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On Study View handle larger number of resource files (#5034)
Fixes cBioPortal/cbioportal#11004 (associated backend PR is merged, see cBioPortal/cbioportal#11051). This PR modifies the FilesAndLinks table on the Study View to use the new resource-data-all endpoint, which reduces the number of API requests and enables showing thousands of resource files without performance degradation
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7 files changed

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‎packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal-docs.json‎

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"operationId": "getAllStudyResourceDataInStudyUsingGET"
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}
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},
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"/api/studies/{studyId}/resource-data-all": {
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"get": {
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"produces": [
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"application/json"
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],
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"parameters": [
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{
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"description": "Study ID e.g. acc_tcga",
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"in": "path",
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"name": "studyId",
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"required": true,
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"type": "string"
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},
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{
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"description": "Resource ID",
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"in": "query",
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"name": "resourceId",
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"required": false,
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"type": "string"
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},
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{
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"default": "SUMMARY",
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"description": "Level of detail of the response",
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"enum": [
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"ID",
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"SUMMARY",
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"DETAILED",
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"META"
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],
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"in": "query",
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"name": "projection",
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"required": false,
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"type": "string"
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},
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{
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"default": 10000000,
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"description": "Page size of the result list",
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"format": "int32",
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"in": "query",
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"maximum": 10000000,
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"minimum": 1,
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"name": "pageSize",
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"required": false,
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"type": "integer"
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},
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{
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"default": 0,
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"description": "Page number of the result list",
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"format": "int32",
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"in": "query",
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"minimum": 0,
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"name": "pageNumber",
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"required": false,
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"type": "integer"
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},
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{
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"description": "Name of the property that the result list is sorted by",
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"enum": [
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"ResourceId",
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"url"
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],
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"in": "query",
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"name": "sortBy",
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"required": false,
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"type": "string"
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},
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{
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"default": "ASC",
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"description": "Direction of the sort",
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"enum": [
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"ASC",
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"DESC"
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],
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"in": "query",
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"name": "direction",
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"required": false,
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"type": "string"
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}
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],
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"responses": {
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"200": {
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"description": "OK",
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"schema": {
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"items": {
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"$ref": "#/definitions/ResourceData"
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},
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"type": "array"
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}
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}
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},
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"tags": [
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"Resource Data"
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],
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"description": "Get all resource data for for all patients and all samples within a study",
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"operationId": "getAllStudyResourceDataInStudyPatientSampleUsingGET"
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}
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},
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"/api/studies/{studyId}/resource-definitions": {
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"get": {
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"produces": [

‎packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal.ts‎

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@@ -6746,6 +6746,159 @@ export default class CBioPortalAPIInternal {
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return response.body;
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});
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};
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getAllStudyResourceDataInStudyPatientSampleUsingGETURL(parameters: {
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'studyId': string,
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'resourceId' ? : string,
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'projection' ? : "ID" | "SUMMARY" | "DETAILED" | "META",
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'pageSize' ? : number,
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'pageNumber' ? : number,
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'sortBy' ? : "ResourceId" | "url",
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'direction' ? : "ASC" | "DESC",
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$queryParameters ? : any
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}): string {
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let queryParameters: any = {};
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let path = '/api/studies/{studyId}/resource-data-all';
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path = path.replace('{studyId}', parameters['studyId'] + '');
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if (parameters['resourceId'] !== undefined) {
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queryParameters['resourceId'] = parameters['resourceId'];
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}
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if (parameters['projection'] !== undefined) {
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queryParameters['projection'] = parameters['projection'];
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}
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if (parameters['pageSize'] !== undefined) {
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queryParameters['pageSize'] = parameters['pageSize'];
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}
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if (parameters['pageNumber'] !== undefined) {
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queryParameters['pageNumber'] = parameters['pageNumber'];
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}
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if (parameters['sortBy'] !== undefined) {
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queryParameters['sortBy'] = parameters['sortBy'];
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}
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if (parameters['direction'] !== undefined) {
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queryParameters['direction'] = parameters['direction'];
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}
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if (parameters.$queryParameters) {
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Object.keys(parameters.$queryParameters).forEach(function(parameterName) {
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var parameter = parameters.$queryParameters[parameterName];
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queryParameters[parameterName] = parameter;
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});
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}
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let keys = Object.keys(queryParameters);
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return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : '');
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};
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/**
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* Get all resource data for for all patients and all samples within a study
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* @method
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* @name CBioPortalAPIInternal#getAllStudyResourceDataInStudyPatientSampleUsingGET
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* @param {string} studyId - Study ID e.g. acc_tcga
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* @param {string} resourceId - Resource ID
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* @param {string} projection - Level of detail of the response
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* @param {integer} pageSize - Page size of the result list
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* @param {integer} pageNumber - Page number of the result list
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* @param {string} sortBy - Name of the property that the result list is sorted by
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* @param {string} direction - Direction of the sort
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*/
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getAllStudyResourceDataInStudyPatientSampleUsingGETWithHttpInfo(parameters: {
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'studyId': string,
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'resourceId' ? : string,
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'projection' ? : "ID" | "SUMMARY" | "DETAILED" | "META",
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'pageSize' ? : number,
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'pageNumber' ? : number,
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'sortBy' ? : "ResourceId" | "url",
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'direction' ? : "ASC" | "DESC",
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$queryParameters ? : any,
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$domain ? : string
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}): Promise < request.Response > {
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const domain = parameters.$domain ? parameters.$domain : this.domain;
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const errorHandlers = this.errorHandlers;
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const request = this.request;
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let path = '/api/studies/{studyId}/resource-data-all';
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let body: any;
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let queryParameters: any = {};
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let headers: any = {};
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let form: any = {};
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return new Promise(function(resolve, reject) {
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headers['Accept'] = 'application/json';
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path = path.replace('{studyId}', parameters['studyId'] + '');
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if (parameters['studyId'] === undefined) {
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reject(new Error('Missing required parameter: studyId'));
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return;
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}
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if (parameters['resourceId'] !== undefined) {
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queryParameters['resourceId'] = parameters['resourceId'];
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}
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if (parameters['projection'] !== undefined) {
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queryParameters['projection'] = parameters['projection'];
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}
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if (parameters['pageSize'] !== undefined) {
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queryParameters['pageSize'] = parameters['pageSize'];
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}
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if (parameters['pageNumber'] !== undefined) {
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queryParameters['pageNumber'] = parameters['pageNumber'];
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}
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if (parameters['sortBy'] !== undefined) {
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queryParameters['sortBy'] = parameters['sortBy'];
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}
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if (parameters['direction'] !== undefined) {
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queryParameters['direction'] = parameters['direction'];
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}
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if (parameters.$queryParameters) {
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Object.keys(parameters.$queryParameters).forEach(function(parameterName) {
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var parameter = parameters.$queryParameters[parameterName];
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queryParameters[parameterName] = parameter;
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});
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}
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request('GET', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers);
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});
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};
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/**
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* Get all resource data for for all patients and all samples within a study
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* @method
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* @name CBioPortalAPIInternal#getAllStudyResourceDataInStudyPatientSampleUsingGET
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* @param {string} studyId - Study ID e.g. acc_tcga
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* @param {string} resourceId - Resource ID
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* @param {string} projection - Level of detail of the response
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* @param {integer} pageSize - Page size of the result list
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* @param {integer} pageNumber - Page number of the result list
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* @param {string} sortBy - Name of the property that the result list is sorted by
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* @param {string} direction - Direction of the sort
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*/
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getAllStudyResourceDataInStudyPatientSampleUsingGET(parameters: {
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'studyId': string,
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'resourceId' ? : string,
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'projection' ? : "ID" | "SUMMARY" | "DETAILED" | "META",
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'pageSize' ? : number,
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'pageNumber' ? : number,
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'sortBy' ? : "ResourceId" | "url",
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'direction' ? : "ASC" | "DESC",
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$queryParameters ? : any,
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$domain ? : string
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}): Promise < Array < ResourceData >
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> {
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return this.getAllStudyResourceDataInStudyPatientSampleUsingGETWithHttpInfo(parameters).then(function(response: request.Response) {
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return response.body;
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});
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};
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getAllResourceDefinitionsInStudyUsingGETURL(parameters: {
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'studyId': string,
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'projection' ? : "ID" | "SUMMARY" | "DETAILED" | "META",

‎packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPI-docs.json‎

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},
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"ncitCode": {
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"type": "string"
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},
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"synonyms": {
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"type": "array",
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"items": {
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"type": "string"
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}
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},
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"uuid": {
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"type": "string"
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}
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}
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},

‎packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPI.ts‎

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'ncitCode': string
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'synonyms': Array < string >
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'uuid': string
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};
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export type EnsemblFilter = {
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'geneIds': Array < string >

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