Example usage for com.mongodb.client MongoCollection getNamespace

List of usage examples for com.mongodb.client MongoCollection getNamespace

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Introduction

In this page you can find the example usage for com.mongodb.client MongoCollection getNamespace.

Prototype

MongoNamespace getNamespace();

Source Link

Document

Gets the namespace of this collection.

Usage

From source file:org.radarcns.mongo.util.MongoHelper.java

License:Apache License

/**
 * Creates given index on the collection, if it is not already created for given collection.
 * Having indexes created in background prevents other operations being blocked.
 * @param collection mongoCollection to index.
 * @param index index to be created.//ww w  .j a va2s . c  o  m
 */
private static void createIndexIfNotAvailable(MongoCollection<Document> collection, Bson index) {
    if (indexMap.containsKey(collection.getNamespace().getCollectionName())) {
        List<String> availableIndexes = indexMap.get(collection.getNamespace().getCollectionName());
        if (!availableIndexes.contains(index.toString())) {
            collection.createIndex(index, new IndexOptions().background(true));
            availableIndexes.add(index.toString());
        }

    } else {
        collection.createIndex(index, new IndexOptions().background(true));
        List<String> indexList = new ArrayList<>();
        indexList.add(index.toString());
        indexMap.put(collection.getNamespace().getCollectionName(), indexList);
    }
}

From source file:rapture.lock.mongodb.MongoLockHandler2.java

License:Open Source License

@Override
public LockHandle acquireLock(String lockHolder, String lockName, long secondsToWait, long secondsToHold) {
    log.debug("Mongo acquire lock2  " + lockName + ":" + secondsToHold + ":" + secondsToWait);
    long start = System.currentTimeMillis();

    MongoCollection<Document> coll = getLockCollection(lockName);
    log.debug("lock COLLECTION for " + lockName + "IS " + coll.getNamespace().getFullName());

    long bailTime = System.currentTimeMillis() + secondsToWait * 1000;
    long leaseTime = System.currentTimeMillis() + secondsToHold * 1000;

    Document lockFile = new Document();
    lockFile.put("lockName", lockName);
    lockFile.put("lockHolder", lockHolder);
    lockFile.put("lease", leaseTime);

    long myLockID = System.currentTimeMillis();
    lockFile.put("_id", "" + myLockID);
    log.debug("id is " + myLockID);
    log.debug("bailtime " + bailTime);

    while (bailTime > System.currentTimeMillis()) {
        try {/*from w w w. j  a v  a 2  s  . c  o  m*/
            myLockID = System.currentTimeMillis();
            lockFile.put("_id", "" + myLockID);
            lockFile.put("lease", myLockID + secondsToHold * 1000);

            coll.withWriteConcern(WriteConcern.ACKNOWLEDGED).insertOne(lockFile);
            log.debug("inserted file" + lockFile);

            break;
        } catch (MongoServerException e) {
            log.error(ExceptionToString.format(e));
            try {
                Thread.sleep(50);
            } catch (InterruptedException e1) {
                e1.printStackTrace();
            }
        }
    }

    // loop until we acquire lock or timeout
    while (bailTime > System.currentTimeMillis()) {
        // we have the lock if no lock file exists with a smaller number
        FindIterable<Document> results = coll
                .find(new Document("lease", new Document("$gt", System.currentTimeMillis())))
                .sort(new Document("_id", 1)).limit(1);

        Document lock = results.first();
        if (lock != null && ((String) lock.get("_id")).equals("" + myLockID)) {
            log.debug("* i have the lock" + lock.get("_id") + ":" + myLockID);
            LockHandle lockHandle = new LockHandle();
            lockHandle.setLockName(lockName);
            lockHandle.setHandle("" + myLockID);
            lockHandle.setLockHolder(lockHolder);
            long end = System.currentTimeMillis();
            log.debug("* NG acquired lock in " + (end - start));
            return lockHandle;
        } else {
            // log.info("* waiting for lock held by "+ lock.get("_id"));
            try {
                Thread.sleep(100);
            } catch (InterruptedException e) {
                e.printStackTrace();
            }
        }

    }
    // ran out of time trying to get lock.
    log.debug("giving up " + myLockID);
    long end2 = System.currentTimeMillis();
    log.debug("denied lock in " + (end2 - start));
    return null;
}

From source file:uk.ac.ebi.eva.dbmigration.mongodb.ExtractAnnotationFromVariant.java

License:Apache License

@ChangeSet(order = "001", id = "migrateAnnotation", author = "EVA")
public void migrateAnnotation(MongoDatabase mongoDatabase) {
    final MongoCollection<Document> variantsCollection = mongoDatabase
            .getCollection(databaseParameters.getDbCollectionsVariantsName());
    final MongoCollection<Document> annotationCollection = mongoDatabase
            .getCollection(databaseParameters.getDbCollectionsAnnotationsName());
    logger.info("1) migrate annotation from collection {}", variantsCollection.getNamespace());

    long annotationsReadCount = 0;
    long annotationsWrittenCount = 0;
    BulkWriteOptions unorderedBulk = new BulkWriteOptions().ordered(false);
    Document onlyAnnotatedVariants = new Document(ANNOT_FIELD, EXISTS);
    try (MongoCursor<Document> cursor = variantsCollection.find(onlyAnnotatedVariants).iterator()) {
        while (true) {
            List<InsertOneModel<Document>> annotationsToInsert = getBatch(cursor, BULK_SIZE).stream()
                    .map(this::buildInsertionDocument).collect(toList());

            if (annotationsToInsert.isEmpty()) {
                break;
            }/*  w  w w.j a va 2 s  .c  om*/

            annotationsReadCount += annotationsToInsert.size();
            BulkWriteResult bulkInsert = annotationCollection.bulkWrite(annotationsToInsert, unorderedBulk);
            annotationsWrittenCount += bulkInsert.getInsertedCount();
        }
    }

    //before executing the next changeSet check that the count of read and written annotation documents match
    if (annotationsReadCount != annotationsWrittenCount) {
        throw new RuntimeException("The number of processed Variants (" + annotationsReadCount
                + ") is different from the number of new annotation inserted (" + annotationsWrittenCount
                + "). The '" + ANNOT_FIELD + "' field will not be removed from the "
                + variantsCollection.getNamespace() + " collection.");
    }
}

From source file:uk.ac.ebi.eva.dbmigration.mongodb.ExtractAnnotationFromVariant.java

License:Apache License

@ChangeSet(order = "002", id = "dropIndexes", author = "EVA")
public void dropIndexes(MongoDatabase mongoDatabase) {
    final MongoCollection<Document> variantsCollection = mongoDatabase
            .getCollection(databaseParameters.getDbCollectionsVariantsName());
    logger.info("2) drop indexes from annot field from collection {}", variantsCollection.getNamespace());

    variantsCollection.dropIndex(LEGACY_ANNOTATION_CT_SO_INDEX);
    variantsCollection.dropIndex(LEGACY_ANNOTATION_XREF_ID_INDEX);
}

From source file:uk.ac.ebi.eva.dbmigration.mongodb.ExtractAnnotationFromVariant.java

License:Apache License

@ChangeSet(order = "003", id = "reduceAnnotationFromVariants", author = "EVA")
public void reduceAnnotationFromVariants(MongoDatabase mongoDatabase) {
    final MongoCollection<Document> variantsCollection = mongoDatabase
            .getCollection(databaseParameters.getDbCollectionsVariantsName());
    logger.info("3) reduce annotation field from collection {}", variantsCollection.getNamespace());

    long annotationsReadCount = 0;
    long annotationsUpdatedCount = 0;
    BulkWriteOptions unorderedBulk = new BulkWriteOptions().ordered(false);
    Document onlyAnnotatedVariants = new Document(ANNOT_FIELD, EXISTS);
    try (MongoCursor<Document> cursor = variantsCollection.find(onlyAnnotatedVariants).iterator()) {
        while (true) {
            List<UpdateOneModel<Document>> annotationsToUpdate = getBatch(cursor, BULK_SIZE).stream()
                    .map(this::buildUpdateDocument).collect(toList());

            if (annotationsToUpdate.isEmpty()) {
                break;
            }// www.  j  a  v  a  2s.c  o  m
            annotationsReadCount += annotationsToUpdate.size();
            BulkWriteResult bulkInsert = variantsCollection.bulkWrite(annotationsToUpdate, unorderedBulk);
            annotationsUpdatedCount += bulkInsert.getModifiedCount();
        }
    }
    if (annotationsReadCount != annotationsUpdatedCount) {
        throw new RuntimeException("The number of processed Variants (" + annotationsReadCount
                + ") is different from the number of annotation " + "updated (" + annotationsUpdatedCount
                + ").");
    }
}

From source file:uk.ac.ebi.eva.dbmigration.mongodb.ExtractAnnotationFromVariant.java

License:Apache License

@ChangeSet(order = "004", id = "updateAnnotationMetadata", author = "EVA")
public void updateAnnotationMetadata(MongoDatabase mongoDatabase) {
    final MongoCollection<Document> annotationMetadataCollection = mongoDatabase
            .getCollection(databaseParameters.getDbCollectionsAnnotationMetadataName());
    logger.info("4) update annotation metadata in collection {}", annotationMetadataCollection.getNamespace());

    String id = databaseParameters.getVepVersion() + "_" + databaseParameters.getVepCacheVersion();
    Document metadata = new Document(ID_FIELD, id);
    if (annotationMetadataCollection.count(metadata) == 0) {
        metadata.append(VEP_VERSION_FIELD, databaseParameters.getVepVersion()).append(CACHE_VERSION_FIELD,
                databaseParameters.getVepCacheVersion());

        annotationMetadataCollection.insertOne(metadata);
    }/*from  www . j  av  a  2  s.c o m*/
}

From source file:uk.ac.ebi.eva.dbmigration.mongodb.ExtractAnnotationFromVariant.java

License:Apache License

@ChangeSet(order = "005", id = "createIndexes", author = "EVA")
public void createIndexes(MongoDatabase mongoDatabase) {
    final MongoCollection<Document> variantsCollection = mongoDatabase
            .getCollection(databaseParameters.getDbCollectionsVariantsName());
    final MongoCollection<Document> annotationsCollection = mongoDatabase
            .getCollection(databaseParameters.getDbCollectionsAnnotationsName());
    logger.info("5) create indexes collections {} and {}", annotationsCollection.getNamespace(),
            variantsCollection.getNamespace());

    IndexOptions background = new IndexOptions().background(true);
    variantsCollection.createIndex(new Document(ANNOT_FIELD + "." + XREFS_FIELD, 1), background);
    variantsCollection.createIndex(new Document(ANNOT_FIELD + "." + SO_FIELD, 1), background);

    annotationsCollection.createIndex(new Document(CONSEQUENCE_TYPE_FIELD + "." + SO_FIELD, 1), background);
    annotationsCollection.createIndex(new Document(XREFS_FIELD + "." + XREF_ID_FIELD, 1), background);
    annotationsCollection.createIndex(/* ww  w.  j a v  a  2  s  .c o m*/
            new Document(CHROMOSOME_FIELD, 1).append(START_FIELD, 1).append(END_FIELD, 1), background);
}

From source file:uk.ac.ebi.eva.dbmigration.mongodb.ExtractAnnotationFromVariant.java

License:Apache License

@ChangeSet(order = "006", id = "addDefaultVersionInAnnotationMetadata", author = "EVA")
public void addDefaultVersion(MongoDatabase mongoDatabase) {
    final MongoCollection<Document> annotationMetadataCollection = mongoDatabase
            .getCollection(databaseParameters.getDbCollectionsAnnotationMetadataName());
    logger.info("6) add default annotation version to collection {} ",
            annotationMetadataCollection.getNamespace());

    Document allVersions = new Document();
    Document setDefaultToFalse = new Document("$set", new Document(DEFAULT_VERSION_FIELD, false));
    annotationMetadataCollection.updateMany(allVersions, setDefaultToFalse);

    String id = databaseParameters.getVepVersion() + "_" + databaseParameters.getVepCacheVersion();
    Document defaultVersionDocument = new Document(ID_FIELD, id);
    Document setDefaultToTrue = new Document("$set", new Document(DEFAULT_VERSION_FIELD, true));
    UpdateResult updateResult = annotationMetadataCollection.updateOne(defaultVersionDocument,
            setDefaultToTrue);//from w  w  w  .  j a  v  a  2 s  .c om
    Assert.state(updateResult.getModifiedCount() == 1, "Only one modification was expected");
}