Merge branch 'TASK-6013' of github.com:opencb/opencga into TASK-6013

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

@@ -1,5 +1,5 @@
 /*
-* Copyright 2015-2024-04-10 OpenCB
+* Copyright 2015-2024-04-29 OpenCB
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
@@ -85,7 +85,7 @@ public abstract class OpenCgaCompleter implements Completer {
             .map(Candidate::new)
             .collect(toList());
 
-    private List<Candidate> usersList = asList( "anonymous","create","login","password","info","configs","configs-update","filters","password-reset","update")
+    private List<Candidate> usersList = asList( "anonymous","create","login","password","search","info","configs","configs-update","filters","password-reset","update")
             .stream()
             .map(Candidate::new)
             .collect(toList());

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

@@ -1,5 +1,5 @@
 /*
-* Copyright 2015-2024-04-10 OpenCB
+* Copyright 2015-2024-04-29 OpenCB
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
@@ -229,6 +229,7 @@ public OpencgaCliOptionsParser() {
         usersSubCommands.addCommand("create", usersCommandOptions.createCommandOptions);
         usersSubCommands.addCommand("login", usersCommandOptions.loginCommandOptions);
         usersSubCommands.addCommand("password", usersCommandOptions.passwordCommandOptions);
+        usersSubCommands.addCommand("search", usersCommandOptions.searchCommandOptions);
         usersSubCommands.addCommand("info", usersCommandOptions.infoCommandOptions);
         usersSubCommands.addCommand("configs", usersCommandOptions.configsCommandOptions);
         usersSubCommands.addCommand("configs-update", usersCommandOptions.updateConfigsCommandOptions);

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

@@ -262,7 +262,6 @@ private RestResponse<Sample> searchUsers() throws Exception {
         queryParams.putIfNotNull("count", commandOptions.count);
         queryParams.putIfNotEmpty("organization", commandOptions.organization);
         queryParams.putIfNotEmpty("user", commandOptions.user);
-        queryParams.putIfNotEmpty("account", commandOptions.account);
         queryParams.putIfNotEmpty("authenticationId", commandOptions.authenticationId);
 
         return openCGAClient.getAdminClient().searchUsers(queryParams);

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

@@ -22,6 +22,7 @@
 import org.opencb.opencga.core.models.organizations.OrganizationConfiguration;
 import org.opencb.opencga.core.models.organizations.OrganizationCreateParams;
 import org.opencb.opencga.core.models.organizations.OrganizationUpdateParams;
+import org.opencb.opencga.core.models.organizations.TokenConfiguration;
 import org.opencb.opencga.core.response.QueryType;
 import org.opencb.opencga.core.response.RestResponse;
 

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

@@ -77,6 +77,9 @@ public void execute() throws Exception {
             case "password":
                 queryResponse = password();
                 break;
+            case "search":
+                queryResponse = search();
+                break;
             case "info":
                 queryResponse = info();
                 break;
@@ -188,6 +191,24 @@ private RestResponse<User> password() throws Exception {
         return openCGAClient.getUserClient().password(passwordChangeParams);
     }
 
+    private RestResponse<User> search() throws Exception {
+        logger.debug("Executing search in Users command line");
+
+        UsersCommandOptions.SearchCommandOptions commandOptions = usersCommandOptions.searchCommandOptions;
+
+        ObjectMap queryParams = new ObjectMap();
+        queryParams.putIfNotEmpty("include", commandOptions.include);
+        queryParams.putIfNotEmpty("exclude", commandOptions.exclude);
+        queryParams.putIfNotNull("limit", commandOptions.limit);
+        queryParams.putIfNotNull("skip", commandOptions.skip);
+        queryParams.putIfNotNull("count", commandOptions.count);
+        queryParams.putIfNotEmpty("organization", commandOptions.organization);
+        queryParams.putIfNotEmpty("id", commandOptions.id);
+        queryParams.putIfNotEmpty("authenticationId", commandOptions.authenticationId);
+
+        return openCGAClient.getUserClient().search(queryParams);
+    }
+
     private RestResponse<User> info() throws Exception {
         logger.debug("Executing info in Users command line");
 
@@ -284,7 +305,6 @@ private RestResponse<User> update() throws Exception {
             ObjectMap beanParams = new ObjectMap();
             putNestedIfNotEmpty(beanParams, "name",commandOptions.name, true);
             putNestedIfNotEmpty(beanParams, "email",commandOptions.email, true);
-            putNestedIfNotEmpty(beanParams, "organization",commandOptions.organization, true);
             putNestedIfNotNull(beanParams, "attributes",commandOptions.attributes, true);
 
             userUpdateParams = JacksonUtils.getDefaultObjectMapper().copy()

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

@@ -243,9 +243,6 @@ public class SearchUsersCommandOptions {
         @Parameter(names = {"--user", "-u"}, description = "User ID", required = false, arity = 1)
         public String user; 
 
-        @Parameter(names = {"--account"}, description = "Account type [GUEST, FULL, ADMINISTRATOR]", required = false, arity = 1)
-        public String account; 
-
         @Parameter(names = {"--authentication-id"}, description = "Authentication origin ID", required = false, arity = 1)
         public String authenticationId; 
 

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

@@ -37,6 +37,7 @@ public class UsersCommandOptions extends CustomUsersCommandOptions {
         public CreateCommandOptions createCommandOptions;
         public LoginCommandOptions loginCommandOptions;
         public PasswordCommandOptions passwordCommandOptions;
+        public SearchCommandOptions searchCommandOptions;
         public InfoCommandOptions infoCommandOptions;
         public ConfigsCommandOptions configsCommandOptions;
         public UpdateConfigsCommandOptions updateConfigsCommandOptions;
@@ -52,6 +53,7 @@ public UsersCommandOptions(CommonCommandOptions commonCommandOptions, JCommander
         this.createCommandOptions = new CreateCommandOptions();
         this.loginCommandOptions = new LoginCommandOptions();
         this.passwordCommandOptions = new PasswordCommandOptions();
+        this.searchCommandOptions = new SearchCommandOptions();
         this.infoCommandOptions = new InfoCommandOptions();
         this.configsCommandOptions = new ConfigsCommandOptions();
         this.updateConfigsCommandOptions = new UpdateConfigsCommandOptions();
@@ -136,6 +138,38 @@ public class PasswordCommandOptions {
 
     }
 
+    @Parameters(commandNames = {"search"}, commandDescription ="User search method")
+    public class SearchCommandOptions {
+
+        @ParametersDelegate
+        public CommonCommandOptions commonOptions = commonCommandOptions;
+
+        @Parameter(names = {"--include", "-I"}, description = "Fields included in the response, whole JSON path must be provided", required = false, arity = 1)
+        public String include; 
+
+        @Parameter(names = {"--exclude", "-E"}, description = "Fields excluded in the response, whole JSON path must be provided", required = false, arity = 1)
+        public String exclude; 
+
+        @Parameter(names = {"--limit"}, description = "Number of results to be returned", required = false, arity = 1)
+        public Integer limit; 
+
+        @Parameter(names = {"--skip"}, description = "Number of results to skip", required = false, arity = 1)
+        public Integer skip; 
+
+        @Parameter(names = {"--count"}, description = "Get the total number of results matching the query. Deactivated by default.", required = false, help = true, arity = 0)
+        public boolean count = false; 
+
+        @Parameter(names = {"--organization"}, description = "Organization id", required = false, arity = 1)
+        public String organization; 
+
+        @Parameter(names = {"--id"}, description = "Comma separated list user 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.", required = false, arity = 1)
+        public String id; 
+
+        @Parameter(names = {"--authentication-id"}, description = "Authentication origin ID", required = false, arity = 1)
+        public String authenticationId; 
+
+    }
+
     @Parameters(commandNames = {"info"}, commandDescription ="Return the user information including its projects and studies")
     public class InfoCommandOptions {
 
@@ -251,9 +285,6 @@ public class UpdateCommandOptions {
         @Parameter(names = {"--email"}, description = "The body web service email parameter", required = false, arity = 1)
         public String email;
 
-        @Parameter(names = {"--organization"}, description = "The body web service organization parameter", required = false, arity = 1)
-        public String organization;
-
         @DynamicParameter(names = {"--attributes"}, description = "The body web service attributes parameter. Use: --attributes key=value", required = false)
         public java.util.Map<java.lang.String,java.lang.Object> attributes = new HashMap<>(); //Dynamic parameters must be initialized;
 

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

@@ -47,9 +47,6 @@ public class AdminManager extends AbstractManager {
 
     public OpenCGAResult<User> userSearch(String organizationId, Query query, QueryOptions options, String token)
             throws CatalogException {
-        query = ParamUtils.defaultObject(query, Query::new);
-        options = ParamUtils.defaultObject(options, QueryOptions::new);
-
         ObjectMap auditParams = new ObjectMap()
                 .append("organizationId", organizationId)
                 .append("query", query)
@@ -58,30 +55,23 @@ public OpenCGAResult<User> userSearch(String organizationId, Query query, QueryO
         JwtPayload jwtPayload = catalogManager.getUserManager().validateToken(token);
         try {
             authorizationManager.checkIsOpencgaAdministrator(jwtPayload);
-
-            // Fix query object
-            if (query.containsKey(ParamConstants.USER)) {
-                query.put(UserDBAdaptor.QueryParams.ID.key(), query.get(ParamConstants.USER));
-                query.remove(ParamConstants.USER);
-            }
-            if (query.containsKey(ParamConstants.USER_AUTHENTICATION_ORIGIN)) {
-                query.put(UserDBAdaptor.QueryParams.ACCOUNT_AUTHENTICATION_ID.key(), query.get(ParamConstants.USER_AUTHENTICATION_ORIGIN));
-                query.remove(ParamConstants.USER_AUTHENTICATION_ORIGIN);
-            }
-            if (query.containsKey(ParamConstants.USER_CREATION_DATE)) {
-                query.put(UserDBAdaptor.QueryParams.ACCOUNT_CREATION_DATE.key(), query.get(ParamConstants.USER_CREATION_DATE));
-                query.remove(ParamConstants.USER_CREATION_DATE);
-            }
-
-            OpenCGAResult<User> userDataResult = getUserDBAdaptor(organizationId).get(query, options);
-            auditManager.auditSearch(organizationId, jwtPayload.getUserId(organizationId), Enums.Resource.USER, "", "", auditParams,
-                    new AuditRecord.Status(AuditRecord.Status.Result.SUCCESS));
-            return userDataResult;
         } catch (CatalogException e) {
             auditManager.auditSearch(organizationId, jwtPayload.getUserId(organizationId), Enums.Resource.USER, "", "", auditParams,
                     new AuditRecord.Status(AuditRecord.Status.Result.ERROR, e.getError()));
             throw e;
         }
+
+        // Fix query object
+        if (query.containsKey(ParamConstants.USER)) {
+            query.put(UserDBAdaptor.QueryParams.ID.key(), query.get(ParamConstants.USER));
+            query.remove(ParamConstants.USER);
+        }
+        if (query.containsKey(ParamConstants.USER_CREATION_DATE)) {
+            query.put(UserDBAdaptor.QueryParams.ACCOUNT_CREATION_DATE.key(), query.get(ParamConstants.USER_CREATION_DATE));
+            query.remove(ParamConstants.USER_CREATION_DATE);
+        }
+
+        return catalogManager.getUserManager().search(organizationId, query, options, token);
     }
 
     public OpenCGAResult<Group> updateGroups(String organizationId, String userId, List<String> studyIds, List<String> groupIds,

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

@@ -215,6 +215,47 @@ public OpenCGAResult<User> create(String id, String name, String email, String p
         return create(user, password, token);
     }
 
+    /**
+     * Search users from Organization. Token must belong to at least an Organization administrator.
+     *
+     * @param organizationId Organization id.
+     * @param query          Query object.
+     * @param options        QueryOptions object.
+     * @param token          JWT token.
+     * @return               OpenCGAResult with the list of users.
+     * @throws CatalogException if the token does not belong to an Organization administrator or there are any parameters wrong.
+     */
+    public OpenCGAResult<User> search(@Nullable String organizationId, Query query, QueryOptions options, String token)
+            throws CatalogException {
+        JwtPayload tokenPayload = catalogManager.getUserManager().validateToken(token);
+        ObjectMap auditParams = new ObjectMap()
+                .append("organizationId", organizationId)
+                .append("query", query)
+                .append("options", options)
+                .append("token", token);
+
+        options = ParamUtils.defaultObject(options, QueryOptions::new);
+        String myOrganizationId = StringUtils.isNotEmpty(organizationId) ? organizationId : tokenPayload.getOrganization();
+        try {
+            authorizationManager.checkIsAtLeastOrganizationOwnerOrAdmin(myOrganizationId, tokenPayload.getUserId(myOrganizationId));
+
+            // Fix query params
+            if (query.containsKey(ParamConstants.USER_AUTHENTICATION_ORIGIN)) {
+                query.put(UserDBAdaptor.QueryParams.ACCOUNT_AUTHENTICATION_ID.key(), query.get(ParamConstants.USER_AUTHENTICATION_ORIGIN));
+                query.remove(ParamConstants.USER_AUTHENTICATION_ORIGIN);
+            }
+
+            OpenCGAResult<User> result = getUserDBAdaptor(myOrganizationId).get(query, options);
+            auditManager.auditSearch(myOrganizationId, tokenPayload.getUserId(myOrganizationId), Enums.Resource.USER, "", "", auditParams,
+                    new AuditRecord.Status(AuditRecord.Status.Result.SUCCESS));
+            return result;
+        } catch (Exception e) {
+            auditManager.auditSearch(myOrganizationId, tokenPayload.getUserId(myOrganizationId), Enums.Resource.USER, "", "", auditParams,
+                    new AuditRecord.Status(AuditRecord.Status.Result.ERROR, new Error(0, "User search", e.getMessage())));
+            throw e;
+        }
+    }
+
     public JwtPayload validateToken(String token) throws CatalogException {
         JwtPayload jwtPayload = new JwtPayload(token);
         ParamUtils.checkParameter(jwtPayload.getUserId(), "jwt user");

opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/CatalogManagerTest.java

@@ -103,6 +103,35 @@ public void testAdminUserExists() throws Exception {
         assertEquals(ParamConstants.ADMIN_ORGANIZATION, payload.getOrganization());
     }
 
+    @Test
+    public void searchUsersTest() throws CatalogException {
+        OpenCGAResult<User> search = catalogManager.getUserManager().search(organizationId, new Query(), QueryOptions.empty(), opencgaToken);
+        assertEquals(8, search.getNumResults());
+        for (User user : search.getResults()) {
+            if (noAccessUserId1.equals(user.getId())) {
+                assertEquals(0, user.getProjects().size());
+            } else if (user.getId().startsWith("normalUser")) {
+                assertEquals(1, user.getProjects().size());
+            } else {
+                assertEquals(2, user.getProjects().size());
+            }
+        }
+
+        search = catalogManager.getUserManager().search(null, new Query(), QueryOptions.empty(), ownerToken);
+        assertEquals(8, search.getNumResults());
+
+        search = catalogManager.getUserManager().search(null, new Query(), QueryOptions.empty(), orgAdminToken2);
+        assertEquals(8, search.getNumResults());
+
+        search = catalogManager.getUserManager().search(null, new Query(), QueryOptions.empty(), orgAdminToken1);
+        assertEquals(8, search.getNumResults());
+
+        assertThrows(CatalogAuthorizationException.class, () -> catalogManager.getUserManager().search(null, new Query(),
+                QueryOptions.empty(), studyAdminToken1));
+        assertThrows(CatalogAuthorizationException.class, () -> catalogManager.getUserManager().search(null, new Query(),
+                QueryOptions.empty(), normalToken1));
+    }
+
     @Test
     public void testGetToken() throws Exception {
         String token = catalogManager.getUserManager().loginAsAdmin(TestParamConstants.ADMIN_PASSWORD).getToken();

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

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2024-04-10
+#    Autogenerated on: 2024-04-29
 #    
 #    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.
@@ -26,7 +26,7 @@
 #' | createUsers | /{apiVersion}/admin/users/create | body[*] |
 #' | importUsers | /{apiVersion}/admin/users/import | organization, body[*] |
 #' | permissionsUsers | /{apiVersion}/admin/users/permissions | study, entryIds, permissions, category |
-#' | searchUsers | /{apiVersion}/admin/users/search | include, exclude, limit, skip, count, organization, user, account, authenticationId |
+#' | searchUsers | /{apiVersion}/admin/users/search | include, exclude, limit, skip, count, organization, user, authenticationId |
 #' | syncUsers | /{apiVersion}/admin/users/sync | organization, body[*] |
 #' | usersUpdateGroups | /{apiVersion}/admin/users/{user}/groups/update | organization, user[*], action, body[*] |
 #'
@@ -97,7 +97,6 @@ setMethod("adminClient", "OpencgaR", function(OpencgaR, user, endpointName, para
         #' @param count Get the total number of results matching the query. Deactivated by default.
         #' @param organization Organization id.
         #' @param user User ID.
-        #' @param account Account type [GUEST, FULL, ADMINISTRATOR].
         #' @param authenticationId Authentication origin ID.
         searchUsers=fetchOpenCGA(object=OpencgaR, category="admin", categoryId=NULL, subcategory="users",
                 subcategoryId=NULL, action="search", params=params, httpMethod="GET", as.queryParam=NULL, ...),

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

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2024-04-10
+#    Autogenerated on: 2024-04-29
 #    
 #    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.