverFilter': string - - 'driverFilterAnn': string - - 'driverTiersFilter': string - - 'driverTiersFilterAnn': string - - 'eventInfo': string - - 'externalAnnotation': string - - 'length': number - - 'molecularProfileId': string - - 'ncbiBuild': string - - 'normalPairedEndReadCount': number - - 'normalReadCount': number - - 'normalSplitReadCount': number - - 'normalVariantCount': number - - 'patientId': string - - 'rnaSupport': string - - 'sampleId': string - - 'site1Chromosome': string - - 'site1Description': string - - 'site1EnsemblTranscriptId': string - - 'site1EntrezGeneId': number - - 'site1Exon': number - - 'site1HugoSymbol': string - - 'site1Position': number - - 'site2Chromosome': string - - 'site2Description': string - - 'site2EffectOnFrame': string - - 'site2EnsemblTranscriptId': string - - 'site2EntrezGeneId': number - - 'site2Exon': number - - 'site2HugoSymbol': string - - 'site2Position': number - - 'studyId': string - - 'tumorPairedEndReadCount': number - - 'tumorReadCount': number - - 'tumorSplitReadCount': number - - 'tumorVariantCount': number - - 'uniquePatientKey': string - - 'uniqueSampleKey': string - - 'variantClass': string - -}; -export type StructuralVariantFilter = { - 'entrezGeneIds': Array < number > - - 'molecularProfileIds': Array < string > - - 'sampleMolecularIdentifiers': Array < SampleMolecularIdentifier > +export type ServerStatusMessage = { + 'status': string }; export type StudyViewFilter = { @@ -1866,6 +1796,279 @@ export default class CBioPortalAPI { return response.body; }); }; + getGenericAssayDataInMolecularProfileUsingGETURL(parameters: { + 'genericAssayStableId': string, + 'molecularProfileId': string, + 'projection' ? : "ID" | "SUMMARY" | "DETAILED" | "META", + $queryParameters ? : any + }): string { + let queryParameters: any = {}; + let path = '/generic-assay-data/{molecularProfileId}/generic-assay/{genericAssayStableId}'; + + path = path.replace('{genericAssayStableId}', parameters['genericAssayStableId'] + ''); + + path = path.replace('{molecularProfileId}', parameters['molecularProfileId'] + ''); + if (parameters['projection'] !== undefined) { + queryParameters['projection'] = parameters['projection']; + } + + if (parameters.$queryParameters) { + Object.keys(parameters.$queryParameters).forEach(function(parameterName) { + var parameter = parameters.$queryParameters[parameterName]; + queryParameters[parameterName] = parameter; + }); + } + let keys = Object.keys(queryParameters); + return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); + }; + + /** + * Get generic_assay_data in a molecular profile + * @method + * @name CBioPortalAPI#getGenericAssayDataInMolecularProfileUsingGET + * @param {string} genericAssayStableId - Generic Assay stable ID + * @param {string} molecularProfileId - Molecular Profile ID + * @param {string} projection - Level of detail of the response + */ + getGenericAssayDataInMolecularProfileUsingGETWithHttpInfo(parameters: { + 'genericAssayStableId': string, + 'molecularProfileId': string, + 'projection' ? : "ID" | "SUMMARY" | "DETAILED" | "META", + $queryParameters ? : any, + $domain ? : string + }): Promise < request.Response > { + const domain = parameters.$domain ? parameters.$domain : this.domain; + const errorHandlers = this.errorHandlers; + const request = this.request; + let path = '/generic-assay-data/{molecularProfileId}/generic-assay/{genericAssayStableId}'; + let body: any; + let queryParameters: any = {}; + let headers: any = {}; + let form: any = {}; + return new Promise(function(resolve, reject) { + headers['Accept'] = 'application/json'; + + path = path.replace('{genericAssayStableId}', parameters['genericAssayStableId'] + ''); + + if (parameters['genericAssayStableId'] === undefined) { + reject(new Error('Missing required parameter: genericAssayStableId')); + return; + } + + path = path.replace('{molecularProfileId}', parameters['molecularProfileId'] + ''); + + if (parameters['molecularProfileId'] === undefined) { + reject(new Error('Missing required parameter: molecularProfileId')); + return; + } + + if (parameters['projection'] !== undefined) { + queryParameters['projection'] = parameters['projection']; + } + + if (parameters.$queryParameters) { + Object.keys(parameters.$queryParameters).forEach(function(parameterName) { + var parameter = parameters.$queryParameters[parameterName]; + queryParameters[parameterName] = parameter; + }); + } + + request('GET', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); + + }); + }; + + /** + * Get generic_assay_data in a molecular profile + * @method + * @name CBioPortalAPI#getGenericAssayDataInMolecularProfileUsingGET + * @param {string} genericAssayStableId - Generic Assay stable ID + * @param {string} molecularProfileId - Molecular Profile ID + * @param {string} projection - Level of detail of the response + */ + getGenericAssayDataInMolecularProfileUsingGET(parameters: { + 'genericAssayStableId': string, + 'molecularProfileId': string, + 'projection' ? : "ID" | "SUMMARY" | "DETAILED" | "META", + $queryParameters ? : any, + $domain ? : string + }): Promise < Array < GenericAssayData > + > { + return this.getGenericAssayDataInMolecularProfileUsingGETWithHttpInfo(parameters).then(function(response: request.Response) { + return response.body; + }); + }; + getGenericAssayMeta_gaUsingGETURL(parameters: { + 'genericAssayStableId' ? : string, + 'projection' ? : "ID" | "SUMMARY" | "DETAILED" | "META", + $queryParameters ? : any + }): string { + let queryParameters: any = {}; + let path = '/generic-assay-meta/generic-assay/{genericAssayStableId}'; + + path = path.replace('{genericAssayStableId}', parameters['genericAssayStableId'] + ''); + if (parameters['projection'] !== undefined) { + queryParameters['projection'] = parameters['projection']; + } + + if (parameters.$queryParameters) { + Object.keys(parameters.$queryParameters).forEach(function(parameterName) { + var parameter = parameters.$queryParameters[parameterName]; + queryParameters[parameterName] = parameter; + }); + } + let keys = Object.keys(queryParameters); + return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); + }; + + /** + * Fetch meta data for generic-assay by ID + * @method + * @name CBioPortalAPI#getGenericAssayMeta_gaUsingGET + * @param {string} genericAssayStableId - Generic Assay stable ID + * @param {string} projection - Level of detail of the response + */ + getGenericAssayMeta_gaUsingGETWithHttpInfo(parameters: { + 'genericAssayStableId' ? : string, + 'projection' ? : "ID" | "SUMMARY" | "DETAILED" | "META", + $queryParameters ? : any, + $domain ? : string + }): Promise < request.Response > { + const domain = parameters.$domain ? parameters.$domain : this.domain; + const errorHandlers = this.errorHandlers; + const request = this.request; + let path = '/generic-assay-meta/generic-assay/{genericAssayStableId}'; + let body: any; + let queryParameters: any = {}; + let headers: any = {}; + let form: any = {}; + return new Promise(function(resolve, reject) { + headers['Accept'] = 'application/json'; + + path = path.replace('{genericAssayStableId}', parameters['genericAssayStableId'] + ''); + + if (parameters['projection'] !== undefined) { + queryParameters['projection'] = parameters['projection']; + } + + if (parameters.$queryParameters) { + Object.keys(parameters.$queryParameters).forEach(function(parameterName) { + var parameter = parameters.$queryParameters[parameterName]; + queryParameters[parameterName] = parameter; + }); + } + + request('GET', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); + + }); + }; + + /** + * Fetch meta data for generic-assay by ID + * @method + * @name CBioPortalAPI#getGenericAssayMeta_gaUsingGET + * @param {string} genericAssayStableId - Generic Assay stable ID + * @param {string} projection - Level of detail of the response + */ + getGenericAssayMeta_gaUsingGET(parameters: { + 'genericAssayStableId' ? : string, + 'projection' ? : "ID" | "SUMMARY" | "DETAILED" | "META", + $queryParameters ? : any, + $domain ? : string + }): Promise < Array < GenericAssayMeta > + > { + return this.getGenericAssayMeta_gaUsingGETWithHttpInfo(parameters).then(function(response: request.Response) { + return response.body; + }); + }; + getGenericAssayMetaUsingGETURL(parameters: { + 'molecularProfileId': string, + 'projection' ? : "ID" | "SUMMARY" | "DETAILED" | "META", + $queryParameters ? : any + }): string { + let queryParameters: any = {}; + let path = '/generic-assay-meta/{molecularProfileId}'; + + path = path.replace('{molecularProfileId}', parameters['molecularProfileId'] + ''); + if (parameters['projection'] !== undefined) { + queryParameters['projection'] = parameters['projection']; + } + + if (parameters.$queryParameters) { + Object.keys(parameters.$queryParameters).forEach(function(parameterName) { + var parameter = parameters.$queryParameters[parameterName]; + queryParameters[parameterName] = parameter; + }); + } + let keys = Object.keys(queryParameters); + return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); + }; + + /** + * Fetch meta data for generic-assay by ID + * @method + * @name CBioPortalAPI#getGenericAssayMetaUsingGET + * @param {string} molecularProfileId - Molecular Profile ID + * @param {string} projection - Level of detail of the response + */ + getGenericAssayMetaUsingGETWithHttpInfo(parameters: { + 'molecularProfileId': string, + 'projection' ? : "ID" | "SUMMARY" | "DETAILED" | "META", + $queryParameters ? : any, + $domain ? : string + }): Promise < request.Response > { + const domain = parameters.$domain ? parameters.$domain : this.domain; + const errorHandlers = this.errorHandlers; + const request = this.request; + let path = '/generic-assay-meta/{molecularProfileId}'; + let body: any; + let queryParameters: any = {}; + let headers: any = {}; + let form: any = {}; + return new Promise(function(resolve, reject) { + headers['Accept'] = 'application/json'; + + path = path.replace('{molecularProfileId}', parameters['molecularProfileId'] + ''); + + if (parameters['molecularProfileId'] === undefined) { + reject(new Error('Missing required parameter: molecularProfileId')); + return; + } + + if (parameters['projection'] !== undefined) { + queryParameters['projection'] = parameters['projection']; + } + + if (parameters.$queryParameters) { + Object.keys(parameters.$queryParameters).forEach(function(parameterName) { + var parameter = parameters.$queryParameters[parameterName]; + queryParameters[parameterName] = parameter; + }); + } + + request('GET', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); + + }); + }; + + /** + * Fetch meta data for generic-assay by ID + * @method + * @name CBioPortalAPI#getGenericAssayMetaUsingGET + * @param {string} molecularProfileId - Molecular Profile ID + * @param {string} projection - Level of detail of the response + */ + getGenericAssayMetaUsingGET(parameters: { + 'molecularProfileId': string, + 'projection' ? : "ID" | "SUMMARY" | "DETAILED" | "META", + $queryParameters ? : any, + $domain ? : string + }): Promise < Array < GenericAssayMeta > + > { + return this.getGenericAssayMetaUsingGETWithHttpInfo(parameters).then(function(response: request.Response) { + return response.body; + }); + }; fetchGenericAssayDataInMultipleMolecularProfilesUsingPOSTURL(parameters: { 'genericAssayDataMultipleStudyFilter': GenericAssayDataMultipleStudyFilter, 'projection' ? : "ID" | "SUMMARY" | "DETAILED" | "META", @@ -2059,7 +2262,7 @@ export default class CBioPortalAPI { return response.body; }); }; - fetchGenericAssayMetaDataUsingPOSTURL(parameters: { + fetchGenericAssayMetaUsingPOSTURL(parameters: { 'genericAssayMetaFilter': GenericAssayMetaFilter, 'projection' ? : "ID" | "SUMMARY" | "DETAILED" | "META", $queryParameters ? : any @@ -2084,11 +2287,11 @@ export default class CBioPortalAPI { /** * Fetch meta data for generic-assay by ID * @method - * @name CBioPortalAPI#fetchGenericAssayMetaDataUsingPOST + * @name CBioPortalAPI#fetchGenericAssayMetaUsingPOST * @param {} genericAssayMetaFilter - List of Molecular Profile ID or List of Stable ID * @param {string} projection - Level of detail of the response */ - fetchGenericAssayMetaDataUsingPOSTWithHttpInfo(parameters: { + fetchGenericAssayMetaUsingPOSTWithHttpInfo(parameters: { 'genericAssayMetaFilter': GenericAssayMetaFilter, 'projection' ? : "ID" | "SUMMARY" | "DETAILED" | "META", $queryParameters ? : any, @@ -2134,18 +2337,18 @@ export default class CBioPortalAPI { /** * Fetch meta data for generic-assay by ID * @method - * @name CBioPortalAPI#fetchGenericAssayMetaDataUsingPOST + * @name CBioPortalAPI#fetchGenericAssayMetaUsingPOST * @param {} genericAssayMetaFilter - List of Molecular Profile ID or List of Stable ID * @param {string} projection - Level of detail of the response */ - fetchGenericAssayMetaDataUsingPOST(parameters: { + fetchGenericAssayMetaUsingPOST(parameters: { 'genericAssayMetaFilter': GenericAssayMetaFilter, 'projection' ? : "ID" | "SUMMARY" | "DETAILED" | "META", $queryParameters ? : any, $domain ? : string }): Promise < Array < GenericAssayMeta > > { - return this.fetchGenericAssayMetaDataUsingPOSTWithHttpInfo(parameters).then(function(response: request.Response) { + return this.fetchGenericAssayMetaUsingPOSTWithHttpInfo(parameters).then(function(response: request.Response) { return response.body; }); }; @@ -2554,6 +2757,128 @@ export default class CBioPortalAPI { return response.body; }); }; + getServerStatusUsingGETURL(parameters: { + $queryParameters ? : any + }): string { + let queryParameters: any = {}; + let path = '/health'; + + if (parameters.$queryParameters) { + Object.keys(parameters.$queryParameters).forEach(function(parameterName) { + var parameter = parameters.$queryParameters[parameterName]; + queryParameters[parameterName] = parameter; + }); + } + let keys = Object.keys(queryParameters); + return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); + }; + + /** + * Get the running status of the server + * @method + * @name CBioPortalAPI#getServerStatusUsingGET + */ + getServerStatusUsingGETWithHttpInfo(parameters: { + $queryParameters ? : any, + $domain ? : string + }): Promise < request.Response > { + const domain = parameters.$domain ? parameters.$domain : this.domain; + const errorHandlers = this.errorHandlers; + const request = this.request; + let path = '/health'; + let body: any; + let queryParameters: any = {}; + let headers: any = {}; + let form: any = {}; + return new Promise(function(resolve, reject) { + headers['Accept'] = 'application/json'; + + if (parameters.$queryParameters) { + Object.keys(parameters.$queryParameters).forEach(function(parameterName) { + var parameter = parameters.$queryParameters[parameterName]; + queryParameters[parameterName] = parameter; + }); + } + + request('GET', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); + + }); + }; + + /** + * Get the running status of the server + * @method + * @name CBioPortalAPI#getServerStatusUsingGET + */ + getServerStatusUsingGET(parameters: { + $queryParameters ? : any, + $domain ? : string + }): Promise < ServerStatusMessage > { + return this.getServerStatusUsingGETWithHttpInfo(parameters).then(function(response: request.Response) { + return response.body; + }); + }; + getInfoUsingGETURL(parameters: { + $queryParameters ? : any + }): string { + let queryParameters: any = {}; + let path = '/info'; + + if (parameters.$queryParameters) { + Object.keys(parameters.$queryParameters).forEach(function(parameterName) { + var parameter = parameters.$queryParameters[parameterName]; + queryParameters[parameterName] = parameter; + }); + } + let keys = Object.keys(queryParameters); + return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); + }; + + /** + * Get information about the running instance + * @method + * @name CBioPortalAPI#getInfoUsingGET + */ + getInfoUsingGETWithHttpInfo(parameters: { + $queryParameters ? : any, + $domain ? : string + }): Promise < request.Response > { + const domain = parameters.$domain ? parameters.$domain : this.domain; + const errorHandlers = this.errorHandlers; + const request = this.request; + let path = '/info'; + let body: any; + let queryParameters: any = {}; + let headers: any = {}; + let form: any = {}; + return new Promise(function(resolve, reject) { + headers['Accept'] = 'application/json'; + + if (parameters.$queryParameters) { + Object.keys(parameters.$queryParameters).forEach(function(parameterName) { + var parameter = parameters.$queryParameters[parameterName]; + queryParameters[parameterName] = parameter; + }); + } + + request('GET', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); + + }); + }; + + /** + * Get information about the running instance + * @method + * @name CBioPortalAPI#getInfoUsingGET + */ + getInfoUsingGET(parameters: { + $queryParameters ? : any, + $domain ? : string + }): Promise < Info > { + return this.getInfoUsingGETWithHttpInfo(parameters).then(function(response: request.Response) { + return response.body; + }); + }; fetchMolecularDataInMultipleMolecularProfilesUsingPOSTURL(parameters: { 'molecularDataMultipleStudyFilter': MolecularDataMultipleStudyFilter, 'projection' ? : "ID" | "SUMMARY" | "DETAILED" | "META", @@ -4767,134 +5092,6 @@ export default class CBioPortalAPI { return response.body; }); }; - fetchStructuralVariantsUsingPOSTURL(parameters: { - 'entrezGeneIds' ? : Array < number > , - 'molecularProfileIds' ? : Array < string > , - 'sampleMolecularIdentifiers0MolecularProfileId' ? : string, - 'sampleMolecularIdentifiers0SampleId' ? : string, - 'structuralVariantFilter': StructuralVariantFilter, - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/structural-variant/fetch'; - if (parameters['entrezGeneIds'] !== undefined) { - queryParameters['entrezGeneIds'] = parameters['entrezGeneIds']; - } - - if (parameters['molecularProfileIds'] !== undefined) { - queryParameters['molecularProfileIds'] = parameters['molecularProfileIds']; - } - - if (parameters['sampleMolecularIdentifiers0MolecularProfileId'] !== undefined) { - queryParameters['sampleMolecularIdentifiers[0].molecularProfileId'] = parameters['sampleMolecularIdentifiers0MolecularProfileId']; - } - - if (parameters['sampleMolecularIdentifiers0SampleId'] !== undefined) { - queryParameters['sampleMolecularIdentifiers[0].sampleId'] = parameters['sampleMolecularIdentifiers0SampleId']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Fetch structural variants for entrezGeneIds and molecularProfileIds or sampleMolecularIdentifiers - * @method - * @name CBioPortalAPI#fetchStructuralVariantsUsingPOST - * @param {array} entrezGeneIds - A web service for supplying JSON formatted data to cBioPortal clients. Please note that this API is currently in beta and subject to change. - * @param {array} molecularProfileIds - A web service for supplying JSON formatted data to cBioPortal clients. Please note that this API is currently in beta and subject to change. - * @param {string} sampleMolecularIdentifiers0MolecularProfileId - A web service for supplying JSON formatted data to cBioPortal clients. Please note that this API is currently in beta and subject to change. - * @param {string} sampleMolecularIdentifiers0SampleId - A web service for supplying JSON formatted data to cBioPortal clients. Please note that this API is currently in beta and subject to change. - * @param {} structuralVariantFilter - List of entrezGeneIds and molecularProfileIds or sampleMolecularIdentifiers - */ - fetchStructuralVariantsUsingPOSTWithHttpInfo(parameters: { - 'entrezGeneIds' ? : Array < number > , - 'molecularProfileIds' ? : Array < string > , - 'sampleMolecularIdentifiers0MolecularProfileId' ? : string, - 'sampleMolecularIdentifiers0SampleId' ? : string, - 'structuralVariantFilter': StructuralVariantFilter, - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/structural-variant/fetch'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - if (parameters['entrezGeneIds'] !== undefined) { - queryParameters['entrezGeneIds'] = parameters['entrezGeneIds']; - } - - if (parameters['molecularProfileIds'] !== undefined) { - queryParameters['molecularProfileIds'] = parameters['molecularProfileIds']; - } - - if (parameters['sampleMolecularIdentifiers0MolecularProfileId'] !== undefined) { - queryParameters['sampleMolecularIdentifiers[0].molecularProfileId'] = parameters['sampleMolecularIdentifiers0MolecularProfileId']; - } - - if (parameters['sampleMolecularIdentifiers0SampleId'] !== undefined) { - queryParameters['sampleMolecularIdentifiers[0].sampleId'] = parameters['sampleMolecularIdentifiers0SampleId']; - } - - if (parameters['structuralVariantFilter'] !== undefined) { - body = parameters['structuralVariantFilter']; - } - - if (parameters['structuralVariantFilter'] === undefined) { - reject(new Error('Missing required parameter: structuralVariantFilter')); - return; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('POST', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Fetch structural variants for entrezGeneIds and molecularProfileIds or sampleMolecularIdentifiers - * @method - * @name CBioPortalAPI#fetchStructuralVariantsUsingPOST - * @param {array} entrezGeneIds - A web service for supplying JSON formatted data to cBioPortal clients. Please note that this API is currently in beta and subject to change. - * @param {array} molecularProfileIds - A web service for supplying JSON formatted data to cBioPortal clients. Please note that this API is currently in beta and subject to change. - * @param {string} sampleMolecularIdentifiers0MolecularProfileId - A web service for supplying JSON formatted data to cBioPortal clients. Please note that this API is currently in beta and subject to change. - * @param {string} sampleMolecularIdentifiers0SampleId - A web service for supplying JSON formatted data to cBioPortal clients. Please note that this API is currently in beta and subject to change. - * @param {} structuralVariantFilter - List of entrezGeneIds and molecularProfileIds or sampleMolecularIdentifiers - */ - fetchStructuralVariantsUsingPOST(parameters: { - 'entrezGeneIds' ? : Array < number > , - 'molecularProfileIds' ? : Array < string > , - 'sampleMolecularIdentifiers0MolecularProfileId' ? : string, - 'sampleMolecularIdentifiers0SampleId' ? : string, - 'structuralVariantFilter': StructuralVariantFilter, - $queryParameters ? : any, - $domain ? : string - }): Promise < Array < StructuralVariant > - > { - return this.fetchStructuralVariantsUsingPOSTWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; getAllStudiesUsingGETURL(parameters: { 'authenticated' ? : boolean, 'authorities0Authority' ? : string, diff --git a/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal-docs.json b/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal-docs.json index 1dfa4518359..ff1467894f9 100644 --- a/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal-docs.json +++ b/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal-docs.json @@ -75,10 +75,6 @@ "name": "Gene Sets", "description": " " }, - { - "name": "Info", - "description": " " - }, { "name": "Mutation Spectrums", "description": " " @@ -99,10 +95,6 @@ "name": "Resource Definitions", "description": " " }, - { - "name": "Server running status", - "description": "This end point does not require authentication" - }, { "name": "Significant Copy Number Regions", "description": " " @@ -111,6 +103,10 @@ "name": "Significantly Mutated Genes", "description": " " }, + { + "name": "Structural Variants", + "description": " " + }, { "name": "Study View", "description": " " @@ -1746,48 +1742,6 @@ "deprecated": false } }, - "/health": { - "get": { - "tags": [ - "Server running status" - ], - "summary": "Get the running status of the server", - "operationId": "getServerStatusUsingGET", - "produces": [ - "application/json" - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "$ref": "#/definitions/ServerStatusMessage" - } - } - }, - "deprecated": false - } - }, - "/info": { - "get": { - "tags": [ - "Info" - ], - "summary": "Get information about the running instance", - "operationId": "getInfoUsingGET", - "produces": [ - "application/json" - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "$ref": "#/definitions/Info" - } - } - }, - "deprecated": false - } - }, "/molecular-profile-sample-counts/fetch": { "post": { "tags": [ @@ -2380,6 +2334,81 @@ "deprecated": false } }, + "/structural-variant/fetch": { + "post": { + "tags": [ + "Structural Variants" + ], + "summary": "Fetch structural variants for entrezGeneIds and molecularProfileIds or sampleMolecularIdentifiers", + "operationId": "fetchStructuralVariantsUsingPOST", + "consumes": [ + "application/json" + ], + "produces": [ + "application/json" + ], + "parameters": [ + { + "name": "entrezGeneIds", + "in": "query", + "required": false, + "type": "array", + "items": { + "type": "integer", + "format": "int32" + }, + "collectionFormat": "multi", + "maximum": 10000000, + "minimum": 0 + }, + { + "name": "molecularProfileIds", + "in": "query", + "required": false, + "type": "array", + "items": { + "type": "string" + }, + "collectionFormat": "multi", + "maximum": 10000000, + "minimum": 0 + }, + { + "name": "sampleMolecularIdentifiers[0].molecularProfileId", + "in": "query", + "required": false, + "type": "string" + }, + { + "name": "sampleMolecularIdentifiers[0].sampleId", + "in": "query", + "required": false, + "type": "string" + }, + { + "in": "body", + "name": "structuralVariantFilter", + "description": "List of entrezGeneIds and molecularProfileIds or sampleMolecularIdentifiers", + "required": true, + "schema": { + "$ref": "#/definitions/StructuralVariantFilter" + } + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "array", + "items": { + "$ref": "#/definitions/StructuralVariant" + } + } + } + }, + "deprecated": false + } + }, "/structuralvariant-genes/fetch": { "post": { "tags": [ @@ -4786,62 +4815,6 @@ }, "title": "GroupStatistics" }, - "Info": { - "type": "object", - "required": [ - "dbVersion", - "gitBranch", - "gitCommitId", - "gitCommitIdAbbrev", - "gitCommitIdDescribe", - "gitCommitIdDescribeShort", - "gitCommitMessageFull", - "gitCommitMessageShort", - "gitCommitMessageUserEmail", - "gitCommitMessageUserName", - "gitDirty", - "portalVersion" - ], - "properties": { - "dbVersion": { - "type": "string" - }, - "gitBranch": { - "type": "string" - }, - "gitCommitId": { - "type": "string" - }, - "gitCommitIdAbbrev": { - "type": "string" - }, - "gitCommitIdDescribe": { - "type": "string" - }, - "gitCommitIdDescribeShort": { - "type": "string" - }, - "gitCommitMessageFull": { - "type": "string" - }, - "gitCommitMessageShort": { - "type": "string" - }, - "gitCommitMessageUserEmail": { - "type": "string" - }, - "gitCommitMessageUserName": { - "type": "string" - }, - "gitDirty": { - "type": "boolean" - }, - "portalVersion": { - "type": "string" - } - }, - "title": "Info" - }, "MolecularProfileCaseIdentifier": { "type": "object", "required": [ @@ -5294,6 +5267,18 @@ }, "title": "SampleIdentifier" }, + "SampleMolecularIdentifier": { + "type": "object", + "properties": { + "molecularProfileId": { + "type": "string" + }, + "sampleId": { + "type": "string" + } + }, + "title": "SampleMolecularIdentifier" + }, "SampleTreatmentFilter": { "type": "object", "properties": { @@ -5310,14 +5295,188 @@ }, "title": "SampleTreatmentFilter" }, - "ServerStatusMessage": { + "StructuralVariant": { "type": "object", "properties": { - "status": { + "annotation": { + "type": "string" + }, + "breakpointType": { + "type": "string" + }, + "center": { + "type": "string" + }, + "comments": { + "type": "string" + }, + "connectionType": { + "type": "string" + }, + "dnaSupport": { + "type": "string" + }, + "driverFilter": { + "type": "string" + }, + "driverFilterAnn": { + "type": "string" + }, + "driverTiersFilter": { + "type": "string" + }, + "driverTiersFilterAnn": { + "type": "string" + }, + "eventInfo": { + "type": "string" + }, + "externalAnnotation": { + "type": "string" + }, + "length": { + "type": "integer", + "format": "int32" + }, + "molecularProfileId": { + "type": "string" + }, + "ncbiBuild": { + "type": "string" + }, + "normalPairedEndReadCount": { + "type": "integer", + "format": "int32" + }, + "normalReadCount": { + "type": "integer", + "format": "int32" + }, + "normalSplitReadCount": { + "type": "integer", + "format": "int32" + }, + "normalVariantCount": { + "type": "integer", + "format": "int32" + }, + "patientId": { + "type": "string" + }, + "rnaSupport": { + "type": "string" + }, + "sampleId": { + "type": "string" + }, + "site1Chromosome": { + "type": "string" + }, + "site1Description": { + "type": "string" + }, + "site1EnsemblTranscriptId": { + "type": "string" + }, + "site1EntrezGeneId": { + "type": "integer", + "format": "int32" + }, + "site1Exon": { + "type": "integer", + "format": "int32" + }, + "site1HugoSymbol": { "type": "string" + }, + "site1Position": { + "type": "integer", + "format": "int32" + }, + "site2Chromosome": { + "type": "string" + }, + "site2Description": { + "type": "string" + }, + "site2EffectOnFrame": { + "type": "string" + }, + "site2EnsemblTranscriptId": { + "type": "string" + }, + "site2EntrezGeneId": { + "type": "integer", + "format": "int32" + }, + "site2Exon": { + "type": "integer", + "format": "int32" + }, + "site2HugoSymbol": { + "type": "string" + }, + "site2Position": { + "type": "integer", + "format": "int32" + }, + "studyId": { + "type": "string" + }, + "tumorPairedEndReadCount": { + "type": "integer", + "format": "int32" + }, + "tumorReadCount": { + "type": "integer", + "format": "int32" + }, + "tumorSplitReadCount": { + "type": "integer", + "format": "int32" + }, + "tumorVariantCount": { + "type": "integer", + "format": "int32" + }, + "uniquePatientKey": { + "type": "string" + }, + "uniqueSampleKey": { + "type": "string" + }, + "variantClass": { + "type": "string" + } + }, + "title": "StructuralVariant" + }, + "StructuralVariantFilter": { + "type": "object", + "properties": { + "entrezGeneIds": { + "type": "array", + "items": { + "type": "integer", + "format": "int32", + "minimum": 0, + "maximum": 10000000 + } + }, + "molecularProfileIds": { + "type": "array", + "items": { + "type": "string" + } + }, + "sampleMolecularIdentifiers": { + "type": "array", + "items": { + "$ref": "#/definitions/SampleMolecularIdentifier" + } } }, - "title": "ServerStatusMessage" + "title": "StructuralVariantFilter" }, "StudyViewFilter": { "type": "object", diff --git a/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal.ts b/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal.ts index d8b25ecb701..2af7e8dfa31 100644 --- a/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal.ts +++ b/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal.ts @@ -641,32 +641,6 @@ export type GroupStatistics = { 'standardDeviation': number -}; -export type Info = { - 'dbVersion': string - - 'gitBranch': string - - 'gitCommitId': string - - 'gitCommitIdAbbrev': string - - 'gitCommitIdDescribe': string - - 'gitCommitIdDescribeShort': string - - 'gitCommitMessageFull': string - - 'gitCommitMessageShort': string - - 'gitCommitMessageUserEmail': string - - 'gitCommitMessageUserName': string - - 'gitDirty': boolean - - 'portalVersion': string - }; export type MolecularProfileCaseIdentifier = { 'caseId': string @@ -859,6 +833,12 @@ export type SampleIdentifier = { 'studyId': string +}; +export type SampleMolecularIdentifier = { + 'molecularProfileId': string + + 'sampleId': string + }; export type SampleTreatmentFilter = { 'time': "Pre" | "Post" @@ -866,8 +846,104 @@ export type SampleTreatmentFilter = { 'treatment': string }; -export type ServerStatusMessage = { - 'status': string +export type StructuralVariant = { + 'annotation': string + + 'breakpointType': string + + 'center': string + + 'comments': string + + 'connectionType': string + + 'dnaSupport': string + + 'driverFilter': string + + 'driverFilterAnn': string + + 'driverTiersFilter': string + + 'driverTiersFilterAnn': string + + 'eventInfo': string + + 'externalAnnotation': string + + 'length': number + + 'molecularProfileId': string + + 'ncbiBuild': string + + 'normalPairedEndReadCount': number + + 'normalReadCount': number + + 'normalSplitReadCount': number + + 'normalVariantCount': number + + 'patientId': string + + 'rnaSupport': string + + 'sampleId': string + + 'site1Chromosome': string + + 'site1Description': string + + 'site1EnsemblTranscriptId': string + + 'site1EntrezGeneId': number + + 'site1Exon': number + + 'site1HugoSymbol': string + + 'site1Position': number + + 'site2Chromosome': string + + 'site2Description': string + + 'site2EffectOnFrame': string + + 'site2EnsemblTranscriptId': string + + 'site2EntrezGeneId': number + + 'site2Exon': number + + 'site2HugoSymbol': string + + 'site2Position': number + + 'studyId': string + + 'tumorPairedEndReadCount': number + + 'tumorReadCount': number + + 'tumorSplitReadCount': number + + 'tumorVariantCount': number + + 'uniquePatientKey': string + + 'uniqueSampleKey': string + + 'variantClass': string + +}; +export type StructuralVariantFilter = { + 'entrezGeneIds': Array < number > + + 'molecularProfileIds': Array < string > + + 'sampleMolecularIdentifiers': Array < SampleMolecularIdentifier > }; export type StudyViewFilter = { @@ -4117,128 +4193,6 @@ export default class CBioPortalAPIInternal { return response.body; }); }; - getServerStatusUsingGETURL(parameters: { - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/health'; - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Get the running status of the server - * @method - * @name CBioPortalAPIInternal#getServerStatusUsingGET - */ - getServerStatusUsingGETWithHttpInfo(parameters: { - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/health'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('GET', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Get the running status of the server - * @method - * @name CBioPortalAPIInternal#getServerStatusUsingGET - */ - getServerStatusUsingGET(parameters: { - $queryParameters ? : any, - $domain ? : string - }): Promise < ServerStatusMessage > { - return this.getServerStatusUsingGETWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - getInfoUsingGETURL(parameters: { - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/info'; - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Get information about the running instance - * @method - * @name CBioPortalAPIInternal#getInfoUsingGET - */ - getInfoUsingGETWithHttpInfo(parameters: { - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/info'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('GET', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Get information about the running instance - * @method - * @name CBioPortalAPIInternal#getInfoUsingGET - */ - getInfoUsingGET(parameters: { - $queryParameters ? : any, - $domain ? : string - }): Promise < Info > { - return this.getInfoUsingGETWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; fetchMolecularProfileSampleCountsUsingPOSTURL(parameters: { 'studyViewFilter': StudyViewFilter, $queryParameters ? : any @@ -5399,6 +5353,134 @@ export default class CBioPortalAPIInternal { return response.body; }); }; + fetchStructuralVariantsUsingPOSTURL(parameters: { + 'entrezGeneIds' ? : Array < number > , + 'molecularProfileIds' ? : Array < string > , + 'sampleMolecularIdentifiers0MolecularProfileId' ? : string, + 'sampleMolecularIdentifiers0SampleId' ? : string, + 'structuralVariantFilter': StructuralVariantFilter, + $queryParameters ? : any + }): string { + let queryParameters: any = {}; + let path = '/structural-variant/fetch'; + if (parameters['entrezGeneIds'] !== undefined) { + queryParameters['entrezGeneIds'] = parameters['entrezGeneIds']; + } + + if (parameters['molecularProfileIds'] !== undefined) { + queryParameters['molecularProfileIds'] = parameters['molecularProfileIds']; + } + + if (parameters['sampleMolecularIdentifiers0MolecularProfileId'] !== undefined) { + queryParameters['sampleMolecularIdentifiers[0].molecularProfileId'] = parameters['sampleMolecularIdentifiers0MolecularProfileId']; + } + + if (parameters['sampleMolecularIdentifiers0SampleId'] !== undefined) { + queryParameters['sampleMolecularIdentifiers[0].sampleId'] = parameters['sampleMolecularIdentifiers0SampleId']; + } + + if (parameters.$queryParameters) { + Object.keys(parameters.$queryParameters).forEach(function(parameterName) { + var parameter = parameters.$queryParameters[parameterName]; + queryParameters[parameterName] = parameter; + }); + } + let keys = Object.keys(queryParameters); + return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); + }; + + /** + * Fetch structural variants for entrezGeneIds and molecularProfileIds or sampleMolecularIdentifiers + * @method + * @name CBioPortalAPIInternal#fetchStructuralVariantsUsingPOST + * @param {array} entrezGeneIds - A web service for supplying JSON formatted data to cBioPortal clients. Please note that interal API is currently in beta and subject to change. + * @param {array} molecularProfileIds - A web service for supplying JSON formatted data to cBioPortal clients. Please note that interal API is currently in beta and subject to change. + * @param {string} sampleMolecularIdentifiers0MolecularProfileId - A web service for supplying JSON formatted data to cBioPortal clients. Please note that interal API is currently in beta and subject to change. + * @param {string} sampleMolecularIdentifiers0SampleId - A web service for supplying JSON formatted data to cBioPortal clients. Please note that interal API is currently in beta and subject to change. + * @param {} structuralVariantFilter - List of entrezGeneIds and molecularProfileIds or sampleMolecularIdentifiers + */ + fetchStructuralVariantsUsingPOSTWithHttpInfo(parameters: { + 'entrezGeneIds' ? : Array < number > , + 'molecularProfileIds' ? : Array < string > , + 'sampleMolecularIdentifiers0MolecularProfileId' ? : string, + 'sampleMolecularIdentifiers0SampleId' ? : string, + 'structuralVariantFilter': StructuralVariantFilter, + $queryParameters ? : any, + $domain ? : string + }): Promise < request.Response > { + const domain = parameters.$domain ? parameters.$domain : this.domain; + const errorHandlers = this.errorHandlers; + const request = this.request; + let path = '/structural-variant/fetch'; + let body: any; + let queryParameters: any = {}; + let headers: any = {}; + let form: any = {}; + return new Promise(function(resolve, reject) { + headers['Accept'] = 'application/json'; + headers['Content-Type'] = 'application/json'; + + if (parameters['entrezGeneIds'] !== undefined) { + queryParameters['entrezGeneIds'] = parameters['entrezGeneIds']; + } + + if (parameters['molecularProfileIds'] !== undefined) { + queryParameters['molecularProfileIds'] = parameters['molecularProfileIds']; + } + + if (parameters['sampleMolecularIdentifiers0MolecularProfileId'] !== undefined) { + queryParameters['sampleMolecularIdentifiers[0].molecularProfileId'] = parameters['sampleMolecularIdentifiers0MolecularProfileId']; + } + + if (parameters['sampleMolecularIdentifiers0SampleId'] !== undefined) { + queryParameters['sampleMolecularIdentifiers[0].sampleId'] = parameters['sampleMolecularIdentifiers0SampleId']; + } + + if (parameters['structuralVariantFilter'] !== undefined) { + body = parameters['structuralVariantFilter']; + } + + if (parameters['structuralVariantFilter'] === undefined) { + reject(new Error('Missing required parameter: structuralVariantFilter')); + return; + } + + if (parameters.$queryParameters) { + Object.keys(parameters.$queryParameters).forEach(function(parameterName) { + var parameter = parameters.$queryParameters[parameterName]; + queryParameters[parameterName] = parameter; + }); + } + + request('POST', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); + + }); + }; + + /** + * Fetch structural variants for entrezGeneIds and molecularProfileIds or sampleMolecularIdentifiers + * @method + * @name CBioPortalAPIInternal#fetchStructuralVariantsUsingPOST + * @param {array} entrezGeneIds - A web service for supplying JSON formatted data to cBioPortal clients. Please note that interal API is currently in beta and subject to change. + * @param {array} molecularProfileIds - A web service for supplying JSON formatted data to cBioPortal clients. Please note that interal API is currently in beta and subject to change. + * @param {string} sampleMolecularIdentifiers0MolecularProfileId - A web service for supplying JSON formatted data to cBioPortal clients. Please note that interal API is currently in beta and subject to change. + * @param {string} sampleMolecularIdentifiers0SampleId - A web service for supplying JSON formatted data to cBioPortal clients. Please note that interal API is currently in beta and subject to change. + * @param {} structuralVariantFilter - List of entrezGeneIds and molecularProfileIds or sampleMolecularIdentifiers + */ + fetchStructuralVariantsUsingPOST(parameters: { + 'entrezGeneIds' ? : Array < number > , + 'molecularProfileIds' ? : Array < string > , + 'sampleMolecularIdentifiers0MolecularProfileId' ? : string, + 'sampleMolecularIdentifiers0SampleId' ? : string, + 'structuralVariantFilter': StructuralVariantFilter, + $queryParameters ? : any, + $domain ? : string + }): Promise < Array < StructuralVariant > + > { + return this.fetchStructuralVariantsUsingPOSTWithHttpInfo(parameters).then(function(response: request.Response) { + return response.body; + }); + }; fetchStructuralVariantGenesUsingPOSTURL(parameters: { 'studyViewFilter': StudyViewFilter, $queryParameters ? : any diff --git a/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPI-docs.json b/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPI-docs.json index 234b7589f71..825d767cb03 100644 --- a/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPI-docs.json +++ b/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPI-docs.json @@ -1864,6 +1864,12 @@ "items": { "type": "string" } + }, + "protein": { + "type": "array", + "items": { + "type": "string" + } } } }, diff --git a/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPI.ts b/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPI.ts index 209d6640ba9..73c97ccf4ca 100644 --- a/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPI.ts +++ b/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPI.ts @@ -340,6 +340,8 @@ export type Hgvs = { 'genomic': Array < string > + 'protein': Array < string > + }; export type Homozygotes = { 'hom': number diff --git a/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPIInternal-docs.json b/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPIInternal-docs.json index d4ee38c582d..61f039828d6 100644 --- a/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPIInternal-docs.json +++ b/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPIInternal-docs.json @@ -1486,6 +1486,12 @@ "items": { "type": "string" } + }, + "protein": { + "type": "array", + "items": { + "type": "string" + } } } }, diff --git a/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPIInternal.ts b/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPIInternal.ts index 1c0c8abb4be..0ee75093d4c 100644 --- a/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPIInternal.ts +++ b/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPIInternal.ts @@ -242,6 +242,8 @@ export type Hgvs = { 'genomic': Array < string > + 'protein': Array < string > + }; export type Homozygotes = { 'hom': number diff --git a/yarn.lock b/yarn.lock index e9cebab5fbf..178138d7b76 100644 --- a/yarn.lock +++ b/yarn.lock @@ -20533,16 +20533,6 @@ react-column-resizer@^1.1.9: resolved "https://registry.yarnpkg.com/react-column-resizer/-/react-column-resizer-1.1.9.tgz#b3e591003d1373ae9a9f85ef9d855813743773dd" integrity sha512-l25LPyN3Gu33RC726cv3ZnS9EaI/B+ZIY1MrJiiHcBqsY4BKRYNBbrZolUfzBjjWDwHOBMc/fZLiSxmDGPqCrQ== -react-dom@16.14.0, react-dom@^16.6: - version "16.14.0" - resolved "https://registry.yarnpkg.com/react-dom/-/react-dom-16.14.0.tgz#7ad838ec29a777fb3c75c3a190f661cf92ab8b89" - integrity sha512-1gCeQXDLoIqMgqD3IO2Ah9bnf0w9kzhwN5q4FGnHZ67hBm9yePzB5JJAIQCc8x3pFnNlwFq4RidZggNAAkzWWw== - dependencies: - loose-envify "^1.1.0" - object-assign "^4.1.1" - prop-types "^15.6.2" - scheduler "^0.19.1" - react-dom@^15.3.1: version "15.6.2" resolved "https://registry.yarnpkg.com/react-dom/-/react-dom-15.6.2.tgz#41cfadf693b757faf2708443a1d1fd5a02bef730" @@ -20553,6 +20543,16 @@ react-dom@^15.3.1: object-assign "^4.1.0" prop-types "^15.5.10" +react-dom@^16.6: + version "16.14.0" + resolved "https://registry.yarnpkg.com/react-dom/-/react-dom-16.14.0.tgz#7ad838ec29a777fb3c75c3a190f661cf92ab8b89" + integrity sha512-1gCeQXDLoIqMgqD3IO2Ah9bnf0w9kzhwN5q4FGnHZ67hBm9yePzB5JJAIQCc8x3pFnNlwFq4RidZggNAAkzWWw== + dependencies: + loose-envify "^1.1.0" + object-assign "^4.1.1" + prop-types "^15.6.2" + scheduler "^0.19.1" + react-dom@^16.7.0: version "16.8.4" resolved "https://registry.yarnpkg.com/react-dom/-/react-dom-16.8.4.tgz#1061a8e01a2b3b0c8160037441c3bf00a0e3bc48"