diff --git a/env/master.sh b/env/master.sh index 49f303e188b..6c589976526 100644 --- a/env/master.sh +++ b/env/master.sh @@ -1,3 +1,3 @@ -export CBIOPORTAL_URL="${CBIOPORTAL_URL:-https://beta.cbioportal.org}" +export CBIOPORTAL_URL="${CBIOPORTAL_URL:-https://www.cbioportal.org}" export GENOME_NEXUS_URL="${GENOME_NEXUS_URL:-https://www.genomenexus.org}" export BACKEND=cbioportal:demo-fix-clinical-table-sorting \ No newline at end of file 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 c325e47f998..540248d96d8 100644 --- a/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPI-docs.json +++ b/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPI-docs.json @@ -3945,208 +3945,6 @@ "description": "Get the tags of a study", "operationId": "getTagsUsingGET" } - }, - "/api/treatments/display-patient": { - "post": { - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "default": "Agent", - "enum": [ - "Agent", - "AgentClass", - "AgentTarget" - ], - "in": "query", - "name": "tier", - "required": false, - "type": "string" - }, - { - "in": "body", - "name": "studyIds", - "required": true, - "schema": { - "description": "List of Study IDs", - "items": { - "maxLength": 10000000, - "minLength": 1, - "type": "string" - }, - "maxItems": 10000000, - "minItems": 1, - "type": "array", - "uniqueItems": true - } - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "type": "boolean" - } - } - }, - "tags": [ - "Treatments" - ], - "description": "Should patient level treatments be displayed", - "operationId": "getContainsTreatmentDataUsingPOST" - } - }, - "/api/treatments/display-sample": { - "post": { - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "default": "Agent", - "enum": [ - "Agent", - "AgentClass", - "AgentTarget" - ], - "in": "query", - "name": "tier", - "required": false, - "type": "string" - }, - { - "in": "body", - "name": "studyIds", - "required": true, - "schema": { - "description": "List of Study IDs", - "items": { - "maxLength": 10000000, - "minLength": 1, - "type": "string" - }, - "maxItems": 10000000, - "minItems": 1, - "type": "array", - "uniqueItems": true - } - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "type": "boolean" - } - } - }, - "tags": [ - "Treatments" - ], - "description": "Should sample level treatments be displayed", - "operationId": "getContainsSampleTreatmentDataUsingPOST" - } - }, - "/api/treatments/patient": { - "post": { - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "default": "Agent", - "enum": [ - "Agent", - "AgentClass", - "AgentTarget" - ], - "in": "query", - "name": "tier", - "required": false, - "type": "string" - }, - { - "in": "body", - "name": "studyViewFilter", - "schema": { - "$ref": "#/definitions/StudyViewFilter" - } - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "items": { - "$ref": "#/definitions/PatientTreatmentRow" - }, - "type": "array" - } - } - }, - "tags": [ - "Treatments" - ], - "description": "Get all patient level treatments", - "operationId": "getAllPatientTreatmentsUsingPOST" - } - }, - "/api/treatments/sample": { - "post": { - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "default": "Agent", - "enum": [ - "Agent", - "AgentClass", - "AgentTarget" - ], - "in": "query", - "name": "tier", - "required": false, - "type": "string" - }, - { - "in": "body", - "name": "studyViewFilter", - "schema": { - "$ref": "#/definitions/StudyViewFilter" - } - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "items": { - "$ref": "#/definitions/SampleTreatmentRow" - }, - "type": "array" - } - } - }, - "tags": [ - "Treatments" - ], - "description": "Get all sample level treatments", - "operationId": "getAllSampleTreatmentsUsingPOST" - } } }, "definitions": { @@ -4185,75 +3983,6 @@ }, "type": "object" }, - "AlterationFilter": { - "properties": { - "copyNumberAlterationEventTypes": { - "additionalProperties": { - "type": "boolean" - }, - "type": "object" - }, - "includeDriver": { - "type": "boolean" - }, - "includeGermline": { - "type": "boolean" - }, - "includeSomatic": { - "type": "boolean" - }, - "includeUnknownOncogenicity": { - "type": "boolean" - }, - "includeUnknownStatus": { - "type": "boolean" - }, - "includeUnknownTier": { - "type": "boolean" - }, - "includeVUS": { - "type": "boolean" - }, - "mutationEventTypes": { - "additionalProperties": { - "type": "boolean" - }, - "type": "object" - }, - "structuralVariants": { - "type": "boolean" - }, - "tiersBooleanMap": { - "additionalProperties": { - "type": "boolean" - }, - "type": "object" - } - }, - "type": "object" - }, - "AndedPatientTreatmentFilters": { - "properties": { - "filters": { - "items": { - "$ref": "#/definitions/OredPatientTreatmentFilters" - }, - "type": "array" - } - }, - "type": "object" - }, - "AndedSampleTreatmentFilters": { - "properties": { - "filters": { - "items": { - "$ref": "#/definitions/OredSampleTreatmentFilters" - }, - "type": "array" - } - }, - "type": "object" - }, "CancerStudy": { "properties": { "allSampleCount": { @@ -4439,20 +4168,6 @@ ], "type": "object" }, - "ClinicalDataFilter": { - "properties": { - "attributeId": { - "type": "string" - }, - "values": { - "items": { - "$ref": "#/definitions/DataFilterValue" - }, - "type": "array" - } - }, - "type": "object" - }, "ClinicalDataIdentifier": { "properties": { "entityId": { @@ -4514,24 +4229,6 @@ }, "type": "object" }, - "ClinicalEventSample": { - "properties": { - "patientId": { - "type": "string" - }, - "sampleId": { - "type": "string" - }, - "studyId": { - "type": "string" - }, - "timeTaken": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, "CopyNumberSeg": { "properties": { "chromosome": { @@ -4580,31 +4277,6 @@ ], "type": "object" }, - "DataFilter": { - "properties": { - "values": { - "items": { - "$ref": "#/definitions/DataFilterValue" - }, - "type": "array" - } - }, - "type": "object" - }, - "DataFilterValue": { - "properties": { - "end": { - "type": "number" - }, - "start": { - "type": "number" - }, - "value": { - "type": "string" - } - }, - "type": "object" - }, "DiscreteCopyNumberData": { "properties": { "alteration": { @@ -4696,97 +4368,24 @@ "properties": { "entrezGeneId": { "format": "int32", - "type": "integer" - }, - "geneticEntityId": { - "format": "int32", - "type": "integer" - }, - "hugoGeneSymbol": { - "type": "string" - }, - "type": { - "type": "string" - } - }, - "required": [ - "entrezGeneId", - "geneticEntityId", - "hugoGeneSymbol" - ], - "type": "object" - }, - "GeneFilter": { - "properties": { - "geneQueries": { - "items": { - "items": { - "$ref": "#/definitions/GeneFilterQuery" - }, - "type": "array" - }, - "type": "array" - }, - "molecularProfileIds": { - "items": { - "type": "string" - }, - "type": "array", - "uniqueItems": true - } - }, - "type": "object" - }, - "GeneFilterQuery": { - "properties": { - "alterations": { - "items": { - "enum": [ - "AMP", - "GAIN", - "DIPLOID", - "HETLOSS", - "HOMDEL" - ], - "type": "string" - }, - "type": "array" + "type": "integer" }, - "entrezGeneId": { + "geneticEntityId": { "format": "int32", "type": "integer" }, "hugoGeneSymbol": { "type": "string" }, - "includeDriver": { - "type": "boolean" - }, - "includeGermline": { - "type": "boolean" - }, - "includeSomatic": { - "type": "boolean" - }, - "includeUnknownOncogenicity": { - "type": "boolean" - }, - "includeUnknownStatus": { - "type": "boolean" - }, - "includeUnknownTier": { - "type": "boolean" - }, - "includeVUS": { - "type": "boolean" - }, - "tiersBooleanMap": { - "additionalProperties": { - "type": "boolean" - }, - "type": "object" + "type": { + "type": "string" } }, + "required": [ + "entrezGeneId", + "geneticEntityId", + "hugoGeneSymbol" + ], "type": "object" }, "GenePanel": { @@ -4944,23 +4543,6 @@ ], "type": "object" }, - "GenericAssayDataFilter": { - "properties": { - "profileType": { - "type": "string" - }, - "stableId": { - "type": "string" - }, - "values": { - "items": { - "$ref": "#/definitions/DataFilterValue" - }, - "type": "array" - } - }, - "type": "object" - }, "GenericAssayDataMultipleStudyFilter": { "description": "List of Molecular Profile ID and Sample ID pairs or List of MolecularProfile IDs and Generic Assay IDs", "properties": { @@ -5063,23 +4645,6 @@ }, "type": "object" }, - "GenomicDataFilter": { - "properties": { - "hugoGeneSymbol": { - "type": "string" - }, - "profileType": { - "type": "string" - }, - "values": { - "items": { - "$ref": "#/definitions/DataFilterValue" - }, - "type": "array" - } - }, - "type": "object" - }, "Info": { "properties": { "dbVersion": { @@ -5418,36 +4983,6 @@ ], "type": "object" }, - "MutationDataFilter": { - "properties": { - "categorization": { - "enum": [ - "MUTATED", - "MUTATION_TYPE" - ], - "type": "string" - }, - "hugoGeneSymbol": { - "type": "string" - }, - "profileType": { - "type": "string" - }, - "values": { - "items": { - "items": { - "$ref": "#/definitions/DataFilterValue" - }, - "type": "array" - }, - "type": "array" - } - }, - "required": [ - "categorization" - ], - "type": "object" - }, "MutationFilter": { "description": "List of Sample IDs/Sample List ID and Entrez Gene IDs", "properties": { @@ -5550,28 +5085,6 @@ ], "type": "object" }, - "OredPatientTreatmentFilters": { - "properties": { - "filters": { - "items": { - "$ref": "#/definitions/PatientTreatmentFilter" - }, - "type": "array" - } - }, - "type": "object" - }, - "OredSampleTreatmentFilters": { - "properties": { - "filters": { - "items": { - "$ref": "#/definitions/SampleTreatmentFilter" - }, - "type": "array" - } - }, - "type": "object" - }, "Patient": { "properties": { "cancerStudy": { @@ -5631,33 +5144,6 @@ }, "type": "object" }, - "PatientTreatmentFilter": { - "properties": { - "treatment": { - "type": "string" - } - }, - "type": "object" - }, - "PatientTreatmentRow": { - "properties": { - "count": { - "format": "int32", - "type": "integer" - }, - "samples": { - "items": { - "$ref": "#/definitions/ClinicalEventSample" - }, - "type": "array", - "uniqueItems": true - }, - "treatment": { - "type": "string" - } - }, - "type": "object" - }, "Sample": { "properties": { "copyNumberSegmentPresent": { @@ -5790,47 +5276,6 @@ }, "type": "object" }, - "SampleTreatmentFilter": { - "properties": { - "time": { - "enum": [ - "Pre", - "Post" - ], - "type": "string" - }, - "treatment": { - "type": "string" - } - }, - "type": "object" - }, - "SampleTreatmentRow": { - "properties": { - "count": { - "format": "int32", - "type": "integer" - }, - "samples": { - "items": { - "$ref": "#/definitions/ClinicalEventSample" - }, - "type": "array", - "uniqueItems": true - }, - "time": { - "enum": [ - "Pre", - "Post" - ], - "type": "string" - }, - "treatment": { - "type": "string" - } - }, - "type": "object" - }, "ServerStatusMessage": { "properties": { "status": { @@ -5839,195 +5284,6 @@ }, "type": "object" }, - "StructuralVariantFilterQuery": { - "properties": { - "gene1Query": { - "$ref": "#/definitions/StructuralVariantGeneSubQuery" - }, - "gene2Query": { - "$ref": "#/definitions/StructuralVariantGeneSubQuery" - }, - "includeDriver": { - "type": "boolean" - }, - "includeGermline": { - "type": "boolean" - }, - "includeSomatic": { - "type": "boolean" - }, - "includeUnknownOncogenicity": { - "type": "boolean" - }, - "includeUnknownStatus": { - "type": "boolean" - }, - "includeUnknownTier": { - "type": "boolean" - }, - "includeVUS": { - "type": "boolean" - }, - "tiersBooleanMap": { - "additionalProperties": { - "type": "boolean" - }, - "type": "object" - } - }, - "type": "object" - }, - "StructuralVariantGeneSubQuery": { - "properties": { - "entrezId": { - "format": "int32", - "type": "integer" - }, - "hugoSymbol": { - "type": "string" - }, - "specialValue": { - "enum": [ - "ANY_GENE", - "NO_GENE" - ], - "type": "string" - } - }, - "type": "object" - }, - "StudyViewFilter": { - "description": "Study view filter", - "properties": { - "alterationFilter": { - "$ref": "#/definitions/AlterationFilter" - }, - "caseLists": { - "items": { - "items": { - "type": "string" - }, - "type": "array" - }, - "type": "array" - }, - "clinicalDataFilters": { - "items": { - "$ref": "#/definitions/ClinicalDataFilter" - }, - "type": "array" - }, - "clinicalEventFilters": { - "items": { - "$ref": "#/definitions/DataFilter" - }, - "type": "array" - }, - "customDataFilters": { - "items": { - "$ref": "#/definitions/ClinicalDataFilter" - }, - "type": "array" - }, - "geneFilters": { - "items": { - "$ref": "#/definitions/GeneFilter" - }, - "type": "array" - }, - "genericAssayDataFilters": { - "items": { - "$ref": "#/definitions/GenericAssayDataFilter" - }, - "type": "array" - }, - "genomicDataFilters": { - "items": { - "$ref": "#/definitions/GenomicDataFilter" - }, - "type": "array" - }, - "genomicProfiles": { - "items": { - "items": { - "type": "string" - }, - "type": "array" - }, - "type": "array" - }, - "mutationDataFilters": { - "items": { - "$ref": "#/definitions/MutationDataFilter" - }, - "type": "array" - }, - "patientTreatmentFilters": { - "$ref": "#/definitions/AndedPatientTreatmentFilters" - }, - "patientTreatmentGroupFilters": { - "$ref": "#/definitions/AndedPatientTreatmentFilters" - }, - "patientTreatmentTargetFilters": { - "$ref": "#/definitions/AndedPatientTreatmentFilters" - }, - "sampleIdentifiers": { - "items": { - "$ref": "#/definitions/SampleIdentifier" - }, - "maxItems": 2147483647, - "minItems": 1, - "type": "array" - }, - "sampleTreatmentFilters": { - "$ref": "#/definitions/AndedSampleTreatmentFilters" - }, - "sampleTreatmentGroupFilters": { - "$ref": "#/definitions/AndedSampleTreatmentFilters" - }, - "sampleTreatmentTargetFilters": { - "$ref": "#/definitions/AndedSampleTreatmentFilters" - }, - "structuralVariantFilters": { - "items": { - "$ref": "#/definitions/StudyViewStructuralVariantFilter" - }, - "type": "array" - }, - "studyIds": { - "items": { - "maxLength": 2147483647, - "minLength": 1, - "type": "string" - }, - "maxItems": 2147483647, - "minItems": 1, - "type": "array" - } - }, - "type": "object" - }, - "StudyViewStructuralVariantFilter": { - "properties": { - "molecularProfileIds": { - "items": { - "type": "string" - }, - "type": "array", - "uniqueItems": true - }, - "structVarQueries": { - "items": { - "items": { - "$ref": "#/definitions/StructuralVariantFilterQuery" - }, - "type": "array" - }, - "type": "array" - } - }, - "type": "object" - }, "TypeOfCancer": { "properties": { "cancerTypeId": { diff --git a/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPI.ts b/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPI.ts index 63f16a5bdb1..a58d3829e47 100644 --- a/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPI.ts +++ b/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPI.ts @@ -18,38 +18,6 @@ export type AlleleSpecificCopyNumber = { 'totalCopyNumber': number -}; -export type AlterationFilter = { - 'copyNumberAlterationEventTypes': {} - - 'includeDriver': boolean - - 'includeGermline': boolean - - 'includeSomatic': boolean - - 'includeUnknownOncogenicity': boolean - - 'includeUnknownStatus': boolean - - 'includeUnknownTier': boolean - - 'includeVUS': boolean - - 'mutationEventTypes': {} - - 'structuralVariants': boolean - - 'tiersBooleanMap': {} - -}; -export type AndedPatientTreatmentFilters = { - 'filters': Array < OredPatientTreatmentFilters > - -}; -export type AndedSampleTreatmentFilters = { - 'filters': Array < OredSampleTreatmentFilters > - }; export type CancerStudy = { 'allSampleCount': number @@ -148,12 +116,6 @@ export type ClinicalData = { 'value': string -}; -export type ClinicalDataFilter = { - 'attributeId': string - - 'values': Array < DataFilterValue > - }; export type ClinicalDataIdentifier = { 'entityId': string @@ -172,16 +134,6 @@ export type ClinicalDataSingleStudyFilter = { 'ids': Array < string > -}; -export type ClinicalEventSample = { - 'patientId': string - - 'sampleId': string - - 'studyId': string - - 'timeTaken': number - }; export type CopyNumberSeg = { 'chromosome': string @@ -204,18 +156,6 @@ export type CopyNumberSeg = { 'uniqueSampleKey': string -}; -export type DataFilter = { - 'values': Array < DataFilterValue > - -}; -export type DataFilterValue = { - 'end': number - - 'start': number - - 'value': string - }; export type DiscreteCopyNumberData = { 'alteration': number @@ -264,37 +204,6 @@ export type Gene = { 'type': string -}; -export type GeneFilter = { - 'geneQueries': Array < Array < GeneFilterQuery > - > - - 'molecularProfileIds': Array < string > - -}; -export type GeneFilterQuery = { - 'alterations': Array < "AMP" | "GAIN" | "DIPLOID" | "HETLOSS" | "HOMDEL" > - - 'entrezGeneId': number - - 'hugoGeneSymbol': string - - 'includeDriver': boolean - - 'includeGermline': boolean - - 'includeSomatic': boolean - - 'includeUnknownOncogenicity': boolean - - 'includeUnknownStatus': boolean - - 'includeUnknownTier': boolean - - 'includeVUS': boolean - - 'tiersBooleanMap': {} - }; export type GenePanel = { 'description': string @@ -359,14 +268,6 @@ export type GenericAssayData = { 'value': string -}; -export type GenericAssayDataFilter = { - 'profileType': string - - 'stableId': string - - 'values': Array < DataFilterValue > - }; export type GenericAssayDataMultipleStudyFilter = { 'genericAssayStableIds': Array < string > @@ -397,14 +298,6 @@ export type GenericAssayMetaFilter = { 'molecularProfileIds': Array < string > -}; -export type GenomicDataFilter = { - 'hugoGeneSymbol': string - - 'profileType': string - - 'values': Array < DataFilterValue > - }; export type Info = { 'dbVersion': string @@ -551,17 +444,6 @@ export type Mutation = { 'variantType': string -}; -export type MutationDataFilter = { - 'categorization': "MUTATED" | "MUTATION_TYPE" - - 'hugoGeneSymbol': string - - 'profileType': string - - 'values': Array < Array < DataFilterValue > - > - }; export type MutationFilter = { 'entrezGeneIds': Array < number > @@ -598,14 +480,6 @@ export type NumericGeneMolecularData = { 'value': number -}; -export type OredPatientTreatmentFilters = { - 'filters': Array < PatientTreatmentFilter > - -}; -export type OredSampleTreatmentFilters = { - 'filters': Array < SampleTreatmentFilter > - }; export type Patient = { 'cancerStudy': CancerStudy @@ -630,18 +504,6 @@ export type PatientIdentifier = { 'studyId': string -}; -export type PatientTreatmentFilter = { - 'treatment': string - -}; -export type PatientTreatmentRow = { - 'count': number - - 'samples': Array < ClinicalEventSample > - - 'treatment': string - }; export type Sample = { 'copyNumberSegmentPresent': boolean @@ -696,105 +558,10 @@ export type SampleMolecularIdentifier = { 'sampleId': string -}; -export type SampleTreatmentFilter = { - 'time': "Pre" | "Post" - - 'treatment': string - -}; -export type SampleTreatmentRow = { - 'count': number - - 'samples': Array < ClinicalEventSample > - - 'time': "Pre" | "Post" - - 'treatment': string - }; export type ServerStatusMessage = { 'status': string -}; -export type StructuralVariantFilterQuery = { - 'gene1Query': StructuralVariantGeneSubQuery - - 'gene2Query': StructuralVariantGeneSubQuery - - 'includeDriver': boolean - - 'includeGermline': boolean - - 'includeSomatic': boolean - - 'includeUnknownOncogenicity': boolean - - 'includeUnknownStatus': boolean - - 'includeUnknownTier': boolean - - 'includeVUS': boolean - - 'tiersBooleanMap': {} - -}; -export type StructuralVariantGeneSubQuery = { - 'entrezId': number - - 'hugoSymbol': string - - 'specialValue': "ANY_GENE" | "NO_GENE" - -}; -export type StudyViewFilter = { - 'alterationFilter': AlterationFilter - - 'caseLists': Array < Array < string > - > - - 'clinicalDataFilters': Array < ClinicalDataFilter > - - 'clinicalEventFilters': Array < DataFilter > - - 'customDataFilters': Array < ClinicalDataFilter > - - 'geneFilters': Array < GeneFilter > - - 'genericAssayDataFilters': Array < GenericAssayDataFilter > - - 'genomicDataFilters': Array < GenomicDataFilter > - - 'genomicProfiles': Array < Array < string > - > - - 'mutationDataFilters': Array < MutationDataFilter > - - 'patientTreatmentFilters': AndedPatientTreatmentFilters - - 'patientTreatmentGroupFilters': AndedPatientTreatmentFilters - - 'patientTreatmentTargetFilters': AndedPatientTreatmentFilters - - 'sampleIdentifiers': Array < SampleIdentifier > - - 'sampleTreatmentFilters': AndedSampleTreatmentFilters - - 'sampleTreatmentGroupFilters': AndedSampleTreatmentFilters - - 'sampleTreatmentTargetFilters': AndedSampleTreatmentFilters - - 'structuralVariantFilters': Array < StudyViewStructuralVariantFilter > - - 'studyIds': Array < string > - -}; -export type StudyViewStructuralVariantFilter = { - 'molecularProfileIds': Array < string > - - 'structVarQueries': Array < Array < StructuralVariantFilterQuery > - > - }; export type TypeOfCancer = { 'cancerTypeId': string @@ -7457,348 +7224,4 @@ export default class CBioPortalAPI { return response.body; }); }; - getContainsTreatmentDataUsingPOSTURL(parameters: { - 'tier' ? : "Agent" | "AgentClass" | "AgentTarget", - 'studyIds': Array < string > , - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/api/treatments/display-patient'; - if (parameters['tier'] !== undefined) { - queryParameters['tier'] = parameters['tier']; - } - - if (parameters.$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('&')) : ''); - }; - - /** - * Should patient level treatments be displayed - * @method - * @name CBioPortalAPI#getContainsTreatmentDataUsingPOST - * @param {string} tier - 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 {} studyIds - A web service for supplying JSON formatted data to cBioPortal clients. Please note that this API is currently in beta and subject to change. - */ - getContainsTreatmentDataUsingPOSTWithHttpInfo(parameters: { - 'tier' ? : "Agent" | "AgentClass" | "AgentTarget", - 'studyIds': Array < string > , - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/api/treatments/display-patient'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - if (parameters['tier'] !== undefined) { - queryParameters['tier'] = parameters['tier']; - } - - if (parameters['studyIds'] !== undefined) { - body = parameters['studyIds']; - } - - if (parameters['studyIds'] === undefined) { - reject(new Error('Missing required parameter: studyIds')); - return; - } - - if (parameters.$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); - - }); - }; - - /** - * Should patient level treatments be displayed - * @method - * @name CBioPortalAPI#getContainsTreatmentDataUsingPOST - * @param {string} tier - 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 {} studyIds - A web service for supplying JSON formatted data to cBioPortal clients. Please note that this API is currently in beta and subject to change. - */ - getContainsTreatmentDataUsingPOST(parameters: { - 'tier' ? : "Agent" | "AgentClass" | "AgentTarget", - 'studyIds': Array < string > , - $queryParameters ? : any, - $domain ? : string - }): Promise < boolean > { - return this.getContainsTreatmentDataUsingPOSTWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - getContainsSampleTreatmentDataUsingPOSTURL(parameters: { - 'tier' ? : "Agent" | "AgentClass" | "AgentTarget", - 'studyIds': Array < string > , - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/api/treatments/display-sample'; - if (parameters['tier'] !== undefined) { - queryParameters['tier'] = parameters['tier']; - } - - if (parameters.$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('&')) : ''); - }; - - /** - * Should sample level treatments be displayed - * @method - * @name CBioPortalAPI#getContainsSampleTreatmentDataUsingPOST - * @param {string} tier - 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 {} studyIds - A web service for supplying JSON formatted data to cBioPortal clients. Please note that this API is currently in beta and subject to change. - */ - getContainsSampleTreatmentDataUsingPOSTWithHttpInfo(parameters: { - 'tier' ? : "Agent" | "AgentClass" | "AgentTarget", - 'studyIds': Array < string > , - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/api/treatments/display-sample'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - if (parameters['tier'] !== undefined) { - queryParameters['tier'] = parameters['tier']; - } - - if (parameters['studyIds'] !== undefined) { - body = parameters['studyIds']; - } - - if (parameters['studyIds'] === undefined) { - reject(new Error('Missing required parameter: studyIds')); - return; - } - - if (parameters.$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); - - }); - }; - - /** - * Should sample level treatments be displayed - * @method - * @name CBioPortalAPI#getContainsSampleTreatmentDataUsingPOST - * @param {string} tier - 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 {} studyIds - A web service for supplying JSON formatted data to cBioPortal clients. Please note that this API is currently in beta and subject to change. - */ - getContainsSampleTreatmentDataUsingPOST(parameters: { - 'tier' ? : "Agent" | "AgentClass" | "AgentTarget", - 'studyIds': Array < string > , - $queryParameters ? : any, - $domain ? : string - }): Promise < boolean > { - return this.getContainsSampleTreatmentDataUsingPOSTWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - getAllPatientTreatmentsUsingPOSTURL(parameters: { - 'tier' ? : "Agent" | "AgentClass" | "AgentTarget", - 'studyViewFilter' ? : StudyViewFilter, - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/api/treatments/patient'; - if (parameters['tier'] !== undefined) { - queryParameters['tier'] = parameters['tier']; - } - - if (parameters.$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 all patient level treatments - * @method - * @name CBioPortalAPI#getAllPatientTreatmentsUsingPOST - * @param {string} tier - 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 {} studyViewFilter - A web service for supplying JSON formatted data to cBioPortal clients. Please note that this API is currently in beta and subject to change. - */ - getAllPatientTreatmentsUsingPOSTWithHttpInfo(parameters: { - 'tier' ? : "Agent" | "AgentClass" | "AgentTarget", - 'studyViewFilter' ? : StudyViewFilter, - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/api/treatments/patient'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - if (parameters['tier'] !== undefined) { - queryParameters['tier'] = parameters['tier']; - } - - if (parameters['studyViewFilter'] !== undefined) { - body = parameters['studyViewFilter']; - } - - if (parameters.$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); - - }); - }; - - /** - * Get all patient level treatments - * @method - * @name CBioPortalAPI#getAllPatientTreatmentsUsingPOST - * @param {string} tier - 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 {} studyViewFilter - A web service for supplying JSON formatted data to cBioPortal clients. Please note that this API is currently in beta and subject to change. - */ - getAllPatientTreatmentsUsingPOST(parameters: { - 'tier' ? : "Agent" | "AgentClass" | "AgentTarget", - 'studyViewFilter' ? : StudyViewFilter, - $queryParameters ? : any, - $domain ? : string - }): Promise < Array < PatientTreatmentRow > - > { - return this.getAllPatientTreatmentsUsingPOSTWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - getAllSampleTreatmentsUsingPOSTURL(parameters: { - 'tier' ? : "Agent" | "AgentClass" | "AgentTarget", - 'studyViewFilter' ? : StudyViewFilter, - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/api/treatments/sample'; - if (parameters['tier'] !== undefined) { - queryParameters['tier'] = parameters['tier']; - } - - if (parameters.$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 all sample level treatments - * @method - * @name CBioPortalAPI#getAllSampleTreatmentsUsingPOST - * @param {string} tier - 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 {} studyViewFilter - A web service for supplying JSON formatted data to cBioPortal clients. Please note that this API is currently in beta and subject to change. - */ - getAllSampleTreatmentsUsingPOSTWithHttpInfo(parameters: { - 'tier' ? : "Agent" | "AgentClass" | "AgentTarget", - 'studyViewFilter' ? : StudyViewFilter, - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/api/treatments/sample'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - if (parameters['tier'] !== undefined) { - queryParameters['tier'] = parameters['tier']; - } - - if (parameters['studyViewFilter'] !== undefined) { - body = parameters['studyViewFilter']; - } - - if (parameters.$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); - - }); - }; - - /** - * Get all sample level treatments - * @method - * @name CBioPortalAPI#getAllSampleTreatmentsUsingPOST - * @param {string} tier - 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 {} studyViewFilter - A web service for supplying JSON formatted data to cBioPortal clients. Please note that this API is currently in beta and subject to change. - */ - getAllSampleTreatmentsUsingPOST(parameters: { - 'tier' ? : "Agent" | "AgentClass" | "AgentTarget", - 'studyViewFilter' ? : StudyViewFilter, - $queryParameters ? : any, - $domain ? : string - }): Promise < Array < SampleTreatmentRow > - > { - return this.getAllSampleTreatmentsUsingPOSTWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; } \ No newline at end of file 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 cbdd0fbf7fc..a8616dca66f 100644 --- a/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal-docs.json +++ b/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal-docs.json @@ -3239,6 +3239,208 @@ "description": "Get the last time each static resource was updated", "operationId": "getAllTimestampsUsingGET" } + }, + "/api/treatments/display-patient": { + "post": { + "consumes": [ + "application/json" + ], + "produces": [ + "application/json" + ], + "parameters": [ + { + "default": "Agent", + "enum": [ + "Agent", + "AgentClass", + "AgentTarget" + ], + "in": "query", + "name": "tier", + "required": false, + "type": "string" + }, + { + "in": "body", + "name": "studyIds", + "required": true, + "schema": { + "description": "List of Study IDs", + "items": { + "maxLength": 10000000, + "minLength": 1, + "type": "string" + }, + "maxItems": 10000000, + "minItems": 1, + "type": "array", + "uniqueItems": true + } + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "boolean" + } + } + }, + "tags": [ + "Treatments" + ], + "description": "Should patient level treatments be displayed", + "operationId": "getContainsTreatmentDataUsingPOST" + } + }, + "/api/treatments/display-sample": { + "post": { + "consumes": [ + "application/json" + ], + "produces": [ + "application/json" + ], + "parameters": [ + { + "default": "Agent", + "enum": [ + "Agent", + "AgentClass", + "AgentTarget" + ], + "in": "query", + "name": "tier", + "required": false, + "type": "string" + }, + { + "in": "body", + "name": "studyIds", + "required": true, + "schema": { + "description": "List of Study IDs", + "items": { + "maxLength": 10000000, + "minLength": 1, + "type": "string" + }, + "maxItems": 10000000, + "minItems": 1, + "type": "array", + "uniqueItems": true + } + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "type": "boolean" + } + } + }, + "tags": [ + "Treatments" + ], + "description": "Should sample level treatments be displayed", + "operationId": "getContainsSampleTreatmentDataUsingPOST" + } + }, + "/api/treatments/patient": { + "post": { + "consumes": [ + "application/json" + ], + "produces": [ + "application/json" + ], + "parameters": [ + { + "default": "Agent", + "enum": [ + "Agent", + "AgentClass", + "AgentTarget" + ], + "in": "query", + "name": "tier", + "required": false, + "type": "string" + }, + { + "in": "body", + "name": "studyViewFilter", + "schema": { + "$ref": "#/definitions/StudyViewFilter" + } + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "items": { + "$ref": "#/definitions/PatientTreatmentRow" + }, + "type": "array" + } + } + }, + "tags": [ + "Treatments" + ], + "description": "Get all patient level treatments", + "operationId": "getAllPatientTreatmentsUsingPOST" + } + }, + "/api/treatments/sample": { + "post": { + "consumes": [ + "application/json" + ], + "produces": [ + "application/json" + ], + "parameters": [ + { + "default": "Agent", + "enum": [ + "Agent", + "AgentClass", + "AgentTarget" + ], + "in": "query", + "name": "tier", + "required": false, + "type": "string" + }, + { + "in": "body", + "name": "studyViewFilter", + "schema": { + "$ref": "#/definitions/StudyViewFilter" + } + } + ], + "responses": { + "200": { + "description": "OK", + "schema": { + "items": { + "$ref": "#/definitions/SampleTreatmentRow" + }, + "type": "array" + } + } + }, + "tags": [ + "Treatments" + ], + "description": "Get all sample level treatments", + "operationId": "getAllSampleTreatmentsUsingPOST" + } } }, "definitions": { @@ -3771,6 +3973,24 @@ ], "type": "object" }, + "ClinicalEventSample": { + "properties": { + "patientId": { + "type": "string" + }, + "sampleId": { + "type": "string" + }, + "studyId": { + "type": "string" + }, + "timeTaken": { + "format": "int32", + "type": "integer" + } + }, + "type": "object" + }, "ClinicalEventTypeCount": { "properties": { "count": { @@ -5252,6 +5472,25 @@ }, "type": "object" }, + "PatientTreatmentRow": { + "properties": { + "count": { + "format": "int32", + "type": "integer" + }, + "samples": { + "items": { + "$ref": "#/definitions/ClinicalEventSample" + }, + "type": "array", + "uniqueItems": true + }, + "treatment": { + "type": "string" + } + }, + "type": "object" + }, "ReferenceGenomeGene": { "properties": { "chromosome": { @@ -5451,6 +5690,32 @@ }, "type": "object" }, + "SampleTreatmentRow": { + "properties": { + "count": { + "format": "int32", + "type": "integer" + }, + "samples": { + "items": { + "$ref": "#/definitions/ClinicalEventSample" + }, + "type": "array", + "uniqueItems": true + }, + "time": { + "enum": [ + "Pre", + "Post" + ], + "type": "string" + }, + "treatment": { + "type": "string" + } + }, + "type": "object" + }, "StructuralVariant": { "properties": { "annotation": { diff --git a/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal.ts b/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal.ts index 43e68255e06..02610206a86 100644 --- a/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal.ts +++ b/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal.ts @@ -244,6 +244,16 @@ export type ClinicalEventData = { 'value': string +}; +export type ClinicalEventSample = { + 'patientId': string + + 'sampleId': string + + 'studyId': string + + 'timeTaken': number + }; export type ClinicalEventTypeCount = { 'count': number @@ -890,6 +900,14 @@ export type OredSampleTreatmentFilters = { export type PatientTreatmentFilter = { 'treatment': string +}; +export type PatientTreatmentRow = { + 'count': number + + 'samples': Array < ClinicalEventSample > + + 'treatment': string + }; export type ReferenceGenomeGene = { 'chromosome': string @@ -980,6 +998,16 @@ export type SampleTreatmentFilter = { 'treatment': string +}; +export type SampleTreatmentRow = { + 'count': number + + 'samples': Array < ClinicalEventSample > + + 'time': "Pre" | "Post" + + 'treatment': string + }; export type StructuralVariant = { 'annotation': string @@ -7347,4 +7375,348 @@ export default class CBioPortalAPIInternal { return response.body; }); }; + getContainsTreatmentDataUsingPOSTURL(parameters: { + 'tier' ? : "Agent" | "AgentClass" | "AgentTarget", + 'studyIds': Array < string > , + $queryParameters ? : any + }): string { + let queryParameters: any = {}; + let path = '/api/treatments/display-patient'; + if (parameters['tier'] !== undefined) { + queryParameters['tier'] = parameters['tier']; + } + + if (parameters.$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('&')) : ''); + }; + + /** + * Should patient level treatments be displayed + * @method + * @name CBioPortalAPIInternal#getContainsTreatmentDataUsingPOST + * @param {string} tier - 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 {} studyIds - A web service for supplying JSON formatted data to cBioPortal clients. Please note that this API is currently in beta and subject to change. + */ + getContainsTreatmentDataUsingPOSTWithHttpInfo(parameters: { + 'tier' ? : "Agent" | "AgentClass" | "AgentTarget", + 'studyIds': Array < string > , + $queryParameters ? : any, + $domain ? : string + }): Promise < request.Response > { + const domain = parameters.$domain ? parameters.$domain : this.domain; + const errorHandlers = this.errorHandlers; + const request = this.request; + let path = '/api/treatments/display-patient'; + let body: any; + let queryParameters: any = {}; + let headers: any = {}; + let form: any = {}; + return new Promise(function(resolve, reject) { + headers['Accept'] = 'application/json'; + headers['Content-Type'] = 'application/json'; + + if (parameters['tier'] !== undefined) { + queryParameters['tier'] = parameters['tier']; + } + + if (parameters['studyIds'] !== undefined) { + body = parameters['studyIds']; + } + + if (parameters['studyIds'] === undefined) { + reject(new Error('Missing required parameter: studyIds')); + return; + } + + if (parameters.$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); + + }); + }; + + /** + * Should patient level treatments be displayed + * @method + * @name CBioPortalAPIInternal#getContainsTreatmentDataUsingPOST + * @param {string} tier - 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 {} studyIds - A web service for supplying JSON formatted data to cBioPortal clients. Please note that this API is currently in beta and subject to change. + */ + getContainsTreatmentDataUsingPOST(parameters: { + 'tier' ? : "Agent" | "AgentClass" | "AgentTarget", + 'studyIds': Array < string > , + $queryParameters ? : any, + $domain ? : string + }): Promise < boolean > { + return this.getContainsTreatmentDataUsingPOSTWithHttpInfo(parameters).then(function(response: request.Response) { + return response.body; + }); + }; + getContainsSampleTreatmentDataUsingPOSTURL(parameters: { + 'tier' ? : "Agent" | "AgentClass" | "AgentTarget", + 'studyIds': Array < string > , + $queryParameters ? : any + }): string { + let queryParameters: any = {}; + let path = '/api/treatments/display-sample'; + if (parameters['tier'] !== undefined) { + queryParameters['tier'] = parameters['tier']; + } + + if (parameters.$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('&')) : ''); + }; + + /** + * Should sample level treatments be displayed + * @method + * @name CBioPortalAPIInternal#getContainsSampleTreatmentDataUsingPOST + * @param {string} tier - 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 {} studyIds - A web service for supplying JSON formatted data to cBioPortal clients. Please note that this API is currently in beta and subject to change. + */ + getContainsSampleTreatmentDataUsingPOSTWithHttpInfo(parameters: { + 'tier' ? : "Agent" | "AgentClass" | "AgentTarget", + 'studyIds': Array < string > , + $queryParameters ? : any, + $domain ? : string + }): Promise < request.Response > { + const domain = parameters.$domain ? parameters.$domain : this.domain; + const errorHandlers = this.errorHandlers; + const request = this.request; + let path = '/api/treatments/display-sample'; + let body: any; + let queryParameters: any = {}; + let headers: any = {}; + let form: any = {}; + return new Promise(function(resolve, reject) { + headers['Accept'] = 'application/json'; + headers['Content-Type'] = 'application/json'; + + if (parameters['tier'] !== undefined) { + queryParameters['tier'] = parameters['tier']; + } + + if (parameters['studyIds'] !== undefined) { + body = parameters['studyIds']; + } + + if (parameters['studyIds'] === undefined) { + reject(new Error('Missing required parameter: studyIds')); + return; + } + + if (parameters.$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); + + }); + }; + + /** + * Should sample level treatments be displayed + * @method + * @name CBioPortalAPIInternal#getContainsSampleTreatmentDataUsingPOST + * @param {string} tier - 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 {} studyIds - A web service for supplying JSON formatted data to cBioPortal clients. Please note that this API is currently in beta and subject to change. + */ + getContainsSampleTreatmentDataUsingPOST(parameters: { + 'tier' ? : "Agent" | "AgentClass" | "AgentTarget", + 'studyIds': Array < string > , + $queryParameters ? : any, + $domain ? : string + }): Promise < boolean > { + return this.getContainsSampleTreatmentDataUsingPOSTWithHttpInfo(parameters).then(function(response: request.Response) { + return response.body; + }); + }; + getAllPatientTreatmentsUsingPOSTURL(parameters: { + 'tier' ? : "Agent" | "AgentClass" | "AgentTarget", + 'studyViewFilter' ? : StudyViewFilter, + $queryParameters ? : any + }): string { + let queryParameters: any = {}; + let path = '/api/treatments/patient'; + if (parameters['tier'] !== undefined) { + queryParameters['tier'] = parameters['tier']; + } + + if (parameters.$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 all patient level treatments + * @method + * @name CBioPortalAPIInternal#getAllPatientTreatmentsUsingPOST + * @param {string} tier - 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 {} studyViewFilter - A web service for supplying JSON formatted data to cBioPortal clients. Please note that this API is currently in beta and subject to change. + */ + getAllPatientTreatmentsUsingPOSTWithHttpInfo(parameters: { + 'tier' ? : "Agent" | "AgentClass" | "AgentTarget", + 'studyViewFilter' ? : StudyViewFilter, + $queryParameters ? : any, + $domain ? : string + }): Promise < request.Response > { + const domain = parameters.$domain ? parameters.$domain : this.domain; + const errorHandlers = this.errorHandlers; + const request = this.request; + let path = '/api/treatments/patient'; + let body: any; + let queryParameters: any = {}; + let headers: any = {}; + let form: any = {}; + return new Promise(function(resolve, reject) { + headers['Accept'] = 'application/json'; + headers['Content-Type'] = 'application/json'; + + if (parameters['tier'] !== undefined) { + queryParameters['tier'] = parameters['tier']; + } + + if (parameters['studyViewFilter'] !== undefined) { + body = parameters['studyViewFilter']; + } + + if (parameters.$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); + + }); + }; + + /** + * Get all patient level treatments + * @method + * @name CBioPortalAPIInternal#getAllPatientTreatmentsUsingPOST + * @param {string} tier - 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 {} studyViewFilter - A web service for supplying JSON formatted data to cBioPortal clients. Please note that this API is currently in beta and subject to change. + */ + getAllPatientTreatmentsUsingPOST(parameters: { + 'tier' ? : "Agent" | "AgentClass" | "AgentTarget", + 'studyViewFilter' ? : StudyViewFilter, + $queryParameters ? : any, + $domain ? : string + }): Promise < Array < PatientTreatmentRow > + > { + return this.getAllPatientTreatmentsUsingPOSTWithHttpInfo(parameters).then(function(response: request.Response) { + return response.body; + }); + }; + getAllSampleTreatmentsUsingPOSTURL(parameters: { + 'tier' ? : "Agent" | "AgentClass" | "AgentTarget", + 'studyViewFilter' ? : StudyViewFilter, + $queryParameters ? : any + }): string { + let queryParameters: any = {}; + let path = '/api/treatments/sample'; + if (parameters['tier'] !== undefined) { + queryParameters['tier'] = parameters['tier']; + } + + if (parameters.$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 all sample level treatments + * @method + * @name CBioPortalAPIInternal#getAllSampleTreatmentsUsingPOST + * @param {string} tier - 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 {} studyViewFilter - A web service for supplying JSON formatted data to cBioPortal clients. Please note that this API is currently in beta and subject to change. + */ + getAllSampleTreatmentsUsingPOSTWithHttpInfo(parameters: { + 'tier' ? : "Agent" | "AgentClass" | "AgentTarget", + 'studyViewFilter' ? : StudyViewFilter, + $queryParameters ? : any, + $domain ? : string + }): Promise < request.Response > { + const domain = parameters.$domain ? parameters.$domain : this.domain; + const errorHandlers = this.errorHandlers; + const request = this.request; + let path = '/api/treatments/sample'; + let body: any; + let queryParameters: any = {}; + let headers: any = {}; + let form: any = {}; + return new Promise(function(resolve, reject) { + headers['Accept'] = 'application/json'; + headers['Content-Type'] = 'application/json'; + + if (parameters['tier'] !== undefined) { + queryParameters['tier'] = parameters['tier']; + } + + if (parameters['studyViewFilter'] !== undefined) { + body = parameters['studyViewFilter']; + } + + if (parameters.$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); + + }); + }; + + /** + * Get all sample level treatments + * @method + * @name CBioPortalAPIInternal#getAllSampleTreatmentsUsingPOST + * @param {string} tier - 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 {} studyViewFilter - A web service for supplying JSON formatted data to cBioPortal clients. Please note that this API is currently in beta and subject to change. + */ + getAllSampleTreatmentsUsingPOST(parameters: { + 'tier' ? : "Agent" | "AgentClass" | "AgentTarget", + 'studyViewFilter' ? : StudyViewFilter, + $queryParameters ? : any, + $domain ? : string + }): Promise < Array < SampleTreatmentRow > + > { + return this.getAllSampleTreatmentsUsingPOSTWithHttpInfo(parameters).then(function(response: request.Response) { + return response.body; + }); + }; } \ No newline at end of file diff --git a/packages/cbioportal-ts-api-client/src/index.tsx b/packages/cbioportal-ts-api-client/src/index.tsx index 304c48e8295..5965c0a825d 100644 --- a/packages/cbioportal-ts-api-client/src/index.tsx +++ b/packages/cbioportal-ts-api-client/src/index.tsx @@ -77,5 +77,20 @@ export { StructuralVariantFilter, StructuralVariantQuery, StructuralVariantGeneSubQuery, + StructuralVariantFilterQuery, + GeneFilterQuery, + AndedSampleTreatmentFilters, + AndedPatientTreatmentFilters, + DataFilter, + OredPatientTreatmentFilters, + OredSampleTreatmentFilters, + StudyViewStructuralVariantFilter, + SampleTreatmentRow, + SampleTreatmentFilter, + PatientTreatmentFilter, + PatientTreatmentRow, + MutationDataFilter, + GenericAssayDataFilter, + AlterationFilter, default as CBioPortalAPIInternal, } from './generated/CBioPortalAPIInternal'; diff --git a/src/pages/studyView/StudyViewPageStore.ts b/src/pages/studyView/StudyViewPageStore.ts index 7ccfe01d7bf..5e9aa544412 100644 --- a/src/pages/studyView/StudyViewPageStore.ts +++ b/src/pages/studyView/StudyViewPageStore.ts @@ -10507,7 +10507,7 @@ export class StudyViewPageStore await: () => [this.shouldDisplaySampleTreatments], invoke: () => { if (this.shouldDisplaySampleTreatments.result) { - return defaultClient.getAllSampleTreatmentsUsingPOST({ + return internalClient.getAllSampleTreatmentsUsingPOST({ studyViewFilter: this.filters, }); } @@ -10518,7 +10518,7 @@ export class StudyViewPageStore public readonly shouldDisplayPatientTreatments = remoteData({ await: () => [this.queriedPhysicalStudyIds], invoke: () => { - return defaultClient.getContainsTreatmentDataUsingPOST({ + return internalClient.getContainsTreatmentDataUsingPOST({ studyIds: toJS(this.queriedPhysicalStudyIds.result), }); }, @@ -10527,7 +10527,7 @@ export class StudyViewPageStore public readonly shouldDisplaySampleTreatments = remoteData({ await: () => [this.queriedPhysicalStudyIds], invoke: () => { - return defaultClient.getContainsSampleTreatmentDataUsingPOST({ + return internalClient.getContainsSampleTreatmentDataUsingPOST({ studyIds: toJS(this.queriedPhysicalStudyIds.result), }); }, @@ -10539,7 +10539,7 @@ export class StudyViewPageStore await: () => [this.shouldDisplayPatientTreatments], invoke: () => { if (this.shouldDisplayPatientTreatments.result) { - return defaultClient.getAllPatientTreatmentsUsingPOST({ + return internalClient.getAllPatientTreatmentsUsingPOST({ studyViewFilter: this.filters, }); } @@ -10551,7 +10551,7 @@ export class StudyViewPageStore await: () => [this.shouldDisplaySampleTreatmentGroups], invoke: () => { if (this.shouldDisplaySampleTreatmentGroups.result) { - return defaultClient.getAllSampleTreatmentsUsingPOST({ + return internalClient.getAllSampleTreatmentsUsingPOST({ studyViewFilter: this.filters, tier: 'AgentClass', }); @@ -10566,7 +10566,7 @@ export class StudyViewPageStore if (!getServerConfig().enable_treatment_groups) { return Promise.resolve(false); } - return defaultClient.getContainsTreatmentDataUsingPOST({ + return internalClient.getContainsTreatmentDataUsingPOST({ studyIds: toJS(this.queriedPhysicalStudyIds.result), tier: 'AgentClass', }); @@ -10579,7 +10579,7 @@ export class StudyViewPageStore if (!getServerConfig().enable_treatment_groups) { return Promise.resolve(false); } - return defaultClient.getContainsSampleTreatmentDataUsingPOST({ + return internalClient.getContainsSampleTreatmentDataUsingPOST({ studyIds: toJS(this.queriedPhysicalStudyIds.result), tier: 'AgentClass', }); @@ -10592,7 +10592,7 @@ export class StudyViewPageStore await: () => [this.shouldDisplayPatientTreatmentGroups], invoke: () => { if (this.shouldDisplayPatientTreatmentGroups.result) { - return defaultClient.getAllPatientTreatmentsUsingPOST({ + return internalClient.getAllPatientTreatmentsUsingPOST({ studyViewFilter: this.filters, tier: 'AgentClass', }); @@ -10605,7 +10605,7 @@ export class StudyViewPageStore await: () => [this.shouldDisplaySampleTreatmentTarget], invoke: () => { if (this.shouldDisplaySampleTreatmentTarget.result) { - return defaultClient.getAllSampleTreatmentsUsingPOST({ + return internalClient.getAllSampleTreatmentsUsingPOST({ studyViewFilter: this.filters, tier: 'AgentTarget', }); @@ -10620,7 +10620,7 @@ export class StudyViewPageStore if (!getServerConfig().enable_treatment_groups) { return Promise.resolve(false); } - return defaultClient.getContainsTreatmentDataUsingPOST({ + return internalClient.getContainsTreatmentDataUsingPOST({ studyIds: toJS(this.queriedPhysicalStudyIds.result), tier: 'AgentTarget', }); @@ -10633,7 +10633,7 @@ export class StudyViewPageStore if (!getServerConfig().enable_treatment_groups) { return Promise.resolve(false); } - return defaultClient.getContainsSampleTreatmentDataUsingPOST({ + return internalClient.getContainsSampleTreatmentDataUsingPOST({ studyIds: toJS(this.queriedPhysicalStudyIds.result), tier: 'AgentTarget', }); @@ -10646,7 +10646,7 @@ export class StudyViewPageStore await: () => [this.shouldDisplayPatientTreatmentTarget], invoke: () => { if (this.shouldDisplayPatientTreatmentTarget.result) { - return defaultClient.getAllPatientTreatmentsUsingPOST({ + return internalClient.getAllPatientTreatmentsUsingPOST({ studyViewFilter: this.filters, tier: 'AgentTarget', });