diff --git a/end-to-end-test/local/screenshots/reference/add_custom_data_tab_should_have_numerical_and_categorical_selector_element_chrome_1600x1000.png b/end-to-end-test/local/screenshots/reference/add_custom_data_tab_should_have_numerical_and_categorical_selector_element_chrome_1600x1000.png index 4ef6109c7db..21e98a4f85e 100644 Binary files a/end-to-end-test/local/screenshots/reference/add_custom_data_tab_should_have_numerical_and_categorical_selector_element_chrome_1600x1000.png and b/end-to-end-test/local/screenshots/reference/add_custom_data_tab_should_have_numerical_and_categorical_selector_element_chrome_1600x1000.png differ diff --git a/end-to-end-test/local/screenshots/reference/breadcrumbs_are_editable_for_mutation_count_chart_element_chrome_1600x1000.png b/end-to-end-test/local/screenshots/reference/breadcrumbs_are_editable_for_mutation_count_chart_element_chrome_1600x1000.png index 6e01ebfb629..0dda25a3a62 100644 Binary files a/end-to-end-test/local/screenshots/reference/breadcrumbs_are_editable_for_mutation_count_chart_element_chrome_1600x1000.png and b/end-to-end-test/local/screenshots/reference/breadcrumbs_are_editable_for_mutation_count_chart_element_chrome_1600x1000.png differ diff --git a/end-to-end-test/local/screenshots/reference/show_binary_vs_mutation_count_plot_element_chrome_1600x1000.png b/end-to-end-test/local/screenshots/reference/show_binary_vs_mutation_count_plot_element_chrome_1600x1000.png index abf789ba0e4..d5e892c9f77 100644 Binary files a/end-to-end-test/local/screenshots/reference/show_binary_vs_mutation_count_plot_element_chrome_1600x1000.png and b/end-to-end-test/local/screenshots/reference/show_binary_vs_mutation_count_plot_element_chrome_1600x1000.png differ diff --git a/end-to-end-test/local/screenshots/reference/show_category_vs_mutation_count_plot_element_chrome_1600x1000.png b/end-to-end-test/local/screenshots/reference/show_category_vs_mutation_count_plot_element_chrome_1600x1000.png index abf789ba0e4..d5e892c9f77 100644 Binary files a/end-to-end-test/local/screenshots/reference/show_category_vs_mutation_count_plot_element_chrome_1600x1000.png and b/end-to-end-test/local/screenshots/reference/show_category_vs_mutation_count_plot_element_chrome_1600x1000.png differ diff --git a/end-to-end-test/local/screenshots/reference/shows_box_plot_for_numerical_data_element_chrome_1600x1000.png b/end-to-end-test/local/screenshots/reference/shows_box_plot_for_numerical_data_element_chrome_1600x1000.png index 4f6c960e3e5..07827352f79 100644 Binary files a/end-to-end-test/local/screenshots/reference/shows_box_plot_for_numerical_data_element_chrome_1600x1000.png and b/end-to-end-test/local/screenshots/reference/shows_box_plot_for_numerical_data_element_chrome_1600x1000.png differ diff --git a/end-to-end-test/local/specs/study-view-custom-bins.screenshot.spec.js b/end-to-end-test/local/specs/study-view-custom-bins.screenshot.spec.js index 2c7465f9fee..52d8eae85d8 100644 --- a/end-to-end-test/local/specs/study-view-custom-bins.screenshot.spec.js +++ b/end-to-end-test/local/specs/study-view-custom-bins.screenshot.spec.js @@ -35,6 +35,7 @@ describe('Custom Bins menu in study view chart header', function() { selectMenuOption('label=Median split'); clickUpdate(); $('body').moveTo(); + browser.pause(2000); const res = checkElementWithMouseDisabled(MUTATION_COUNT_CHART); assertScreenShotMatch(res); }); diff --git a/end-to-end-test/remote/specs/core/quickSearch.spec.js b/end-to-end-test/remote/specs/core/quickSearch.spec.js index d92eb08e254..ea38e00fcf5 100644 --- a/end-to-end-test/remote/specs/core/quickSearch.spec.js +++ b/end-to-end-test/remote/specs/core/quickSearch.spec.js @@ -55,7 +55,8 @@ describe('Quick Search', () => { }); it('should give results for genes', async () => { - await clickElement('strong=454 more genes (click to load 20 more)'); + //browser.debug(); + await clickElement('strong=458 more genes (click to load 20 more)'); await (await getElement('strong=ADAM12')).waitForExist(); await clickElement('strong=ADAM15'); await (await getElement('a=ADAM15')).waitForExist({ timeout: 60000 }); diff --git a/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal-docs.json b/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal-docs.json index 4b857f37010..31052fbd0ac 100644 --- a/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal-docs.json +++ b/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal-docs.json @@ -628,93 +628,6 @@ "operationId": "fetchCNAGenesUsingPOST" } }, - "/api/column-store/treatments/patient-counts/fetch": { - "post": { - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "default": "Agent", - "enum": [ - "Agent", - "AgentClass", - "AgentTarget" - ], - "in": "query", - "name": "tier", - "required": false, - "type": "string" - }, - { - "in": "body", - "name": "studyViewFilter", - "schema": { - "$ref": "#/definitions/StudyViewFilter" - } - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "$ref": "#/definitions/PatientTreatmentReport" - } - } - }, - "tags": [ - "study-view-column-store-controller" - ], - "description": "Get all patient level treatments", - "operationId": "fetchPatientTreatmentCountsUsingPOST" - } - }, - "/api/column-store/treatments/sample-counts/fetch": { - "post": { - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "default": "Agent", - "enum": [ - "Agent", - "AgentClass", - "AgentTarget" - ], - "in": "query", - "name": "tier", - "required": false, - "type": "string" - }, - { - "in": "body", - "name": "studyViewFilter", - "schema": { - "$ref": "#/definitions/StudyViewFilter" - } - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "$ref": "#/definitions/SampleTreatmentReport" - } - } - }, - "tags": [ - "study-view-column-store-controller" - ], - "operationId": "fetchSampleTreatmentCountsUsingPOST" - } - }, "/api/cosmic-counts/fetch": { "post": { "consumes": [ @@ -5791,18 +5704,6 @@ }, "type": "object" }, - "PatientTreatment": { - "properties": { - "count": { - "format": "int32", - "type": "integer" - }, - "treatment": { - "type": "string" - } - }, - "type": "object" - }, "PatientTreatmentFilter": { "properties": { "treatment": { @@ -5811,25 +5712,6 @@ }, "type": "object" }, - "PatientTreatmentReport": { - "properties": { - "patientTreatments": { - "items": { - "$ref": "#/definitions/PatientTreatment" - }, - "type": "array" - }, - "totalPatients": { - "format": "int32", - "type": "integer" - }, - "totalSamples": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, "PatientTreatmentRow": { "properties": { "count": { @@ -6048,21 +5930,6 @@ }, "type": "object" }, - "SampleTreatmentReport": { - "properties": { - "totalSamples": { - "format": "int32", - "type": "integer" - }, - "treatments": { - "items": { - "$ref": "#/definitions/SampleTreatmentRow" - }, - "type": "array" - } - }, - "type": "object" - }, "SampleTreatmentRow": { "properties": { "count": { diff --git a/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal.ts b/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal.ts index 7abb932cccc..7db0e3b4e3f 100644 --- a/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal.ts +++ b/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal.ts @@ -920,24 +920,10 @@ export type PatientIdentifier = { 'studyId': string -}; -export type PatientTreatment = { - 'count': number - - 'treatment': string - }; export type PatientTreatmentFilter = { 'treatment': string -}; -export type PatientTreatmentReport = { - 'patientTreatments': Array < PatientTreatment > - - 'totalPatients': number - - 'totalSamples': number - }; export type PatientTreatmentRow = { 'count': number @@ -1036,12 +1022,6 @@ export type SampleTreatmentFilter = { 'treatment': string -}; -export type SampleTreatmentReport = { - 'totalSamples': number - - 'treatments': Array < SampleTreatmentRow > - }; export type SampleTreatmentRow = { 'count': number @@ -2539,172 +2519,6 @@ export default class CBioPortalAPIInternal { return response.body; }); }; - fetchPatientTreatmentCountsUsingPOSTURL(parameters: { - 'tier' ? : "Agent" | "AgentClass" | "AgentTarget", - 'studyViewFilter' ? : StudyViewFilter, - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/api/column-store/treatments/patient-counts/fetch'; - if (parameters['tier'] !== undefined) { - queryParameters['tier'] = parameters['tier']; - } - - if (parameters.$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#fetchPatientTreatmentCountsUsingPOST - * @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. - */ - fetchPatientTreatmentCountsUsingPOSTWithHttpInfo(parameters: { - 'tier' ? : "Agent" | "AgentClass" | "AgentTarget", - 'studyViewFilter' ? : StudyViewFilter, - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/api/column-store/treatments/patient-counts/fetch'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - if (parameters['tier'] !== undefined) { - queryParameters['tier'] = parameters['tier']; - } - - if (parameters['studyViewFilter'] !== undefined) { - body = parameters['studyViewFilter']; - } - - if (parameters.$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#fetchPatientTreatmentCountsUsingPOST - * @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. - */ - fetchPatientTreatmentCountsUsingPOST(parameters: { - 'tier' ? : "Agent" | "AgentClass" | "AgentTarget", - 'studyViewFilter' ? : StudyViewFilter, - $queryParameters ? : any, - $domain ? : string - }): Promise < PatientTreatmentReport > { - return this.fetchPatientTreatmentCountsUsingPOSTWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - fetchSampleTreatmentCountsUsingPOSTURL(parameters: { - 'tier' ? : "Agent" | "AgentClass" | "AgentTarget", - 'studyViewFilter' ? : StudyViewFilter, - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/api/column-store/treatments/sample-counts/fetch'; - if (parameters['tier'] !== undefined) { - queryParameters['tier'] = parameters['tier']; - } - - if (parameters.$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('&')) : ''); - }; - - /** - * - * @method - * @name CBioPortalAPIInternal#fetchSampleTreatmentCountsUsingPOST - * @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. - */ - fetchSampleTreatmentCountsUsingPOSTWithHttpInfo(parameters: { - 'tier' ? : "Agent" | "AgentClass" | "AgentTarget", - 'studyViewFilter' ? : StudyViewFilter, - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/api/column-store/treatments/sample-counts/fetch'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - if (parameters['tier'] !== undefined) { - queryParameters['tier'] = parameters['tier']; - } - - if (parameters['studyViewFilter'] !== undefined) { - body = parameters['studyViewFilter']; - } - - if (parameters.$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); - - }); - }; - - /** - * - * @method - * @name CBioPortalAPIInternal#fetchSampleTreatmentCountsUsingPOST - * @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. - */ - fetchSampleTreatmentCountsUsingPOST(parameters: { - 'tier' ? : "Agent" | "AgentClass" | "AgentTarget", - 'studyViewFilter' ? : StudyViewFilter, - $queryParameters ? : any, - $domain ? : string - }): Promise < SampleTreatmentReport > { - return this.fetchSampleTreatmentCountsUsingPOSTWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; fetchCosmicCountsUsingPOSTURL(parameters: { 'keywords': Array < string > , $queryParameters ? : any diff --git a/packages/oncokb-ts-api-client/src/generated/OncoKbAPI-docs.json b/packages/oncokb-ts-api-client/src/generated/OncoKbAPI-docs.json index 312261803f0..4e79ae4d8dc 100644 --- a/packages/oncokb-ts-api-client/src/generated/OncoKbAPI-docs.json +++ b/packages/oncokb-ts-api-client/src/generated/OncoKbAPI-docs.json @@ -97,7 +97,7 @@ { "name": "evidenceType", "in": "query", - "description": "Evidence type to compute. This could help to improve the performance if you only look for sub-content. Example: ONCOGENIC. All available evidence type are GENE_SUMMARY, MUTATION_SUMMARY, TUMOR_TYPE_SUMMARY, PROGNOSTIC_SUMMARY, DIAGNOSTIC_SUMMARY, ONCOGENIC, MUTATION_EFFECT, PROGNOSTIC_IMPLICATION, DIAGNOSTIC_IMPLICATION, STANDARD_THERAPEUTIC_IMPLICATIONS_FOR_DRUG_SENSITIVITY, STANDARD_THERAPEUTIC_IMPLICATIONS_FOR_DRUG_RESISTANCE, INVESTIGATIONAL_THERAPEUTIC_IMPLICATIONS_DRUG_SENSITIVITY, INVESTIGATIONAL_THERAPEUTIC_IMPLICATIONS_DRUG_RESISTANCE. For multiple evidence types query, use ',' as separator.", + "description": "DEPRECATED. We do not recommend using this parameter and it will eventually be removed.", "required": false, "type": "string" } @@ -181,7 +181,7 @@ { "name": "genomicLocation", "in": "query", - "description": "Genomic location. Example: 7,140453136,140453136,A,T", + "description": "Genomic location following TCGA MAF format. Example: 7,140453136,140453136,A,T", "required": true, "type": "string" }, @@ -203,7 +203,7 @@ { "name": "evidenceType", "in": "query", - "description": "Evidence type to compute. This could help to improve the performance if you only look for sub-content. Example: ONCOGENIC. All available evidence type are GENE_SUMMARY, MUTATION_SUMMARY, TUMOR_TYPE_SUMMARY, PROGNOSTIC_SUMMARY, DIAGNOSTIC_SUMMARY, ONCOGENIC, MUTATION_EFFECT, PROGNOSTIC_IMPLICATION, DIAGNOSTIC_IMPLICATION, STANDARD_THERAPEUTIC_IMPLICATIONS_FOR_DRUG_SENSITIVITY, STANDARD_THERAPEUTIC_IMPLICATIONS_FOR_DRUG_RESISTANCE, INVESTIGATIONAL_THERAPEUTIC_IMPLICATIONS_DRUG_SENSITIVITY, INVESTIGATIONAL_THERAPEUTIC_IMPLICATIONS_DRUG_RESISTANCE. For multiple evidence types query, use ',' as separator.", + "description": "DEPRECATED. We do not recommend using this parameter and it will eventually be removed.", "required": false, "type": "string" } @@ -287,7 +287,7 @@ { "name": "hgvsg", "in": "query", - "description": "HGVS genomic format. Example: 7:g.140453136A>T", + "description": "HGVS genomic format following HGVS nomenclature. Example: 7:g.140453136A>T", "required": true, "type": "string" }, @@ -309,7 +309,7 @@ { "name": "evidenceType", "in": "query", - "description": "Evidence type to compute. This could help to improve the performance if you only look for sub-content. Example: ONCOGENIC. All available evidence type are GENE_SUMMARY, MUTATION_SUMMARY, TUMOR_TYPE_SUMMARY, PROGNOSTIC_SUMMARY, DIAGNOSTIC_SUMMARY, ONCOGENIC, MUTATION_EFFECT, PROGNOSTIC_IMPLICATION, DIAGNOSTIC_IMPLICATION, STANDARD_THERAPEUTIC_IMPLICATIONS_FOR_DRUG_SENSITIVITY, STANDARD_THERAPEUTIC_IMPLICATIONS_FOR_DRUG_RESISTANCE, INVESTIGATIONAL_THERAPEUTIC_IMPLICATIONS_DRUG_SENSITIVITY, INVESTIGATIONAL_THERAPEUTIC_IMPLICATIONS_DRUG_RESISTANCE. For multiple evidence types query, use ',' as separator.", + "description": "DEPRECATED. We do not recommend using this parameter and it will eventually be removed.", "required": false, "type": "string" } @@ -334,7 +334,7 @@ "Annotations" ], "summary": "annotateMutationsByHGVSgPost", - "description": "Annotate mutations by genomic change.", + "description": "Annotate mutations by HGVSg.", "operationId": "annotateMutationsByHGVSgPostUsingPOST_1", "consumes": [ "application/json" @@ -465,7 +465,7 @@ { "name": "evidenceType", "in": "query", - "description": "Evidence type to compute. This could help to improve the performance if you only look for sub-content. Example: ONCOGENIC. All available evidence type are GENE_SUMMARY, MUTATION_SUMMARY, TUMOR_TYPE_SUMMARY, PROGNOSTIC_SUMMARY, DIAGNOSTIC_SUMMARY, ONCOGENIC, MUTATION_EFFECT, PROGNOSTIC_IMPLICATION, DIAGNOSTIC_IMPLICATION, STANDARD_THERAPEUTIC_IMPLICATIONS_FOR_DRUG_SENSITIVITY, STANDARD_THERAPEUTIC_IMPLICATIONS_FOR_DRUG_RESISTANCE, INVESTIGATIONAL_THERAPEUTIC_IMPLICATIONS_DRUG_SENSITIVITY, INVESTIGATIONAL_THERAPEUTIC_IMPLICATIONS_DRUG_RESISTANCE. For multiple evidence types query, use ',' as separator.", + "description": "DEPRECATED. We do not recommend using this parameter and it will eventually be removed.", "required": false, "type": "string" } @@ -618,7 +618,7 @@ { "name": "evidenceType", "in": "query", - "description": "Evidence type to compute. This could help to improve the performance if you only look for sub-content. Example: ONCOGENIC. All available evidence type are GENE_SUMMARY, MUTATION_SUMMARY, TUMOR_TYPE_SUMMARY, PROGNOSTIC_SUMMARY, DIAGNOSTIC_SUMMARY, ONCOGENIC, MUTATION_EFFECT, PROGNOSTIC_IMPLICATION, DIAGNOSTIC_IMPLICATION, STANDARD_THERAPEUTIC_IMPLICATIONS_FOR_DRUG_SENSITIVITY, STANDARD_THERAPEUTIC_IMPLICATIONS_FOR_DRUG_RESISTANCE, INVESTIGATIONAL_THERAPEUTIC_IMPLICATIONS_DRUG_SENSITIVITY, INVESTIGATIONAL_THERAPEUTIC_IMPLICATIONS_DRUG_RESISTANCE. For multiple evidence types query, use ',' as separator.", + "description": "DEPRECATED. We do not recommend using this parameter and it will eventually be removed.", "required": false, "type": "string" } diff --git a/packages/oncokb-ts-api-client/src/generated/OncoKbAPI.ts b/packages/oncokb-ts-api-client/src/generated/OncoKbAPI.ts index 7719c131c06..6b2e57a747a 100644 --- a/packages/oncokb-ts-api-client/src/generated/OncoKbAPI.ts +++ b/packages/oncokb-ts-api-client/src/generated/OncoKbAPI.ts @@ -484,7 +484,7 @@ export default class OncoKbAPI { * @param {string} copyNameAlterationType - Copy number alteration type * @param {string} referenceGenome - Reference genome, either GRCh37 or GRCh38. The default is GRCh37 * @param {string} tumorType - OncoTree(http://oncotree.info) tumor type name. The field supports OncoTree Code, OncoTree Name and OncoTree Main type. Example: Melanoma - * @param {string} evidenceType - Evidence type to compute. This could help to improve the performance if you only look for sub-content. Example: ONCOGENIC. All available evidence type are GENE_SUMMARY, MUTATION_SUMMARY, TUMOR_TYPE_SUMMARY, PROGNOSTIC_SUMMARY, DIAGNOSTIC_SUMMARY, ONCOGENIC, MUTATION_EFFECT, PROGNOSTIC_IMPLICATION, DIAGNOSTIC_IMPLICATION, STANDARD_THERAPEUTIC_IMPLICATIONS_FOR_DRUG_SENSITIVITY, STANDARD_THERAPEUTIC_IMPLICATIONS_FOR_DRUG_RESISTANCE, INVESTIGATIONAL_THERAPEUTIC_IMPLICATIONS_DRUG_SENSITIVITY, INVESTIGATIONAL_THERAPEUTIC_IMPLICATIONS_DRUG_RESISTANCE. For multiple evidence types query, use ',' as separator. + * @param {string} evidenceType - DEPRECATED. We do not recommend using this parameter and it will eventually be removed. */ annotateCopyNumberAlterationsGetUsingGET_1WithHttpInfo(parameters: { 'hugoSymbol' ? : string, @@ -558,7 +558,7 @@ export default class OncoKbAPI { * @param {string} copyNameAlterationType - Copy number alteration type * @param {string} referenceGenome - Reference genome, either GRCh37 or GRCh38. The default is GRCh37 * @param {string} tumorType - OncoTree(http://oncotree.info) tumor type name. The field supports OncoTree Code, OncoTree Name and OncoTree Main type. Example: Melanoma - * @param {string} evidenceType - Evidence type to compute. This could help to improve the performance if you only look for sub-content. Example: ONCOGENIC. All available evidence type are GENE_SUMMARY, MUTATION_SUMMARY, TUMOR_TYPE_SUMMARY, PROGNOSTIC_SUMMARY, DIAGNOSTIC_SUMMARY, ONCOGENIC, MUTATION_EFFECT, PROGNOSTIC_IMPLICATION, DIAGNOSTIC_IMPLICATION, STANDARD_THERAPEUTIC_IMPLICATIONS_FOR_DRUG_SENSITIVITY, STANDARD_THERAPEUTIC_IMPLICATIONS_FOR_DRUG_RESISTANCE, INVESTIGATIONAL_THERAPEUTIC_IMPLICATIONS_DRUG_SENSITIVITY, INVESTIGATIONAL_THERAPEUTIC_IMPLICATIONS_DRUG_RESISTANCE. For multiple evidence types query, use ',' as separator. + * @param {string} evidenceType - DEPRECATED. We do not recommend using this parameter and it will eventually be removed. */ annotateCopyNumberAlterationsGetUsingGET_1(parameters: { 'hugoSymbol' ? : string, @@ -690,10 +690,10 @@ export default class OncoKbAPI { * Annotate mutation by genomic change. * @method * @name OncoKbAPI#annotateMutationsByGenomicChangeGetUsingGET_1 - * @param {string} genomicLocation - Genomic location. Example: 7,140453136,140453136,A,T + * @param {string} genomicLocation - Genomic location following TCGA MAF format. Example: 7,140453136,140453136,A,T * @param {string} referenceGenome - Reference genome, either GRCh37 or GRCh38. The default is GRCh37 * @param {string} tumorType - OncoTree(http://oncotree.info) tumor type name. The field supports OncoTree Code, OncoTree Name and OncoTree Main type. Example: Melanoma - * @param {string} evidenceType - Evidence type to compute. This could help to improve the performance if you only look for sub-content. Example: ONCOGENIC. All available evidence type are GENE_SUMMARY, MUTATION_SUMMARY, TUMOR_TYPE_SUMMARY, PROGNOSTIC_SUMMARY, DIAGNOSTIC_SUMMARY, ONCOGENIC, MUTATION_EFFECT, PROGNOSTIC_IMPLICATION, DIAGNOSTIC_IMPLICATION, STANDARD_THERAPEUTIC_IMPLICATIONS_FOR_DRUG_SENSITIVITY, STANDARD_THERAPEUTIC_IMPLICATIONS_FOR_DRUG_RESISTANCE, INVESTIGATIONAL_THERAPEUTIC_IMPLICATIONS_DRUG_SENSITIVITY, INVESTIGATIONAL_THERAPEUTIC_IMPLICATIONS_DRUG_RESISTANCE. For multiple evidence types query, use ',' as separator. + * @param {string} evidenceType - DEPRECATED. We do not recommend using this parameter and it will eventually be removed. */ annotateMutationsByGenomicChangeGetUsingGET_1WithHttpInfo(parameters: { 'genomicLocation': string, @@ -752,10 +752,10 @@ export default class OncoKbAPI { * Annotate mutation by genomic change. * @method * @name OncoKbAPI#annotateMutationsByGenomicChangeGetUsingGET_1 - * @param {string} genomicLocation - Genomic location. Example: 7,140453136,140453136,A,T + * @param {string} genomicLocation - Genomic location following TCGA MAF format. Example: 7,140453136,140453136,A,T * @param {string} referenceGenome - Reference genome, either GRCh37 or GRCh38. The default is GRCh37 * @param {string} tumorType - OncoTree(http://oncotree.info) tumor type name. The field supports OncoTree Code, OncoTree Name and OncoTree Main type. Example: Melanoma - * @param {string} evidenceType - Evidence type to compute. This could help to improve the performance if you only look for sub-content. Example: ONCOGENIC. All available evidence type are GENE_SUMMARY, MUTATION_SUMMARY, TUMOR_TYPE_SUMMARY, PROGNOSTIC_SUMMARY, DIAGNOSTIC_SUMMARY, ONCOGENIC, MUTATION_EFFECT, PROGNOSTIC_IMPLICATION, DIAGNOSTIC_IMPLICATION, STANDARD_THERAPEUTIC_IMPLICATIONS_FOR_DRUG_SENSITIVITY, STANDARD_THERAPEUTIC_IMPLICATIONS_FOR_DRUG_RESISTANCE, INVESTIGATIONAL_THERAPEUTIC_IMPLICATIONS_DRUG_SENSITIVITY, INVESTIGATIONAL_THERAPEUTIC_IMPLICATIONS_DRUG_RESISTANCE. For multiple evidence types query, use ',' as separator. + * @param {string} evidenceType - DEPRECATED. We do not recommend using this parameter and it will eventually be removed. */ annotateMutationsByGenomicChangeGetUsingGET_1(parameters: { 'genomicLocation': string, @@ -885,10 +885,10 @@ export default class OncoKbAPI { * Annotate mutation by HGVSg. * @method * @name OncoKbAPI#annotateMutationsByHGVSgGetUsingGET_1 - * @param {string} hgvsg - HGVS genomic format. Example: 7:g.140453136A>T + * @param {string} hgvsg - HGVS genomic format following HGVS nomenclature. Example: 7:g.140453136A>T * @param {string} referenceGenome - Reference genome, either GRCh37 or GRCh38. The default is GRCh37 * @param {string} tumorType - OncoTree(http://oncotree.info) tumor type name. The field supports OncoTree Code, OncoTree Name and OncoTree Main type. Example: Melanoma - * @param {string} evidenceType - Evidence type to compute. This could help to improve the performance if you only look for sub-content. Example: ONCOGENIC. All available evidence type are GENE_SUMMARY, MUTATION_SUMMARY, TUMOR_TYPE_SUMMARY, PROGNOSTIC_SUMMARY, DIAGNOSTIC_SUMMARY, ONCOGENIC, MUTATION_EFFECT, PROGNOSTIC_IMPLICATION, DIAGNOSTIC_IMPLICATION, STANDARD_THERAPEUTIC_IMPLICATIONS_FOR_DRUG_SENSITIVITY, STANDARD_THERAPEUTIC_IMPLICATIONS_FOR_DRUG_RESISTANCE, INVESTIGATIONAL_THERAPEUTIC_IMPLICATIONS_DRUG_SENSITIVITY, INVESTIGATIONAL_THERAPEUTIC_IMPLICATIONS_DRUG_RESISTANCE. For multiple evidence types query, use ',' as separator. + * @param {string} evidenceType - DEPRECATED. We do not recommend using this parameter and it will eventually be removed. */ annotateMutationsByHGVSgGetUsingGET_1WithHttpInfo(parameters: { 'hgvsg': string, @@ -947,10 +947,10 @@ export default class OncoKbAPI { * Annotate mutation by HGVSg. * @method * @name OncoKbAPI#annotateMutationsByHGVSgGetUsingGET_1 - * @param {string} hgvsg - HGVS genomic format. Example: 7:g.140453136A>T + * @param {string} hgvsg - HGVS genomic format following HGVS nomenclature. Example: 7:g.140453136A>T * @param {string} referenceGenome - Reference genome, either GRCh37 or GRCh38. The default is GRCh37 * @param {string} tumorType - OncoTree(http://oncotree.info) tumor type name. The field supports OncoTree Code, OncoTree Name and OncoTree Main type. Example: Melanoma - * @param {string} evidenceType - Evidence type to compute. This could help to improve the performance if you only look for sub-content. Example: ONCOGENIC. All available evidence type are GENE_SUMMARY, MUTATION_SUMMARY, TUMOR_TYPE_SUMMARY, PROGNOSTIC_SUMMARY, DIAGNOSTIC_SUMMARY, ONCOGENIC, MUTATION_EFFECT, PROGNOSTIC_IMPLICATION, DIAGNOSTIC_IMPLICATION, STANDARD_THERAPEUTIC_IMPLICATIONS_FOR_DRUG_SENSITIVITY, STANDARD_THERAPEUTIC_IMPLICATIONS_FOR_DRUG_RESISTANCE, INVESTIGATIONAL_THERAPEUTIC_IMPLICATIONS_DRUG_SENSITIVITY, INVESTIGATIONAL_THERAPEUTIC_IMPLICATIONS_DRUG_RESISTANCE. For multiple evidence types query, use ',' as separator. + * @param {string} evidenceType - DEPRECATED. We do not recommend using this parameter and it will eventually be removed. */ annotateMutationsByHGVSgGetUsingGET_1(parameters: { 'hgvsg': string, @@ -982,7 +982,7 @@ export default class OncoKbAPI { }; /** - * Annotate mutations by genomic change. + * Annotate mutations by HGVSg. * @method * @name OncoKbAPI#annotateMutationsByHGVSgPostUsingPOST_1 * @param {} body - List of queries. Please see swagger.json for request body format. @@ -1026,7 +1026,7 @@ export default class OncoKbAPI { }; /** - * Annotate mutations by genomic change. + * Annotate mutations by HGVSg. * @method * @name OncoKbAPI#annotateMutationsByHGVSgPostUsingPOST_1 * @param {} body - List of queries. Please see swagger.json for request body format. @@ -1113,7 +1113,7 @@ export default class OncoKbAPI { * @param {integer} proteinStart - Protein Start. Example: 600 * @param {integer} proteinEnd - Protein End. Example: 600 * @param {string} tumorType - OncoTree(http://oncotree.info) tumor type name. The field supports OncoTree Code, OncoTree Name and OncoTree Main type. Example: Melanoma - * @param {string} evidenceType - Evidence type to compute. This could help to improve the performance if you only look for sub-content. Example: ONCOGENIC. All available evidence type are GENE_SUMMARY, MUTATION_SUMMARY, TUMOR_TYPE_SUMMARY, PROGNOSTIC_SUMMARY, DIAGNOSTIC_SUMMARY, ONCOGENIC, MUTATION_EFFECT, PROGNOSTIC_IMPLICATION, DIAGNOSTIC_IMPLICATION, STANDARD_THERAPEUTIC_IMPLICATIONS_FOR_DRUG_SENSITIVITY, STANDARD_THERAPEUTIC_IMPLICATIONS_FOR_DRUG_RESISTANCE, INVESTIGATIONAL_THERAPEUTIC_IMPLICATIONS_DRUG_SENSITIVITY, INVESTIGATIONAL_THERAPEUTIC_IMPLICATIONS_DRUG_RESISTANCE. For multiple evidence types query, use ',' as separator. + * @param {string} evidenceType - DEPRECATED. We do not recommend using this parameter and it will eventually be removed. */ annotateMutationsByProteinChangeGetUsingGET_1WithHttpInfo(parameters: { 'hugoSymbol' ? : string, @@ -1200,7 +1200,7 @@ export default class OncoKbAPI { * @param {integer} proteinStart - Protein Start. Example: 600 * @param {integer} proteinEnd - Protein End. Example: 600 * @param {string} tumorType - OncoTree(http://oncotree.info) tumor type name. The field supports OncoTree Code, OncoTree Name and OncoTree Main type. Example: Melanoma - * @param {string} evidenceType - Evidence type to compute. This could help to improve the performance if you only look for sub-content. Example: ONCOGENIC. All available evidence type are GENE_SUMMARY, MUTATION_SUMMARY, TUMOR_TYPE_SUMMARY, PROGNOSTIC_SUMMARY, DIAGNOSTIC_SUMMARY, ONCOGENIC, MUTATION_EFFECT, PROGNOSTIC_IMPLICATION, DIAGNOSTIC_IMPLICATION, STANDARD_THERAPEUTIC_IMPLICATIONS_FOR_DRUG_SENSITIVITY, STANDARD_THERAPEUTIC_IMPLICATIONS_FOR_DRUG_RESISTANCE, INVESTIGATIONAL_THERAPEUTIC_IMPLICATIONS_DRUG_SENSITIVITY, INVESTIGATIONAL_THERAPEUTIC_IMPLICATIONS_DRUG_RESISTANCE. For multiple evidence types query, use ',' as separator. + * @param {string} evidenceType - DEPRECATED. We do not recommend using this parameter and it will eventually be removed. */ annotateMutationsByProteinChangeGetUsingGET_1(parameters: { 'hugoSymbol' ? : string, @@ -1368,7 +1368,7 @@ export default class OncoKbAPI { * @param {boolean} isFunctionalFusion - Whether is functional fusion * @param {string} referenceGenome - Reference genome, either GRCh37 or GRCh38. The default is GRCh37 * @param {string} tumorType - OncoTree(http://oncotree.info) tumor type name. The field supports OncoTree Code, OncoTree Name and OncoTree Main type. Example: Melanoma - * @param {string} evidenceType - Evidence type to compute. This could help to improve the performance if you only look for sub-content. Example: ONCOGENIC. All available evidence type are GENE_SUMMARY, MUTATION_SUMMARY, TUMOR_TYPE_SUMMARY, PROGNOSTIC_SUMMARY, DIAGNOSTIC_SUMMARY, ONCOGENIC, MUTATION_EFFECT, PROGNOSTIC_IMPLICATION, DIAGNOSTIC_IMPLICATION, STANDARD_THERAPEUTIC_IMPLICATIONS_FOR_DRUG_SENSITIVITY, STANDARD_THERAPEUTIC_IMPLICATIONS_FOR_DRUG_RESISTANCE, INVESTIGATIONAL_THERAPEUTIC_IMPLICATIONS_DRUG_SENSITIVITY, INVESTIGATIONAL_THERAPEUTIC_IMPLICATIONS_DRUG_RESISTANCE. For multiple evidence types query, use ',' as separator. + * @param {string} evidenceType - DEPRECATED. We do not recommend using this parameter and it will eventually be removed. */ annotateStructuralVariantsGetUsingGET_1WithHttpInfo(parameters: { 'hugoSymbolA' ? : string, @@ -1465,7 +1465,7 @@ export default class OncoKbAPI { * @param {boolean} isFunctionalFusion - Whether is functional fusion * @param {string} referenceGenome - Reference genome, either GRCh37 or GRCh38. The default is GRCh37 * @param {string} tumorType - OncoTree(http://oncotree.info) tumor type name. The field supports OncoTree Code, OncoTree Name and OncoTree Main type. Example: Melanoma - * @param {string} evidenceType - Evidence type to compute. This could help to improve the performance if you only look for sub-content. Example: ONCOGENIC. All available evidence type are GENE_SUMMARY, MUTATION_SUMMARY, TUMOR_TYPE_SUMMARY, PROGNOSTIC_SUMMARY, DIAGNOSTIC_SUMMARY, ONCOGENIC, MUTATION_EFFECT, PROGNOSTIC_IMPLICATION, DIAGNOSTIC_IMPLICATION, STANDARD_THERAPEUTIC_IMPLICATIONS_FOR_DRUG_SENSITIVITY, STANDARD_THERAPEUTIC_IMPLICATIONS_FOR_DRUG_RESISTANCE, INVESTIGATIONAL_THERAPEUTIC_IMPLICATIONS_DRUG_SENSITIVITY, INVESTIGATIONAL_THERAPEUTIC_IMPLICATIONS_DRUG_RESISTANCE. For multiple evidence types query, use ',' as separator. + * @param {string} evidenceType - DEPRECATED. We do not recommend using this parameter and it will eventually be removed. */ annotateStructuralVariantsGetUsingGET_1(parameters: { 'hugoSymbolA' ? : string, diff --git a/src/pages/studyView/StudyViewPageStore.ts b/src/pages/studyView/StudyViewPageStore.ts index eeac06a3581..746d3591a1f 100644 --- a/src/pages/studyView/StudyViewPageStore.ts +++ b/src/pages/studyView/StudyViewPageStore.ts @@ -10456,11 +10456,12 @@ export class StudyViewPageStore } // a row represents a list of patients that either have or have not recieved // a specific treatment - public readonly sampleTreatments = remoteData({ + public readonly sampleTreatments = remoteData({ await: () => [this.shouldDisplaySampleTreatments], invoke: async () => { if (this.shouldDisplaySampleTreatments.result) { if (isClickhouseMode()) { + // @ts-ignore (will be available when go live with Clickhouse for all portals) return await this.internalClient.fetchSampleTreatmentCountsUsingPOST( { studyViewFilter: this.filters, @@ -10500,11 +10501,12 @@ export class StudyViewPageStore // a row represents a list of samples that ether have or have not recieved // a specific treatment - public readonly patientTreatments = remoteData({ + public readonly patientTreatments = remoteData({ await: () => [this.shouldDisplayPatientTreatments], invoke: async () => { if (this.shouldDisplayPatientTreatments.result) { if (isClickhouseMode()) { + // @ts-ignore (will be available when go live with Clickhouse for all portals) return await this.internalClient.fetchPatientTreatmentCountsUsingPOST( { studyViewFilter: this.filters, @@ -10565,28 +10567,31 @@ export class StudyViewPageStore // a row represents a list of samples that ether have or have not recieved // a specific treatment - public readonly patientTreatmentGroups = remoteData({ - await: () => [this.shouldDisplayPatientTreatmentGroups], - invoke: () => { - if (this.shouldDisplayPatientTreatmentGroups.result) { - if (isClickhouseMode()) { - return this.internalClient.fetchPatientTreatmentCountsUsingPOST( - { - studyViewFilter: this.filters, - tier: 'AgentClass', - } - ); - } else { - return getPatientTreatmentReport( - this.filters, - 'AgentClass', - this.internalClient - ); + public readonly patientTreatmentGroups = remoteData( + { + await: () => [this.shouldDisplayPatientTreatmentGroups], + invoke: () => { + if (this.shouldDisplayPatientTreatmentGroups.result) { + if (isClickhouseMode()) { + // @ts-ignore (will be available when go live with Clickhouse for all portals) + return this.internalClient.fetchPatientTreatmentCountsUsingPOST( + { + studyViewFilter: this.filters, + tier: 'AgentClass', + } + ); + } else { + return getPatientTreatmentReport( + this.filters, + 'AgentClass', + this.internalClient + ); + } } - } - return Promise.resolve(undefined); - }, - }); + return Promise.resolve(undefined); + }, + } + ); public readonly sampleTreatmentTarget = remoteData({ await: () => [this.shouldDisplaySampleTreatmentTarget], @@ -10637,26 +10642,29 @@ export class StudyViewPageStore // a row represents a list of samples that ether have or have not recieved // a specific treatment - public readonly patientTreatmentTarget = remoteData({ - await: () => [this.shouldDisplayPatientTreatmentTarget], - invoke: async () => { - if (isClickhouseMode()) { - return await this.internalClient.fetchPatientTreatmentCountsUsingPOST( - { - studyViewFilter: this.filters, - tier: 'AgentTarget', - } - ); - } else { - //we need to transform pre-clickhouse response into new SampleTreatmentReport - return await getPatientTreatmentReport( - this.filters, - 'AgentTarget', - this.internalClient - ); - } - }, - }); + public readonly patientTreatmentTarget = remoteData( + { + await: () => [this.shouldDisplayPatientTreatmentTarget], + invoke: async () => { + if (isClickhouseMode()) { + // @ts-ignore (will be available when go live with Clickhouse for all portals) + return await this.internalClient.fetchPatientTreatmentCountsUsingPOST( + { + studyViewFilter: this.filters, + tier: 'AgentTarget', + } + ); + } else { + //we need to transform pre-clickhouse response into new SampleTreatmentReport + return await getPatientTreatmentReport( + this.filters, + 'AgentTarget', + this.internalClient + ); + } + }, + } + ); @action.bound public onTreatmentSelection(meta: ChartMeta, values: string[][]): void {