client: regenerate clients, #TASK-6568

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OrganizationsCommandExecutor.java

@@ -12,6 +12,7 @@
 import org.opencb.opencga.app.cli.main.options.OrganizationsCommandOptions;
 import org.opencb.opencga.catalog.exceptions.CatalogAuthenticationException;
 import org.opencb.opencga.catalog.utils.ParamUtils.AddRemoveAction;
+import org.opencb.opencga.catalog.utils.ParamUtils.BasicUpdateAction;
 import org.opencb.opencga.catalog.utils.ParamUtils.UpdateAction;
 import org.opencb.opencga.client.exceptions.ClientException;
 import org.opencb.opencga.core.common.JacksonUtils;
@@ -214,6 +215,7 @@ private RestResponse<Note> updateNotes() throws Exception {
         ObjectMap queryParams = new ObjectMap();
         queryParams.putIfNotEmpty("include", commandOptions.include);
         queryParams.putIfNotEmpty("exclude", commandOptions.exclude);
+        queryParams.putIfNotNull("tagsAction", commandOptions.tagsAction);
         queryParams.putIfNotNull("includeResult", commandOptions.includeResult);
 
 

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/StudiesCommandExecutor.java

@@ -448,6 +448,7 @@ private RestResponse<Note> updateNotes() throws Exception {
         ObjectMap queryParams = new ObjectMap();
         queryParams.putIfNotEmpty("include", commandOptions.include);
         queryParams.putIfNotEmpty("exclude", commandOptions.exclude);
+        queryParams.putIfNotNull("tagsAction", commandOptions.tagsAction);
         queryParams.putIfNotNull("includeResult", commandOptions.includeResult);
 
 

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/OrganizationsCommandOptions.java

@@ -214,6 +214,9 @@ public class UpdateNotesCommandOptions {
         @Parameter(names = {"--id"}, description = "Note unique identifier.", required = true, arity = 1)
         public String id; 
 
+        @Parameter(names = {"--tags-action"}, description = "Action to be performed if the array of tags is being updated.", required = false, arity = 1)
+        public String tagsAction = "ADD"; 
+
         @Parameter(names = {"--include-result"}, description = "Flag indicating to include the created or updated document result in the response", required = false, help = true, arity = 0)
         public boolean includeResult = false; 
 

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/StudiesCommandOptions.java

@@ -505,6 +505,9 @@ public class UpdateNotesCommandOptions {
         @Parameter(names = {"--id"}, description = "Note unique identifier.", required = true, arity = 1)
         public String id; 
 
+        @Parameter(names = {"--tags-action"}, description = "Action to be performed if the array of tags is being updated.", required = false, arity = 1)
+        public String tagsAction = "ADD"; 
+
         @Parameter(names = {"--include-result"}, description = "Flag indicating to include the created or updated document result in the response", required = false, help = true, arity = 0)
         public boolean includeResult = false; 
 

opencga-client/src/main/R/R/Organization-methods.R

@@ -23,7 +23,7 @@
 #' | createNotes | /{apiVersion}/organizations/notes/create | include, exclude, includeResult, body[*] |
 #' | searchNotes | /{apiVersion}/organizations/notes/search | include, exclude, creationDate, modificationDate, id, scope, visibility, uuid, userId, tags, version |
 #' | deleteNotes | /{apiVersion}/organizations/notes/{id}/delete | id[*], includeResult |
-#' | updateNotes | /{apiVersion}/organizations/notes/{id}/update | include, exclude, id[*], includeResult, body[*] |
+#' | updateNotes | /{apiVersion}/organizations/notes/{id}/update | include, exclude, id[*], tagsAction, includeResult, body[*] |
 #' | userUpdateStatus | /{apiVersion}/organizations/user/{user}/status/update | include, exclude, user[*], organization, includeResult, body[*] |
 #' | updateUser | /{apiVersion}/organizations/user/{user}/update | include, exclude, user[*], organization, includeResult, body[*] |
 #' | updateConfiguration | /{apiVersion}/organizations/{organization}/configuration/update | include, exclude, organization[*], includeResult, authenticationOriginsAction, body[*] |
@@ -85,6 +85,7 @@ setMethod("organizationClient", "OpencgaR", function(OpencgaR, id, organization,
         #' @param include Fields included in the response, whole JSON path must be provided.
         #' @param exclude Fields excluded in the response, whole JSON path must be provided.
         #' @param id Note unique identifier.
+        #' @param tagsAction Action to be performed if the array of tags is being updated. Allowed values: ['ADD SET REMOVE']
         #' @param includeResult Flag indicating to include the created or updated document result in the response.
         #' @param data JSON containing the Note fields to be updated.
         updateNotes=fetchOpenCGA(object=OpencgaR, category="organizations", categoryId=NULL, subcategory="notes",

opencga-client/src/main/R/R/Study-methods.R

@@ -31,7 +31,7 @@
 #' | createNotes | /{apiVersion}/studies/{study}/notes/create | include, exclude, study[*], includeResult, body[*] |
 #' | searchNotes | /{apiVersion}/studies/{study}/notes/search | include, exclude, study[*], creationDate, modificationDate, id, uuid, userId, tags, visibility, version |
 #' | deleteNotes | /{apiVersion}/studies/{study}/notes/{id}/delete | study[*], id[*], includeResult |
-#' | updateNotes | /{apiVersion}/studies/{study}/notes/{id}/update | include, exclude, study[*], id[*], includeResult, body[*] |
+#' | updateNotes | /{apiVersion}/studies/{study}/notes/{id}/update | include, exclude, study[*], id[*], tagsAction, includeResult, body[*] |
 #' | permissionRules | /{apiVersion}/studies/{study}/permissionRules | study[*], entity[*] |
 #' | updatePermissionRules | /{apiVersion}/studies/{study}/permissionRules/update | study[*], entity[*], action, body[*] |
 #' | runTemplates | /{apiVersion}/studies/{study}/templates/run | study[*], jobId, jobDependsOn, jobDescription, jobTags, jobScheduledStartTime, jobPriority, jobDryRun, body[*] |
@@ -191,6 +191,7 @@ setMethod("studyClient", "OpencgaR", function(OpencgaR, group, id, members, stud
         #' @param exclude Fields excluded in the response, whole JSON path must be provided.
         #' @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
         #' @param id Note unique identifier.
+        #' @param tagsAction Action to be performed if the array of tags is being updated. Allowed values: ['ADD SET REMOVE']
         #' @param includeResult Flag indicating to include the created or updated document result in the response.
         #' @param data JSON containing the Note fields to be updated.
         updateNotes=fetchOpenCGA(object=OpencgaR, category="studies", categoryId=study, subcategory="notes",

opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/OrganizationClient.java

@@ -128,6 +128,7 @@ public RestResponse<Note> deleteNotes(String id, ObjectMap params) throws Client
      * @param params Map containing any of the following optional parameters.
      *       include: Fields included in the response, whole JSON path must be provided.
      *       exclude: Fields excluded in the response, whole JSON path must be provided.
+     *       tagsAction: Action to be performed if the array of tags is being updated.
      *       includeResult: Flag indicating to include the created or updated document result in the response.
      * @return a RestResponse object.
      * @throws ClientException ClientException if there is any server error.

opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java

@@ -288,6 +288,7 @@ public RestResponse<Note> deleteNotes(String study, String id, ObjectMap params)
      * @param params Map containing any of the following optional parameters.
      *       include: Fields included in the response, whole JSON path must be provided.
      *       exclude: Fields excluded in the response, whole JSON path must be provided.
+     *       tagsAction: Action to be performed if the array of tags is being updated.
      *       includeResult: Flag indicating to include the created or updated document result in the response.
      * @return a RestResponse object.
      * @throws ClientException ClientException if there is any server error.

opencga-client/src/main/javascript/Organization.js

@@ -97,6 +97,8 @@ export default class Organization extends OpenCGAParentClass {
     * @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 {"ADD SET REMOVE"} [params.tagsAction = "ADD"] - Action to be performed if the array of tags 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.

opencga-client/src/main/javascript/Study.js

@@ -219,6 +219,8 @@ export default class Study extends OpenCGAParentClass {
     * @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 {"ADD SET REMOVE"} [params.tagsAction = "ADD"] - Action to be performed if the array of tags 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.

opencga-client/src/main/python/pyopencga/rest_clients/organization_client.py

@@ -104,6 +104,8 @@ def update_notes(self, id, data=None, **options):
             must be provided.
         :param str exclude: Fields excluded in the response, whole JSON path
             must be provided.
+        :param str tags_action: Action to be performed if the array of tags is
+            being updated. Allowed values: ['ADD SET REMOVE']
         :param bool include_result: Flag indicating to include the created or
             updated document result in the response.
         """

opencga-client/src/main/python/pyopencga/rest_clients/study_client.py

@@ -270,6 +270,8 @@ def update_notes(self, study, id, data=None, **options):
             must be provided.
         :param str exclude: Fields excluded in the response, whole JSON path
             must be provided.
+        :param str tags_action: Action to be performed if the array of tags is
+            being updated. Allowed values: ['ADD SET REMOVE']
         :param bool include_result: Flag indicating to include the created or
             updated document result in the response.
         """