server: move reset password WS, #TASK-7200 #TASK-7130

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

@@ -89,7 +89,7 @@ public abstract class OpenCgaCompleter implements Completer {
             .map(Candidate::new)
             .collect(toList());
 
-    private List<Candidate> organizationsList = asList( "create","notes-create","notes-search","notes-delete","notes-update","update-status-user","user-update","configuration-update","info","update")
+    private List<Candidate> organizationsList = asList( "create","notes-create","notes-search","notes-delete","notes-update","password-reset","update-status-user","user-update","configuration-update","info","update")
             .stream()
             .map(Candidate::new)
             .collect(toList());

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

@@ -273,6 +273,7 @@ public OpencgaCliOptionsParser() {
         organizationsSubCommands.addCommand("notes-search", organizationsCommandOptions.searchNotesCommandOptions);
         organizationsSubCommands.addCommand("notes-delete", organizationsCommandOptions.deleteNotesCommandOptions);
         organizationsSubCommands.addCommand("notes-update", organizationsCommandOptions.updateNotesCommandOptions);
+        organizationsSubCommands.addCommand("password-reset", organizationsCommandOptions.resetPasswordCommandOptions);
         organizationsSubCommands.addCommand("update-status-user", organizationsCommandOptions.userUpdateStatusCommandOptions);
         organizationsSubCommands.addCommand("user-update", organizationsCommandOptions.updateUserCommandOptions);
         organizationsSubCommands.addCommand("configuration-update", organizationsCommandOptions.updateConfigurationCommandOptions);

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

@@ -81,6 +81,9 @@ public void execute() throws Exception {
             case "notes-update":
                 queryResponse = updateNotes();
                 break;
+            case "password-reset":
+                queryResponse = resetPassword();
+                break;
             case "update-status-user":
                 queryResponse = userUpdateStatus();
                 break;
@@ -240,6 +243,17 @@ private RestResponse<Note> updateNotes() throws Exception {
         return openCGAClient.getOrganizationClient().updateNotes(commandOptions.id, noteUpdateParams, queryParams);
     }
 
+    private RestResponse<ObjectMap> resetPassword() throws Exception {
+        logger.debug("Executing resetPassword in Organizations command line");
+
+        OrganizationsCommandOptions.ResetPasswordCommandOptions commandOptions = organizationsCommandOptions.resetPasswordCommandOptions;
+
+        ObjectMap queryParams = new ObjectMap();
+        queryParams.putIfNotEmpty("userId", commandOptions.userId);
+
+        return openCGAClient.getOrganizationClient().resetPassword(queryParams);
+    }
+
     private RestResponse<User> userUpdateStatus() throws Exception {
         logger.debug("Executing userUpdateStatus in Organizations command line");
 

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

@@ -38,6 +38,7 @@ public class OrganizationsCommandOptions {
         public SearchNotesCommandOptions searchNotesCommandOptions;
         public DeleteNotesCommandOptions deleteNotesCommandOptions;
         public UpdateNotesCommandOptions updateNotesCommandOptions;
+        public ResetPasswordCommandOptions resetPasswordCommandOptions;
         public UserUpdateStatusCommandOptions userUpdateStatusCommandOptions;
         public UpdateUserCommandOptions updateUserCommandOptions;
         public UpdateConfigurationCommandOptions updateConfigurationCommandOptions;
@@ -54,6 +55,7 @@ public OrganizationsCommandOptions(CommonCommandOptions commonCommandOptions, JC
         this.searchNotesCommandOptions = new SearchNotesCommandOptions();
         this.deleteNotesCommandOptions = new DeleteNotesCommandOptions();
         this.updateNotesCommandOptions = new UpdateNotesCommandOptions();
+        this.resetPasswordCommandOptions = new ResetPasswordCommandOptions();
         this.userUpdateStatusCommandOptions = new UserUpdateStatusCommandOptions();
         this.updateUserCommandOptions = new UpdateUserCommandOptions();
         this.updateConfigurationCommandOptions = new UpdateConfigurationCommandOptions();
@@ -228,6 +230,23 @@ public class UpdateNotesCommandOptions {
 
     }
 
+    @Parameters(commandNames = {"password-reset"}, commandDescription ="Reset user's password")
+    public class ResetPasswordCommandOptions {
+
+        @ParametersDelegate
+        public CommonCommandOptions commonOptions = commonCommandOptions;
+
+        @Parameter(names = {"--json-file"}, description = "File with the body data in JSON format. Note, that using this parameter will ignore all the other parameters.", required = false, arity = 1)
+        public String jsonFile;
+
+        @Parameter(names = {"--json-data-model"}, description = "Show example of file structure for body data.", help = true, arity = 0)
+        public Boolean jsonDataModel = false;
+
+        @Parameter(names = {"--user-id"}, description = "User whose password needs to be reset", required = false, arity = 1)
+        public String userId; 
+
+    }
+
     @Parameters(commandNames = {"update-status-user"}, commandDescription ="Update the user status")
     public class UserUpdateStatusCommandOptions {
 

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

@@ -244,7 +244,7 @@ public class FiltersCommandOptions {
 
     }
 
-    @Parameters(commandNames = {"password-reset"}, commandDescription ="Reset password")
+    @Parameters(commandNames = {"password-reset"}, commandDescription ="[DEPRECATED]")
     public class ResetPasswordCommandOptions {
 
         @ParametersDelegate

opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/OrganizationManager.java

@@ -292,6 +292,26 @@ public OpenCGAResult<Organization> update(String organizationId, OrganizationUpd
         return result;
     }
 
+    public OpenCGAResult<?> resetUserPassword(String userId, String token) throws CatalogException {
+        ParamUtils.checkParameter(userId, "userId");
+        ParamUtils.checkParameter(token, "token");
+        JwtPayload jwtPayload = catalogManager.getUserManager().validateToken(token);
+        String organizationId = jwtPayload.getOrganization();
+        try {
+            authorizationManager.checkIsAtLeastOrganizationOwnerOrAdmin(organizationId, jwtPayload.getUserId());
+            String authOrigin = catalogManager.getUserManager().getAuthenticationOriginId(organizationId, userId);
+            OpenCGAResult<?> writeResult = authenticationFactory.resetPassword(organizationId, authOrigin, userId);
+
+            auditManager.auditUser(organizationId, jwtPayload.getUserId(organizationId), Enums.Action.RESET_USER_PASSWORD, userId,
+                    new AuditRecord.Status(AuditRecord.Status.Result.SUCCESS));
+            return writeResult;
+        } catch (CatalogException e) {
+            auditManager.auditUser(organizationId, jwtPayload.getUserId(organizationId), Enums.Action.RESET_USER_PASSWORD, userId,
+                    new AuditRecord.Status(AuditRecord.Status.Result.ERROR, e.getError()));
+            throw e;
+        }
+    }
+
     public OpenCGAResult<User> updateUser(@Nullable String organizationId, String userId, OrganizationUserUpdateParams updateParams,
                                           QueryOptions options, String token) throws CatalogException {
         JwtPayload tokenPayload = catalogManager.getUserManager().validateToken(token);

opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/UserManager.java

@@ -773,26 +773,6 @@ public OpenCGAResult<User> restore(String ids, QueryOptions options, String sess
         throw new UnsupportedOperationException();
     }
 
-    public OpenCGAResult resetPassword(String userId, String token) throws CatalogException {
-        ParamUtils.checkParameter(userId, "userId");
-        ParamUtils.checkParameter(token, "token");
-        JwtPayload jwtPayload = validateToken(token);
-        String organizationId = jwtPayload.getOrganization();
-        try {
-            authorizationManager.checkIsAtLeastOrganizationOwnerOrAdmin(organizationId, jwtPayload.getUserId());
-            String authOrigin = getAuthenticationOriginId(organizationId, userId);
-            OpenCGAResult writeResult = authenticationFactory.resetPassword(organizationId, authOrigin, userId);
-
-            auditManager.auditUser(organizationId, jwtPayload.getUserId(organizationId), Enums.Action.RESET_USER_PASSWORD, userId,
-                    new AuditRecord.Status(AuditRecord.Status.Result.SUCCESS));
-            return writeResult;
-        } catch (CatalogException e) {
-            auditManager.auditUser(organizationId, jwtPayload.getUserId(organizationId), Enums.Action.RESET_USER_PASSWORD, userId,
-                    new AuditRecord.Status(AuditRecord.Status.Result.ERROR, e.getError()));
-            throw e;
-        }
-    }
-
     public AuthenticationResponse loginAsAdmin(String password) throws CatalogException {
         return login(ParamConstants.ADMIN_ORGANIZATION, OPENCGA, password);
     }
@@ -1533,7 +1513,7 @@ private void checkUserExists(String organizationId, String userId) throws Catalo
         }
     }
 
-    private String getAuthenticationOriginId(String organizationId, String userId) throws CatalogException {
+    String getAuthenticationOriginId(String organizationId, String userId) throws CatalogException {
         OpenCGAResult<User> user = getUserDBAdaptor(organizationId).get(userId, new QueryOptions());
         if (user == null || user.getNumResults() == 0) {
             throw new CatalogException(userId + " user not found");

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

@@ -24,6 +24,7 @@
 #' | 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[*], tagsAction, includeResult, body[*] |
+#' | resetPassword | /{apiVersion}/organizations/password/reset | userId |
 #' | 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[*] |
@@ -91,6 +92,12 @@ setMethod("organizationClient", "OpencgaR", function(OpencgaR, id, organization,
         updateNotes=fetchOpenCGA(object=OpencgaR, category="organizations", categoryId=NULL, subcategory="notes",
                 subcategoryId=id, action="update", params=params, httpMethod="POST", as.queryParam=NULL, ...),
 
+        #' @section Endpoint /{apiVersion}/organizations/password/reset:
+        #' Reset user's password.
+        #' @param userId User whose password needs to be reset.
+        resetPassword=fetchOpenCGA(object=OpencgaR, category="organizations", categoryId=NULL, subcategory="password",
+                subcategoryId=NULL, action="reset", params=params, httpMethod="POST", as.queryParam=NULL, ...),
+
         #' @section Endpoint /{apiVersion}/organizations/user/{user}/status/update:
         #' Update the user status.
         #' @param include Fields included in the response, whole JSON path must be provided.

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

@@ -128,7 +128,7 @@ setMethod("userClient", "OpencgaR", function(OpencgaR, filterId, user, users, en
                 subcategoryId=filterId, action="update", params=params, httpMethod="POST", as.queryParam=NULL, ...),
 
         #' @section Endpoint /{apiVersion}/users/{user}/password/reset:
-        #' Reset password.
+        #' [DEPRECATED].
         #' @param user User ID.
         resetPassword=fetchOpenCGA(object=OpencgaR, category="users", categoryId=user, subcategory="password",
                 subcategoryId=NULL, action="reset", params=params, httpMethod="GET", as.queryParam=NULL, ...),

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

@@ -139,6 +139,18 @@ public RestResponse<Note> updateNotes(String id, NoteUpdateParams data, ObjectMa
         return execute("organizations", null, "notes", id, "update", params, POST, Note.class);
     }
 
+    /**
+     * Reset user's password.
+     * @param params Map containing any of the following optional parameters.
+     *       userId: User whose password needs to be reset.
+     * @return a RestResponse object.
+     * @throws ClientException ClientException if there is any server error.
+     */
+    public RestResponse<ObjectMap> resetPassword(ObjectMap params) throws ClientException {
+        params = params != null ? params : new ObjectMap();
+        return execute("organizations", null, "password", null, "reset", params, POST, ObjectMap.class);
+    }
+
     /**
      * Update the user status.
      * @param user User ID.

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

@@ -208,7 +208,7 @@ public RestResponse<UserFilter> updateFilter(String user, String filterId, Filte
     }
 
     /**
-     * Reset password.
+     * [DEPRECATED].
      * @param user User ID.
      * @return a RestResponse object.
      * @throws ClientException ClientException if there is any server error.

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

@@ -107,6 +107,15 @@ export default class Organization extends OpenCGAParentClass {
         return this._post("organizations", null, "notes", id, "update", data, params);
     }
 
+    /** Reset user's password
+    * @param {Object} [params] - The Object containing the following optional parameters:
+    * @param {String} [params.userId] - User whose password needs to be reset.
+    * @returns {Promise} Promise object in the form of RestResponse instance.
+    */
+    resetPassword(params) {
+        return this._post("organizations", null, "password", null, "reset", null, params);
+    }
+
     /** Update the user status
     * @param {String} user - User ID.
     * @param {Object} data - JSON containing the User fields to be updated.

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

@@ -149,7 +149,7 @@ export default class User extends OpenCGAParentClass {
         return this._post("users", user, "filters", filterId, "update", data);
     }
 
-    /** Reset password
+    /** [DEPRECATED]
     * @param {String} user - User ID.
     * @returns {Promise} Promise object in the form of RestResponse instance.
     */

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

@@ -112,6 +112,16 @@ def update_notes(self, id, data=None, **options):
 
         return self._post(category='organizations', resource='update', subcategory='notes', second_query_id=id, data=data, **options)
 
+    def reset_password(self, **options):
+        """
+        Reset user's password.
+        PATH: /{apiVersion}/organizations/password/reset
+
+        :param str user_id: User whose password needs to be reset.
+        """
+
+        return self._post(category='organizations', resource='reset', subcategory='password', **options)
+
     def user_update_status(self, user, data=None, **options):
         """
         Update the user status.

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

@@ -165,7 +165,7 @@ def update_filter(self, user, filter_id, data=None, **options):
 
     def reset_password(self, user, **options):
         """
-        Reset password.
+        [DEPRECATED].
         PATH: /{apiVersion}/users/{user}/password/reset
 
         :param str user: User ID. (REQUIRED)

opencga-server/src/main/java/org/opencb/opencga/server/rest/OrganizationWSServer.java

@@ -148,6 +148,20 @@ public Response create(
         }
     }
 
+    @POST
+    @Path("/password/reset")
+    @ApiOperation(value = "Reset user's password",
+            notes = "Reset the user's password and send a new random one to the e-mail stored in catalog.")
+    public Response resetPassword(
+            @ApiParam(value = "User whose password needs to be reset") @QueryParam("userId") String userId) {
+        try {
+            OpenCGAResult<?> result = catalogManager.getOrganizationManager().resetUserPassword(userId, token);
+            return createOkResponse(result, "The new password has been sent to the user's email.");
+        } catch (Exception e) {
+            return createErrorResponse(e);
+        }
+    }
+
     @GET
     @Path("/notes/search")
     @ApiOperation(value = "Search for notes of scope ORGANIZATION", response = Note.class)

opencga-server/src/main/java/org/opencb/opencga/server/rest/UserWSServer.java

@@ -182,14 +182,14 @@ public Response changePassword(
         }
     }
 
+    @Deprecated
     @GET
     @Path("/{user}/password/reset")
-    @ApiOperation(value = "Reset password", hidden = false,
-            notes = "Reset the user's password and send a new random one to the e-mail stored in catalog.", response = User.class)
+    @ApiOperation(value = "[DEPRECATED]", notes = "[DEPRECATED] This WS has been moved to /organizations/password/reset.", response = User.class)
     public Response resetPassword(
             @ApiParam(value = ParamConstants.USER_DESCRIPTION, required = true) @PathParam("user") String userId) {
         try {
-            OpenCGAResult<User> result = catalogManager.getUserManager().resetPassword(userId, token);
+            OpenCGAResult<?> result = catalogManager.getOrganizationManager().resetUserPassword(userId, token);
             return createOkResponse(result, "The new password has been sent to the user's email.");
         } catch (Exception e) {
             return createErrorResponse(e);