Java tutorial
/* * Copyright 2015-2016 OpenCB * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package org.opencb.opencga.storage.mongodb.metadata; import com.mongodb.DuplicateKeyException; import com.mongodb.MongoWriteException; import com.mongodb.ReadPreference; import com.mongodb.WriteConcern; import com.mongodb.client.model.Projections; import com.mongodb.client.model.Updates; import com.mongodb.client.result.UpdateResult; import org.bson.Document; import org.bson.conversions.Bson; import org.opencb.commons.datastore.core.QueryOptions; import org.opencb.commons.datastore.core.QueryResult; import org.opencb.commons.datastore.mongodb.MongoDBCollection; import org.opencb.commons.datastore.mongodb.MongoDataStore; import org.opencb.commons.datastore.mongodb.MongoDataStoreManager; import org.opencb.opencga.storage.core.metadata.StudyConfiguration; import org.opencb.opencga.storage.core.metadata.StudyConfigurationManager; import org.opencb.opencga.storage.mongodb.auth.MongoCredentials; import org.opencb.opencga.storage.mongodb.utils.MongoLock; import org.opencb.opencga.storage.mongodb.variant.converters.DocumentToStudyConfigurationConverter; import java.net.UnknownHostException; import java.util.ArrayList; import java.util.Collections; import java.util.List; import java.util.Map; import java.util.concurrent.TimeoutException; import java.util.stream.Collectors; import static com.mongodb.client.model.Updates.set; import static org.opencb.commons.datastore.mongodb.MongoDBCollection.UPSERT; /** * @author Jacobo Coll <jacobo167@gmail.com> */ public class MongoDBStudyConfigurationManager extends StudyConfigurationManager { private final MongoDataStoreManager mongoManager; private final boolean closeConnection; private final DocumentToStudyConfigurationConverter studyConfigurationConverter = new DocumentToStudyConfigurationConverter(); private final MongoLock mongoLock; private final MongoDBCollection collection; public MongoDBStudyConfigurationManager(MongoCredentials credentials, String collectionName) throws UnknownHostException { this(new MongoDataStoreManager(credentials.getDataStoreServerAddresses()), true, credentials, collectionName); } public MongoDBStudyConfigurationManager(MongoDataStoreManager mongoManager, MongoCredentials credentials, String collectionName) throws UnknownHostException { this(mongoManager, false, credentials, collectionName); } private MongoDBStudyConfigurationManager(MongoDataStoreManager mongoManager, boolean closeConnection, MongoCredentials credentials, String collectionName) throws UnknownHostException { super(null); // Mongo configuration this.mongoManager = mongoManager; this.closeConnection = closeConnection; MongoDataStore db = mongoManager.get(credentials.getMongoDbName(), credentials.getMongoDBConfiguration()); collection = db.getCollection(collectionName).withReadPreference(ReadPreference.primary()) .withWriteConcern(WriteConcern.ACKNOWLEDGED); mongoLock = new MongoLock(collection, "_lock"); } @Override protected QueryResult<StudyConfiguration> internalGetStudyConfiguration(String studyName, Long timeStamp, QueryOptions options) { return internalGetStudyConfiguration(null, studyName, timeStamp, options); } @Override protected QueryResult<StudyConfiguration> internalGetStudyConfiguration(int studyId, Long timeStamp, QueryOptions options) { return internalGetStudyConfiguration(studyId, null, timeStamp, options); } @Override public long lockStudy(int studyId, long lockDuration, long timeout) throws InterruptedException, TimeoutException { try { // Ensure document exists collection.update(new Document("_id", studyId), set("id", studyId), new QueryOptions(MongoDBCollection.UPSERT, true)); } catch (MongoWriteException e) { // Duplicated key exception if (e.getError().getCode() != 11000) { throw e; } } catch (DuplicateKeyException ignore) { // Ignore this exception. // With UPSERT=true, this command should never throw DuplicatedKeyException. // See https://jira.mongodb.org/browse/SERVER-14322 } return mongoLock.lock(studyId, lockDuration, timeout); } @Override public void unLockStudy(int studyId, long lockId) { mongoLock.unlock(studyId, lockId); } private QueryResult<StudyConfiguration> internalGetStudyConfiguration(Integer studyId, String studyName, Long timeStamp, QueryOptions options) { long start = System.currentTimeMillis(); StudyConfiguration studyConfiguration; Document query = new Document(); if (studyId != null) { query.append("_id", studyId); } if (studyName != null) { query.append("studyName", studyName); } if (timeStamp != null) { query.append("timeStamp", new Document("$ne", timeStamp)); } QueryResult<StudyConfiguration> queryResult = collection.find(query, null, studyConfigurationConverter, null); if (queryResult.getResult().isEmpty()) { studyConfiguration = null; } else { if (queryResult.first().getStudyName() == null) { // If the studyName is null, it may be only a lock instead of a real study configuration studyConfiguration = null; } else { studyConfiguration = queryResult.first(); } } if (studyConfiguration == null) { return new QueryResult<>(studyName, ((int) (System.currentTimeMillis() - start)), 0, 0, "", "", Collections.emptyList()); } else { return new QueryResult<>(studyName, ((int) (System.currentTimeMillis() - start)), 1, 1, "", "", Collections.singletonList(studyConfiguration)); } } @Override public QueryResult internalUpdateStudyConfiguration(StudyConfiguration studyConfiguration, QueryOptions options) { Document studyMongo = new DocumentToStudyConfigurationConverter().convertToStorageType(studyConfiguration); // Update field by field, instead of replacing the whole object to preserve existing fields like "_lock" Document query = new Document("_id", studyConfiguration.getStudyId()); List<Bson> updates = new ArrayList<>(studyMongo.size()); studyMongo.forEach((s, o) -> updates.add(new Document("$set", new Document(s, o)))); QueryResult<UpdateResult> queryResult = collection.update(query, Updates.combine(updates), new QueryOptions(UPSERT, true)); // studyConfigurationMap.put(studyConfiguration.getStudyId(), studyConfiguration); return queryResult; } @Override public List<String> getStudyNames(QueryOptions options) { List<String> studyNames = collection.distinct("studyName", null).getResult(); return studyNames.stream().map(Object::toString).collect(Collectors.toList()); } @Override public List<Integer> getStudyIds(QueryOptions options) { return collection.distinct("_id", null, Integer.class).getResult(); } @Override public Map<String, Integer> getStudies(QueryOptions options) { QueryResult<StudyConfiguration> queryResult = collection.find(new Document(), Projections.include("studyId", "studyName"), studyConfigurationConverter, null); return queryResult.getResult().stream() .collect(Collectors.toMap(StudyConfiguration::getStudyName, StudyConfiguration::getStudyId)); } @Override public void close() { if (closeConnection) { mongoManager.close(); } } }