public VariantMongoDBAdaptor(String species, String assembly, MongoDataStore mongoDataStore) { super(species, assembly, mongoDataStore); mongoDBCollection = mongoDataStore.getCollection("variation"); caddDBCollection = mongoDataStore.getCollection("variation_functional_score"); logger.debug("VariationMongoDBAdaptor: in 'constructor'"); }
public MongoDBCollection getStageCollection(int studyId) { String stageCollectionName = configuration.getString(COLLECTION_STAGE.key(), COLLECTION_STAGE.defaultValue()); // Ensure retro-compatibility. // If a "stage" collection exists, continue using one single stage collection for all the studies. // Otherwise, build the stage collection name as: 'stage_study_<study-id>' if (db.getCollectionNames().contains(stageCollectionName)) { return db.getCollection(stageCollectionName); } else { return db.getCollection(stageCollectionName + "_study_" + studyId); } }
public ProteinMongoDBAdaptor(String species, String assembly, MongoDataStore mongoDataStore) { super(species, assembly, mongoDataStore); mongoDBCollection = mongoDataStore.getCollection("protein"); proteinSubstitutionMongoDBCollection = mongoDataStore.getCollection("protein_functional_prediction"); logger.debug("ProteinMongoDBAdaptor: in 'constructor'"); }
public GeneMongoDBAdaptor(String species, String assembly, MongoDataStore mongoDataStore) { super(species, assembly, mongoDataStore); mongoDBCollection = mongoDataStore.getCollection(GENE); logger.debug("GeneMongoDBAdaptor: in 'constructor'"); }
public ProteinProteinInteractionMongoDBAdaptor(String species, String assembly, MongoDataStore mongoDataStore) { super(species, assembly, mongoDataStore); mongoDBCollection = mongoDataStore.getCollection("variation"); logger.debug("ProteinProteinInteractionMongoDBAdaptor: in 'constructor'"); }
public ProteinProteinInteractionMongoDBAdaptor(String species, String assembly, MongoDataStore mongoDataStore) { super(species, assembly, mongoDataStore); mongoDBCollection = mongoDataStore.getCollection("variation"); logger.debug("ProteinProteinInteractionMongoDBAdaptor: in 'constructor'"); }
public ClinicalMongoDBAdaptor(String species, String assembly, MongoDataStore mongoDataStore) { super(species, assembly, mongoDataStore); mongoDBCollection = mongoDataStore.getCollection("clinical_variants"); logger.debug("ClinicalMongoDBAdaptor: in 'constructor'"); }
public ClinicalLegacyMongoDBAdaptor(String species, String assembly, MongoDataStore mongoDataStore) { super(species, assembly, mongoDataStore); mongoDBCollection = mongoDataStore.getCollection("clinical"); logger.debug("ClinicalLegacyMongoDBAdaptor: in 'constructor'"); }
public MetaMongoDBAdaptor(String species, String assembly, MongoDataStore mongoDataStore) { super(species, assembly, mongoDataStore); mongoDBCollection = mongoDataStore.getCollection("metadata"); logger.debug("MetaMongoDBAdaptor: in 'constructor'"); }
public ConservationMongoDBAdaptor(String species, String assembly, MongoDataStore mongoDataStore) { super(species, assembly, mongoDataStore); mongoDBCollection = mongoDataStore.getCollection("conservation"); logger.debug("ConservationMongoDBAdaptor: in 'constructor'"); }
public XRefMongoDBAdaptor(String species, String assembly, MongoDataStore mongoDataStore) { super(species, assembly, mongoDataStore); mongoDBCollection = mongoDataStore.getCollection("gene"); logger.debug("XRefMongoDBAdaptor: in 'constructor'"); }
public ConservationMongoDBAdaptor(String species, String assembly, MongoDataStore mongoDataStore) { super(species, assembly, mongoDataStore); mongoDBCollection = mongoDataStore.getCollection("conservation"); logger.debug("ConservationMongoDBAdaptor: in 'constructor'"); }
public XRefMongoDBAdaptor(String species, String assembly, MongoDataStore mongoDataStore) { super(species, assembly, mongoDataStore); mongoDBCollection = mongoDataStore.getCollection("gene"); logger.debug("XRefMongoDBAdaptor: in 'constructor'"); }
public ClinicalMongoDBAdaptor(String species, String assembly, MongoDataStore mongoDataStore) { super(species, assembly, mongoDataStore); mongoDBCollection = mongoDataStore.getCollection("clinical_variants"); logger.debug("ClinicalMongoDBAdaptor: in 'constructor'"); }
public TranscriptMongoDBAdaptor(String species, String assembly, MongoDataStore mongoDataStore) { super(species, assembly, mongoDataStore); mongoDBCollection = mongoDataStore.getCollection("gene"); logger.debug("TranscriptMongoDBAdaptor: in 'constructor'"); }
public MongoDBCollection createCollection(String collectionName) { if (!Arrays.asList(db.listCollectionNames()).contains(collectionName)) { db.createCollection(collectionName); } return getCollection(collectionName); }
@Override public void delete(int study, int file) { String id = DocumentToVariantFileMetadataConverter.buildId(study, file); MongoDBCollection coll = db.getCollection(collectionName); DeleteResult deleteResult = coll.remove(Filters.eq("_id", id), null).first(); if (deleteResult.getDeletedCount() != 1) { throw new IllegalArgumentException("Unable to delete VariantSource " + id); } }
public MongoDBStudyConfigurationDBAdaptor(MongoDataStore db, String collectionName) { collection = db.getCollection(collectionName) .withReadPreference(ReadPreference.primary()) .withWriteConcern(WriteConcern.ACKNOWLEDGED); collection.createIndex(new Document("studyName", 1), new ObjectMap(MongoDBCollection.UNIQUE, true)); mongoLock = new MongoLock(collection, "_lock"); }
@Override public void updateVariantFileMetadata(String studyId, VariantFileMetadata metadata) { MongoDBCollection coll = db.getCollection(collectionName); if (Integer.valueOf(metadata.getId()) <= 0) { throw new IllegalArgumentException("FileIds must be integer positive"); } Document document = variantFileMetadataConverter.convertToStorageType(studyId, metadata); String id = document.getString("_id"); document.append("_id", id); QueryOptions options = new QueryOptions(MongoDBCollection.REPLACE, true).append(MongoDBCollection.UPSERT, true); coll.update(Filters.eq("_id", id), document, options); }
public MongoDBProjectMetadataDBAdaptor(MongoDataStore db, String collectionName) { converter = new GenericDocumentComplexConverter<>(ProjectMetadata.class); this.collection = db.getCollection(collectionName) .withReadPreference(ReadPreference.primary()) .withWriteConcern(WriteConcern.ACKNOWLEDGED); mongoLock = new MongoLock(collection, "_lock"); }