Example usage for com.mongodb BasicDBObject BasicDBObject

Introduction

In this page you can find the example usage for com.mongodb BasicDBObject BasicDBObject.

Prototype

public BasicDBObject()

Source Link

Document

Creates an empty object.

Usage

From source file:act.server.MongoDB.java

License:Open Source License

private Cofactor getCofactorFromDB(String field, Object val) {
    BasicDBObject query = new BasicDBObject();
    query.put(field, val);
    BasicDBObject keys = new BasicDBObject();
    DBObject o = this.dbCofactors.findOne(query, keys);
    if (o == null)
        return null;
    return convertDBObjectToCofactor(o);
}

From source file:act.server.MongoDB.java

License:Open Source License

public Reaction getReactionFromUUID(Long reactionUUID) {
    if (reactionUUID < 0) {
        throw new RuntimeException(String.format(
                "getReactionFromUUID called with a negaive number (%d).  It used to reverse the reaction.",
                reactionUUID));//from  w  w w  . j  a v  a2 s.c om
    }
    BasicDBObject query = new BasicDBObject();
    query.put("_id", reactionUUID);

    BasicDBObject keys = new BasicDBObject();
    DBObject o = this.dbReactions.findOne(query, keys);
    if (o == null)
        return null;
    return convertDBObjectToReaction(o);
}

From source file:act.server.MongoDB.java

License:Open Source License

public Iterator<Seq> getSeqIterator(BasicDBObject query) {
    final DBIterator iter = getDbIteratorOverSeq(query, new BasicDBObject());

    return new Iterator<Seq>() {
        @Override//from   ww  w  .ja va2 s  .  c o  m
        public boolean hasNext() {
            boolean hasNext = iter.hasNext();
            if (!hasNext)
                iter.close();
            return hasNext;
        }

        @Override
        public Seq next() {
            DBObject o = iter.next();
            return convertDBObjectToSeq(o);
        }
    };
}

From source file:act.server.MongoDB.java

License:Open Source License

public BasicDBObject getRangeUUIDRestriction(Long lowUUID, Long highUUID) {
    BasicDBObject restrictTo = new BasicDBObject();
    // need to encode { "_id" : { $gte : lowUUID, $lte : highUUID } }
    BasicDBObject range = new BasicDBObject();
    if (lowUUID != null)
        range.put("$gte", lowUUID);
    if (highUUID != null)
        range.put("$lte", highUUID);
    restrictTo.put("_id", range);
    return restrictTo;
}

From source file:act.server.MongoDB.java

License:Open Source License

public List<Long> getAllCollectionUUIDs(DBCollection collection) {

    List<Long> ids = new ArrayList<Long>();

    BasicDBObject query = new BasicDBObject();
    BasicDBObject keys = new BasicDBObject();
    keys.put("_id", 1); // 0 means exclude, rest are included
    DBCursor cur = collection.find(query, keys);

    while (cur.hasNext()) {
        DBObject o = cur.next();//from  w ww. j a v  a  2  s.  c  o m
        long uuid = (Integer) o.get("_id"); // checked: db type IS int
        ids.add(uuid);
    }
    cur.close();

    return ids;
}

From source file:act.server.MongoDB.java

License:Open Source License

public Seq getSeqFromID(Long seqID) {
    BasicDBObject query = new BasicDBObject();
    query.put("_id", seqID);

    BasicDBObject keys = new BasicDBObject();
    DBObject o = this.dbSeq.findOne(query, keys);
    if (o == null)
        return null;
    return convertDBObjectToSeq(o);
}

From source file:act.server.MongoDB.java

License:Open Source License

public List<Seq> getSeqFromSeqEcOrg(String seq, String ec, String organism) {
    List<Seq> seqs = new ArrayList<>();
    BasicDBObject query = new BasicDBObject();
    query.put("seq", seq);
    query.put("ecnum", ec);
    query.put("org", organism);

    DBCursor cur = this.dbSeq.find(query, new BasicDBObject());
    try {//from w  w w  .j  av  a  2  s.  com
        while (cur.hasNext()) {
            DBObject o = cur.next();
            seqs.add(convertDBObjectToSeq(o));
        }
    } finally {
        if (cur != null) {
            cur.close();
        }
    }

    return seqs;
}

From source file:act.server.MongoDB.java

License:Open Source License

public List<Seq> getSeqFromGenbankProtAccession(String accession) {
    List<Seq> seqs = new ArrayList<>();
    BasicDBObject query = new BasicDBObject();
    query.put("metadata.accession.genbank_protein",
            new BasicDBObject("$elemMatch", new BasicDBObject("$eq", accession)));

    DBCursor cur = this.dbSeq.find(query, new BasicDBObject());
    try {//from   ww  w .  j a va2 s  .  c o m
        while (cur.hasNext()) {
            DBObject o = cur.next();
            seqs.add(convertDBObjectToSeq(o));
        }
    } finally {
        if (cur != null) {
            cur.close();
        }
    }

    return seqs;
}

From source file:act.server.MongoDB.java

License:Open Source License

public List<Seq> getSeqFromGenbankNucAccessionSeq(String accession, String seq) {
    List<Seq> seqs = new ArrayList<>();
    BasicDBObject query = new BasicDBObject();
    query.put("seq", seq);
    query.put("metadata.accession.genbank_nucleotide",
            new BasicDBObject("$elemMatch", new BasicDBObject("$eq", accession)));

    DBCursor cur = this.dbSeq.find(query, new BasicDBObject());
    try {/*from  www  .j a v a  2 s .co  m*/
        while (cur.hasNext()) {
            DBObject o = cur.next();
            seqs.add(convertDBObjectToSeq(o));
        }
    } finally {
        if (cur != null) {
            cur.close();
        }
    }

    return seqs;
}

From source file:act.server.MongoDB.java

License:Open Source License

public List<Seq> getSeqWithSARConstraints() {
    List<Seq> seqs = new ArrayList<Seq>();
    BasicDBObject query = new BasicDBObject();
    query.put("sar_constraints", new BasicDBObject("$exists", true));

    BasicDBObject keys = new BasicDBObject();

    DBCursor cur = this.dbSeq.find(query, keys);
    while (cur.hasNext()) {
        DBObject o = cur.next();//from   w w w.j  a v  a2s.com
        seqs.add(convertDBObjectToSeq(o));
    }
    cur.close();

    return seqs;
}