public String getCatalogDatabase() { return catalogDBAdaptorFactory.getCatalogDatabase(configuration.getDatabasePrefix()); }
private void init() { try { this.database = catalogManager.getConfiguration().getDatabasePrefix() + "_clinical"; this.clinicalVariantEngine = getClinicalStorageEngine(); } catch (IllegalAccessException | InstantiationException | ClassNotFoundException e) { e.printStackTrace(); } }
public ObjectMap getDatabaseStatus() { if (existsCatalogDB()) { return catalogDBAdaptorFactory.getDatabaseStatus(); } else { return new ObjectMap("error", "Database " + configuration.getDatabasePrefix() + "_opencga not found"); } }
public MongoDBAdaptorFactory(Configuration catalogConfiguration) throws CatalogDBException { MongoDBConfiguration mongoDBConfiguration = MongoDBConfiguration.builder() .setUserPassword( catalogConfiguration.getCatalog().getDatabase().getUser(), catalogConfiguration.getCatalog().getDatabase().getPassword()) .load(catalogConfiguration.getCatalog().getDatabase().getOptions()) .build(); List<DataStoreServerAddress> dataStoreServerAddresses = new LinkedList<>(); for (String hostPort : catalogConfiguration.getCatalog().getDatabase().getHosts()) { if (hostPort.contains(":")) { String[] split = hostPort.split(":"); int port = Integer.valueOf(split[1]); dataStoreServerAddresses.add(new DataStoreServerAddress(split[0], port)); } else { dataStoreServerAddresses.add(new DataStoreServerAddress(hostPort, 27017)); } } this.mongoManager = new MongoDataStoreManager(dataStoreServerAddresses); this.configuration = mongoDBConfiguration; this.database = getCatalogDatabase(catalogConfiguration.getDatabasePrefix()); logger = LoggerFactory.getLogger(this.getClass()); connect(); }
getConfiguration().getDatabasePrefix() + "_" + CatalogSolrManager.SAMPLE_SOLR_COLLECTION);
public CatalogSolrManager(CatalogManager catalogManager) { this.catalogManager = catalogManager; SearchConfiguration searchConfiguration = catalogManager.getConfiguration().getCatalog().getSearch(); this.solrManager = new SolrManager(searchConfiguration.getHosts(), searchConfiguration.getMode(), searchConfiguration.getTimeout()); insertBatchSize = searchConfiguration.getInsertBatchSize() > 0 ? searchConfiguration.getInsertBatchSize() : DEFAULT_INSERT_BATCH_SIZE; DATABASE_PREFIX = catalogManager.getConfiguration().getDatabasePrefix() + "_"; populateConfigCollectionMap(); logger = LoggerFactory.getLogger(CatalogSolrManager.class); }
public static DataStore getDataStoreByProjectId(CatalogManager catalogManager, String projectStr, File.Bioformat bioformat, String sessionId) throws CatalogException { DataStore dataStore; QueryOptions queryOptions = new QueryOptions(QueryOptions.INCLUDE, Arrays.asList(ProjectDBAdaptor.QueryParams.ID.key(), ProjectDBAdaptor.QueryParams.DATASTORES.key())); Project project = catalogManager.getProjectManager().get(projectStr, queryOptions, sessionId).first(); if (project.getDataStores() != null && project.getDataStores().containsKey(bioformat)) { dataStore = project.getDataStores().get(bioformat); } else { //get default datastore //Must use the UserByStudyId instead of the file owner. String userId = catalogManager.getProjectManager().getOwner(project.getUid()); // Replace possible dots at the userId. Usually a special character in almost all databases. See #532 userId = userId.replace('.', '_'); String databasePrefix = catalogManager.getConfiguration().getDatabasePrefix(); String dbName = buildDatabaseName(databasePrefix, userId, project.getId()); dataStore = new DataStore(StorageEngineFactory.get().getDefaultStorageEngineId(), dbName); } return dataStore; }
if(StringUtils.isNotEmpty(configuration.getDatabasePrefix())) { if (!configuration.getDatabasePrefix().endsWith("_")) { database = configuration.getDatabasePrefix() + "_catalog"; } else { database = configuration.getDatabasePrefix() + "catalog";
@Override public void before() throws Exception { super.before(); Path rootDir = getOpencgaHome(); // Copy configuration copyConfiguration("cohort-managed-schema.xml", CatalogSolrManager.COHORT_CONF_SET); copyConfiguration("family-managed-schema.xml", CatalogSolrManager.FAMILY_CONF_SET); copyConfiguration("file-managed-schema.xml", CatalogSolrManager.FILE_CONF_SET); copyConfiguration("individual-managed-schema.xml", CatalogSolrManager.INDIVIDUAL_CONF_SET); copyConfiguration("sample-managed-schema.xml", CatalogSolrManager.SAMPLE_CONF_SET); String solrHome = rootDir.resolve("solr").toString(); solrClient = create(solrHome, rootDir.resolve("solr/configsets").toString()); CoreAdminRequest.Create request = new CoreAdminRequest.Create(); request.setCoreName(getConfiguration().getDatabasePrefix() + "_" + CatalogSolrManager.COHORT_SOLR_COLLECTION); request.setConfigSet(CatalogSolrManager.COHORT_CONF_SET); request.process(solrClient); request.setCoreName(getConfiguration().getDatabasePrefix() + "_" + CatalogSolrManager.SAMPLE_SOLR_COLLECTION); request.setConfigSet(CatalogSolrManager.SAMPLE_CONF_SET); request.process(solrClient); request.setCoreName(getConfiguration().getDatabasePrefix() + "_" + CatalogSolrManager.INDIVIDUAL_SOLR_COLLECTION); request.setConfigSet(CatalogSolrManager.INDIVIDUAL_CONF_SET); request.process(solrClient); request.setCoreName(getConfiguration().getDatabasePrefix() + "_" + CatalogSolrManager.FILE_SOLR_COLLECTION); request.setConfigSet(CatalogSolrManager.FILE_CONF_SET); request.process(solrClient); request.setCoreName(getConfiguration().getDatabasePrefix() + "_" + CatalogSolrManager.FAMILY_SOLR_COLLECTION); request.setConfigSet(CatalogSolrManager.FAMILY_CONF_SET); request.process(solrClient); }
if(StringUtils.isNotEmpty(configuration.getDatabasePrefix())) { if (!configuration.getDatabasePrefix().endsWith("_")) { database = configuration.getDatabasePrefix() + "_catalog"; } else { database = configuration.getDatabasePrefix() + "catalog";
protected DummyVariantStorageEngine mockVariantStorageManager() { DummyVariantStorageEngine vsm = spy(new DummyVariantStorageEngine()); vsm.setConfiguration(opencga.getStorageConfiguration(), DummyVariantStorageEngine.STORAGE_ENGINE_ID, StorageOperation.buildDatabaseName(catalogManager.getConfiguration().getDatabasePrefix(), userId, projectAlias)); StorageEngineFactory.get(opencga.getStorageConfiguration()).registerVariantStorageEngine(vsm); vsm.setConfiguration(opencga.getStorageConfiguration(), DummyVariantStorageEngine.STORAGE_ENGINE_ID, DB_NAME); StorageEngineFactory.get(opencga.getStorageConfiguration()).registerVariantStorageEngine(vsm); return vsm; }