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 dc13a5fdfae..e3bc4db4b7b 100644 --- a/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPI-docs.json +++ b/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPI-docs.json @@ -5418,6 +5418,36 @@ ], "type": "object" }, + "MutationDataFilter": { + "properties": { + "categorization": { + "enum": [ + "MUTATED", + "EVENT" + ], + "type": "string" + }, + "hugoGeneSymbol": { + "type": "string" + }, + "profileType": { + "type": "string" + }, + "values": { + "items": { + "items": { + "$ref": "#/definitions/DataFilterValue" + }, + "type": "array" + }, + "type": "array" + } + }, + "required": [ + "categorization" + ], + "type": "object" + }, "MutationFilter": { "description": "List of Sample IDs/Sample List ID and Entrez Gene IDs", "properties": { @@ -5926,6 +5956,12 @@ }, "type": "array" }, + "mutationDataFilters": { + "items": { + "$ref": "#/definitions/MutationDataFilter" + }, + "type": "array" + }, "patientTreatmentFilters": { "$ref": "#/definitions/AndedPatientTreatmentFilters" }, diff --git a/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPI.ts b/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPI.ts index 9206ee6b534..b9b9a112105 100644 --- a/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPI.ts +++ b/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPI.ts @@ -551,6 +551,17 @@ export type Mutation = { 'variantType': string +}; +export type MutationDataFilter = { + 'categorization': "MUTATED" | "EVENT" + + 'hugoGeneSymbol': string + + 'profileType': string + + 'values': Array < Array < DataFilterValue > + > + }; export type MutationFilter = { 'entrezGeneIds': Array < number > @@ -757,6 +768,8 @@ export type StudyViewFilter = { 'genomicProfiles': Array < Array < string > > + 'mutationDataFilters': Array < MutationDataFilter > + 'patientTreatmentFilters': AndedPatientTreatmentFilters 'patientTreatmentGroupFilters': AndedPatientTreatmentFilters diff --git a/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal-docs.json b/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal-docs.json index 2f1cf95e502..dc27c974f83 100644 --- a/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal-docs.json +++ b/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal-docs.json @@ -2039,6 +2039,52 @@ "operationId": "fetchMutationCountsByPositionUsingPOST" } }, + "/api/mutation-data-counts/fetch": { + "post": { + "consumes": [ + "application/json" + ], + "produces": [ + "application/json" + ], + "parameters": [ + { + "default": "SUMMARY", + "description": "Level of detail of the response", + "enum": [ + "ID", + "SUMMARY", + "DETAILED", + "META" + ], + "in": "query", + "name": "projection", + "required": false, + "type": "string" + }, + { + "in": "body", + "name": "genomicDataCountFilter", + "schema": { + "$ref": "#/definitions/GenomicDataCountFilter" + } + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "$ref": "#/definitions/ResponseEntityListGenomicDataCountItem" + } + } + }, + "tags": [ + "Study View" + ], + "description": "Fetch mutation data counts by GenomicDataCountFilter", + "operationId": "fetchMutationDataCountsUsingPOST" + } + }, "/api/reference-genome-genes/{genomeName}": { "get": { "produces": [ @@ -3893,6 +3939,53 @@ }, "type": "object" }, + "ContentDisposition": { + "properties": { + "attachment": { + "type": "boolean" + }, + "charset": { + "properties": { + "registered": { + "type": "boolean" + } + }, + "type": "object" + }, + "creationDate": { + "format": "date-time", + "type": "string" + }, + "filename": { + "type": "string" + }, + "formData": { + "type": "boolean" + }, + "inline": { + "type": "boolean" + }, + "modificationDate": { + "format": "date-time", + "type": "string" + }, + "name": { + "type": "string" + }, + "readDate": { + "format": "date-time", + "type": "string" + }, + "size": { + "format": "int64", + "type": "integer" + }, + "type": { + "type": "string" + } + }, + "type": "object" + }, "CopyNumberCount": { "properties": { "alteration": { @@ -4714,6 +4807,10 @@ "label": { "type": "string" }, + "uniqueCount": { + "format": "int32", + "type": "integer" + }, "value": { "type": "string" } @@ -4908,6 +5005,76 @@ ], "type": "object" }, + "HttpMethod": { + "type": "object" + }, + "HttpRange": { + "type": "object" + }, + "HttpStatusCode": { + "properties": { + "error": { + "type": "boolean" + }, + "is1xxInformational": { + "type": "boolean" + }, + "is2xxSuccessful": { + "type": "boolean" + }, + "is3xxRedirection": { + "type": "boolean" + }, + "is4xxClientError": { + "type": "boolean" + }, + "is5xxServerError": { + "type": "boolean" + } + }, + "type": "object" + }, + "MediaType": { + "properties": { + "parameters": { + "additionalProperties": { + "type": "string" + }, + "type": "object" + }, + "charset": { + "properties": { + "registered": { + "type": "boolean" + } + }, + "type": "object" + }, + "concrete": { + "type": "boolean" + }, + "qualityValue": { + "format": "double", + "type": "number" + }, + "subtype": { + "type": "string" + }, + "subtypeSuffix": { + "type": "string" + }, + "type": { + "type": "string" + }, + "wildcardSubtype": { + "type": "boolean" + }, + "wildcardType": { + "type": "boolean" + } + }, + "type": "object" + }, "MolecularProfileCaseIdentifier": { "properties": { "caseId": { @@ -5061,6 +5228,36 @@ ], "type": "object" }, + "MutationDataFilter": { + "properties": { + "categorization": { + "enum": [ + "MUTATED", + "EVENT" + ], + "type": "string" + }, + "hugoGeneSymbol": { + "type": "string" + }, + "profileType": { + "type": "string" + }, + "values": { + "items": { + "items": { + "$ref": "#/definitions/DataFilterValue" + }, + "type": "array" + }, + "type": "array" + } + }, + "required": [ + "categorization" + ], + "type": "object" + }, "MutationPositionIdentifier": { "properties": { "entrezGeneId": { @@ -5291,6 +5488,401 @@ ], "type": "object" }, + "ResponseEntityListGenomicDataCountItem": { + "properties": { + "body": { + "items": { + "$ref": "#/definitions/GenomicDataCountItem" + }, + "type": "array" + }, + "headers": { + "additionalProperties": { + "items": { + "type": "string" + }, + "type": "array" + }, + "properties": { + "host": { + "properties": { + "address": { + "properties": { + "address": { + "items": { + "format": "byte", + "type": "string" + }, + "type": "array" + }, + "anyLocalAddress": { + "type": "boolean" + }, + "canonicalHostName": { + "type": "string" + }, + "hostAddress": { + "type": "string" + }, + "hostName": { + "type": "string" + }, + "linkLocalAddress": { + "type": "boolean" + }, + "loopbackAddress": { + "type": "boolean" + }, + "mcglobal": { + "type": "boolean" + }, + "mclinkLocal": { + "type": "boolean" + }, + "mcnodeLocal": { + "type": "boolean" + }, + "mcorgLocal": { + "type": "boolean" + }, + "mcsiteLocal": { + "type": "boolean" + }, + "multicastAddress": { + "type": "boolean" + }, + "siteLocalAddress": { + "type": "boolean" + } + }, + "type": "object" + }, + "hostName": { + "type": "string" + }, + "hostString": { + "type": "string" + }, + "port": { + "format": "int32", + "type": "integer" + }, + "unresolved": { + "type": "boolean" + } + }, + "type": "object" + }, + "accept": { + "items": { + "$ref": "#/definitions/MediaType" + }, + "type": "array" + }, + "acceptCharset": { + "items": { + "properties": { + "registered": { + "type": "boolean" + } + }, + "type": "object" + }, + "type": "array" + }, + "acceptLanguage": { + "items": { + "properties": { + "range": { + "type": "string" + }, + "weight": { + "format": "double", + "type": "number" + } + }, + "type": "object" + }, + "type": "array" + }, + "acceptLanguageAsLocales": { + "items": { + "properties": { + "country": { + "type": "string" + }, + "displayCountry": { + "type": "string" + }, + "displayLanguage": { + "type": "string" + }, + "displayName": { + "type": "string" + }, + "displayScript": { + "type": "string" + }, + "displayVariant": { + "type": "string" + }, + "extensionKeys": { + "items": { + "type": "string" + }, + "type": "array", + "uniqueItems": true + }, + "iso3Country": { + "type": "string" + }, + "iso3Language": { + "type": "string" + }, + "language": { + "type": "string" + }, + "script": { + "type": "string" + }, + "unicodeLocaleAttributes": { + "items": { + "type": "string" + }, + "type": "array", + "uniqueItems": true + }, + "unicodeLocaleKeys": { + "items": { + "type": "string" + }, + "type": "array", + "uniqueItems": true + }, + "variant": { + "type": "string" + } + }, + "type": "object" + }, + "type": "array" + }, + "acceptPatch": { + "items": { + "$ref": "#/definitions/MediaType" + }, + "type": "array" + }, + "accessControlAllowCredentials": { + "type": "boolean" + }, + "accessControlAllowHeaders": { + "items": { + "type": "string" + }, + "type": "array" + }, + "accessControlAllowMethods": { + "items": { + "$ref": "#/definitions/HttpMethod" + }, + "type": "array" + }, + "accessControlAllowOrigin": { + "type": "string" + }, + "accessControlExposeHeaders": { + "items": { + "type": "string" + }, + "type": "array" + }, + "accessControlMaxAge": { + "format": "int64", + "type": "integer" + }, + "accessControlRequestHeaders": { + "items": { + "type": "string" + }, + "type": "array" + }, + "accessControlRequestMethod": { + "$ref": "#/definitions/HttpMethod" + }, + "all": { + "additionalProperties": { + "type": "string" + }, + "type": "object" + }, + "allow": { + "items": { + "$ref": "#/definitions/HttpMethod" + }, + "type": "array", + "uniqueItems": true + }, + "basicAuth": { + "type": "string" + }, + "bearerAuth": { + "type": "string" + }, + "cacheControl": { + "type": "string" + }, + "connection": { + "items": { + "type": "string" + }, + "type": "array" + }, + "contentDisposition": { + "$ref": "#/definitions/ContentDisposition" + }, + "contentLanguage": { + "properties": { + "country": { + "type": "string" + }, + "displayCountry": { + "type": "string" + }, + "displayLanguage": { + "type": "string" + }, + "displayName": { + "type": "string" + }, + "displayScript": { + "type": "string" + }, + "displayVariant": { + "type": "string" + }, + "extensionKeys": { + "items": { + "type": "string" + }, + "type": "array", + "uniqueItems": true + }, + "iso3Country": { + "type": "string" + }, + "iso3Language": { + "type": "string" + }, + "language": { + "type": "string" + }, + "script": { + "type": "string" + }, + "unicodeLocaleAttributes": { + "items": { + "type": "string" + }, + "type": "array", + "uniqueItems": true + }, + "unicodeLocaleKeys": { + "items": { + "type": "string" + }, + "type": "array", + "uniqueItems": true + }, + "variant": { + "type": "string" + } + }, + "type": "object" + }, + "contentLength": { + "format": "int64", + "type": "integer" + }, + "contentType": { + "$ref": "#/definitions/MediaType" + }, + "date": { + "format": "int64", + "type": "integer" + }, + "empty": { + "type": "boolean" + }, + "etag": { + "type": "string" + }, + "expires": { + "format": "int64", + "type": "integer" + }, + "ifMatch": { + "items": { + "type": "string" + }, + "type": "array" + }, + "ifModifiedSince": { + "format": "int64", + "type": "integer" + }, + "ifNoneMatch": { + "items": { + "type": "string" + }, + "type": "array" + }, + "ifUnmodifiedSince": { + "format": "int64", + "type": "integer" + }, + "lastModified": { + "format": "int64", + "type": "integer" + }, + "location": { + "format": "uri", + "type": "string" + }, + "origin": { + "type": "string" + }, + "pragma": { + "type": "string" + }, + "range": { + "items": { + "$ref": "#/definitions/HttpRange" + }, + "type": "array" + }, + "upgrade": { + "type": "string" + }, + "vary": { + "items": { + "type": "string" + }, + "type": "array" + } + }, + "type": "object" + }, + "statusCode": { + "$ref": "#/definitions/HttpStatusCode" + }, + "statusCodeValue": { + "format": "int32", + "type": "integer" + } + }, + "type": "object" + }, "Sample": { "properties": { "copyNumberSegmentPresent": { @@ -5709,6 +6301,12 @@ }, "type": "array" }, + "mutationDataFilters": { + "items": { + "$ref": "#/definitions/MutationDataFilter" + }, + "type": "array" + }, "patientTreatmentFilters": { "$ref": "#/definitions/AndedPatientTreatmentFilters" }, diff --git a/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal.ts b/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal.ts index e9e830b05af..fb14d2aa810 100644 --- a/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal.ts +++ b/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal.ts @@ -316,6 +316,33 @@ export type CoExpressionFilter = { 'sampleListId': string +}; +export type ContentDisposition = { + 'attachment': boolean + + 'charset': { + 'registered': boolean + + } + + 'creationDate': string + + 'filename': string + + 'formData': boolean + + 'inline': boolean + + 'modificationDate': string + + 'name': string + + 'readDate': string + + 'size': number + + 'type': string + }; export type CopyNumberCount = { 'alteration': number @@ -689,6 +716,8 @@ export type GenomicDataCount = { 'label': string + 'uniqueCount': number + 'value': string }; @@ -767,6 +796,45 @@ export type GroupStatistics = { 'standardDeviation': number +}; +export type HttpMethod = {}; +export type HttpRange = {}; +export type HttpStatusCode = { + 'error': boolean + + 'is1xxInformational': boolean + + 'is2xxSuccessful': boolean + + 'is3xxRedirection': boolean + + 'is4xxClientError': boolean + + 'is5xxServerError': boolean + +}; +export type MediaType = { + 'parameters': {} + + 'charset': { + 'registered': boolean + + } + + 'concrete': boolean + + 'qualityValue': number + + 'subtype': string + + 'subtypeSuffix': string + + 'type': string + + 'wildcardSubtype': boolean + + 'wildcardType': boolean + }; export type MolecularProfileCaseIdentifier = { 'caseId': string @@ -831,6 +899,17 @@ export type MutationCountByPosition = { 'proteinPosStart': number +}; +export type MutationDataFilter = { + 'categorization': "MUTATED" | "EVENT" + + 'hugoGeneSymbol': string + + 'profileType': string + + 'values': Array < Array < DataFilterValue > + > + }; export type MutationPositionIdentifier = { 'entrezGeneId': number @@ -933,6 +1012,201 @@ export type ResourceDefinition = { 'studyId': string +}; +export type ResponseEntityListGenomicDataCountItem = { + 'body': Array < GenomicDataCountItem > + + 'headers': { + 'host': { + 'address': { + 'address': Array < string > + + 'anyLocalAddress': boolean + + 'canonicalHostName': string + + 'hostAddress': string + + 'hostName': string + + 'linkLocalAddress': boolean + + 'loopbackAddress': boolean + + 'mcglobal': boolean + + 'mclinkLocal': boolean + + 'mcnodeLocal': boolean + + 'mcorgLocal': boolean + + 'mcsiteLocal': boolean + + 'multicastAddress': boolean + + 'siteLocalAddress': boolean + + } + + 'hostName': string + + 'hostString': string + + 'port': number + + 'unresolved': boolean + + } + + 'accept': Array < MediaType > + + 'acceptCharset': Array < { + 'registered': boolean + + } > + + 'acceptLanguage': Array < { + 'range': string + + 'weight': number + + } > + + 'acceptLanguageAsLocales': Array < { + 'country': string + + 'displayCountry': string + + 'displayLanguage': string + + 'displayName': string + + 'displayScript': string + + 'displayVariant': string + + 'extensionKeys': Array < string > + + 'iso3Country': string + + 'iso3Language': string + + 'language': string + + 'script': string + + 'unicodeLocaleAttributes': Array < string > + + 'unicodeLocaleKeys': Array < string > + + 'variant': string + + } > + + 'acceptPatch': Array < MediaType > + + 'accessControlAllowCredentials': boolean + + 'accessControlAllowHeaders': Array < string > + + 'accessControlAllowMethods': Array < HttpMethod > + + 'accessControlAllowOrigin': string + + 'accessControlExposeHeaders': Array < string > + + 'accessControlMaxAge': number + + 'accessControlRequestHeaders': Array < string > + + 'accessControlRequestMethod': HttpMethod + + 'all': {} + + 'allow': Array < HttpMethod > + + 'basicAuth': string + + 'bearerAuth': string + + 'cacheControl': string + + 'connection': Array < string > + + 'contentDisposition': ContentDisposition + + 'contentLanguage': { + 'country': string + + 'displayCountry': string + + 'displayLanguage': string + + 'displayName': string + + 'displayScript': string + + 'displayVariant': string + + 'extensionKeys': Array < string > + + 'iso3Country': string + + 'iso3Language': string + + 'language': string + + 'script': string + + 'unicodeLocaleAttributes': Array < string > + + 'unicodeLocaleKeys': Array < string > + + 'variant': string + + } + + 'contentLength': number + + 'contentType': MediaType + + 'date': number + + 'empty': boolean + + 'etag': string + + 'expires': number + + 'ifMatch': Array < string > + + 'ifModifiedSince': number + + 'ifNoneMatch': Array < string > + + 'ifUnmodifiedSince': number + + 'lastModified': number + + 'location': string + + 'origin': string + + 'pragma': string + + 'range': Array < HttpRange > + + 'upgrade': string + + 'vary': Array < string > + + } + + 'statusCode': HttpStatusCode + + 'statusCodeValue': number + }; export type Sample = { 'copyNumberSegmentPresent': boolean @@ -1137,6 +1411,8 @@ export type StudyViewFilter = { 'genomicProfiles': Array < Array < string > > + 'mutationDataFilters': Array < MutationDataFilter > + 'patientTreatmentFilters': AndedPatientTreatmentFilters 'patientTreatmentGroupFilters': AndedPatientTreatmentFilters @@ -5266,6 +5542,89 @@ export default class CBioPortalAPIInternal { return response.body; }); }; + fetchMutationDataCountsUsingPOSTURL(parameters: { + 'projection' ? : "ID" | "SUMMARY" | "DETAILED" | "META", + 'genomicDataCountFilter' ? : GenomicDataCountFilter, + $queryParameters ? : any + }): string { + let queryParameters: any = {}; + let path = '/api/mutation-data-counts/fetch'; + if (parameters['projection'] !== undefined) { + queryParameters['projection'] = parameters['projection']; + } + + if (parameters.$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 mutation data counts by GenomicDataCountFilter + * @method + * @name CBioPortalAPIInternal#fetchMutationDataCountsUsingPOST + * @param {string} projection - Level of detail of the response + * @param {} genomicDataCountFilter - A web service for supplying JSON formatted data to cBioPortal clients. Please note that this API is currently in beta and subject to change. + */ + fetchMutationDataCountsUsingPOSTWithHttpInfo(parameters: { + 'projection' ? : "ID" | "SUMMARY" | "DETAILED" | "META", + 'genomicDataCountFilter' ? : GenomicDataCountFilter, + $queryParameters ? : any, + $domain ? : string + }): Promise < request.Response > { + const domain = parameters.$domain ? parameters.$domain : this.domain; + const errorHandlers = this.errorHandlers; + const request = this.request; + let path = '/api/mutation-data-counts/fetch'; + let body: any; + let queryParameters: any = {}; + let headers: any = {}; + let form: any = {}; + return new Promise(function(resolve, reject) { + headers['Accept'] = 'application/json'; + headers['Content-Type'] = 'application/json'; + + if (parameters['projection'] !== undefined) { + queryParameters['projection'] = parameters['projection']; + } + + if (parameters['genomicDataCountFilter'] !== undefined) { + body = parameters['genomicDataCountFilter']; + } + + if (parameters.$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 mutation data counts by GenomicDataCountFilter + * @method + * @name CBioPortalAPIInternal#fetchMutationDataCountsUsingPOST + * @param {string} projection - Level of detail of the response + * @param {} genomicDataCountFilter - A web service for supplying JSON formatted data to cBioPortal clients. Please note that this API is currently in beta and subject to change. + */ + fetchMutationDataCountsUsingPOST(parameters: { + 'projection' ? : "ID" | "SUMMARY" | "DETAILED" | "META", + 'genomicDataCountFilter' ? : GenomicDataCountFilter, + $queryParameters ? : any, + $domain ? : string + }): Promise < ResponseEntityListGenomicDataCountItem > { + return this.fetchMutationDataCountsUsingPOSTWithHttpInfo(parameters).then(function(response: request.Response) { + return response.body; + }); + }; getAllReferenceGenomeGenesUsingGETURL(parameters: { 'genomeName': string, $queryParameters ? : any