diff --git a/src/core/clients/opencga/api/Admin.js b/src/core/clients/opencga/api/Admin.js index 57f9329561..05a71e5ced 100644 --- a/src/core/clients/opencga/api/Admin.js +++ b/src/core/clients/opencga/api/Admin.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2022-08-11 16:30:01 + * Autogenerated on: 2024-02-02 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -116,4 +116,15 @@ export default class Admin extends OpenCGAParentClass { return this._post("admin", null, "users", null, "sync", data); } + /** Add or remove users from existing groups + * @param {String} user - User ID. + * @param {Object} data - JSON containing the parameters. + * @param {Object} [params] - The Object containing the following optional parameters: + * @param {"ADD REMOVE"} [params.action = "ADD"] - Action to be performed: ADD or REMOVE user to/from groups. The default value is ADD. + * @returns {Promise} Promise object in the form of RestResponse instance. + */ + usersUpdateGroups(user, data, params) { + return this._post("admin/users", user, "groups", null, "update", data, params); + } + } \ No newline at end of file diff --git a/src/core/clients/opencga/api/Alignment.js b/src/core/clients/opencga/api/Alignment.js index 3ade900cd7..1075d6d854 100644 --- a/src/core/clients/opencga/api/Alignment.js +++ b/src/core/clients/opencga/api/Alignment.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2022-08-11 16:30:01 + * Autogenerated on: 2024-02-02 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -188,10 +188,9 @@ export default class Alignment extends OpenCGAParentClass { return this._post("analysis", null, "alignment/picard", null, "run", data, params); } - /** Compute quality control (QC) metrics for a given alignment file (including samtools stats, samtools flag stats, FastQC and HS metrics) - * @param {Object} data - Alignment quality control (QC) parameters. It computes: stats, flag stats, fastqc and hybrid-selection metrics. - * The BAM file is mandatory ever but the BED fileand the dictionary files are only mandatory for computing hybrid-selection (HS) - * metrics. In order to skip some metrics, use the following keywords (separated by commas): stats, flagstats, fastqc and hsmetrics. + /** Compute quality control (QC) metrics for a given alignment file: samtools stats, samtools flag stats and FastQC metrics. + * @param {Object} data - Alignment quality control (QC) parameters. It computes: stats, flag stats and fastqc metrics. The BAM file ID + * is mandatory and in order to skip some metrics, use the following keywords (separated by commas): stats, flagstats, fastqc. * @param {Object} [params] - The Object containing the following optional parameters: * @param {String} [params.study] - study. * @param {String} [params.jobId] - Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not diff --git a/src/core/clients/opencga/api/Clinical.js b/src/core/clients/opencga/api/Clinical.js deleted file mode 100644 index 2c695aacd9..0000000000 --- a/src/core/clients/opencga/api/Clinical.js +++ /dev/null @@ -1,807 +0,0 @@ -/** - * Copyright 2015-2020 OpenCB - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * http://www.apache.org/licenses/LICENSE-2.0 - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * WARNING: AUTOGENERATED CODE - * - * This code was generated by a tool. - * Autogenerated on: 2022-08-02 08:25:32 ->>>>>>> develop ->>>>>>> release-2.4.x ->>>>>>> release-2.4.x - * - * Manual changes to this file may cause unexpected behavior in your application. - * Manual changes to this file will be overwritten if the code is regenerated. - * -**/ - -import OpenCGAParentClass from "./../opencga-parent-class.js"; - - -/** - * This class contains the methods for the "Clinical" resource - */ - -export default class Clinical extends OpenCGAParentClass { - - constructor(config) { - super(config); - } - - /** Update the set of permissions granted for the member - * @param {String} members - Comma separated list of user or group IDs. - * @param {Object} data - JSON containing the parameters to add ACLs. - * @param {String} action = "ADD" - Action to be performed [ADD, SET, REMOVE or RESET]. The default value is ADD. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {Boolean} [params.propagate = "false"] - Propagate permissions to related families, individuals, samples and files. The default - * value is false. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - updateAcl(members, action, data, params) { - return this._post("analysis", null, "clinical/acl", members, "update", data, {action, ...params}); - } - - /** Update Clinical Analysis configuration. - * @param {Object} [data] - Configuration params to update. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - updateClinicalConfiguration(data, params) { - return this._post("analysis", null, "clinical/clinical/configuration", null, "update", data, params); - } - - /** Create a new clinical analysis - * @param {Object} data - JSON containing clinical analysis information. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.include] - Fields included in the response, whole JSON path must be provided. - * @param {String} [params.exclude] - Fields excluded in the response, whole JSON path must be provided. - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {Boolean} [params.skipCreateDefaultInterpretation] - Flag to skip creating and initialise an empty default primary - * interpretation (Id will be '{clinicalAnalysisId}.1'). This flag is only considered if no Interpretation object is passed. - * @param {Boolean} [params.includeResult = "false"] - Flag indicating to include the created or updated document result in the response. - * The default value is false. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - create(data, params) { - return this._post("analysis", null, "clinical", null, "create", data, params); - } - - /** Clinical Analysis distinct method - * @param {String} field - Field for which to obtain the distinct values. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list of Clinical Analysis IDs up to a maximum of 100. - * @param {String} [params.uuid] - Comma separated list of Clinical Analysis UUIDs up to a maximum of 100. - * @param {String} [params.type] - Clinical Analysis type. - * @param {String} [params.disorder] - Clinical Analysis disorder. - * @param {String} [params.files] - Clinical Analysis files. - * @param {String} [params.sample] - Sample associated to the proband or any member of a family. - * @param {String} [params.individual] - Proband or any member of a family. - * @param {String} [params.proband] - Clinical Analysis proband. - * @param {String} [params.probandSamples] - Clinical Analysis proband samples. - * @param {String} [params.family] - Clinical Analysis family. - * @param {String} [params.familyMembers] - Clinical Analysis family members. - * @param {String} [params.familyMemberSamples] - Clinical Analysis family members samples. - * @param {String} [params.panels] - Clinical Analysis panels. - * @param {Boolean} [params.locked] - Locked Clinical Analyses. - * @param {String} [params.analystId] - Clinical Analysis analyst id. - * @param {String} [params.priority] - Clinical Analysis priority. - * @param {String} [params.flags] - Clinical Analysis flags. - * @param {String} [params.creationDate] - Clinical Analysis Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - * @param {String} [params.modificationDate] - Clinical Analysis Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, - * <201805. - * @param {String} [params.dueDate] - Clinical Analysis due date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - * @param {String} [params.qualityControlSummary] - Clinical Analysis quality control summary. - * @param {String} [params.release] - Release when it was created. - * @param {String} [params.status] - Filter by status. - * @param {String} [params.internalStatus] - Filter by internal status. - * @param {Boolean} [params.deleted] - Boolean to retrieve deleted entries. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - distinct(field, params) { - return this._get("analysis", null, "clinical", null, "distinct", {field, ...params}); - } - - /** Interpretation distinct method - * @param {String} field - Field for which to obtain the distinct values. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list of Interpretation IDs up to a maximum of 100. - * @param {String} [params.uuid] - Comma separated list of Interpretation UUIDs up to a maximum of 100. - * @param {String} [params.clinicalAnalysisId] - Clinical Analysis id. - * @param {String} [params.analystId] - Analyst ID. - * @param {String} [params.methodName] - Interpretation method name. - * @param {String} [params.panels] - Interpretation panels. - * @param {String} [params.primaryFindings] - Interpretation primary findings. - * @param {String} [params.secondaryFindings] - Interpretation secondary findings. - * @param {String} [params.creationDate] - Interpretation Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - * @param {String} [params.modificationDate] - Interpretation Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, - * <201805. - * @param {String} [params.status] - Filter by status. - * @param {String} [params.internalStatus] - Filter by internal status. - * @param {String} [params.release] - Release when it was created. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - distinctInterpretation(field, params) { - return this._get("analysis", null, "clinical/interpretation", null, "distinct", {field, ...params}); - } - - /** Search clinical interpretations - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.include] - Fields included in the response, whole JSON path must be provided. - * @param {String} [params.exclude] - Fields excluded in the response, whole JSON path must be provided. - * @param {Number} [params.limit] - Number of results to be returned. - * @param {Number} [params.skip] - Number of results to skip. - * @param {Boolean} [params.sort] - Sort the results. - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list of Interpretation IDs up to a maximum of 100. - * @param {String} [params.uuid] - Comma separated list of Interpretation UUIDs up to a maximum of 100. - * @param {String} [params.clinicalAnalysisId] - Clinical Analysis id. - * @param {String} [params.analystId] - Analyst ID. - * @param {String} [params.methodName] - Interpretation method name. - * @param {String} [params.panels] - Interpretation panels. - * @param {String} [params.primaryFindings] - Interpretation primary findings. - * @param {String} [params.secondaryFindings] - Interpretation secondary findings. - * @param {String} [params.creationDate] - Interpretation Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - * @param {String} [params.modificationDate] - Interpretation Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, - * <201805. - * @param {String} [params.status] - Filter by status. - * @param {String} [params.internalStatus] - Filter by internal status. - * @param {String} [params.release] - Release when it was created. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - searchInterpretation(params) { - return this._get("analysis", null, "clinical/interpretation", null, "search", params); - } - - /** Clinical interpretation information - * @param {String} interpretations - Comma separated list of clinical interpretation IDs up to a maximum of 100. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.include] - Fields included in the response, whole JSON path must be provided. - * @param {String} [params.exclude] - Fields excluded in the response, whole JSON path must be provided. - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.version] - Comma separated list of interpretation versions. 'all' to get all the interpretation versions. Not - * supported if multiple interpretation ids are provided. - * @param {Boolean} [params.deleted = "false"] - Boolean to retrieve deleted entries. The default value is false. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - infoInterpretation(interpretations, params) { - return this._get("analysis", null, "clinical/interpretation", interpretations, "info", params); - } - - /** Run cancer tiering interpretation analysis - * @param {Object} data - Cancer tiering interpretation analysis params. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.jobId] - Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not - * provided. - * @param {String} [params.jobDescription] - Job description. - * @param {String} [params.jobDependsOn] - Comma separated list of existing job IDs the job will depend on. - * @param {String} [params.jobTags] - Job tags. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - runInterpreterCancerTiering(data, params) { - return this._post("analysis", null, "clinical/interpreter/cancerTiering", null, "run", data, params); - } - - /** Run exomiser interpretation analysis - * @param {Object} data - Exomizer interpretation analysis params. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.jobId] - Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not - * provided. - * @param {String} [params.jobDescription] - Job description. - * @param {String} [params.jobDependsOn] - Comma separated list of existing job IDs the job will depend on. - * @param {String} [params.jobTags] - Job tags. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - runInterpreterExomiser(data, params) { - return this._post("analysis", null, "clinical/interpreter/exomiser", null, "run", data, params); - } - - /** Run TEAM interpretation analysis - * @param {Object} data - TEAM interpretation analysis params. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.jobId] - Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not - * provided. - * @param {String} [params.jobDescription] - Job description. - * @param {String} [params.jobDependsOn] - Comma separated list of existing job IDs the job will depend on. - * @param {String} [params.jobTags] - Job tags. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - runInterpreterTeam(data, params) { - return this._post("analysis", null, "clinical/interpreter/team", null, "run", data, params); - } - - /** Run tiering interpretation analysis - * @param {Object} data - Tiering interpretation analysis params. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.jobId] - Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not - * provided. - * @param {String} [params.jobDescription] - Job description. - * @param {String} [params.jobDependsOn] - Comma separated list of existing job IDs the job will depend on. - * @param {String} [params.jobTags] - Job tags. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - runInterpreterTiering(data, params) { - return this._post("analysis", null, "clinical/interpreter/tiering", null, "run", data, params); - } - - /** Run Zetta interpretation analysis - * @param {Object} data - Zetta interpretation analysis params. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.jobId] - Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not - * provided. - * @param {String} [params.jobDescription] - Job description. - * @param {String} [params.jobDependsOn] - Comma separated list of existing job IDs the job will depend on. - * @param {String} [params.jobTags] - Job tags. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - runInterpreterZetta(data, params) { - return this._post("analysis", null, "clinical/interpreter/zetta", null, "run", data, params); - } - - /** RGA aggregation stats - * @param {String} field - List of fields separated by semicolons, e.g.: clinicalSignificances;type. For nested fields use >>, e.g.: - * type>>clinicalSignificances;knockoutType. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {Number} [params.limit] - Number of results to be returned. - * @param {Number} [params.skip] - Number of results to skip. - * @param {String} [params.sampleId] - Filter by sample id. - * @param {String} [params.individualId] - Filter by individual id. - * @param {String} [params.sex] - Filter by sex. - * @param {String} [params.phenotypes] - Filter by phenotypes. - * @param {String} [params.disorders] - Filter by disorders. - * @param {String} [params.numParents] - Filter by the number of parents registered. - * @param {String} [params.geneId] - Filter by gene id. - * @param {String} [params.geneName] - Filter by gene name. - * @param {String} [params.chromosome] - Filter by chromosome. - * @param {String} [params.start] - Filter by start position. - * @param {String} [params.end] - Filter by end position. - * @param {String} [params.transcriptId] - Filter by transcript id. - * @param {String} [params.variants] - Filter by variant id. - * @param {String} [params.dbSnps] - Filter by DB_SNP id. - * @param {String} [params.knockoutType] - Filter by knockout type. - * @param {String} [params.filter] - Filter by filter (PASS, NOT_PASS). - * @param {String} [params.type] - Filter by variant type. - * @param {String} [params.clinicalSignificance] - Filter by clinical significance. - * @param {String} [params.populationFrequency] - Filter by population frequency. - * @param {String} [params.consequenceType] - Filter by consequence type. - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - aggregationStatsRga(field, params) { - return this._get("analysis", null, "clinical/rga", null, "aggregationStats", {field, ...params}); - } - - /** Query gene RGA - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.include] - Fields included in the response, whole JSON path must be provided. - * @param {String} [params.exclude] - Fields excluded in the response, whole JSON path must be provided. - * @param {Number} [params.limit] - Number of results to be returned. - * @param {Number} [params.skip] - Number of results to skip. - * @param {Boolean} [params.count] - Get the total number of results matching the query. Deactivated by default. - * @param {String} [params.includeIndividual] - Include only the comma separated list of individuals to the response. - * @param {Number} [params.skipIndividual] - Number of individuals to skip. - * @param {Number} [params.limitIndividual] - Limit number of individuals returned (default: 1000). - * @param {String} [params.sampleId] - Filter by sample id. - * @param {String} [params.individualId] - Filter by individual id. - * @param {String} [params.sex] - Filter by sex. - * @param {String} [params.phenotypes] - Filter by phenotypes. - * @param {String} [params.disorders] - Filter by disorders. - * @param {String} [params.numParents] - Filter by the number of parents registered. - * @param {String} [params.geneId] - Filter by gene id. - * @param {String} [params.geneName] - Filter by gene name. - * @param {String} [params.chromosome] - Filter by chromosome. - * @param {String} [params.start] - Filter by start position. - * @param {String} [params.end] - Filter by end position. - * @param {String} [params.transcriptId] - Filter by transcript id. - * @param {String} [params.variants] - Filter by variant id. - * @param {String} [params.dbSnps] - Filter by DB_SNP id. - * @param {String} [params.knockoutType] - Filter by knockout type. - * @param {String} [params.filter] - Filter by filter (PASS, NOT_PASS). - * @param {String} [params.type] - Filter by variant type. - * @param {String} [params.clinicalSignificance] - Filter by clinical significance. - * @param {String} [params.populationFrequency] - Filter by population frequency. - * @param {String} [params.consequenceType] - Filter by consequence type. - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - queryRgaGene(params) { - return this._get("analysis", null, "clinical/rga/gene", null, "query", params); - } - - /** RGA gene summary stats - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {Number} [params.limit] - Number of results to be returned. - * @param {Number} [params.skip] - Number of results to skip. - * @param {Boolean} [params.count] - Get the total number of results matching the query. Deactivated by default. - * @param {String} [params.sampleId] - Filter by sample id. - * @param {String} [params.individualId] - Filter by individual id. - * @param {String} [params.sex] - Filter by sex. - * @param {String} [params.phenotypes] - Filter by phenotypes. - * @param {String} [params.disorders] - Filter by disorders. - * @param {String} [params.numParents] - Filter by the number of parents registered. - * @param {String} [params.geneId] - Filter by gene id. - * @param {String} [params.geneName] - Filter by gene name. - * @param {String} [params.chromosome] - Filter by chromosome. - * @param {String} [params.start] - Filter by start position. - * @param {String} [params.end] - Filter by end position. - * @param {String} [params.transcriptId] - Filter by transcript id. - * @param {String} [params.variants] - Filter by variant id. - * @param {String} [params.dbSnps] - Filter by DB_SNP id. - * @param {String} [params.knockoutType] - Filter by knockout type. - * @param {String} [params.filter] - Filter by filter (PASS, NOT_PASS). - * @param {String} [params.type] - Filter by variant type. - * @param {String} [params.clinicalSignificance] - Filter by clinical significance. - * @param {String} [params.populationFrequency] - Filter by population frequency. - * @param {String} [params.consequenceType] - Filter by consequence type. - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - summaryRgaGene(params) { - return this._get("analysis", null, "clinical/rga/gene", null, "summary", params); - } - - /** Generate Recessive Gene Analysis secondary index - * @param {Object} data - Recessive Gene Analysis index params. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.jobId] - Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not - * provided. - * @param {String} [params.jobDescription] - Job description. - * @param {String} [params.jobDependsOn] - Comma separated list of existing job IDs the job will depend on. - * @param {String} [params.jobTags] - Job tags. - * @param {Boolean} [params.auxiliarIndex = "false"] - Index auxiliar collection to improve performance assuming RGA is completely - * indexed. The default value is false. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - runRgaIndex(data, params) { - return this._post("analysis", null, "clinical/rga/index", null, "run", data, params); - } - - /** Query individual RGA - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.include] - Fields included in the response, whole JSON path must be provided. - * @param {String} [params.exclude] - Fields excluded in the response, whole JSON path must be provided. - * @param {Number} [params.limit] - Number of results to be returned. - * @param {Number} [params.skip] - Number of results to skip. - * @param {Boolean} [params.count] - Get the total number of results matching the query. Deactivated by default. - * @param {String} [params.sampleId] - Filter by sample id. - * @param {String} [params.individualId] - Filter by individual id. - * @param {String} [params.sex] - Filter by sex. - * @param {String} [params.phenotypes] - Filter by phenotypes. - * @param {String} [params.disorders] - Filter by disorders. - * @param {String} [params.numParents] - Filter by the number of parents registered. - * @param {String} [params.geneId] - Filter by gene id. - * @param {String} [params.geneName] - Filter by gene name. - * @param {String} [params.chromosome] - Filter by chromosome. - * @param {String} [params.start] - Filter by start position. - * @param {String} [params.end] - Filter by end position. - * @param {String} [params.transcriptId] - Filter by transcript id. - * @param {String} [params.variants] - Filter by variant id. - * @param {String} [params.dbSnps] - Filter by DB_SNP id. - * @param {String} [params.knockoutType] - Filter by knockout type. - * @param {String} [params.filter] - Filter by filter (PASS, NOT_PASS). - * @param {String} [params.type] - Filter by variant type. - * @param {String} [params.clinicalSignificance] - Filter by clinical significance. - * @param {String} [params.populationFrequency] - Filter by population frequency. - * @param {String} [params.consequenceType] - Filter by consequence type. - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - queryRgaIndividual(params) { - return this._get("analysis", null, "clinical/rga/individual", null, "query", params); - } - - /** RGA individual summary stats - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {Number} [params.limit] - Number of results to be returned. - * @param {Number} [params.skip] - Number of results to skip. - * @param {Boolean} [params.count] - Get the total number of results matching the query. Deactivated by default. - * @param {String} [params.sampleId] - Filter by sample id. - * @param {String} [params.individualId] - Filter by individual id. - * @param {String} [params.sex] - Filter by sex. - * @param {String} [params.phenotypes] - Filter by phenotypes. - * @param {String} [params.disorders] - Filter by disorders. - * @param {String} [params.numParents] - Filter by the number of parents registered. - * @param {String} [params.geneId] - Filter by gene id. - * @param {String} [params.geneName] - Filter by gene name. - * @param {String} [params.chromosome] - Filter by chromosome. - * @param {String} [params.start] - Filter by start position. - * @param {String} [params.end] - Filter by end position. - * @param {String} [params.transcriptId] - Filter by transcript id. - * @param {String} [params.variants] - Filter by variant id. - * @param {String} [params.dbSnps] - Filter by DB_SNP id. - * @param {String} [params.knockoutType] - Filter by knockout type. - * @param {String} [params.filter] - Filter by filter (PASS, NOT_PASS). - * @param {String} [params.type] - Filter by variant type. - * @param {String} [params.clinicalSignificance] - Filter by clinical significance. - * @param {String} [params.populationFrequency] - Filter by population frequency. - * @param {String} [params.consequenceType] - Filter by consequence type. - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - summaryRgaIndividual(params) { - return this._get("analysis", null, "clinical/rga/individual", null, "summary", params); - } - - /** Query variant RGA - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.include] - Fields included in the response, whole JSON path must be provided. - * @param {String} [params.exclude] - Fields excluded in the response, whole JSON path must be provided. - * @param {Number} [params.limit] - Number of results to be returned. - * @param {Number} [params.skip] - Number of results to skip. - * @param {Boolean} [params.count] - Get the total number of results matching the query. Deactivated by default. - * @param {String} [params.includeIndividual] - Include only the comma separated list of individuals to the response. - * @param {Number} [params.skipIndividual] - Number of individuals to skip. - * @param {Number} [params.limitIndividual] - Limit number of individuals returned (default: 1000). - * @param {String} [params.sampleId] - Filter by sample id. - * @param {String} [params.individualId] - Filter by individual id. - * @param {String} [params.sex] - Filter by sex. - * @param {String} [params.phenotypes] - Filter by phenotypes. - * @param {String} [params.disorders] - Filter by disorders. - * @param {String} [params.numParents] - Filter by the number of parents registered. - * @param {String} [params.geneId] - Filter by gene id. - * @param {String} [params.geneName] - Filter by gene name. - * @param {String} [params.chromosome] - Filter by chromosome. - * @param {String} [params.start] - Filter by start position. - * @param {String} [params.end] - Filter by end position. - * @param {String} [params.transcriptId] - Filter by transcript id. - * @param {String} [params.variants] - Filter by variant id. - * @param {String} [params.dbSnps] - Filter by DB_SNP id. - * @param {String} [params.knockoutType] - Filter by knockout type. - * @param {String} [params.filter] - Filter by filter (PASS, NOT_PASS). - * @param {String} [params.type] - Filter by variant type. - * @param {String} [params.clinicalSignificance] - Filter by clinical significance. - * @param {String} [params.populationFrequency] - Filter by population frequency. - * @param {String} [params.consequenceType] - Filter by consequence type. - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - queryRgaVariant(params) { - return this._get("analysis", null, "clinical/rga/variant", null, "query", params); - } - - /** RGA variant summary stats - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {Number} [params.limit] - Number of results to be returned. - * @param {Number} [params.skip] - Number of results to skip. - * @param {Boolean} [params.count] - Get the total number of results matching the query. Deactivated by default. - * @param {String} [params.sampleId] - Filter by sample id. - * @param {String} [params.individualId] - Filter by individual id. - * @param {String} [params.sex] - Filter by sex. - * @param {String} [params.phenotypes] - Filter by phenotypes. - * @param {String} [params.disorders] - Filter by disorders. - * @param {String} [params.numParents] - Filter by the number of parents registered. - * @param {String} [params.geneId] - Filter by gene id. - * @param {String} [params.geneName] - Filter by gene name. - * @param {String} [params.chromosome] - Filter by chromosome. - * @param {String} [params.start] - Filter by start position. - * @param {String} [params.end] - Filter by end position. - * @param {String} [params.transcriptId] - Filter by transcript id. - * @param {String} [params.variants] - Filter by variant id. - * @param {String} [params.dbSnps] - Filter by DB_SNP id. - * @param {String} [params.knockoutType] - Filter by knockout type. - * @param {String} [params.filter] - Filter by filter (PASS, NOT_PASS). - * @param {String} [params.type] - Filter by variant type. - * @param {String} [params.clinicalSignificance] - Filter by clinical significance. - * @param {String} [params.populationFrequency] - Filter by population frequency. - * @param {String} [params.consequenceType] - Filter by consequence type. - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - summaryRgaVariant(params) { - return this._get("analysis", null, "clinical/rga/variant", null, "summary", params); - } - - /** Clinical analysis search. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.include] - Fields included in the response, whole JSON path must be provided. - * @param {String} [params.exclude] - Fields excluded in the response, whole JSON path must be provided. - * @param {Number} [params.limit] - Number of results to be returned. - * @param {Number} [params.skip] - Number of results to skip. - * @param {Boolean} [params.count = "false"] - Get the total number of results matching the query. Deactivated by default. The default - * value is false. - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list of Clinical Analysis IDs up to a maximum of 100. - * @param {String} [params.uuid] - Comma separated list of Clinical Analysis UUIDs up to a maximum of 100. - * @param {String} [params.type] - Clinical Analysis type. - * @param {String} [params.disorder] - Clinical Analysis disorder. - * @param {String} [params.files] - Clinical Analysis files. - * @param {String} [params.sample] - Sample associated to the proband or any member of a family. - * @param {String} [params.individual] - Proband or any member of a family. - * @param {String} [params.proband] - Clinical Analysis proband. - * @param {String} [params.probandSamples] - Clinical Analysis proband samples. - * @param {String} [params.family] - Clinical Analysis family. - * @param {String} [params.familyMembers] - Clinical Analysis family members. - * @param {String} [params.familyMemberSamples] - Clinical Analysis family members samples. - * @param {String} [params.panels] - Clinical Analysis panels. - * @param {Boolean} [params.locked] - Locked Clinical Analyses. - * @param {String} [params.analystId] - Clinical Analysis analyst id. - * @param {String} [params.priority] - Clinical Analysis priority. - * @param {String} [params.flags] - Clinical Analysis flags. - * @param {String} [params.creationDate] - Clinical Analysis Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - * @param {String} [params.modificationDate] - Clinical Analysis Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, - * <201805. - * @param {String} [params.dueDate] - Clinical Analysis due date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - * @param {String} [params.qualityControlSummary] - Clinical Analysis quality control summary. - * @param {String} [params.release] - Release when it was created. - * @param {String} [params.status] - Filter by status. - * @param {String} [params.internalStatus] - Filter by internal status. - * @param {Boolean} [params.deleted] - Boolean to retrieve deleted entries. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - search(params) { - return this._get("analysis", null, "clinical", null, "search", params); - } - - /** Fetch actionable clinical variants - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.sample] - Sample ID. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - actionableVariant(params) { - return this._get("analysis", null, "clinical/variant", null, "actionable", params); - } - - /** Fetch clinical variants - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.include] - Fields included in the response, whole JSON path must be provided. - * @param {String} [params.exclude] - Fields excluded in the response, whole JSON path must be provided. - * @param {Number} [params.limit] - Number of results to be returned. - * @param {Number} [params.skip] - Number of results to skip. - * @param {Boolean} [params.count] - Get the total number of results matching the query. Deactivated by default. - * @param {Boolean} [params.approximateCount] - Get an approximate count, instead of an exact total count. Reduces execution time. - * @param {Number} [params.approximateCountSamplingSize] - Sampling size to get the approximate count. Larger values increase accuracy - * but also increase execution time. - * @param {String} [params.savedFilter] - Use a saved filter at User level. - * @param {String} [params.id] - List of IDs, these can be rs IDs (dbSNP) or variants in the format chrom:start:ref:alt, e.g. - * rs116600158,19:7177679:C:T. - * @param {String} [params.region] - List of regions, these can be just a single chromosome name or regions in the format chr:start-end, - * e.g.: 2,3:100000-200000. - * @param {String} [params.type] - List of types, accepted values are SNV, MNV, INDEL, SV, COPY_NUMBER, COPY_NUMBER_LOSS, - * COPY_NUMBER_GAIN, INSERTION, DELETION, DUPLICATION, TANDEM_DUPLICATION, BREAKEND, e.g. SNV,INDEL. - * @param {String} [params.study] - Filter variants from the given studies, these can be either the numeric ID or the alias with the - * format user@project:study. - * @param {String} [params.file] - Filter variants from the files specified. This will set includeFile parameter when not provided. - * @param {String} [params.filter] - Specify the FILTER for any of the files. If 'file' filter is provided, will match the file and the - * filter. e.g.: PASS,LowGQX. - * @param {String} [params.qual] - Specify the QUAL for any of the files. If 'file' filter is provided, will match the file and the qual. - * e.g.: >123.4. - * @param {String} [params.fileData] - Filter by file data (i.e. FILTER, QUAL and INFO columns from VCF file). - * [{file}:]{key}{op}{value}[,;]* . If no file is specified, will use all files from "file" filter. e.g. AN>200 or - * file_1.vcf:AN>200;file_2.vcf:AN<10 . Many fields can be combined. e.g. file_1.vcf:AN>200;DB=true;file_2.vcf:AN<10,FILTER=PASS,LowDP. - * @param {String} [params.sample] - Filter variants by sample genotype. This will automatically set 'includeSample' parameter when not - * provided. This filter accepts multiple 3 forms: 1) List of samples: Samples that contain the main variant. Accepts AND (;) and OR (,) - * operators. e.g. HG0097,HG0098 . 2) List of samples with genotypes: {sample}:{gt1},{gt2}. Accepts AND (;) and OR (,) operators. e.g. - * HG0097:0/0;HG0098:0/1,1/1 . Unphased genotypes (e.g. 0/1, 1/1) will also include phased genotypes (e.g. 0|1, 1|0, 1|1), but not vice - * versa. When filtering by multi-allelic genotypes, any secondary allele will match, regardless of its position e.g. 1/2 will match with - * genotypes 1/2, 1/3, 1/4, .... Genotype aliases accepted: HOM_REF, HOM_ALT, HET, HET_REF, HET_ALT, HET_MISS and MISS e.g. - * HG0097:HOM_REF;HG0098:HET_REF,HOM_ALT . 3) Sample with segregation mode: {sample}:{segregation}. Only one sample accepted.Accepted - * segregation modes: [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, - * mendelianError, compoundHeterozygous ]. Value is case insensitive. e.g. HG0097:DeNovo Sample must have parents defined and indexed. . - * @param {String} [params.sampleData] - Filter by any SampleData field from samples. [{sample}:]{key}{op}{value}[,;]* . If no sample is - * specified, will use all samples from "sample" or "genotype" filter. e.g. DP>200 or HG0097:DP>200,HG0098:DP<10 . Many FORMAT fields can - * be combined. e.g. HG0097:DP>200;GT=1/1,0/1,HG0098:DP<10. - * @param {String} [params.sampleAnnotation] - Selects some samples using metadata information from Catalog. e.g. - * age>20;phenotype=hpo:123,hpo:456;name=smith. - * @param {String} [params.cohort] - Select variants with calculated stats for the selected cohorts. - * @param {String} [params.cohortStatsRef] - Reference Allele Frequency: [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4. - * @param {String} [params.cohortStatsAlt] - Alternate Allele Frequency: [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4. - * @param {String} [params.cohortStatsMaf] - Minor Allele Frequency: [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4. - * @param {String} [params.cohortStatsMgf] - Minor Genotype Frequency: [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4. - * @param {String} [params.cohortStatsPass] - Filter PASS frequency: [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL>0.8. - * @param {String} [params.missingAlleles] - Number of missing alleles: [{study:}]{cohort}[<|>|<=|>=]{number}. - * @param {String} [params.missingGenotypes] - Number of missing genotypes: [{study:}]{cohort}[<|>|<=|>=]{number}. - * @param {String} [params.score] - Filter by variant score: [{study:}]{score}[<|>|<=|>=]{number}. - * @param {String} [params.family] - Filter variants where any of the samples from the given family contains the variant (HET or - * HOM_ALT). - * @param {String} [params.familyDisorder] - Specify the disorder to use for the family segregation. - * @param {String} [params.familySegregation] - Filter by segregation mode from a given family. Accepted values: [ autosomalDominant, - * autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, mendelianError, compoundHeterozygous ]. - * @param {String} [params.familyMembers] - Sub set of the members of a given family. - * @param {String} [params.familyProband] - Specify the proband child to use for the family segregation. - * @param {String} [params.gene] - List of genes, most gene IDs are accepted (HGNC, Ensembl gene, ...). This is an alias to 'xref' - * parameter. - * @param {String} [params.ct] - List of SO consequence types, e.g. missense_variant,stop_lost or SO:0001583,SO:0001578. Accepts aliases - * 'loss_of_function' and 'protein_altering'. - * @param {String} [params.xref] - List of any external reference, these can be genes, proteins or variants. Accepted IDs include HGNC, - * Ensembl genes, dbSNP, ClinVar, HPO, Cosmic, ... - * @param {String} [params.biotype] - List of biotypes, e.g. protein_coding. - * @param {String} [params.proteinSubstitution] - Protein substitution scores include SIFT and PolyPhen. You can query using the score - * {protein_score}[<|>|<=|>=]{number} or the description {protein_score}[~=|=]{description} e.g. polyphen>0.1,sift=tolerant. - * @param {String} [params.conservation] - Filter by conservation score: {conservation_score}[<|>|<=|>=]{number} e.g. - * phastCons>0.5,phylop<0.1,gerp>0.1. - * @param {String} [params.populationFrequencyAlt] - Alternate Population Frequency: {study}:{population}[<|>|<=|>=]{number}. e.g. - * 1000G:ALL<0.01. - * @param {String} [params.populationFrequencyRef] - Reference Population Frequency: {study}:{population}[<|>|<=|>=]{number}. e.g. - * 1000G:ALL<0.01. - * @param {String} [params.populationFrequencyMaf] - Population minor allele frequency: {study}:{population}[<|>|<=|>=]{number}. e.g. - * 1000G:ALL<0.01. - * @param {String} [params.transcriptFlag] - List of transcript flags. e.g. canonical, CCDS, basic, LRG, MANE Select, MANE Plus Clinical, - * EGLH_HaemOnc, TSO500. - * @param {String} [params.geneTraitId] - List of gene trait association id. e.g. "umls:C0007222" , "OMIM:269600". - * @param {String} [params.go] - List of GO (Gene Ontology) terms. e.g. "GO:0002020". - * @param {String} [params.expression] - List of tissues of interest. e.g. "lung". - * @param {String} [params.proteinKeyword] - List of Uniprot protein variant annotation keywords. - * @param {String} [params.drug] - List of drug names. - * @param {String} [params.functionalScore] - Functional score: {functional_score}[<|>|<=|>=]{number} e.g. cadd_scaled>5.2 , - * cadd_raw<=0.3. - * @param {String} [params.clinical] - Clinical source: clinvar, cosmic. - * @param {String} [params.clinicalSignificance] - Clinical significance: benign, likely_benign, likely_pathogenic, pathogenic. - * @param {Boolean} [params.clinicalConfirmedStatus] - Clinical confirmed status. - * @param {String} [params.customAnnotation] - Custom annotation: {key}[<|>|<=|>=]{number} or {key}[~=|=]{text}. - * @param {String} [params.panel] - Filter by genes from the given disease panel. - * @param {String} [params.panelModeOfInheritance] - Filter genes from specific panels that match certain mode of inheritance. Accepted - * values : [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, mendelianError, - * compoundHeterozygous ]. - * @param {String} [params.panelConfidence] - Filter genes from specific panels that match certain confidence. Accepted values : [ high, - * medium, low, rejected ]. - * @param {String} [params.panelRoleInCancer] - Filter genes from specific panels that match certain role in cancer. Accepted values : [ - * both, oncogene, tumorSuppressorGene, fusion ]. - * @param {String} [params.panelFeatureType] - Filter elements from specific panels by type. Accepted values : [ gene, region, str, - * variant ]. - * @param {Boolean} [params.panelIntersection] - Intersect panel genes and regions with given genes and regions from que input query. - * This will prevent returning variants from regions out of the panel. - * @param {String} [params.trait] - List of traits, based on ClinVar, HPO, COSMIC, i.e.: IDs, histologies, descriptions,... - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - queryVariant(params) { - return this._get("analysis", null, "clinical/variant", null, "query", params); - } - - /** Returns the acl of the clinical analyses. If member is provided, it will only return the acl for the member. - * @param {String} clinicalAnalyses - Comma separated list of clinical analysis IDs or names up to a maximum of 100. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.member] - User or group ID. - * @param {Boolean} [params.silent = "false"] - Boolean to retrieve all possible entries that are queried for, false to raise an - * exception whenever one of the entries looked for cannot be shown for whichever reason. The default value is false. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - acl(clinicalAnalyses, params) { - return this._get("analysis", null, "clinical", clinicalAnalyses, "acl", params); - } - - /** Delete clinical analyses - * @param {String} clinicalAnalyses - Comma separated list of clinical analysis IDs or names up to a maximum of 100. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {Boolean} [params.force = "false"] - Force deletion if the ClinicalAnalysis contains interpretations or is locked. The default - * value is false. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - delete(clinicalAnalyses, params) { - return this._delete("analysis", null, "clinical", clinicalAnalyses, "delete", params); - } - - /** Update clinical analysis attributes - * @param {String} clinicalAnalyses - Comma separated list of clinical analysis IDs. - * @param {Object} data - JSON containing clinical analysis information. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.include] - Fields included in the response, whole JSON path must be provided. - * @param {String} [params.exclude] - Fields excluded in the response, whole JSON path must be provided. - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {"ADD"|"REMOVE"|"REPLACE"} [params.commentsAction = "ADD"] - Action to be performed if the array of comments is being updated. - * The default value is ADD. - * @param {"ADD"|"SET"|"REMOVE"} [params.flagsAction = "ADD"] - Action to be performed if the array of flags is being updated. The - * default value is ADD. - * @param {"ADD"|"SET"|"REMOVE"} [params.filesAction = "ADD"] - Action to be performed if the array of files is being updated. The - * default value is ADD. - * @param {"ADD"|"SET"|"REMOVE"} [params.panelsAction = "ADD"] - Action to be performed if the array of panels is being updated. The - * default value is ADD. - * @param {Boolean} [params.includeResult = "false"] - Flag indicating to include the created or updated document result in the response. - * The default value is false. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - update(clinicalAnalyses, data, params) { - return this._post("analysis", null, "clinical", clinicalAnalyses, "update", data, params); - } - - /** Clinical analysis info - * @param {String} clinicalAnalysis - Comma separated list of clinical analysis IDs or names up to a maximum of 100. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.include] - Fields included in the response, whole JSON path must be provided. - * @param {String} [params.exclude] - Fields excluded in the response, whole JSON path must be provided. - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {Boolean} [params.deleted = "false"] - Boolean to retrieve deleted entries. The default value is false. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - info(clinicalAnalysis, params) { - return this._get("analysis", null, "clinical", clinicalAnalysis, "info", params); - } - - /** Create a new Interpretation - * @param {String} clinicalAnalysis - Clinical analysis ID. - * @param {Object} data - JSON containing clinical interpretation information. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.include] - Fields included in the response, whole JSON path must be provided. - * @param {String} [params.exclude] - Fields excluded in the response, whole JSON path must be provided. - * @param {String} [params.study] - [[user@]project:]study id. - * @param {"PRIMARY"|"SECONDARY"} [params.setAs = "SECONDARY"] - Set interpretation as. The default value is SECONDARY. - * @param {Boolean} [params.includeResult = "false"] - Flag indicating to include the created or updated document result in the response. - * The default value is false. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - createInterpretation(clinicalAnalysis, data, params) { - return this._post("analysis/clinical", clinicalAnalysis, "interpretation", null, "create", data, params); - } - - /** Clear the fields of the main interpretation of the Clinical Analysis - * @param {String} interpretations - Interpretation IDs of the Clinical Analysis. - * @param {String} clinicalAnalysis - Clinical analysis ID. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.study] - [[user@]project:]study ID. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - clearInterpretation(clinicalAnalysis, interpretations, params) { - return this._post("analysis/clinical", clinicalAnalysis, "interpretation", interpretations, "clear", params); - } - - /** Delete interpretation - * @param {String} clinicalAnalysis - Clinical analysis ID. - * @param {String} interpretations - Interpretation IDs of the Clinical Analysis. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.study] - [[user@]project:]study ID. - * @param {String} [params.setAsPrimary] - Interpretation id to set as primary from the list of secondaries in case of deleting the - * actual primary one. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - deleteInterpretation(clinicalAnalysis, interpretations, params) { - return this._delete("analysis/clinical", clinicalAnalysis, "interpretation", interpretations, "delete", params); - } - - /** Revert to a previous interpretation version - * @param {String} clinicalAnalysis - Clinical analysis ID. - * @param {String} interpretation - Interpretation ID. - * @param {Number} version - Version to revert to. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.study] - [[user@]project:]study ID. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - revertInterpretation(clinicalAnalysis, interpretation, version, params) { - return this._post("analysis/clinical", clinicalAnalysis, "interpretation", interpretation, "revert", {version, ...params}); - } - - /** Update interpretation fields - * @param {String} clinicalAnalysis - Clinical analysis ID. - * @param {String} interpretation - Interpretation ID. - * @param {Object} data - JSON containing clinical interpretation information. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.include] - Fields included in the response, whole JSON path must be provided. - * @param {String} [params.exclude] - Fields excluded in the response, whole JSON path must be provided. - * @param {String} [params.study] - [[user@]project:]study ID. - * @param {"ADD"|"SET"|"REMOVE"|"REPLACE"} [params.primaryFindingsAction = "ADD"] - Action to be performed if the array of primary - * findings is being updated. The default value is ADD. - * @param {"ADD"|"SET"|"REMOVE"} [params.methodsAction = "ADD"] - Action to be performed if the array of methods is being updated. The - * default value is ADD. - * @param {"ADD"|"SET"|"REMOVE"|"REPLACE"} [params.secondaryFindingsAction = "ADD"] - Action to be performed if the array of secondary - * findings is being updated. The default value is ADD. - * @param {"ADD"|"REMOVE"|"REPLACE"} [params.commentsAction = "ADD"] - Action to be performed if the array of comments is being updated. - * To REMOVE or REPLACE, the date will need to be provided to identify the comment. The default value is ADD. - * @param {"ADD"|"SET"|"REMOVE"} [params.panelsAction = "ADD"] - Action to be performed if the array of panels is being updated. The - * default value is ADD. - * @param {"PRIMARY"|"SECONDARY"} [params.setAs] - Set interpretation as. - * @param {Boolean} [params.includeResult = "false"] - Flag indicating to include the created or updated document result in the response. - * The default value is false. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - updateInterpretation(clinicalAnalysis, interpretation, data, params) { - return this._post("analysis/clinical", clinicalAnalysis, "interpretation", interpretation, "update", data, params); - } - -} \ No newline at end of file diff --git a/src/core/clients/opencga/api/ClinicalAnalysis.js b/src/core/clients/opencga/api/ClinicalAnalysis.js index 4b90259256..826196fd98 100644 --- a/src/core/clients/opencga/api/ClinicalAnalysis.js +++ b/src/core/clients/opencga/api/ClinicalAnalysis.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2022-08-11 16:30:01 + * Autogenerated on: 2024-02-02 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -46,6 +46,21 @@ export default class ClinicalAnalysis extends OpenCGAParentClass { return this._post("analysis", null, "clinical/acl", members, "update", data, {action, ...params}); } + /** Load annotation sets from a TSV file + * @param {Object} [data] - JSON containing the 'content' of the TSV file if this has not yet been registered into OpenCGA. + * @param {String} variableSetId - Variable set ID or name. + * @param {String} path - Path where the TSV file is located in OpenCGA or where it should be located. + * @param {Object} [params] - The Object containing the following optional parameters: + * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. + * @param {Boolean} [params.parents] - Flag indicating whether to create parent directories if they don't exist (only when TSV file was + * not previously associated). + * @param {String} [params.annotationSetId] - Annotation set id. If not provided, variableSetId will be used. + * @returns {Promise} Promise object in the form of RestResponse instance. + */ + loadAnnotationSets(variableSetId, path, data, params) { + return this._post("analysis", null, "clinical/annotationSets", null, "load", data, {variableSetId, path, ...params}); + } + /** Update Clinical Analysis configuration. * @param {Object} [data] - Configuration params to update. * @param {Object} [params] - The Object containing the following optional parameters: @@ -73,13 +88,15 @@ export default class ClinicalAnalysis extends OpenCGAParentClass { } /** Clinical Analysis distinct method - * @param {String} field - Field for which to obtain the distinct values. + * @param {String} field - Comma separated list of fields for which to obtain the distinct values. * @param {Object} [params] - The Object containing the following optional parameters: * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list of Clinical Analysis IDs up to a maximum of 100. + * @param {String} [params.id] - Comma separated list of Clinical Analysis IDs up to a maximum of 100. Also admits basic regular + * expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list of Clinical Analysis UUIDs up to a maximum of 100. * @param {String} [params.type] - Clinical Analysis type. - * @param {String} [params.disorder] - Clinical Analysis disorder. + * @param {String} [params.disorder] - Clinical Analysis disorder. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.files] - Clinical Analysis files. * @param {String} [params.sample] - Sample associated to the proband or any member of a family. * @param {String} [params.individual] - Proband or any member of a family. @@ -101,6 +118,8 @@ export default class ClinicalAnalysis extends OpenCGAParentClass { * @param {String} [params.release] - Release when it was created. * @param {String} [params.status] - Filter by status. * @param {String} [params.internalStatus] - Filter by internal status. + * @param {String} [params.annotation] - Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit + * http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0. * @param {Boolean} [params.deleted] - Boolean to retrieve deleted entries. * @returns {Promise} Promise object in the form of RestResponse instance. */ @@ -109,14 +128,16 @@ export default class ClinicalAnalysis extends OpenCGAParentClass { } /** Interpretation distinct method - * @param {String} field - Field for which to obtain the distinct values. + * @param {String} field - Comma separated list of fields for which to obtain the distinct values. * @param {Object} [params] - The Object containing the following optional parameters: * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list of Interpretation IDs up to a maximum of 100. + * @param {String} [params.id] - Comma separated list of Interpretation IDs up to a maximum of 100. Also admits basic regular expressions + * using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list of Interpretation UUIDs up to a maximum of 100. * @param {String} [params.clinicalAnalysisId] - Clinical Analysis id. * @param {String} [params.analystId] - Analyst ID. - * @param {String} [params.methodName] - Interpretation method name. + * @param {String} [params.methodName] - Interpretation method name. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.panels] - Interpretation panels. * @param {String} [params.primaryFindings] - Interpretation primary findings. * @param {String} [params.secondaryFindings] - Interpretation secondary findings. @@ -140,11 +161,13 @@ export default class ClinicalAnalysis extends OpenCGAParentClass { * @param {Number} [params.skip] - Number of results to skip. * @param {Boolean} [params.sort] - Sort the results. * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list of Interpretation IDs up to a maximum of 100. + * @param {String} [params.id] - Comma separated list of Interpretation IDs up to a maximum of 100. Also admits basic regular expressions + * using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list of Interpretation UUIDs up to a maximum of 100. * @param {String} [params.clinicalAnalysisId] - Clinical Analysis id. * @param {String} [params.analystId] - Analyst ID. - * @param {String} [params.methodName] - Interpretation method name. + * @param {String} [params.methodName] - Interpretation method name. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.panels] - Interpretation panels. * @param {String} [params.primaryFindings] - Interpretation primary findings. * @param {String} [params.secondaryFindings] - Interpretation secondary findings. @@ -512,11 +535,14 @@ export default class ClinicalAnalysis extends OpenCGAParentClass { * @param {Number} [params.skip] - Number of results to skip. * @param {Boolean} [params.count = "false"] - Get the total number of results matching the query. Deactivated by default. The default * value is false. + * @param {Boolean} [params.flattenAnnotations = "false"] - Flatten the annotations?. The default value is false. * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list of Clinical Analysis IDs up to a maximum of 100. + * @param {String} [params.id] - Comma separated list of Clinical Analysis IDs up to a maximum of 100. Also admits basic regular + * expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list of Clinical Analysis UUIDs up to a maximum of 100. * @param {String} [params.type] - Clinical Analysis type. - * @param {String} [params.disorder] - Clinical Analysis disorder. + * @param {String} [params.disorder] - Clinical Analysis disorder. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.files] - Clinical Analysis files. * @param {String} [params.sample] - Sample associated to the proband or any member of a family. * @param {String} [params.individual] - Proband or any member of a family. @@ -538,6 +564,8 @@ export default class ClinicalAnalysis extends OpenCGAParentClass { * @param {String} [params.release] - Release when it was created. * @param {String} [params.status] - Filter by status. * @param {String} [params.internalStatus] - Filter by internal status. + * @param {String} [params.annotation] - Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit + * http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0. * @param {Boolean} [params.deleted] - Boolean to retrieve deleted entries. * @returns {Promise} Promise object in the form of RestResponse instance. */ @@ -545,16 +573,6 @@ export default class ClinicalAnalysis extends OpenCGAParentClass { return this._get("analysis", null, "clinical", null, "search", params); } - /** Fetch actionable clinical variants - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.sample] - Sample ID. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - actionableVariant(params) { - return this._get("analysis", null, "clinical/variant", null, "actionable", params); - } - /** Fetch clinical variants * @param {Object} [params] - The Object containing the following optional parameters: * @param {String} [params.include] - Fields included in the response, whole JSON path must be provided. @@ -591,7 +609,8 @@ export default class ClinicalAnalysis extends OpenCGAParentClass { * genotypes 1/2, 1/3, 1/4, .... Genotype aliases accepted: HOM_REF, HOM_ALT, HET, HET_REF, HET_ALT, HET_MISS and MISS e.g. * HG0097:HOM_REF;HG0098:HET_REF,HOM_ALT . 3) Sample with segregation mode: {sample}:{segregation}. Only one sample accepted.Accepted * segregation modes: [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, - * mendelianError, compoundHeterozygous ]. Value is case insensitive. e.g. HG0097:DeNovo Sample must have parents defined and indexed. . + * deNovoStrict, mendelianError, compoundHeterozygous ]. Value is case insensitive. e.g. HG0097:DeNovo Sample must have parents defined + * and indexed. . * @param {String} [params.sampleData] - Filter by any SampleData field from samples. [{sample}:]{key}{op}{value}[,;]* . If no sample is * specified, will use all samples from "sample" or "genotype" filter. e.g. DP>200 or HG0097:DP>200,HG0098:DP<10 . Many FORMAT fields can * be combined. e.g. HG0097:DP>200;GT=1/1,0/1,HG0098:DP<10. @@ -610,7 +629,8 @@ export default class ClinicalAnalysis extends OpenCGAParentClass { * HOM_ALT). * @param {String} [params.familyDisorder] - Specify the disorder to use for the family segregation. * @param {String} [params.familySegregation] - Filter by segregation mode from a given family. Accepted values: [ autosomalDominant, - * autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, mendelianError, compoundHeterozygous ]. + * autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, deNovoStrict, mendelianError, + * compoundHeterozygous ]. * @param {String} [params.familyMembers] - Sub set of the members of a given family. * @param {String} [params.familyProband] - Specify the proband child to use for the family segregation. * @param {String} [params.gene] - List of genes, most gene IDs are accepted (HGNC, Ensembl gene, ...). This is an alias to 'xref' @@ -698,10 +718,14 @@ export default class ClinicalAnalysis extends OpenCGAParentClass { * default value is ADD. * @param {"ADD SET REMOVE"} [params.flagsAction = "ADD"] - Action to be performed if the array of flags is being updated. The default * value is ADD. + * @param {"ADD SET REMOVE"} [params.analystsAction = "ADD"] - Action to be performed if the array of analysts is being updated. The + * default value is ADD. * @param {"ADD SET REMOVE"} [params.filesAction = "ADD"] - Action to be performed if the array of files is being updated. The default * value is ADD. * @param {"ADD SET REMOVE"} [params.panelsAction = "ADD"] - Action to be performed if the array of panels is being updated. The default * value is ADD. + * @param {"ADD SET REMOVE"} [params.annotationSetsAction = "ADD"] - Action to be performed if the array of annotationSets is being + * updated. The default value is ADD. * @param {Boolean} [params.includeResult = "false"] - Flag indicating to include the created or updated document result in the response. * The default value is false. * @returns {Promise} Promise object in the form of RestResponse instance. @@ -710,11 +734,30 @@ export default class ClinicalAnalysis extends OpenCGAParentClass { return this._post("analysis", null, "clinical", clinicalAnalyses, "update", data, params); } + /** Update annotations from an annotationSet + * @param {String} clinicalAnalysis - Clinical analysis ID. + * @param {String} annotationSet - AnnotationSet ID to be updated. + * @param {Object} [data] - Json containing the map of annotations when the action is ADD, SET or REPLACE, a json with only the key + * 'remove' containing the comma separated variables to be removed as a value when the action is REMOVE or a json with only the key + * 'reset' containing the comma separated variables that will be set to the default value when the action is RESET. + * @param {Object} [params] - The Object containing the following optional parameters: + * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. + * @param {"ADD SET REMOVE RESET REPLACE"} [params.action = "ADD"] - Action to be performed: ADD to add new annotations; REPLACE to + * replace the value of an already existing annotation; SET to set the new list of annotations removing any possible old annotations; + * REMOVE to remove some annotations; RESET to set some annotations to the default value configured in the corresponding variables of the + * VariableSet if any. The default value is ADD. + * @returns {Promise} Promise object in the form of RestResponse instance. + */ + updateAnnotationSetsAnnotations(clinicalAnalysis, annotationSet, data, params) { + return this._post("analysis/clinical", clinicalAnalysis, "annotationSets", annotationSet, "annotations/update", data, params); + } + /** Clinical analysis info * @param {String} clinicalAnalysis - Comma separated list of clinical analysis IDs or names up to a maximum of 100. * @param {Object} [params] - The Object containing the following optional parameters: * @param {String} [params.include] - Fields included in the response, whole JSON path must be provided. * @param {String} [params.exclude] - Fields excluded in the response, whole JSON path must be provided. + * @param {Boolean} [params.flattenAnnotations = "false"] - Flatten the annotations?. The default value is false. * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. * @param {Boolean} [params.deleted = "false"] - Boolean to retrieve deleted entries. The default value is false. * @returns {Promise} Promise object in the form of RestResponse instance. @@ -802,4 +845,25 @@ export default class ClinicalAnalysis extends OpenCGAParentClass { return this._post("analysis/clinical", clinicalAnalysis, "interpretation", interpretation, "update", data, params); } + /** Update clinical analysis report + * @param {String} clinicalAnalysis - Clinical analysis ID. + * @param {Object} data - JSON containing clinical report information. + * @param {Object} [params] - The Object containing the following optional parameters: + * @param {String} [params.include] - Fields included in the response, whole JSON path must be provided. + * @param {String} [params.exclude] - Fields excluded in the response, whole JSON path must be provided. + * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. + * @param {"ADD REMOVE REPLACE"} [params.commentsAction = "ADD"] - Action to be performed if the array of comments is being updated. The + * default value is ADD. + * @param {"ADD SET REMOVE"} [params.supportingEvidencesAction = "ADD"] - Action to be performed if the array of supporting evidences is + * being updated. The default value is ADD. + * @param {"ADD SET REMOVE"} [params.filesAction = "ADD"] - Action to be performed if the array of files is being updated. The default + * value is ADD. + * @param {Boolean} [params.includeResult = "false"] - Flag indicating to include the created or updated document result in the response. + * The default value is false. + * @returns {Promise} Promise object in the form of RestResponse instance. + */ + updateReport(clinicalAnalysis, data, params) { + return this._post("analysis/clinical", clinicalAnalysis, "report", null, "update", data, params); + } + } \ No newline at end of file diff --git a/src/core/clients/opencga/api/Cohort.js b/src/core/clients/opencga/api/Cohort.js index fb8f34ca7d..f11d56a865 100644 --- a/src/core/clients/opencga/api/Cohort.js +++ b/src/core/clients/opencga/api/Cohort.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2022-08-11 16:30:01 + * Autogenerated on: 2024-02-02 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -98,14 +98,15 @@ export default class Cohort extends OpenCGAParentClass { } /** Cohort distinct method - * @param {String} field - Field for which to obtain the distinct values. + * @param {String} field - Comma separated list of fields for which to obtain the distinct values. * @param {Object} [params] - The Object containing the following optional parameters: * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list of cohort IDs up to a maximum of 100. - * @param {String} [params.name] - Comma separated list of cohort names up to a maximum of 100. + * @param {String} [params.id] - Comma separated list of cohort IDs up to a maximum of 100. Also admits basic regular expressions using + * the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.name] - Comma separated list of cohort names up to a maximum of 100. Also admits basic regular expressions + * using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list of cohort IDs up to a maximum of 100. - * @param {"CASE_CONTROL CASE_SET CONTROL_SET PAIRED PAIRED_TUMOR AGGREGATE TIME_SERIES FAMILY TRIO COLLECTION"} [params.type] - Cohort - * type. + * @param {String} [params.type] - Cohort type. * @param {String} [params.creationDate] - creationDate. * @param {String} [params.modificationDate] - modificationDate. * @param {Boolean} [params.deleted] - deleted. @@ -136,7 +137,8 @@ export default class Cohort extends OpenCGAParentClass { * @param {String} [params.modificationDate] - Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * @param {String} [params.internalStatus] - Filter by internal status. * @param {String} [params.status] - Filter by status. - * @param {String} [params.phenotypes] - Comma separated list of phenotype ids or names. + * @param {String} [params.phenotypes] - Comma separated list of phenotype ids or names. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.annotation] - Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit * http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0. * @param {String} [params.acl] - Filter entries for which a user has the provided permissions. Format: acl={user}:{permissions}. @@ -162,11 +164,12 @@ export default class Cohort extends OpenCGAParentClass { * value is false. * @param {Boolean} [params.flattenAnnotations = "false"] - Flatten the annotations?. The default value is false. * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list of cohort IDs up to a maximum of 100. - * @param {String} [params.name] - Comma separated list of cohort names up to a maximum of 100. + * @param {String} [params.id] - Comma separated list of cohort IDs up to a maximum of 100. Also admits basic regular expressions using + * the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.name] - Comma separated list of cohort names up to a maximum of 100. Also admits basic regular expressions + * using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list of cohort IDs up to a maximum of 100. - * @param {"CASE_CONTROL CASE_SET CONTROL_SET PAIRED PAIRED_TUMOR AGGREGATE TIME_SERIES FAMILY TRIO COLLECTION"} [params.type] - Cohort - * type. + * @param {String} [params.type] - Cohort type. * @param {String} [params.creationDate] - creationDate. * @param {String} [params.modificationDate] - modificationDate. * @param {Boolean} [params.deleted] - deleted. diff --git a/src/core/clients/opencga/api/DiseasePanel.js b/src/core/clients/opencga/api/DiseasePanel.js index acb306b818..aa4346dce4 100644 --- a/src/core/clients/opencga/api/DiseasePanel.js +++ b/src/core/clients/opencga/api/DiseasePanel.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2022-08-11 16:30:01 + * Autogenerated on: 2024-02-02 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -59,20 +59,30 @@ export default class DiseasePanel extends OpenCGAParentClass { } /** Panel distinct method - * @param {String} field - Field for which to obtain the distinct values. + * @param {String} field - Comma separated list of fields for which to obtain the distinct values. * @param {Object} [params] - The Object containing the following optional parameters: * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list of panel IDs up to a maximum of 100. + * @param {String} [params.id] - Comma separated list of panel IDs up to a maximum of 100. Also admits basic regular expressions using + * the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list of panel UUIDs up to a maximum of 100. - * @param {String} [params.name] - Comma separated list of panel names up to a maximum of 100. + * @param {String} [params.name] - Comma separated list of panel names up to a maximum of 100. Also admits basic regular expressions + * using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.internalStatus] - Filter by internal status. - * @param {String} [params.disorders] - Comma separated list of disorder ids or names. - * @param {String} [params.variants] - Comma separated list of variant ids. - * @param {String} [params.genes] - Comma separated list of gene ids. + * @param {String} [params.disorders] - Comma separated list of disorder ids or names. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.. Also admits basic + * regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive + * search. + * @param {String} [params.variants] - Comma separated list of variant ids. Also admits basic regular expressions using the operator '~', + * i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.genes] - Comma separated list of gene ids. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.source] - Comma separated list of source ids or names. - * @param {String} [params.regions] - Comma separated list of regions. - * @param {String} [params.categories] - Comma separated list of category names. - * @param {String} [params.tags] - Panel tags. + * @param {String} [params.regions] - Comma separated list of regions. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.categories] - Comma separated list of category names. Also admits basic regular expressions using the operator + * '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.tags] - Panel tags. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. + * '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {Boolean} [params.deleted = "false"] - Boolean to retrieve deleted entries. The default value is false. * @param {String} [params.status] - Filter by status. * @param {String} [params.creationDate] - Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. @@ -112,17 +122,27 @@ export default class DiseasePanel extends OpenCGAParentClass { * @param {Boolean} [params.count = "false"] - Get the total number of results matching the query. Deactivated by default. The default * value is false. * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list of panel IDs up to a maximum of 100. + * @param {String} [params.id] - Comma separated list of panel IDs up to a maximum of 100. Also admits basic regular expressions using + * the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list of panel UUIDs up to a maximum of 100. - * @param {String} [params.name] - Comma separated list of panel names up to a maximum of 100. + * @param {String} [params.name] - Comma separated list of panel names up to a maximum of 100. Also admits basic regular expressions + * using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.internalStatus] - Filter by internal status. - * @param {String} [params.disorders] - Comma separated list of disorder ids or names. - * @param {String} [params.variants] - Comma separated list of variant ids. - * @param {String} [params.genes] - Comma separated list of gene ids. + * @param {String} [params.disorders] - Comma separated list of disorder ids or names. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.. Also admits basic + * regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive + * search. + * @param {String} [params.variants] - Comma separated list of variant ids. Also admits basic regular expressions using the operator '~', + * i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.genes] - Comma separated list of gene ids. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.source] - Comma separated list of source ids or names. - * @param {String} [params.regions] - Comma separated list of regions. - * @param {String} [params.categories] - Comma separated list of category names. - * @param {String} [params.tags] - Panel tags. + * @param {String} [params.regions] - Comma separated list of regions. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.categories] - Comma separated list of category names. Also admits basic regular expressions using the operator + * '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.tags] - Panel tags. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. + * '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {Boolean} [params.deleted = "false"] - Boolean to retrieve deleted entries. The default value is false. * @param {String} [params.status] - Filter by status. * @param {String} [params.creationDate] - Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. diff --git a/src/core/clients/opencga/api/Family.js b/src/core/clients/opencga/api/Family.js index 2904307a2c..51ceba74de 100644 --- a/src/core/clients/opencga/api/Family.js +++ b/src/core/clients/opencga/api/Family.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2022-08-11 16:30:01 + * Autogenerated on: 2024-02-02 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -101,17 +101,21 @@ export default class Family extends OpenCGAParentClass { } /** Family distinct method - * @param {String} field - Field for which to obtain the distinct values. + * @param {String} field - Comma separated list of fields for which to obtain the distinct values. * @param {Object} [params] - The Object containing the following optional parameters: * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list family IDs up to a maximum of 100. - * @param {String} [params.name] - Comma separated list family names up to a maximum of 100. + * @param {String} [params.id] - Comma separated list family IDs up to a maximum of 100. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.name] - Comma separated list family names up to a maximum of 100. Also admits basic regular expressions using + * the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list family UUIDs up to a maximum of 100. * @param {String} [params.members] - Comma separated list of family members. * @param {Number} [params.expectedSize] - Expected size of the family (number of members). * @param {String} [params.samples] - Comma separated list of member's samples. - * @param {String} [params.phenotypes] - Comma separated list of phenotype ids or names. - * @param {String} [params.disorders] - Comma separated list of disorder ids or names. + * @param {String} [params.phenotypes] - Comma separated list of phenotype ids or names. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.disorders] - Comma separated list of disorder ids or names. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.creationDate] - Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * @param {String} [params.modificationDate] - Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * @param {Boolean} [params.deleted = "false"] - Boolean to retrieve deleted entries. The default value is false. @@ -140,14 +144,18 @@ export default class Family extends OpenCGAParentClass { * value is false. * @param {Boolean} [params.flattenAnnotations = "false"] - Flatten the annotations?. The default value is false. * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list family IDs up to a maximum of 100. - * @param {String} [params.name] - Comma separated list family names up to a maximum of 100. + * @param {String} [params.id] - Comma separated list family IDs up to a maximum of 100. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.name] - Comma separated list family names up to a maximum of 100. Also admits basic regular expressions using + * the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list family UUIDs up to a maximum of 100. * @param {String} [params.members] - Comma separated list of family members. * @param {Number} [params.expectedSize] - Expected size of the family (number of members). * @param {String} [params.samples] - Comma separated list of member's samples. - * @param {String} [params.phenotypes] - Comma separated list of phenotype ids or names. - * @param {String} [params.disorders] - Comma separated list of disorder ids or names. + * @param {String} [params.phenotypes] - Comma separated list of phenotype ids or names. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.disorders] - Comma separated list of disorder ids or names. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.creationDate] - Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * @param {String} [params.modificationDate] - Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * @param {Boolean} [params.deleted = "false"] - Boolean to retrieve deleted entries. The default value is false. @@ -213,6 +221,7 @@ export default class Family extends OpenCGAParentClass { * @param {String} [params.exclude] - Fields excluded in the response, whole JSON path must be provided. * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. * @param {Boolean} [params.updateRoles = "false"] - Update the member roles within the family. The default value is false. + * @param {Boolean} [params.updatePedigreeGraph = "false"] - Update the family pedigree graph. The default value is false. * @param {"ADD SET REMOVE"} [params.annotationSetsAction = "ADD"] - Action to be performed if the array of annotationSets is being * updated. The default value is ADD. * @param {Boolean} [params.includeResult = "false"] - Flag indicating to include the created or updated document result in the response. diff --git a/src/core/clients/opencga/api/File.js b/src/core/clients/opencga/api/File.js index 5b050521d7..7793fe8997 100644 --- a/src/core/clients/opencga/api/File.js +++ b/src/core/clients/opencga/api/File.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2022-08-11 16:30:01 + * Autogenerated on: 2024-02-02 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -109,14 +109,18 @@ export default class File extends OpenCGAParentClass { } /** File distinct method - * @param {String} field - Field for which to obtain the distinct values. + * @param {String} field - Comma separated list of fields for which to obtain the distinct values. * @param {Object} [params] - The Object containing the following optional parameters: * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list of file IDs up to a maximum of 100. + * @param {String} [params.id] - Comma separated list of file IDs up to a maximum of 100. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list file UUIDs up to a maximum of 100. - * @param {String} [params.name] - Comma separated list of file names. - * @param {String} [params.path] - Comma separated list of paths. - * @param {String} [params.uri] - Comma separated list of uris. + * @param {String} [params.name] - Comma separated list of file names. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.path] - Comma separated list of paths. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.uri] - Comma separated list of uris. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.type] - File type, either FILE or DIRECTORY. * @param {String} [params.bioformat] - Comma separated Bioformat values. For existing Bioformats see files/bioformats. * @param {String} [params.format] - Comma separated Format values. For existing Formats see files/formats. @@ -129,7 +133,8 @@ export default class File extends OpenCGAParentClass { * @param {String} [params.creationDate] - Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * @param {String} [params.modificationDate] - Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * @param {String} [params.description] - Description. - * @param {String} [params.tags] - Tags. + * @param {String} [params.tags] - Tags. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' + * for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.size] - File size. * @param {String} [params.sampleIds] - Comma separated list sample IDs or UUIDs up to a maximum of 100. * @param {String} [params.jobId] - Job ID that created the file(s) or folder(s). @@ -220,11 +225,15 @@ export default class File extends OpenCGAParentClass { * value is false. * @param {Boolean} [params.flattenAnnotations = "false"] - Boolean indicating to flatten the annotations. The default value is false. * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list of file IDs up to a maximum of 100. + * @param {String} [params.id] - Comma separated list of file IDs up to a maximum of 100. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list file UUIDs up to a maximum of 100. - * @param {String} [params.name] - Comma separated list of file names. - * @param {String} [params.path] - Comma separated list of paths. - * @param {String} [params.uri] - Comma separated list of uris. + * @param {String} [params.name] - Comma separated list of file names. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.path] - Comma separated list of paths. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.uri] - Comma separated list of uris. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.type] - File type, either FILE or DIRECTORY. * @param {String} [params.bioformat] - Comma separated Bioformat values. For existing Bioformats see files/bioformats. * @param {String} [params.format] - Comma separated Format values. For existing Formats see files/formats. @@ -237,7 +246,8 @@ export default class File extends OpenCGAParentClass { * @param {String} [params.creationDate] - Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * @param {String} [params.modificationDate] - Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * @param {String} [params.description] - Description. - * @param {String} [params.tags] - Tags. + * @param {String} [params.tags] - Tags. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' + * for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.size] - File size. * @param {String} [params.sampleIds] - Comma separated list sample IDs or UUIDs up to a maximum of 100. * @param {String} [params.jobId] - Job ID that created the file(s) or folder(s). @@ -257,9 +267,9 @@ export default class File extends OpenCGAParentClass { /** Resource to upload a file by chunks * @param {Object} [params] - The Object containing the following optional parameters: * @param {InputStream} [params.file] - File to upload. - * @param {String} [params.filename] - File name to overwrite the input fileName. + * @param {String} [params.fileName] - File name to overwrite the input fileName. * @param {"VCF BCF GVCF TBI BIGWIG SAM BAM BAI CRAM CRAI FASTQ FASTA PED TAB_SEPARATED_VALUES COMMA_SEPARATED_VALUES XML PROTOCOL_BUFFER - * JSON AVRO PARQUET IMAGE PLAIN BINARY NONE UNKNOWN"} [params.fileFormat] - File format. + * JSON AVRO PARQUET PDF IMAGE PLAIN BINARY NONE UNKNOWN"} [params.fileFormat] - File format. * @param {"MICROARRAY_EXPRESSION_ONECHANNEL_AGILENT MICROARRAY_EXPRESSION_ONECHANNEL_AFFYMETRIX MICROARRAY_EXPRESSION_ONECHANNEL_GENEPIX * MICROARRAY_EXPRESSION_TWOCHANNELS_AGILENT MICROARRAY_EXPRESSION_TWOCHANNELS_GENEPIX DATAMATRIX_EXPRESSION IDLIST IDLIST_RANKED * ANNOTATION_GENEVSANNOTATION OTHER_NEWICK OTHER_BLAST OTHER_INTERACTION OTHER_GENOTYPE OTHER_PLINK OTHER_VCF OTHER_PED VCF4 VARIANT diff --git a/src/core/clients/opencga/api/GA4GH.js b/src/core/clients/opencga/api/GA4GH.js index f065546133..a875626c28 100644 --- a/src/core/clients/opencga/api/GA4GH.js +++ b/src/core/clients/opencga/api/GA4GH.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2022-08-11 16:30:01 + * Autogenerated on: 2024-02-02 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/src/core/clients/opencga/api/Individual.js b/src/core/clients/opencga/api/Individual.js index 612c32db62..19ab182bff 100644 --- a/src/core/clients/opencga/api/Individual.js +++ b/src/core/clients/opencga/api/Individual.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2022-08-11 16:30:01 + * Autogenerated on: 2024-02-02 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -108,23 +108,30 @@ export default class Individual extends OpenCGAParentClass { } /** Individual distinct method - * @param {String} field - Field for which to obtain the distinct values. + * @param {String} field - Comma separated list of fields for which to obtain the distinct values. * @param {Object} [params] - The Object containing the following optional parameters: * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list individual IDs up to a maximum of 100. + * @param {String} [params.id] - Comma separated list individual IDs up to a maximum of 100. Also admits basic regular expressions using + * the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list individual UUIDs up to a maximum of 100. - * @param {String} [params.name] - Comma separated list individual names up to a maximum of 100. + * @param {String} [params.name] - Comma separated list individual names up to a maximum of 100. Also admits basic regular expressions + * using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.familyIds] - Comma separated list of family ids the individuals may belong to. * @param {String} [params.father] - Father ID, name or UUID. * @param {String} [params.mother] - Mother ID, name or UUID. * @param {String} [params.samples] - Sample ID, name or UUID. * @param {String} [params.sex] - Individual sex. - * @param {String} [params.ethnicity] - Individual ethnicity. + * @param {String} [params.ethnicity] - Individual ethnicity. Also admits basic regular expressions using the operator '~', i.e. '~{perl- + * regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.dateOfBirth] - Individual date of birth. - * @param {String} [params.disorders] - Comma separated list of disorder ids or names. - * @param {String} [params.phenotypes] - Comma separated list of phenotype ids or names. - * @param {String} [params.populationName] - Population name. - * @param {String} [params.populationSubpopulation] - Subpopulation name. + * @param {String} [params.disorders] - Comma separated list of disorder ids or names. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.phenotypes] - Comma separated list of phenotype ids or names. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.populationName] - Population name. Also admits basic regular expressions using the operator '~', i.e. '~{perl- + * regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.populationSubpopulation] - Subpopulation name. Also admits basic regular expressions using the operator '~', + * i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.karyotypicSex] - Individual karyotypic sex. * @param {String} [params.lifeStatus] - Individual life status. * @param {String} [params.internalStatus] - Filter by internal status. @@ -155,20 +162,27 @@ export default class Individual extends OpenCGAParentClass { * value is false. * @param {Boolean} [params.flattenAnnotations = "false"] - Flatten the annotations?. The default value is false. * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list individual IDs up to a maximum of 100. + * @param {String} [params.id] - Comma separated list individual IDs up to a maximum of 100. Also admits basic regular expressions using + * the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list individual UUIDs up to a maximum of 100. - * @param {String} [params.name] - Comma separated list individual names up to a maximum of 100. + * @param {String} [params.name] - Comma separated list individual names up to a maximum of 100. Also admits basic regular expressions + * using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.father] - Father ID, name or UUID. * @param {String} [params.mother] - Mother ID, name or UUID. * @param {String} [params.samples] - Sample ID, name or UUID. * @param {String} [params.familyIds] - Comma separated list of family ids the individuals may belong to. * @param {String} [params.sex] - Individual sex. * @param {String} [params.dateOfBirth] - Individual date of birth. - * @param {String} [params.ethnicity] - Individual ethnicity. - * @param {String} [params.disorders] - Comma separated list of disorder ids or names. - * @param {String} [params.phenotypes] - Comma separated list of phenotype ids or names. - * @param {String} [params.populationName] - Population name. - * @param {String} [params.populationSubpopulation] - Subpopulation name. + * @param {String} [params.ethnicity] - Individual ethnicity. Also admits basic regular expressions using the operator '~', i.e. '~{perl- + * regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.disorders] - Comma separated list of disorder ids or names. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.phenotypes] - Comma separated list of phenotype ids or names. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.populationName] - Population name. Also admits basic regular expressions using the operator '~', i.e. '~{perl- + * regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.populationSubpopulation] - Subpopulation name. Also admits basic regular expressions using the operator '~', + * i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.karyotypicSex] - Individual karyotypic sex. * @param {String} [params.lifeStatus] - Individual life status. * @param {String} [params.internalStatus] - Filter by internal status. diff --git a/src/core/clients/opencga/api/Job.js b/src/core/clients/opencga/api/Job.js index 844b17017a..2ddbc5e5cd 100644 --- a/src/core/clients/opencga/api/Job.js +++ b/src/core/clients/opencga/api/Job.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2022-08-11 16:30:01 + * Autogenerated on: 2024-02-02 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -80,14 +80,16 @@ export default class Job extends OpenCGAParentClass { } /** Job distinct method - * @param {String} field - Field for which to obtain the distinct values. + * @param {String} field - Comma separated list of fields for which to obtain the distinct values. * @param {Object} [params] - The Object containing the following optional parameters: * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. * @param {Boolean} [params.otherStudies = "false"] - Flag indicating the entries being queried can belong to any related study, not just * the primary one. The default value is false. - * @param {String} [params.id] - Comma separated list of job IDs up to a maximum of 100. + * @param {String} [params.id] - Comma separated list of job IDs up to a maximum of 100. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list of job UUIDs up to a maximum of 100. - * @param {String} [params.toolId] - Tool ID executed by the job. + * @param {String} [params.toolId] - Tool ID executed by the job. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.toolType] - Tool type executed by the job [OPERATION, ANALYSIS]. * @param {String} [params.userId] - User that created the job. * @param {String} [params.priority] - Priority of the job. @@ -136,9 +138,11 @@ export default class Job extends OpenCGAParentClass { * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. * @param {Boolean} [params.otherStudies = "false"] - Flag indicating the entries being queried can belong to any related study, not just * the primary one. The default value is false. - * @param {String} [params.id] - Comma separated list of job IDs up to a maximum of 100. + * @param {String} [params.id] - Comma separated list of job IDs up to a maximum of 100. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list of job UUIDs up to a maximum of 100. - * @param {String} [params.toolId] - Tool ID executed by the job. + * @param {String} [params.toolId] - Tool ID executed by the job. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.toolType] - Tool type executed by the job [OPERATION, ANALYSIS]. * @param {String} [params.userId] - User that created the job. * @param {String} [params.priority] - Priority of the job. @@ -168,7 +172,8 @@ export default class Job extends OpenCGAParentClass { * @param {String} [params.internalStatus] - Filter by internal status. * @param {String} [params.priority] - Priority of the job. * @param {String} [params.userId] - User that created the job. - * @param {String} [params.toolId] - Tool ID executed by the job. + * @param {String} [params.toolId] - Tool ID executed by the job. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @returns {Promise} Promise object in the form of RestResponse instance. */ top(params) { diff --git a/src/core/clients/opencga/api/Meta.js b/src/core/clients/opencga/api/Meta.js index a0711edbbc..35a8a7bea3 100644 --- a/src/core/clients/opencga/api/Meta.js +++ b/src/core/clients/opencga/api/Meta.js @@ -10,12 +10,12 @@ * See the License for the specific language governing permissions and * limitations under the License. * WARNING: AUTOGENERATED CODE - * + * * This code was generated by a tool. - * Autogenerated on: 2022-08-11 16:30:01 - * + * Autogenerated on: 2024-02-02 + * * Manual changes to this file may cause unexpected behavior in your application. - * Manual changes to this file will be overwritten if the code is regenerated. + * Manual changes to this file will be overwritten if the code is regenerated. * **/ @@ -33,7 +33,7 @@ export default class Meta extends OpenCGAParentClass { } /** Returns info about current OpenCGA code. - * + * * @returns {Promise} Promise object in the form of RestResponse instance. */ about() { @@ -50,7 +50,7 @@ export default class Meta extends OpenCGAParentClass { } /** Ping Opencga webservices. - * + * * @returns {Promise} Promise object in the form of RestResponse instance. */ fail() { @@ -59,6 +59,7 @@ export default class Meta extends OpenCGAParentClass { /** Opencga model webservices. * @param {Object} [params] - The Object containing the following optional parameters: + * @param {String} [params.model] - Model description. * @returns {Promise} Promise object in the form of RestResponse instance. */ model(params) { @@ -66,7 +67,7 @@ export default class Meta extends OpenCGAParentClass { } /** Ping Opencga webservices. - * + * * @returns {Promise} Promise object in the form of RestResponse instance. */ ping() { @@ -74,11 +75,11 @@ export default class Meta extends OpenCGAParentClass { } /** Database status. - * + * * @returns {Promise} Promise object in the form of RestResponse instance. */ status() { return this._get("meta", null, null, null, "status"); } -} +} \ No newline at end of file diff --git a/src/core/clients/opencga/api/Project.js b/src/core/clients/opencga/api/Project.js index 98a522b2e9..d11f75b8d2 100644 --- a/src/core/clients/opencga/api/Project.js +++ b/src/core/clients/opencga/api/Project.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2022-08-11 16:30:01 + * Autogenerated on: 2024-02-02 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/src/core/clients/opencga/api/Sample.js b/src/core/clients/opencga/api/Sample.js index 70ff05ded5..cde2fc5698 100644 --- a/src/core/clients/opencga/api/Sample.js +++ b/src/core/clients/opencga/api/Sample.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2022-08-11 16:30:01 + * Autogenerated on: 2024-02-02 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -100,10 +100,11 @@ export default class Sample extends OpenCGAParentClass { } /** Sample distinct method - * @param {String} field - Field for which to obtain the distinct values. + * @param {String} field - Comma separated list of fields for which to obtain the distinct values. * @param {Object} [params] - The Object containing the following optional parameters: * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list sample IDs up to a maximum of 100. + * @param {String} [params.id] - Comma separated list sample IDs up to a maximum of 100. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list sample UUIDs up to a maximum of 100. * @param {Boolean} [params.somatic] - Somatic sample. * @param {String} [params.individualId] - Individual ID or UUID. @@ -120,7 +121,8 @@ export default class Sample extends OpenCGAParentClass { * @param {String} [params.collectionFrom] - Collection from. * @param {String} [params.collectionType] - Collection type. * @param {String} [params.collectionMethod] - Collection method. - * @param {String} [params.phenotypes] - Comma separated list of phenotype ids or names. + * @param {String} [params.phenotypes] - Comma separated list of phenotype ids or names. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.annotation] - Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit * http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0. * @param {String} [params.acl] - Filter entries for which a user has the provided permissions. Format: acl={user}:{permissions}. @@ -173,7 +175,8 @@ export default class Sample extends OpenCGAParentClass { * @param {Boolean} [params.includeIndividual = "false"] - Include Individual object as an attribute. The default value is false. * @param {Boolean} [params.flattenAnnotations = "false"] - Flatten the annotations?. The default value is false. * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list sample IDs up to a maximum of 100. + * @param {String} [params.id] - Comma separated list sample IDs up to a maximum of 100. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list sample UUIDs up to a maximum of 100. * @param {Boolean} [params.somatic] - Somatic sample. * @param {String} [params.individualId] - Individual ID or UUID. @@ -190,7 +193,8 @@ export default class Sample extends OpenCGAParentClass { * @param {String} [params.collectionFrom] - Collection from. * @param {String} [params.collectionType] - Collection type. * @param {String} [params.collectionMethod] - Collection method. - * @param {String} [params.phenotypes] - Comma separated list of phenotype ids or names. + * @param {String} [params.phenotypes] - Comma separated list of phenotype ids or names. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.annotation] - Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit * http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0. * @param {String} [params.acl] - Filter entries for which a user has the provided permissions. Format: acl={user}:{permissions}. diff --git a/src/core/clients/opencga/api/Study.js b/src/core/clients/opencga/api/Study.js index 6a7a5ce91e..89bb9f1114 100644 --- a/src/core/clients/opencga/api/Study.js +++ b/src/core/clients/opencga/api/Study.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2022-08-11 16:30:01 + * Autogenerated on: 2024-02-02 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/src/core/clients/opencga/api/User.js b/src/core/clients/opencga/api/User.js index 145d946d69..c7d367f9d9 100644 --- a/src/core/clients/opencga/api/User.js +++ b/src/core/clients/opencga/api/User.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2022-08-11 16:30:01 + * Autogenerated on: 2024-02-02 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -32,14 +32,6 @@ export default class User extends OpenCGAParentClass { super(config); } - /** Create a new user - * @param {Object} data - JSON containing the parameters. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - create(data) { - return this._post("users", null, null, null, "create", data); - } - /** Get identified and gain access to the system * @param {Object} [data] - JSON containing the authentication parameters. * @returns {Promise} Promise object in the form of RestResponse instance. diff --git a/src/core/clients/opencga/api/Variant.js b/src/core/clients/opencga/api/Variant.js index 651e0e287d..8f80259b63 100644 --- a/src/core/clients/opencga/api/Variant.js +++ b/src/core/clients/opencga/api/Variant.js @@ -10,12 +10,12 @@ * See the License for the specific language governing permissions and * limitations under the License. * WARNING: AUTOGENERATED CODE - * + * * This code was generated by a tool. - * Autogenerated on: 2022-12-19 14:56:41 - * + * Autogenerated on: 2024-02-02 + * * Manual changes to this file may cause unexpected behavior in your application. - * Manual changes to this file will be overwritten if the code is regenerated. + * Manual changes to this file will be overwritten if the code is regenerated. * **/ @@ -406,7 +406,7 @@ export default class Variant extends OpenCGAParentClass { return this._post("analysis", null, "variant/mendelianError", null, "run", data, params); } - /** + /** * @param {Object} [params] - The Object containing the following optional parameters: * @param {String} [params.project] - Project [user@]project where project can be either the ID or the alias. * @param {String} [params.study] - Filter variants from the given studies, these can be either the numeric ID or the alias with the @@ -863,4 +863,4 @@ export default class Variant extends OpenCGAParentClass { return this._post("analysis", null, "variant/stats", null, "run", data, params); } -} +} \ No newline at end of file diff --git a/src/core/clients/opencga/api/VariantOperation.js b/src/core/clients/opencga/api/VariantOperation.js index b2fd4211dd..e58c1c5a84 100644 --- a/src/core/clients/opencga/api/VariantOperation.js +++ b/src/core/clients/opencga/api/VariantOperation.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2022-08-11 16:30:01 + * Autogenerated on: 2024-02-02 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -330,7 +330,7 @@ export default class VariantOperation extends OpenCGAParentClass { } /** Creates a secondary index using a search engine. If samples are provided, sample data will be added to the secondary index. (New!) - * @param {Object} [data] - Variant secondary index params. + * @param {Object} [data] - Variant secondary annotation index params. * @param {Object} [params] - The Object containing the following optional parameters: * @param {String} [params.jobId] - Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not * provided. @@ -372,7 +372,7 @@ export default class VariantOperation extends OpenCGAParentClass { } /** DEPRECATED you should use the new annotation index method instead. - * @param {Object} [data] - Variant secondary index params. + * @param {Object} [data] - Variant secondary annotation index params. * @param {Object} [params] - The Object containing the following optional parameters: * @param {String} [params.jobId] - Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not * provided. diff --git a/src/core/clients/opencga/opencga-client.js b/src/core/clients/opencga/opencga-client.js index 34a78d318f..6bf521b1cb 100644 --- a/src/core/clients/opencga/opencga-client.js +++ b/src/core/clients/opencga/opencga-client.js @@ -16,7 +16,7 @@ import Admin from "./api/Admin.js"; import Alignment from "./api/Alignment.js"; -import Clinical from "./api/Clinical.js"; +import ClinicalAnalysis from "./api/ClinicalAnalysis.js"; import Cohort from "./api/Cohort.js"; import DiseasePanel from "./api/DiseasePanel.js"; import Family from "./api/Family.js"; @@ -188,7 +188,7 @@ export class OpenCGAClient { clinical() { if (!this.clients.has("clinical")) { - this.clients.set("clinical", new Clinical(this._config)); + this.clients.set("clinical", new ClinicalAnalysis(this._config)); } return this.clients.get("clinical"); } diff --git a/src/sites/test-app/clients/opencga-client-mock.js b/src/sites/test-app/clients/opencga-client-mock.js index 2f9d7f606d..19a87e69be 100644 --- a/src/sites/test-app/clients/opencga-client-mock.js +++ b/src/sites/test-app/clients/opencga-client-mock.js @@ -16,7 +16,7 @@ import Admin from "./api-mock/Admin"; import Alignment from "./api-mock/Alignment.js"; -import Clinical from "./api-mock/Clinical.js"; +import ClinicalAnalysis from "./api-mock/ClinicalAnalysis.js"; import Cohort from "./api-mock/Cohort.js"; import DiseasePanel from "./api-mock/DiseasePanel.js"; import Family from "./api-mock/Family.js"; @@ -184,7 +184,7 @@ export class OpenCGAClientMock { clinical() { if (!this.clients.has("clinical")) { - this.clients.set("clinical", new Clinical(this._config)); + this.clients.set("clinical", new ClinicalAnalysis(this._config)); } return this.clients.get("clinical"); }