Merge branch 'develop' into TASK-5610

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","info","update")
+    private List<Candidate> organizationsList = asList( "create","notes-create","notes-search","notes-delete","notes-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 +272,7 @@ public OpencgaCliOptionsParser() {
         organizationsSubCommands.addCommand("notes-search", organizationsCommandOptions.searchNotesCommandOptions);
         organizationsSubCommands.addCommand("notes-delete", organizationsCommandOptions.deleteNotesCommandOptions);
         organizationsSubCommands.addCommand("notes-update", organizationsCommandOptions.updateNotesCommandOptions);
+        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

@@ -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.UpdateAction;
 import org.opencb.opencga.client.exceptions.ClientException;
 import org.opencb.opencga.core.common.JacksonUtils;
 import org.opencb.opencga.core.config.Optimizations;
@@ -75,6 +76,9 @@ public void execute() throws Exception {
             case "notes-update":
                 queryResponse = updateNotes();
                 break;
+            case "configuration-update":
+                queryResponse = updateConfiguration();
+                break;
             case "info":
                 queryResponse = info();
                 break;
@@ -223,6 +227,41 @@ private RestResponse<Note> updateNotes() throws Exception {
         return openCGAClient.getOrganizationClient().updateNotes(commandOptions.id, noteUpdateParams, queryParams);
     }
 
+    private RestResponse<OrganizationConfiguration> updateConfiguration() throws Exception {
+        logger.debug("Executing updateConfiguration in Organizations command line");
+
+        OrganizationsCommandOptions.UpdateConfigurationCommandOptions commandOptions = organizationsCommandOptions.updateConfigurationCommandOptions;
+
+        ObjectMap queryParams = new ObjectMap();
+        queryParams.putIfNotEmpty("include", commandOptions.include);
+        queryParams.putIfNotEmpty("exclude", commandOptions.exclude);
+        queryParams.putIfNotNull("includeResult", commandOptions.includeResult);
+        queryParams.putIfNotNull("authenticationOriginsAction", commandOptions.authenticationOriginsAction);
+
+
+        OrganizationConfiguration organizationConfiguration = null;
+        if (commandOptions.jsonDataModel) {
+            RestResponse<OrganizationConfiguration> res = new RestResponse<>();
+            res.setType(QueryType.VOID);
+            PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/organizations/{organization}/configuration/update"));
+            return res;
+        } else if (commandOptions.jsonFile != null) {
+            organizationConfiguration = JacksonUtils.getDefaultObjectMapper()
+                    .readValue(new java.io.File(commandOptions.jsonFile), OrganizationConfiguration.class);
+        } else {
+            ObjectMap beanParams = new ObjectMap();
+            putNestedIfNotNull(beanParams, "optimizations.simplifyPermissions",commandOptions.optimizationsSimplifyPermissions, true);
+            putNestedIfNotEmpty(beanParams, "token.algorithm",commandOptions.tokenAlgorithm, true);
+            putNestedIfNotEmpty(beanParams, "token.secretKey",commandOptions.tokenSecretKey, true);
+            putNestedIfNotNull(beanParams, "token.expiration",commandOptions.tokenExpiration, true);
+
+            organizationConfiguration = JacksonUtils.getDefaultObjectMapper().copy()
+                    .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
+                    .readValue(beanParams.toJson(), OrganizationConfiguration.class);
+        }
+        return openCGAClient.getOrganizationClient().updateConfiguration(commandOptions.organization, organizationConfiguration, queryParams);
+    }
+
     private RestResponse<Organization> info() throws Exception {
         logger.debug("Executing info 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 UpdateConfigurationCommandOptions updateConfigurationCommandOptions;
         public InfoCommandOptions infoCommandOptions;
         public UpdateCommandOptions updateCommandOptions;
 
@@ -51,6 +52,7 @@ public OrganizationsCommandOptions(CommonCommandOptions commonCommandOptions, JC
         this.searchNotesCommandOptions = new SearchNotesCommandOptions();
         this.deleteNotesCommandOptions = new DeleteNotesCommandOptions();
         this.updateNotesCommandOptions = new UpdateNotesCommandOptions();
+        this.updateConfigurationCommandOptions = new UpdateConfigurationCommandOptions();
         this.infoCommandOptions = new InfoCommandOptions();
         this.updateCommandOptions = new UpdateCommandOptions();
 
@@ -216,6 +218,47 @@ public class UpdateNotesCommandOptions {
 
     }
 
+    @Parameters(commandNames = {"configuration-update"}, commandDescription ="Update the Organization configuration attributes")
+    public class UpdateConfigurationCommandOptions {
+
+        @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 = {"--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 = {"--organization"}, description = "Organization id", required = true, arity = 1)
+        public String organization; 
+
+        @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; 
+
+        @Parameter(names = {"--authentication-origins-action"}, description = "Action to be performed if the array of authenticationOrigins is being updated.", required = false, arity = 1)
+        public String authenticationOriginsAction = "ADD"; 
+
+        @Parameter(names = {"--optimizations-simplify-permissions"}, description = "The body web service simplifyPermissions parameter", required = false, help = true, arity = 0)
+        public boolean optimizationsSimplifyPermissions = false;
+
+        @Parameter(names = {"--token-algorithm"}, description = "The body web service algorithm parameter", required = false, arity = 1)
+        public String tokenAlgorithm;
+
+        @Parameter(names = {"--token-secret-key"}, description = "The body web service secretKey parameter", required = false, arity = 1)
+        public String tokenSecretKey;
+
+        @Parameter(names = {"--token-expiration"}, description = "The body web service expiration parameter", required = false, arity = 1)
+        public Long tokenExpiration;
+
+    }
+
     @Parameters(commandNames = {"info"}, commandDescription ="Return the organization information")
     public class InfoCommandOptions {
 

opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_1_0/NoteMigration.java

@@ -6,34 +6,23 @@
 import com.mongodb.client.model.RenameCollectionOptions;
 import com.mongodb.client.model.Updates;
 import com.mongodb.client.result.UpdateResult;
-import org.apache.commons.lang3.StringUtils;
 import org.bson.Document;
 import org.bson.conversions.Bson;
 import org.opencb.commons.datastore.mongodb.MongoDataStore;
 import org.opencb.opencga.catalog.db.api.NoteDBAdaptor;
-import org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptorFactory;
 import org.opencb.opencga.catalog.db.mongodb.OrganizationMongoDBAdaptorFactory;
-import org.opencb.opencga.catalog.exceptions.CatalogDBException;
-import org.opencb.opencga.catalog.io.IOManagerFactory;
-import org.opencb.opencga.catalog.managers.CatalogManager;
 import org.opencb.opencga.catalog.migration.Migration;
 import org.opencb.opencga.catalog.migration.MigrationTool;
-import org.opencb.opencga.core.api.ParamConstants;
 import org.opencb.opencga.core.models.notes.Note;
 
-import java.util.Collections;
-import java.util.List;
-
 @Migration(id = "migrate_notes", description = "Migrate notes #TASK-5836", version = "3.1.0",
         language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20240315)
 public class NoteMigration extends MigrationTool {
 
     @Override
     protected void run() throws Exception {
-        IOManagerFactory ioManagerFactory = new IOManagerFactory();
-        dbAdaptorFactory = new MongoDBAdaptorFactory(configuration, ioManagerFactory);
         // First migrate to add the new values
-        MongoCollection<Document> collection = getMongoCollection(ParamConstants.ADMIN_ORGANIZATION, "notes");
+        MongoCollection<Document> collection = getMongoCollection(organizationId, "notes");
         Bson query = Filters.exists(NoteDBAdaptor.QueryParams.STUDY_UID.key(), false);
         Bson update = Updates.combine(
                 Updates.set(NoteDBAdaptor.QueryParams.STUDY_UID.key(), -1L),
@@ -43,41 +32,20 @@ protected void run() throws Exception {
         );
         UpdateResult updateResult = collection.updateMany(query, update);
         if (updateResult.getModifiedCount() == 0) {
-            // Check there are at least 2 organizations present
-            logger.info("Note data model could not be updated. Detected organizations are: {}", StringUtils.join(dbAdaptorFactory.getOrganizationIds(), ","));
-            if (dbAdaptorFactory.getOrganizationIds().size() == 2) {
-                logger.info("Nothing to migrate");
-                return;
-            } else {
-                throw new CatalogDBException("Notes could not be found to migrate.");
-            }
+            logger.info("Note data model could not be updated. Notes found in organization '{}': {}", organizationId, updateResult.getMatchedCount());
         }
-        renameNoteCollection(Collections.singletonList(ParamConstants.ADMIN_ORGANIZATION));
-
-        dbAdaptorFactory.close();
-        dbAdaptorFactory = new MongoDBAdaptorFactory(configuration, ioManagerFactory);
-        // We run it a second time because the first time it will only rename the "opencga" org as OpenCGA will not be able to know
-        // which other organizations are present in the installation (trying to fetch the information from "note" instead of old "notes")
-        List<String> organizationIds = dbAdaptorFactory.getOrganizationIds();
-        organizationIds.remove(ParamConstants.ADMIN_ORGANIZATION);
-        renameNoteCollection(organizationIds);
-
-        // Reload catalog manager to install missing indexes
-        catalogManager = new CatalogManager(configuration);
-        catalogManager.installIndexes(token);
-    }
 
-    private void renameNoteCollection(List<String> organizationIds) throws CatalogDBException {
+        // Rename Note collection
         RenameCollectionOptions options = new RenameCollectionOptions().dropTarget(true);
         // Rename collection
-        for (String organizationId : organizationIds) {
-            String databaseName = dbAdaptorFactory.getMongoDataStore(organizationId).getDatabaseName();
-            logger.info("Renaming notes collection for organization '{}' -> Database: '{}'", organizationId, databaseName);
-            MongoDataStore mongoDataStore = dbAdaptorFactory.getMongoDataStore(organizationId);
-            mongoDataStore.getDb().getCollection("notes").renameCollection(new MongoNamespace(databaseName, OrganizationMongoDBAdaptorFactory.NOTE_COLLECTION), options);
-            mongoDataStore.getDb().getCollection("notes_archive").renameCollection(new MongoNamespace(databaseName, OrganizationMongoDBAdaptorFactory.NOTE_ARCHIVE_COLLECTION), options);
-            mongoDataStore.getDb().getCollection("notes_deleted").renameCollection(new MongoNamespace(databaseName, OrganizationMongoDBAdaptorFactory.DELETED_NOTE_COLLECTION), options);
-        }
+        String databaseName = dbAdaptorFactory.getMongoDataStore(organizationId).getDatabaseName();
+        logger.info("Renaming notes collection for organization '{}' -> Database: '{}'", organizationId, databaseName);
+        MongoDataStore mongoDataStore = dbAdaptorFactory.getMongoDataStore(organizationId);
+        mongoDataStore.getDb().getCollection("notes").renameCollection(new MongoNamespace(databaseName, OrganizationMongoDBAdaptorFactory.NOTE_COLLECTION), options);
+        mongoDataStore.getDb().getCollection("notes_archive").renameCollection(new MongoNamespace(databaseName, OrganizationMongoDBAdaptorFactory.NOTE_ARCHIVE_COLLECTION), options);
+        mongoDataStore.getDb().getCollection("notes_deleted").renameCollection(new MongoNamespace(databaseName, OrganizationMongoDBAdaptorFactory.DELETED_NOTE_COLLECTION), options);
+
+        catalogManager.installIndexes(organizationId, token);
     }
 
 }

opencga-catalog/src/main/java/org/opencb/opencga/catalog/auth/authentication/AuthenticationManager.java

@@ -28,6 +28,7 @@
 import org.slf4j.LoggerFactory;
 
 import javax.crypto.spec.SecretKeySpec;
+import java.io.Closeable;
 import java.security.Key;
 import java.util.Collections;
 import java.util.Date;
@@ -37,7 +38,7 @@
 /**
  * @author Jacobo Coll <[email protected]>
  */
-public abstract class AuthenticationManager {
+public abstract class AuthenticationManager implements Closeable {
 
     protected JwtManager jwtManager;
 

opencga-catalog/src/main/java/org/opencb/opencga/catalog/auth/authentication/AzureADAuthenticationManager.java

@@ -146,6 +146,15 @@ public AzureADAuthenticationManager(AuthenticationOrigin authenticationOrigin) t
         Configurator.setLevel("com.microsoft.aad.adal4j.AuthenticationAuthority", Level.WARN);
     }
 
+    public static void validateAuthenticationOriginConfiguration(AuthenticationOrigin authenticationOrigin) throws CatalogException {
+        if (authenticationOrigin.getType() != AuthenticationOrigin.AuthenticationType.AzureAD) {
+            throw new CatalogException("Unknown authentication type. Expected type '" + AuthenticationOrigin.AuthenticationType.AzureAD
+                    + "' but received '" + authenticationOrigin.getType() + "'.");
+        }
+        AzureADAuthenticationManager azureADAuthenticationManager = new AzureADAuthenticationManager(authenticationOrigin);
+        azureADAuthenticationManager.close();
+    }
+
     private OIDCProviderMetadata getProviderMetadata(String host) throws IOException, ParseException {
         URL providerConfigurationURL = new URL(host);
         InputStream stream = providerConfigurationURL.openStream();
@@ -420,4 +429,8 @@ public String createNonExpiringToken(String organizationId, String userId, Map<S
         throw new UnsupportedOperationException("Tokens are generated by Azure via authorization code or user-password");
     }
 
+    @Override
+    public void close() {
+        THREAD_POOL.shutdown();
+    }
 }

opencga-catalog/src/main/java/org/opencb/opencga/catalog/auth/authentication/CatalogAuthenticationManager.java

@@ -64,6 +64,17 @@ public CatalogAuthenticationManager(DBAdaptorFactory dbAdaptorFactory, Email ema
         this.logger = LoggerFactory.getLogger(CatalogAuthenticationManager.class);
     }
 
+    public static void validateAuthenticationOriginConfiguration(AuthenticationOrigin authenticationOrigin) throws CatalogException {
+        if (!OPENCGA.equals(authenticationOrigin.getId())) {
+            throw new CatalogException("Unknown authentication origin. Expected origin id '" + OPENCGA + "' but received '"
+                    + authenticationOrigin.getId() + "'.");
+        }
+        if (authenticationOrigin.getType() != AuthenticationOrigin.AuthenticationType.OPENCGA) {
+            throw new CatalogException("Unknown authentication type. Expected type '" + AuthenticationOrigin.AuthenticationType.OPENCGA
+                    + "' but received '" + authenticationOrigin.getType() + "'.");
+        }
+    }
+
     @Override
     public AuthenticationResponse authenticate(String organizationId, String userId, String password)
             throws CatalogAuthenticationException {
@@ -102,12 +113,12 @@ public void newPassword(String organizationId, String userId, String newPassword
 
     @Override
     public String createToken(String organizationId, String userId, Map<String, Object> claims, long expiration) {
-        return jwtManager.createJWTToken(organizationId, userId, claims, expiration);
+        return jwtManager.createJWTToken(organizationId, AuthenticationOrigin.AuthenticationType.OPENCGA, userId, claims, expiration);
     }
 
     @Override
     public String createNonExpiringToken(String organizationId, String userId, Map<String, Object> claims) {
-        return jwtManager.createJWTToken(organizationId, userId, claims, 0L);
+        return jwtManager.createJWTToken(organizationId, AuthenticationOrigin.AuthenticationType.OPENCGA, userId, claims, 0L);
     }
 
     @Override
@@ -145,4 +156,8 @@ public static AuthenticationOrigin createOpencgaAuthenticationOrigin() {
                 .setId(CatalogAuthenticationManager.OPENCGA)
                 .setType(AuthenticationOrigin.AuthenticationType.OPENCGA);
     }
+
+    @Override
+    public void close() {
+    }
 }