Java tutorial
/* * Copyright 2014 EUBrazilCC (EU?Brazil Cloud Connect) * * Licensed under the EUPL, Version 1.1 or - as soon they will be approved by * the European Commission - subsequent versions of the EUPL (the "Licence"); * You may not use this work except in compliance with the Licence. * You may obtain a copy of the Licence at: * * http://ec.europa.eu/idabc/eupl * * Unless required by applicable law or agreed to in writing, software * distributed under the Licence is distributed on an "AS IS" basis, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the Licence for the specific language governing permissions and * limitations under the Licence. * * This product combines work with different licenses. See the "NOTICE" text * file for details on the various modules and licenses. * The "NOTICE" text file is part of the distribution. Any derivative works * that you distribute must include a readable copy of the "NOTICE" text file. */ package eu.eubrazilcc.lvl.storage.dao; import static com.google.common.collect.Lists.transform; import static eu.eubrazilcc.lvl.storage.mongodb.MongoDBConnector.MONGODB_CONN; import static eu.eubrazilcc.lvl.storage.mongodb.MongoDBHelper.toProjection; import static eu.eubrazilcc.lvl.storage.mongodb.jackson.MongoDBJsonMapper.JSON_MAPPER; import static eu.eubrazilcc.lvl.storage.transform.SameTransientStore.startStore; import static org.slf4j.LoggerFactory.getLogger; import java.io.IOException; import java.io.OutputStream; import java.util.List; import javax.annotation.Nullable; import org.apache.commons.lang.mutable.MutableLong; import org.bson.types.ObjectId; import org.slf4j.Logger; import com.fasterxml.jackson.annotation.JsonProperty; import com.fasterxml.jackson.core.JsonProcessingException; import com.fasterxml.jackson.databind.annotation.JsonDeserialize; import com.fasterxml.jackson.databind.annotation.JsonSerialize; import com.google.common.base.Function; import com.google.common.collect.ImmutableList; import com.google.common.collect.ImmutableMap; import com.mongodb.BasicDBObject; import com.mongodb.DBObject; import com.mongodb.util.JSON; import eu.eubrazilcc.lvl.core.Reference; import eu.eubrazilcc.lvl.core.Sorting; import eu.eubrazilcc.lvl.core.geojson.Point; import eu.eubrazilcc.lvl.core.geojson.Polygon; import eu.eubrazilcc.lvl.storage.mongodb.MongoDBDuplicateKeyException; import eu.eubrazilcc.lvl.storage.mongodb.jackson.ObjectIdDeserializer; import eu.eubrazilcc.lvl.storage.mongodb.jackson.ObjectIdSerializer; import eu.eubrazilcc.lvl.storage.transform.SameTransientStore; /** * {@link Reference} DAO. * @author Erik Torres <ertorser@upv.es> */ public enum ReferenceDAO implements BaseDAO<String, Reference> { REFERENCE_DAO; private final static Logger LOGGER = getLogger(ReferenceDAO.class); public static final String COLLECTION = "references"; public static final String DB_PREFIX = "reference."; public static final String PRIMARY_KEY = DB_PREFIX + "pubmedId"; public static final String GEOLOCATION_KEY = DB_PREFIX + "location"; public static final String ORIGINAL_ARTICLE_KEY = DB_PREFIX + "article"; private ReferenceDAO() { MONGODB_CONN.createIndex(PRIMARY_KEY, COLLECTION); MONGODB_CONN.createGeospatialIndex(GEOLOCATION_KEY, COLLECTION); MONGODB_CONN.createTextIndex(ImmutableList.of(DB_PREFIX + "title"), COLLECTION); } @Override public WriteResult<Reference> insert(final Reference reference) { return insert(reference, false); } @Override public WriteResult<Reference> insert(final Reference reference, final boolean ignoreDuplicates) { // remove transient fields from the element before saving it to the database final SameTransientStore<Reference> store = startStore(reference); final DBObject obj = map(store); String id = null; try { id = MONGODB_CONN.insert(obj, COLLECTION); } catch (MongoDBDuplicateKeyException dke) { if (ignoreDuplicates) { final BasicDBObject duplicate = MONGODB_CONN.get(key(reference.getPubmedId()), COLLECTION); id = entity2ObjectId(duplicate); } else { // re-throw exception throw dke; } } // restore transient fields store.restore(); return new WriteResult.Builder<Reference>().id(id).build(); } @Override public Reference update(final Reference reference) { // remove transient fields from the element before saving it to the database final SameTransientStore<Reference> store = startStore(reference); final DBObject obj = map(store); MONGODB_CONN.update(obj, key(reference.getPubmedId()), COLLECTION); // restore transient fields store.restore(); return null; } @Override public void delete(final String pmid) { MONGODB_CONN.remove(key(pmid), COLLECTION); } @Override public List<Reference> findAll() { return list(0, Integer.MAX_VALUE, null, null, null, null); } @Override public Reference find(final String pmid) { final BasicDBObject obj = MONGODB_CONN.get(key(pmid), COLLECTION); return parseBasicDBObjectOrNull(obj); } @Override public List<Reference> list(final int start, final int size, final @Nullable ImmutableMap<String, String> filter, final @Nullable Sorting sorting, final @Nullable ImmutableMap<String, Boolean> projection, final @Nullable MutableLong count) { // execute the query in the database (unsupported filter) return transform( MONGODB_CONN.list(sortCriteria(), COLLECTION, start, size, null, toProjection(projection), count), new Function<BasicDBObject, Reference>() { @Override public Reference apply(final BasicDBObject obj) { return parseBasicDBObject(obj); } }); } @Override public long count() { return MONGODB_CONN.count(COLLECTION); } @Override public List<Reference> getNear(final Point point, final double maxDistance) { throw new UnsupportedOperationException("Geospatial searches are not currently supported in this class"); } @Override public List<Reference> geoWithin(final Polygon polygon) { throw new UnsupportedOperationException("Geospatial searches are not currently supported in this class"); } @Override public void stats(final OutputStream os) throws IOException { MONGODB_CONN.stats(os, COLLECTION); } private BasicDBObject key(final String key) { return new BasicDBObject(PRIMARY_KEY, key); } private BasicDBObject sortCriteria() { return new BasicDBObject(PRIMARY_KEY, 1); } private Reference parseBasicDBObject(final BasicDBObject obj) { return map(obj).getReference(); } private Reference parseBasicDBObjectOrNull(final BasicDBObject obj) { Reference reference = null; if (obj != null) { final ReferenceEntity entity = map(obj); if (entity != null) { reference = entity.getReference(); } } return reference; } private String entity2ObjectId(final BasicDBObject obj) { return map(obj).getId().toString(); } @SuppressWarnings("unused") private Reference parseObject(final Object obj) { final BasicDBObject obj2 = (BasicDBObject) obj; return map((BasicDBObject) obj2.get("obj")).getReference(); } private DBObject map(final SameTransientStore<Reference> store) { DBObject obj = null; try { obj = (DBObject) JSON.parse(JSON_MAPPER.writeValueAsString(new ReferenceEntity(store.purge()))); } catch (JsonProcessingException e) { LOGGER.error("Failed to write reference to DB object", e); } return obj; } private ReferenceEntity map(final BasicDBObject obj) { ReferenceEntity entity = null; try { entity = JSON_MAPPER.readValue(obj.toString(), ReferenceEntity.class); } catch (IOException e) { LOGGER.error("Failed to read reference from DB object", e); } return entity; } /** * Reference entity. * @author Erik Torres <ertorser@upv.es> */ public static class ReferenceEntity { @JsonSerialize(using = ObjectIdSerializer.class) @JsonDeserialize(using = ObjectIdDeserializer.class) @JsonProperty("_id") private ObjectId id; private Reference reference; public ReferenceEntity() { } public ReferenceEntity(final Reference reference) { setReference(reference); } public ObjectId getId() { return id; } public void setId(final ObjectId id) { this.id = id; } public Reference getReference() { return reference; } public void setReference(final Reference reference) { this.reference = reference; } } }