Example usage for com.mongodb DBCursor hasNext

Introduction

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

Prototype

@Override
public boolean hasNext()

Source Link

Document

Checks if there is another object available.

Usage

From source file:act.server.MongoDB.java

License:Open Source License

private List<Reaction> keywordInReaction(String in_field, String keyword) {
    List<Reaction> rxns = new ArrayList<Reaction>();
    BasicDBObject query = new BasicDBObject();
    query.put(in_field, keyword);// w w w.  ja va2s .co m

    BasicDBObject keys = new BasicDBObject();

    DBCursor cur = this.dbReactions.find(query, keys);
    while (cur.hasNext()) {
        DBObject o = cur.next();
        rxns.add(convertDBObjectToReaction(o));
    }
    cur.close();

    return rxns;
}

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 w  w.j  a v  a2  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 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  a2 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> 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 {/*  ww w.ja v a2  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   w  ww .j  a v  a 2 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> 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();//  ww  w. j  av a  2 s  .  co  m
        seqs.add(convertDBObjectToSeq(o));
    }
    cur.close();

    return seqs;
}

From source file:act.server.MongoDB.java

License:Open Source License

public List<Seq> getSeqWithRxnRef(Long rxnId) {
    List<Seq> seqs = new ArrayList<>();
    BasicDBObject query = new BasicDBObject();
    query.put("rxn_refs", rxnId);

    DBCursor cur = this.dbSeq.find(query, new BasicDBObject());
    try {/*from   ww  w. j a  v  a  2  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:AdminServer.ServiceS.java

private ArrayList getData(DBCollection collection, methodS type, String name) {
    ArrayList data = new ArrayList<>();
    DBCursor cursor;

    if (type == methodS.ATM) {
        cursor = collection.find();/*from  w  ww. j  a  v  a  2  s.  c  om*/
        while (cursor.hasNext()) {
            DBObject obj = cursor.next();
            String no = obj.get("SerialNum").toString();
            String ip = obj.get("ipAddr").toString();
            String money = obj.get("money").toString();
            String usr = obj.get("currentUser").toString();
            data.add(new tellerD(no, ip, money, usr));
        }
    } else if (type == methodS.USER) {
        cursor = collection.find(new BasicDBObject("name", name));
        while (cursor.hasNext()) {
            DBObject obj = cursor.next();
            String usr = obj.get("name").toString();
            boolean ip = (boolean) obj.get("locked");
            data.add(new userD(usr, ip));
        }
    } else if (type == methodS.TRADE) {
        cursor = collection.find(new BasicDBObject("ipAddr", name));
        while (cursor.hasNext()) {
            DBObject obj = cursor.next();
            String no = obj.get("serial").toString();
            String ip = obj.get("ipAddr").toString();
            String method = obj.get("type").toString();
            String usr = obj.get("name").toString();
            String delta = obj.get("delta").toString();
            String remains = obj.get("remains").toString();
            String date = obj.get("time").toString();
            data.add(new tradeD(no, ip, usr, method, delta, remains, date));
        }
    }
    return data;
}

From source file:aic2013.extractor.MongoDataAccess.java

public void forAll(Processor<Status> processor) {
    DB db = mongoClient.getDB("twitterdb");
    DBCollection statusCollection = db.getCollection("statuses");
    DBCursor cursor = statusCollection.find();

    while (cursor.hasNext()) {
        try {/*from www .  j a v a  2  s . c om*/
            processor.process(DataObjectFactory.createStatus(cursor.next().toString()));
        } catch (TwitterException ex) {
            Logger.getLogger(MongoDataAccess.class.getName()).log(Level.SEVERE, null, ex);
        }
    }
}

From source file:aic2013.extractor.MongoDataAccess.java

public void forAllByUserId(long id, Processor<Status> processor) {
    DB db = mongoClient.getDB("twitterdb");
    DBCollection statusCollection = db.getCollection("statuses");
    DBCursor cursor = statusCollection.find(new BasicDBObject("user.id", id));

    while (cursor.hasNext()) {
        try {//w ww .  j  a v  a2 s . c o  m
            processor.process(DataObjectFactory.createStatus(cursor.next().toString()));
        } catch (TwitterException ex) {
            Logger.getLogger(MongoDataAccess.class.getName()).log(Level.SEVERE, null, ex);
        }
    }
}