Merge branch 'develop' into TASK-6345-3.2.0

opencga-analysis/src/test/java/org/opencb/opencga/analysis/variant/OpenCGATestExternalResource.java

@@ -214,8 +214,6 @@ public Path isolateOpenCGA() throws IOException {
         Files.createDirectories(conf);
         Files.createDirectories(userHome);
 
-        catalogManagerExternalResource.getConfiguration().getAdmin().setSecretKey(null);
-        catalogManagerExternalResource.getConfiguration().getAdmin().setAlgorithm(null);
         catalogManagerExternalResource.getConfiguration().serialize(
                 new FileOutputStream(conf.resolve("configuration.yml").toFile()));
         InputStream inputStream = StorageManager.class.getClassLoader().getResourceAsStream("storage-configuration.yml");

opencga-app/app/cloud/docker/opencga-init/override_yaml.py

@@ -19,9 +19,6 @@
 parser.add_argument("--catalog-database-authentication-database", required=False, default="admin")
 parser.add_argument("--catalog-database-authentication-mechanism", required=False)
 parser.add_argument("--catalog-database-replica-set", required=False)
-parser.add_argument("--catalog-search-hosts", required=True)
-parser.add_argument("--catalog-search-user", required=False)
-parser.add_argument("--catalog-search-password", required=False)
 parser.add_argument("--rest-host", required=True)
 parser.add_argument("--grpc-host", required=True)
 parser.add_argument("--analysis-execution-mode", required=False)
@@ -138,13 +135,6 @@ def hostOverride(conf,hosts_var):
 if args.catalog_database_authentication_mechanism is not None:
     config["catalog"]["database"]["options"]["authenticationMechanism"] = args.catalog_database_authentication_mechanism
 
-# Inject search database
-hostOverride(config["catalog"]["searchEngine"], args.catalog_search_hosts)
-
-if args.catalog_search_user is not None:
-    config["catalog"]["searchEngine"]["user"] = args.catalog_search_user
-    config["catalog"]["searchEngine"]["password"] = args.catalog_search_password
-
 # Inject execution settings
 config["analysis"]["scratchDir"] = "/tmp/opencga_scratch"
 if args.max_concurrent_jobs is not None:

opencga-app/app/cloud/docker/opencga-init/test/test_override_yaml.py

@@ -1,11 +1,10 @@
+import os
 import subprocess
-from shutil import copyfile
+import sys
 import unittest
 import yaml
 from io import StringIO
-import sys
-import os
-
+from shutil import copyfile
 
 os.chdir(sys.path[0])
 
@@ -40,9 +39,6 @@ def test_end_2_end(self):
                     "--catalog-database-hosts", "test-catalog-database-host1,test-catalog-database-host2,test-catalog-database-host3",
                     "--catalog-database-user", "test-catalog-database-user",
                     "--catalog-database-password", "test-catalog-database-password",
-                    "--catalog-search-hosts", "test-catalog-search-host1,test-catalog-search-host2",
-                    "--catalog-search-user", "test-catalog-search-user",
-                    "--catalog-search-password", "test-catalog-search-password",
                     "--rest-host", "test-rest-host",
                     "--grpc-host", "test-grpc-host",
                     "--max-concurrent-jobs", "25",
@@ -170,18 +166,6 @@ def test_end_2_end(self):
         self.assertEqual(config["catalog"]["database"]["options"]["sslEnabled"], True)
         self.assertEqual(config["catalog"]["database"]["options"]["sslInvalidCertificatesAllowed"], True)
         self.assertEqual(config["catalog"]["database"]["options"]["authenticationDatabase"], "admin")
-        self.assertEqual(
-            config["catalog"]["searchEngine"]["hosts"][0], "test-catalog-search-host1"
-        )
-        self.assertEqual(
-            config["catalog"]["searchEngine"]["hosts"][1], "test-catalog-search-host2"
-        )
-        self.assertEqual(
-            config["catalog"]["searchEngine"]["user"], "test-catalog-search-user"
-        )
-        self.assertEqual(
-            config["catalog"]["searchEngine"]["password"], "test-catalog-search-password"
-        )
         self.assertEqual(config["analysis"]["execution"]["id"], "test-analysis-execution-mode")
         self.assertEqual(config["analysis"]["execution"]["maxConcurrentJobs"]["variant-index"], 25)
         self.assertEqual(client_config["rest"]["hosts"][0]["url"], "test-rest-host")
@@ -200,9 +184,6 @@ def test_azure_batch_execution(self):
                     "--catalog-database-hosts", "test-catalog-database-host1,test-catalog-database-host2,test-catalog-database-host3",
                     "--catalog-database-user", "test-catalog-database-user",
                     "--catalog-database-password", "test-catalog-database-password",
-                    "--catalog-search-hosts", "test-catalog-search-host1,test-catalog-search-host2",
-                    "--catalog-search-user", "test-catalog-search-user",
-                    "--catalog-search-password", "test-catalog-search-password",
                     "--rest-host", "test-rest-host",
                     "--grpc-host", "test-grpc-host",
                     "--analysis-execution-mode", "AZURE",
@@ -273,9 +254,6 @@ def test_kubernetes_execution(self):
                     "--catalog-database-hosts", "test-catalog-database-host1,test-catalog-database-host2,test-catalog-database-host3",
                     "--catalog-database-user", "test-catalog-database-user",
                     "--catalog-database-password", "test-catalog-database-password",
-                    "--catalog-search-hosts", "test-catalog-search-host1,test-catalog-search-host2",
-                    "--catalog-search-user", "test-catalog-search-user",
-                    "--catalog-search-password", "test-catalog-search-password",
                     "--rest-host", "test-rest-host",
                     "--grpc-host", "test-grpc-host",
                     "--analysis-execution-mode", "k8s",
@@ -357,12 +335,6 @@ def test_cellbasedb_with_empty_hosts(self):
                 "test-catalog-database-user",
                 "--catalog-database-password",
                 "test-catalog-database-password",
-                "--catalog-search-hosts",
-                "test-catalog-search-host1,test-catalog-search-host2",
-                "--catalog-search-user",
-                "test-catalog-search-user",
-                "--catalog-search-password",
-                "test-catalog-search-password",
                 "--rest-host",
                 "test-rest-host",
                 "--grpc-host",
@@ -437,12 +409,6 @@ def test_cellbasedb_with_no_db_hosts(self):
                 "test-catalog-database-user",
                 "--catalog-database-password",
                 "test-catalog-database-password",
-                "--catalog-search-hosts",
-                "test-catalog-search-host1,test-catalog-search-host2",
-                "--catalog-search-user",
-                "test-catalog-search-user",
-                "--catalog-search-password",
-                "test-catalog-search-password",
                 "--rest-host",
                 "test-rest-host",
                 "--grpc-host",
@@ -519,12 +485,6 @@ def test_cellbase_rest_set(self):
                 "test-catalog-database-user",
                 "--catalog-database-password",
                 "test-catalog-database-password",
-                "--catalog-search-hosts",
-                "test-catalog-search-host1,test-catalog-search-host2",
-                "--catalog-search-user",
-                "test-catalog-search-user",
-                "--catalog-search-password",
-                "test-catalog-search-password",
                 "--rest-host",
                 "test-rest-host",
                 "--grpc-host",
@@ -604,12 +564,6 @@ def test_cellbase_rest_empty_set(self):
                 "test-catalog-database-user",
                 "--catalog-database-password",
                 "test-catalog-database-password",
-                "--catalog-search-hosts",
-                "test-catalog-search-host1,test-catalog-search-host2",
-                "--catalog-search-user",
-                "test-catalog-search-user",
-                "--catalog-search-password",
-                "test-catalog-search-password",
                 "--rest-host",
                 "test-rest-host",
                 "--grpc-host",
@@ -688,12 +642,6 @@ def test_cellbase_rest_not_set(self):
                 "test-catalog-database-user",
                 "--catalog-database-password",
                 "test-catalog-database-password",
-                "--catalog-search-hosts",
-                "test-catalog-search-host1,test-catalog-search-host2",
-                "--catalog-search-user",
-                "test-catalog-search-user",
-                "--catalog-search-password",
-                "test-catalog-search-password",
                 "--rest-host",
                 "test-rest-host",
                 "--grpc-host",

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

@@ -22,7 +22,6 @@
 import org.opencb.opencga.app.cli.CommandExecutor;
 import org.opencb.opencga.app.cli.admin.AdminCliOptionsParser;
 import org.opencb.opencga.catalog.exceptions.CatalogException;
-import org.opencb.opencga.core.config.Admin;
 
 import java.util.Collections;
 
@@ -82,9 +81,6 @@ protected void setCatalogDatabaseCredentials(String host, String prefix, String
             configuration.getCatalog().getDatabase().setUser(user);
         }
 
-        if (configuration.getAdmin() == null) {
-            configuration.setAdmin(new Admin());
-        }
         if (StringUtils.isNotEmpty(password)) {
             configuration.getCatalog().getDatabase().setPassword(password);
         }

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

@@ -23,13 +23,11 @@
 import org.opencb.commons.datastore.core.QueryOptions;
 import org.opencb.commons.datastore.mongodb.MongoDataStore;
 import org.opencb.opencga.app.cli.admin.AdminCliOptionsParser;
-import org.opencb.opencga.catalog.auth.authentication.JwtManager;
 import org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptorFactory;
 import org.opencb.opencga.catalog.db.mongodb.MongoDBUtils;
 import org.opencb.opencga.catalog.exceptions.CatalogException;
 import org.opencb.opencga.catalog.managers.CatalogManager;
 import org.opencb.opencga.core.common.JacksonUtils;
-import org.opencb.opencga.core.common.PasswordUtils;
 import org.opencb.opencga.master.monitor.MonitorService;
 
 import javax.ws.rs.client.Client;
@@ -173,19 +171,12 @@ private void install() throws CatalogException {
 
         validateConfiguration(commandOptions);
 
-        this.configuration.getAdmin().setAlgorithm("HS256");
-
-        this.configuration.getAdmin().setSecretKey(commandOptions.secretKey);
-        if (StringUtils.isEmpty(configuration.getAdmin().getSecretKey())) {
-            configuration.getAdmin().setSecretKey(PasswordUtils.getStrongRandomPassword(JwtManager.SECRET_KEY_MIN_LENGTH));
-        }
-
         if (StringUtils.isEmpty(commandOptions.commonOptions.adminPassword)) {
             throw new CatalogException("No admin password found. Please, insert your password.");
         }
 
         try (CatalogManager catalogManager = new CatalogManager(configuration)) {
-            catalogManager.installCatalogDB("HS256", configuration.getAdmin().getSecretKey(), commandOptions.commonOptions.adminPassword,
+            catalogManager.installCatalogDB("HS256", commandOptions.secretKey, commandOptions.commonOptions.adminPassword,
                     commandOptions.email, commandOptions.force);
         }
     }

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","configuration-update","info","update")
+    private List<Candidate> organizationsList = asList( "create","notes-create","notes-search","notes-delete","notes-update","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

@@ -272,6 +272,8 @@ public OpencgaCliOptionsParser() {
         organizationsSubCommands.addCommand("notes-search", organizationsCommandOptions.searchNotesCommandOptions);
         organizationsSubCommands.addCommand("notes-delete", organizationsCommandOptions.deleteNotesCommandOptions);
         organizationsSubCommands.addCommand("notes-update", organizationsCommandOptions.updateNotesCommandOptions);
+        organizationsSubCommands.addCommand("update-status-user", organizationsCommandOptions.userUpdateStatusCommandOptions);
+        organizationsSubCommands.addCommand("user-update", organizationsCommandOptions.updateUserCommandOptions);
         organizationsSubCommands.addCommand("configuration-update", organizationsCommandOptions.updateConfigurationCommandOptions);
         organizationsSubCommands.addCommand("info", organizationsCommandOptions.infoCommandOptions);
         organizationsSubCommands.addCommand("update", organizationsCommandOptions.updateCommandOptions);

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

@@ -24,6 +24,10 @@
 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.models.user.OrganizationUserUpdateParams;
+import org.opencb.opencga.core.models.user.User;
+import org.opencb.opencga.core.models.user.UserQuota;
+import org.opencb.opencga.core.models.user.UserStatusUpdateParams;
 import org.opencb.opencga.core.response.QueryType;
 import org.opencb.opencga.core.response.RestResponse;
 
@@ -76,6 +80,12 @@ public void execute() throws Exception {
             case "notes-update":
                 queryResponse = updateNotes();
                 break;
+            case "update-status-user":
+                queryResponse = userUpdateStatus();
+                break;
+            case "user-update":
+                queryResponse = updateUser();
+                break;
             case "configuration-update":
                 queryResponse = updateConfiguration();
                 break;
@@ -120,6 +130,7 @@ private RestResponse<Organization> create() throws Exception {
             putNestedIfNotEmpty(beanParams, "name",commandOptions.name, true);
             putNestedIfNotEmpty(beanParams, "creationDate",commandOptions.creationDate, true);
             putNestedIfNotEmpty(beanParams, "modificationDate",commandOptions.modificationDate, true);
+            putNestedIfNotEmpty(beanParams, "configuration.defaultUserExpirationDate",commandOptions.configurationDefaultUserExpirationDate, true);
             putNestedIfNotNull(beanParams, "attributes",commandOptions.attributes, true);
 
             organizationCreateParams = JacksonUtils.getDefaultObjectMapper().copy()
@@ -227,6 +238,77 @@ private RestResponse<Note> updateNotes() throws Exception {
         return openCGAClient.getOrganizationClient().updateNotes(commandOptions.id, noteUpdateParams, queryParams);
     }
 
+    private RestResponse<User> userUpdateStatus() throws Exception {
+        logger.debug("Executing userUpdateStatus in Organizations command line");
+
+        OrganizationsCommandOptions.UserUpdateStatusCommandOptions commandOptions = organizationsCommandOptions.userUpdateStatusCommandOptions;
+
+        ObjectMap queryParams = new ObjectMap();
+        queryParams.putIfNotEmpty("include", commandOptions.include);
+        queryParams.putIfNotEmpty("exclude", commandOptions.exclude);
+        queryParams.putIfNotEmpty("organization", commandOptions.organization);
+        queryParams.putIfNotNull("includeResult", commandOptions.includeResult);
+
+
+        UserStatusUpdateParams userStatusUpdateParams = null;
+        if (commandOptions.jsonDataModel) {
+            RestResponse<User> res = new RestResponse<>();
+            res.setType(QueryType.VOID);
+            PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/organizations/user/{user}/status/update"));
+            return res;
+        } else if (commandOptions.jsonFile != null) {
+            userStatusUpdateParams = JacksonUtils.getDefaultObjectMapper()
+                    .readValue(new java.io.File(commandOptions.jsonFile), UserStatusUpdateParams.class);
+        } else {
+            ObjectMap beanParams = new ObjectMap();
+            putNestedIfNotEmpty(beanParams, "status",commandOptions.status, true);
+
+            userStatusUpdateParams = JacksonUtils.getDefaultObjectMapper().copy()
+                    .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
+                    .readValue(beanParams.toJson(), UserStatusUpdateParams.class);
+        }
+        return openCGAClient.getOrganizationClient().userUpdateStatus(commandOptions.user, userStatusUpdateParams, queryParams);
+    }
+
+    private RestResponse<User> updateUser() throws Exception {
+        logger.debug("Executing updateUser in Organizations command line");
+
+        OrganizationsCommandOptions.UpdateUserCommandOptions commandOptions = organizationsCommandOptions.updateUserCommandOptions;
+
+        ObjectMap queryParams = new ObjectMap();
+        queryParams.putIfNotEmpty("include", commandOptions.include);
+        queryParams.putIfNotEmpty("exclude", commandOptions.exclude);
+        queryParams.putIfNotEmpty("organization", commandOptions.organization);
+        queryParams.putIfNotNull("includeResult", commandOptions.includeResult);
+
+
+        OrganizationUserUpdateParams organizationUserUpdateParams = null;
+        if (commandOptions.jsonDataModel) {
+            RestResponse<User> res = new RestResponse<>();
+            res.setType(QueryType.VOID);
+            PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/organizations/user/{user}/update"));
+            return res;
+        } else if (commandOptions.jsonFile != null) {
+            organizationUserUpdateParams = JacksonUtils.getDefaultObjectMapper()
+                    .readValue(new java.io.File(commandOptions.jsonFile), OrganizationUserUpdateParams.class);
+        } else {
+            ObjectMap beanParams = new ObjectMap();
+            putNestedIfNotEmpty(beanParams, "name",commandOptions.name, true);
+            putNestedIfNotEmpty(beanParams, "email",commandOptions.email, true);
+            putNestedIfNotNull(beanParams, "quota.diskUsage",commandOptions.quotaDiskUsage, true);
+            putNestedIfNotNull(beanParams, "quota.cpuUsage",commandOptions.quotaCpuUsage, true);
+            putNestedIfNotNull(beanParams, "quota.maxDisk",commandOptions.quotaMaxDisk, true);
+            putNestedIfNotNull(beanParams, "quota.maxCpu",commandOptions.quotaMaxCpu, true);
+            putNestedIfNotEmpty(beanParams, "account.expirationDate",commandOptions.accountExpirationDate, true);
+            putNestedIfNotNull(beanParams, "attributes",commandOptions.attributes, true);
+
+            organizationUserUpdateParams = JacksonUtils.getDefaultObjectMapper().copy()
+                    .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
+                    .readValue(beanParams.toJson(), OrganizationUserUpdateParams.class);
+        }
+        return openCGAClient.getOrganizationClient().updateUser(commandOptions.user, organizationUserUpdateParams, queryParams);
+    }
+
     private RestResponse<OrganizationConfiguration> updateConfiguration() throws Exception {
         logger.debug("Executing updateConfiguration in Organizations command line");
 
@@ -250,6 +332,7 @@ private RestResponse<OrganizationConfiguration> updateConfiguration() throws Exc
                     .readValue(new java.io.File(commandOptions.jsonFile), OrganizationConfiguration.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
+            putNestedIfNotEmpty(beanParams, "defaultUserExpirationDate",commandOptions.defaultUserExpirationDate, true);
             putNestedIfNotNull(beanParams, "optimizations.simplifyPermissions",commandOptions.optimizationsSimplifyPermissions, true);
             putNestedIfNotEmpty(beanParams, "token.algorithm",commandOptions.tokenAlgorithm, true);
             putNestedIfNotEmpty(beanParams, "token.secretKey",commandOptions.tokenSecretKey, true);