TASK-7922 - Fix: update JWT secret key for new environments

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java

@@ -54,7 +54,7 @@ public abstract class OpenCgaCompleter implements Completer {
             .map(Candidate::new)
             .collect(toList());
 
-    private List<Candidate> adminList = asList( "audit-group-by","catalog-install","catalog-jwt","resource-fetch","users-create","users-import","users-permissions","users-search","users-sync","update-groups-users")
+    private List<Candidate> adminList = asList( "audit-group-by","catalog-install","catalog-jwt","organizations-list","resource-fetch","users-create","users-import","users-permissions","users-search","users-sync","update-groups-users")
             .stream()
             .map(Candidate::new)
             .collect(toList());

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java

@@ -180,6 +180,7 @@ public OpencgaCliOptionsParser() {
         adminSubCommands.addCommand("audit-group-by", adminCommandOptions.groupByAuditCommandOptions);
         adminSubCommands.addCommand("catalog-install", adminCommandOptions.installCatalogCommandOptions);
         adminSubCommands.addCommand("catalog-jwt", adminCommandOptions.jwtCatalogCommandOptions);
+        adminSubCommands.addCommand("organizations-list", adminCommandOptions.listOrganizationsCommandOptions);
         adminSubCommands.addCommand("resource-fetch", adminCommandOptions.fetchResourceCommandOptions);
         adminSubCommands.addCommand("users-create", adminCommandOptions.createUsersCommandOptions);
         adminSubCommands.addCommand("users-import", adminCommandOptions.importUsersCommandOptions);

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

@@ -73,6 +73,9 @@ public void execute() throws Exception {
             case "catalog-jwt":
                 queryResponse = jwtCatalog();
                 break;
+            case "organizations-list":
+                queryResponse = listOrganizations();
+                break;
             case "resource-fetch":
                 queryResponse = fetchResource();
                 break;
@@ -175,6 +178,13 @@ private RestResponse<ObjectMap> jwtCatalog() throws Exception {
         return openCGAClient.getAdminClient().jwtCatalog(jWTParams, queryParams);
     }
 
+    private RestResponse<String> listOrganizations() throws Exception {
+        logger.debug("Executing listOrganizations in Admin command line");
+
+        AdminCommandOptions.ListOrganizationsCommandOptions commandOptions = adminCommandOptions.listOrganizationsCommandOptions;
+        return openCGAClient.getAdminClient().listOrganizations();
+    }
+
     private RestResponse<Job> fetchResource() throws Exception {
         logger.debug("Executing fetchResource in Admin command line");
 

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

@@ -36,6 +36,7 @@ public class AdminCommandOptions {
         public GroupByAuditCommandOptions groupByAuditCommandOptions;
         public InstallCatalogCommandOptions installCatalogCommandOptions;
         public JwtCatalogCommandOptions jwtCatalogCommandOptions;
+        public ListOrganizationsCommandOptions listOrganizationsCommandOptions;
         public FetchResourceCommandOptions fetchResourceCommandOptions;
         public CreateUsersCommandOptions createUsersCommandOptions;
         public ImportUsersCommandOptions importUsersCommandOptions;
@@ -52,6 +53,7 @@ public AdminCommandOptions(CommonCommandOptions commonCommandOptions, JCommander
         this.groupByAuditCommandOptions = new GroupByAuditCommandOptions();
         this.installCatalogCommandOptions = new InstallCatalogCommandOptions();
         this.jwtCatalogCommandOptions = new JwtCatalogCommandOptions();
+        this.listOrganizationsCommandOptions = new ListOrganizationsCommandOptions();
         this.fetchResourceCommandOptions = new FetchResourceCommandOptions();
         this.createUsersCommandOptions = new CreateUsersCommandOptions();
         this.importUsersCommandOptions = new ImportUsersCommandOptions();
@@ -137,6 +139,14 @@ public class JwtCatalogCommandOptions {
 
     }
 
+    @Parameters(commandNames = {"organizations-list"}, commandDescription ="List current Organizations")
+    public class ListOrganizationsCommandOptions {
+
+        @ParametersDelegate
+        public CommonCommandOptions commonOptions = commonCommandOptions;
+
+    }
+
     @Parameters(commandNames = {"resource-fetch"}, commandDescription ="Fetch resources from the public server and save them into the OpenCGA local installation")
     public class FetchResourceCommandOptions {
 

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

@@ -22,6 +22,7 @@
 #' | groupByAudit | /{apiVersion}/admin/audit/groupBy | count, limit, fields[*], entity[*], action, before, after, date |
 #' | installCatalog | /{apiVersion}/admin/catalog/install | body[*] |
 #' | jwtCatalog | /{apiVersion}/admin/catalog/jwt | organization, body[*] |
+#' | listOrganizations | /{apiVersion}/admin/organizations/list |  |
 #' | fetchResource | /{apiVersion}/admin/resource/fetch | jobId, jobDescription, jobDependsOn, jobTags, jobScheduledStartTime, jobPriority, jobDryRun, body[*] |
 #' | createUsers | /{apiVersion}/admin/users/create | body[*] |
 #' | importUsers | /{apiVersion}/admin/users/import | organization, body[*] |
@@ -66,6 +67,12 @@ setMethod("adminClient", "OpencgaR", function(OpencgaR, user, endpointName, para
         jwtCatalog=fetchOpenCGA(object=OpencgaR, category="admin", categoryId=NULL, subcategory="catalog",
                 subcategoryId=NULL, action="jwt", params=params, httpMethod="POST", as.queryParam=NULL, ...),
 
+        #' @section Endpoint /{apiVersion}/admin/organizations/list:
+        #' List current Organizations.
+
+        listOrganizations=fetchOpenCGA(object=OpencgaR, category="admin", categoryId=NULL, subcategory="organizations",
+                subcategoryId=NULL, action="list", params=params, httpMethod="GET", as.queryParam=NULL, ...),
+
         #' @section Endpoint /{apiVersion}/admin/resource/fetch:
         #' Fetch resources from the public server and save them into the OpenCGA local installation.
         #' @param jobId Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not provided.

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

@@ -103,6 +103,16 @@ public RestResponse<ObjectMap> jwtCatalog(JWTParams data, ObjectMap params) thro
         return execute("admin", null, "catalog", null, "jwt", params, POST, ObjectMap.class);
     }
 
+    /**
+     * List current Organizations.
+     * @return a RestResponse object.
+     * @throws ClientException ClientException if there is any server error.
+     */
+    public RestResponse<String> listOrganizations() throws ClientException {
+        ObjectMap params = new ObjectMap();
+        return execute("admin", null, "organizations", null, "list", params, GET, String.class);
+    }
+
     /**
      * Fetch resources from the public server and save them into the OpenCGA local installation.
      * @param data Download-resources tool parameters.

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

@@ -69,6 +69,14 @@ export default class Admin extends OpenCGAParentClass {
         return this._post("admin", null, "catalog", null, "jwt", data, params);
     }
 
+    /** List current Organizations
+    * 
+    * @returns {Promise} Promise object in the form of RestResponse instance.
+    */
+    listOrganizations() {
+        return this._get("admin", null, "organizations", null, "list");
+    }
+
     /** Fetch resources from the public server and save them into the OpenCGA local installation
     * @param {Object} data - Download-resources tool parameters.
     * @param {Object} [params] - The Object containing the following optional parameters:

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

@@ -65,6 +65,14 @@ def jwt_catalog(self, data=None, **options):
 
         return self._post(category='admin', resource='jwt', subcategory='catalog', data=data, **options)
 
+    def list_organizations(self, **options):
+        """
+        List current Organizations.
+        PATH: /{apiVersion}/admin/organizations/list
+        """
+
+        return self._get(category='admin', resource='list', subcategory='organizations', **options)
+
     def fetch_resource(self, data=None, **options):
         """
         Fetch resources from the public server and save them into the OpenCGA

opencga-server/src/main/java/org/opencb/opencga/server/rest/admin/AdminWSServer.java

@@ -63,6 +63,18 @@ public AdminWSServer(@Context UriInfo uriInfo, @Context HttpServletRequest httpS
 
     //******************************** USERS **********************************//
 
+    @GET
+    @Path("/organizations/list")
+    @ApiOperation(value = "List current Organizations", response = String.class)
+    public Response organizationList() {
+        try {
+            return createOkResponse(catalogManager.getAdminManager().getOrganizationIds(token));
+        } catch (CatalogException e) {
+            return createErrorResponse(e);
+        }
+
+    }
+
     @GET
     @Path("/users/search")
     @ApiOperation(value = "User search method", response = Sample.class)