328 lines
11 KiB
Java
328 lines
11 KiB
Java
package eu.dnetlib.data.mdstore.modular.mongodb;
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import java.util.List;
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import com.google.common.collect.Lists;
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import com.google.common.primitives.Ints;
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import com.mongodb.BasicDBObject;
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import com.mongodb.BasicDBObjectBuilder;
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import com.mongodb.DBObject;
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import com.mongodb.client.AggregateIterable;
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import com.mongodb.client.MongoCollection;
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import com.mongodb.client.MongoDatabase;
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import com.mongodb.client.model.CreateCollectionOptions;
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import eu.dnetlib.data.mdstore.MDStoreServiceException;
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import eu.dnetlib.data.mdstore.modular.MDStoreDescription;
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import eu.dnetlib.data.mdstore.modular.RecordParser;
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import eu.dnetlib.data.mdstore.modular.RecordParserFactory;
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import eu.dnetlib.data.mdstore.modular.connector.MDStore;
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import eu.dnetlib.data.mdstore.modular.connector.MDStoreDBStatus;
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import eu.dnetlib.data.mdstore.modular.connector.MDStoreDao;
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import eu.dnetlib.data.mdstore.modular.connector.MDStoreTransactionManager;
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import eu.dnetlib.data.mdstore.modular.mongodb.utils.MDStoreUtils;
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import eu.dnetlib.miscutils.collections.FilteredCollection;
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import eu.dnetlib.miscutils.collections.MappedCollection;
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import eu.dnetlib.miscutils.datetime.DateUtils;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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import org.bson.Document;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.beans.factory.annotation.Required;
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/**
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* Factory bean for MongoMDStore instances.
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*
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* @author marko
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*/
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public class MDStoreDaoImpl implements MDStoreDao {
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public static final String MD_ID = "mdId";
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public static final String FORMAT = "format";
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public static final String INTERPRETATION = "interpretation";
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public static final String LAYOUT = "layout";
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public static final String SIZE = "size";
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public static final String METADATA_NAME = "metadata";
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private static final Log log = LogFactory.getLog(MDStoreDaoImpl.class);
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private MongoDatabase db;
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private RecordParserFactory recordParserFactory;
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private boolean discardRecords = true;
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@Autowired
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private MDStoreTransactionManager transactionManager;
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/**
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* {@inheritDoc}
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*/
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@Override
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public void createMDStore(final String mdId, final String format, final String interpretation, final String layout) throws MDStoreServiceException {
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transactionManager.createMDStore(mdId);
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final String internalId = transactionManager.getMDStoreCollection(mdId);
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if (!Lists.newArrayList(getDb().listCollectionNames()).contains(internalId)) {
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log.info(String.format("creating collection %s", internalId));
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getDb().createCollection(internalId, new CreateCollectionOptions());
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}
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final MongoCollection<DBObject> coll = getDb().getCollection(METADATA_NAME, DBObject.class);
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final BasicDBObject obj = new BasicDBObject();
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obj.put(MD_ID, mdId);
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obj.put(FORMAT, format);
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obj.put(INTERPRETATION, interpretation);
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obj.put(LAYOUT, layout);
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obj.put(SIZE, 0);
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coll.insertOne(obj);
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}
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/**
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* {@inheritDoc}
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*/
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@Override
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public void deleteMDStore(final String mdId) throws MDStoreServiceException {
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final MongoCollection<DBObject> metadata = getDb().getCollection(METADATA_NAME, DBObject.class);
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if (metadata == null) throw new MDStoreServiceException("cannot find metadata collection");
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transactionManager.dropMDStore(mdId);
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metadata.deleteOne(new BasicDBObject(MD_ID, mdId));
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log.info("deleted mdId: " + mdId);
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}
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/**
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* {@inheritDoc}
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*/
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@Override
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public MDStore getMDStore(final String mdId) throws MDStoreServiceException {
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final String internalId = transactionManager.getMDStoreCollection(mdId);
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return new MongoMDStore(mdId, getDb().getCollection(internalId, DBObject.class), getRecordParser(), isDiscardRecords(), getDb());
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}
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/**
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* {@inheritDoc}
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*/
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@Override
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public MDStore readMDStore(final String mdId) throws MDStoreServiceException {
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final String internalId = transactionManager.readMdStore(mdId);
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return new MongoMDStore(mdId, getDb().getCollection(internalId, DBObject.class), getRecordParser(), isDiscardRecords(), getDb());
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}
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/**
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* {@inheritDoc}
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*/
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@Override
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public MDStore startTransaction(final String mdId, final boolean refresh) throws MDStoreServiceException {
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final String transactionId = transactionManager.startTransaction(mdId, refresh);
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return new MongoMDStore(transactionId, getDb().getCollection(transactionId, DBObject.class), getRecordParser(), isDiscardRecords(),
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getDb());
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}
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private RecordParser getRecordParser() {
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final RecordParser parser = getRecordParserFactory().newInstance();
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parser.setTimestamp(DateUtils.now());
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return parser;
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}
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/**
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* {@inheritDoc}
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*/
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@Override
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public List<MDStoreDescription> listMDStores() {
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return MappedCollection.listMap(getDb().getCollection(METADATA_NAME, DBObject.class).find(), input -> {
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final String mdId = (String) input.get(MD_ID);
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log.debug("Getting info for " + mdId);
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final String format = (String) input.get(FORMAT);
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final String layout = (String) input.get(LAYOUT);
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final String interpretation = (String) input.get(INTERPRETATION);
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MongoMDStore currentMDStore = null;
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final MDStoreDescription description = new MDStoreDescription();
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try {
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currentMDStore = (MongoMDStore) getMDStore(mdId);
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} catch (final MDStoreServiceException e) {
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log.error("Error on retrieving mdstore for getting info mdId " + mdId);
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}
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int size = 0;
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if (input.containsField(SIZE)) {
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log.debug("Size retrieved from metadata for mdId :" + mdId);
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size = (Integer) input.get(SIZE);
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} else {
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if (currentMDStore != null) {
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log.debug("Size not Found in metadata for mdId :" + mdId + " calling getCount ");
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size = currentMDStore.getSize();
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input.put("size", size);
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getDb().getCollection(METADATA_NAME, DBObject.class).findOneAndReplace(new BasicDBObject(MD_ID, mdId), input);
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}
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}
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if (currentMDStore != null) {
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description.setIndexed(currentMDStore.isIndexed());
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}
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description.setId(mdId);
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description.setFormat(format);
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description.setLayout(layout);
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description.setInterpretation(interpretation);
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description.setSize(size);
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return description;
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});
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}
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/**
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* {@inheritDoc}
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*/
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@Override
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public List<String> listMDStores(final String format, final String layout, final String interpretation) {
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return MappedCollection.listMap(
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FilteredCollection.listFilter(getDb().getCollection(METADATA_NAME, DBObject.class).find(), MDStoreUtils.dboFilter(format, layout, interpretation)),
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MDStoreUtils.mdId());
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}
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/**
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* {@inheritDoc}
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*/
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@Override
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public int getCachedSize(final String id) throws MDStoreServiceException {
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log.debug("retrieve cached size for mdstore: " + id);
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final DBObject desc = getDb().getCollection(METADATA_NAME, DBObject.class).find(new BasicDBObject(MD_ID, id)).first();
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if (!desc.containsField(SIZE)) {
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desc.put(SIZE, getMDStore(id).getSize());
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}
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final Object oSize = desc.get(SIZE);
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return (Integer) oSize;
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}
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/**
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* {@inheritDoc}
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*/
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@Override
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public void refreshSizes() throws MDStoreServiceException {
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for (final MDStoreDescription mdStoreId : listMDStores()) {
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refreshSize(mdStoreId.getId());
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}
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}
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/**
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* {@inheritDoc}
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*/
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@Override
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public int refreshSize(final String mdStoreId) throws MDStoreServiceException {
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final int size = (int) getDb().getCollection(transactionManager.getMDStoreCollection(mdStoreId)).count();
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final MongoCollection<DBObject> metadata = getDb().getCollection(METADATA_NAME, DBObject.class);
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metadata.updateOne(new BasicDBObject(MD_ID, mdStoreId), new BasicDBObject("$set", new BasicDBObject(SIZE, size)));
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return size;
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}
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@Override
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public int getSumOfSizes(final String format, final String layout, final String interpretation) throws MDStoreServiceException {
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final MongoCollection<DBObject> metadata = getDb().getCollection(METADATA_NAME, DBObject.class);
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BasicDBObject matchObj = (BasicDBObject) BasicDBObjectBuilder.start("$match",
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BasicDBObjectBuilder.start("format", format).add("layout", layout).add("interpretation", interpretation).get()).get();
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BasicDBObject groupObj = (BasicDBObject) BasicDBObjectBuilder.start("$group",
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BasicDBObjectBuilder.start("_id", "").add("total", new BasicDBObject("$sum", "$" + SIZE)).get()).get();
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BasicDBObject projectObj = new BasicDBObject("$project", new BasicDBObject("_id", 0).append("total", 1));
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List<BasicDBObject> pipeline = Lists.newArrayList(matchObj, groupObj, projectObj);
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AggregateIterable<DBObject> output = metadata.aggregate(pipeline, DBObject.class);
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DBObject result = output.first();
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if (result == null || !result.containsField("total")) {
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log.debug("No total found");
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return 0;
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} else return (Integer) result.get("total");
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}
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/**
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* {@inheritDoc}
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*/
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@Override
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public void commit(final String transactionId, final String mdId) throws MDStoreServiceException {
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transactionManager.commit(transactionId, mdId, getMDStore(mdId));
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}
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/**
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* Getter for property 'db'.
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*
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* @return Value for property 'db'.
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*/
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public MongoDatabase getDb() {
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return db;
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}
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/**
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* Setter for property 'db'.
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*
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* @param db
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* Value to set for property 'db'.
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*/
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@Required
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public void setDb(final MongoDatabase db) {
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this.db = db;
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}
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/**
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* Getter for property 'recordParser'.
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*
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* @return Value for property 'recordParser'.
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*/
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public RecordParserFactory getRecordParserFactory() {
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return recordParserFactory;
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}
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@Required
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public void setRecordParserFactory(final RecordParserFactory recordParserFactory) {
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this.recordParserFactory = recordParserFactory;
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}
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/**
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* Getter for property 'discardRecords'.
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*
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* @return Value for property 'discardRecords'.
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*/
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public boolean isDiscardRecords() {
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return discardRecords;
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}
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/**
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* Setter for property 'discardRecords'.
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*
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* @param discardRecords
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* Value to set for property 'discardRecords'.
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*/
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public void setDiscardRecords(final boolean discardRecords) {
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this.discardRecords = discardRecords;
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}
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@Override
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public MDStoreDBStatus getDBStatus() {
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final int handledDatastructures = Ints.saturatedCast(getDb().getCollection(METADATA_NAME).count());
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//final int usedDiskSpace = Ints.saturatedCast(getDb().getStats().getLong("storageSize") / (1024 * 1024)); // in MB
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//{ dbStats: 1, scale: 1 }
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BasicDBObject statsQuery = new BasicDBObject("dbStats", 1);
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statsQuery.put("scale", 1024 * 1024); //storageSize in MB
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final Document statsRes = getDb().runCommand(statsQuery);
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log.debug("DBStatus -- " + statsRes.toJson());
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int usedDiskSpace;
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//trying to handle different versions of the mongo server: old version returns storage size as long, new version as double
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//TODO: simplify this when dev, beta, production are aligned with our local, latest, mongo version
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String usedDiskSpaceStr = statsRes.get("storageSize").toString();
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try {
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Long usedDiskSpaceLong = Long.parseLong(usedDiskSpaceStr);
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usedDiskSpace = Ints.saturatedCast(usedDiskSpaceLong);
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} catch (NumberFormatException nfe) {
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Double usedDiskSpaceDbl = Double.parseDouble(usedDiskSpaceStr);
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usedDiskSpace = usedDiskSpaceDbl.intValue();
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}
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final String date = DateUtils.now_ISO8601();
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return new MDStoreDBStatus(handledDatastructures, usedDiskSpace, date);
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}
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@Override
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public void startGarbage() throws MDStoreServiceException {
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this.transactionManager.garbage();
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}
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@Override
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public void invalidTransaction(final String transactionId, final String mdId) throws MDStoreServiceException {
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transactionManager.dropTransaction(mdId, transactionId);
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}
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}
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