Merge branch 'develop' into TASK-5827

package.json

@@ -1,6 +1,6 @@
 {
   "name": "jsorolla",
-  "version": "2.12.3",
+  "version": "3.1.0-dev",
   "description": "JSorolla is a JavaScript bioinformatic library for data analysis and genomic visualization",
   "repository": {
     "type": "git",

src/core/clients/opencga/api/Admin.js

@@ -12,7 +12,7 @@
  * WARNING: AUTOGENERATED CODE
  * 
  * This code was generated by a tool.
- * Autogenerated on: 2024-02-02
+ * Autogenerated on: 2024-03-06
  * 
  * 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. 
@@ -34,8 +34,8 @@ export default class Admin extends OpenCGAParentClass {
 
     /** Group by operation
     * @param {String} fields - Comma separated list of fields by which to group by.
-    * @param {"AUDIT USER PROJECT STUDY FILE SAMPLE JOB INDIVIDUAL COHORT DISEASE_PANEL FAMILY CLINICAL_ANALYSIS INTERPRETATION VARIANT
-    *     ALIGNMENT CLINICAL EXPRESSION RGA FUNCTIONAL"} entity - Entity to be grouped by.
+    * @param {"AUDIT ORGANIZATION USER PROJECT STUDY FILE SAMPLE JOB INDIVIDUAL COHORT DISEASE_PANEL FAMILY CLINICAL_ANALYSIS INTERPRETATION
+    *     VARIANT ALIGNMENT CLINICAL EXPRESSION RGA FUNCTIONAL"} entity - Entity to be grouped by.
     * @param {Object} [params] - The Object containing the following optional parameters:
     * @param {Boolean} [params.count] - Count the number of elements matching the group.
     * @param {Number} [params.limit = "50"] - Maximum number of documents (groups) to be returned. The default value is 50.
@@ -49,16 +49,6 @@ export default class Admin extends OpenCGAParentClass {
         return this._get("admin", null, "audit", null, "groupBy", {fields, entity, ...params});
     }
 
-    /** Sync Catalog into the Solr
-    * @param {Object} [params] - The Object containing the following optional parameters:
-    * @param {String} [params.collection] - Collection to be indexed (file, sample, individual, family, cohort and/or job). If not provided,
-    *     all of them will be indexed.
-    * @returns {Promise} Promise object in the form of RestResponse instance.
-    */
-    indexStatsCatalog(params) {
-        return this._post("admin", null, "catalog", null, "indexStats", params);
-    }
-
     /** Install OpenCGA database
     * @param {Object} data - JSON containing the mandatory parameters.
     * @returns {Promise} Promise object in the form of RestResponse instance.
@@ -69,10 +59,12 @@ export default class Admin extends OpenCGAParentClass {
 
     /** Change JWT secret key
     * @param {Object} data - JSON containing the parameters.
+    * @param {Object} [params] - The Object containing the following optional parameters:
+    * @param {String} [params.organization] - Organization id.
     * @returns {Promise} Promise object in the form of RestResponse instance.
     */
-    jwtCatalog(data) {
-        return this._post("admin", null, "catalog", null, "jwt", data);
+    jwtCatalog(data, params) {
+        return this._post("admin", null, "catalog", null, "jwt", data, params);
     }
 
     /** Create a new user
@@ -85,10 +77,24 @@ export default class Admin extends OpenCGAParentClass {
 
     /** Import users or a group of users from LDAP or AAD
     * @param {Object} data - JSON containing the parameters.
+    * @param {Object} [params] - The Object containing the following optional parameters:
+    * @param {String} [params.organization] - Organization id.
     * @returns {Promise} Promise object in the form of RestResponse instance.
     */
-    importUsers(data) {
-        return this._post("admin", null, "users", null, "import", data);
+    importUsers(data, params) {
+        return this._post("admin", null, "users", null, "import", data, params);
+    }
+
+    /** User permissions
+    * @param {Object} [params] - The Object containing the following optional parameters:
+    * @param {String} [params.study] - Study [[organization@]project:]study where study and project can be either the ID or UUID.
+    * @param {String} [params.entryIds] - Comma separated list of entry ids.
+    * @param {String} [params.permissions] - Comma separated list of permissions to be retrieved.
+    * @param {String} [params.category] - Category corresponding to the id's provided.
+    * @returns {Promise} Promise object in the form of RestResponse instance.
+    */
+    permissionsUsers(params) {
+        return this._get("admin", null, "users", null, "permissions", params);
     }
 
     /** User search method
@@ -99,6 +105,7 @@ export default class Admin 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 {String} [params.organization] - Organization id.
     * @param {String} [params.user] - User ID.
     * @param {String} [params.account] - Account type [GUEST, FULL, ADMINISTRATOR].
     * @param {String} [params.authenticationId] - Authentication origin ID.
@@ -110,16 +117,19 @@ export default class Admin extends OpenCGAParentClass {
 
     /** Synchronise a group of users from an authentication origin with a group in a study from catalog
     * @param {Object} data - JSON containing the parameters.
+    * @param {Object} [params] - The Object containing the following optional parameters:
+    * @param {String} [params.organization] - Organization id.
     * @returns {Promise} Promise object in the form of RestResponse instance.
     */
-    syncUsers(data) {
-        return this._post("admin", null, "users", null, "sync", data);
+    syncUsers(data, params) {
+        return this._post("admin", null, "users", null, "sync", data, params);
     }
 
     /** 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 {String} [params.organization] - Organization id.
     * @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.
     */

src/core/clients/opencga/api/Alignment.js

@@ -12,7 +12,7 @@
  * WARNING: AUTOGENERATED CODE
  * 
  * This code was generated by a tool.
- * Autogenerated on: 2024-02-02
+ * Autogenerated on: 2024-03-06
  * 
  * 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. 
@@ -80,7 +80,7 @@ export default class Alignment extends OpenCGAParentClass {
     /** Query the coverage of an alignment file for regions or genes
     * @param {String} file - File ID.
     * @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.study] - Study [[organization@]project:]study where study and project can be either the ID or UUID.
     * @param {String} [params.region] - Comma separated list of regions 'chr:start-end, e.g.: 2,3:63500-65000.
     * @param {String} [params.gene] - Comma separated list of genes, e.g.: BCRA2,TP53.
     * @param {Number} [params.offset] - Offset to extend the region, gene or exon at up and downstream.
@@ -100,7 +100,7 @@ export default class Alignment extends OpenCGAParentClass {
     * @param {String} file1 - Input file #1 (e.g. somatic file).
     * @param {String} file2 - Input file #2 (e.g. germline file).
     * @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.study] - Study [[organization@]project:]study where study and project can be either the ID or UUID.
     * @param {Boolean} [params.skipLog2] - Do not apply Log2 to normalise the coverage ratio.
     * @param {String} [params.region] - Comma separated list of regions 'chr:start-end, e.g.: 2,3:63500-65000.
     * @param {String} [params.gene] - Comma separated list of genes, e.g.: BCRA2,TP53.
@@ -118,7 +118,7 @@ export default class Alignment extends OpenCGAParentClass {
     * @param {String} file - File ID.
     * @param {String} gene - Comma separated list of genes, e.g.: BCRA2,TP53.
     * @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.study] - Study [[organization@]project:]study where study and project can be either the ID or UUID.
     * @param {Number} [params.threshold] - Only regions whose coverage depth is under this threshold will be reported.
     * @returns {Promise} Promise object in the form of RestResponse instance.
     */
@@ -211,7 +211,7 @@ export default class Alignment 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 {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID.
+    * @param {String} [params.study] - Study [[organization@]project:]study where study and project can be either the ID or UUID.
     * @param {String} [params.region] - Comma separated list of regions 'chr:start-end, e.g.: 2,3:63500-65000.
     * @param {String} [params.gene] - Comma separated list of genes, e.g.: BCRA2,TP53.
     * @param {Number} [params.offset] - Offset to extend the region, gene or exon at up and downstream.