Merge pull request #856 from opencb/TASK-5580

TASK-5580 - Opecga javascript clients added to jsorolla

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);
+    }
+
 }

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

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.

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.