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

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   w  w  w  .  ja v a 2 s  .c  om
        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 DBIterator getDbIteratorOverOrgs(BasicDBObject matchCriterion, BasicDBObject keys) {
    if (keys == null) {
        keys = new BasicDBObject();
    }//from  w w w .j  a  v  a2 s  .  c  o  m

    DBCursor cursor = this.dbOrganismNames.find(matchCriterion, keys);
    cursor = cursor.addOption(Bytes.QUERYOPTION_NOTIMEOUT);
    return new DBIterator(cursor);
}

From source file:act.server.MongoDB.java

License:Open Source License

public String getOrganismNameFromId(Long id) {
    BasicDBObject query = new BasicDBObject();
    query.put("org_id", id);
    BasicDBObject keys = new BasicDBObject();
    keys.put("name", 1);

    if (this.dbOrganismNames != null) {
        DBObject cur = this.dbOrganismNames.findOne(query, keys);
        if (cur == null) {
            //System.out.println("Did not find in organismnames: " + name);
            return null;
        }/*from ww  w  .j av a  2  s  .  co  m*/
        return (String) cur.get("name");
    } else {
        //System.out.println("no organism names collection");
    }
    return null;
}

From source file:act.server.MongoDB.java

License:Open Source License

public long getOrganismId(String name) {
    BasicDBObject query = new BasicDBObject();
    query.put("name", name);
    BasicDBObject keys = new BasicDBObject();
    keys.put("org_id", 1);

    if (this.dbOrganismNames != null) {
        DBObject cur = this.dbOrganismNames.findOne(query, keys);
        if (cur == null) {
            //System.out.println("Did not find in organismnames: " + name);
            return -1;
        }//  w w  w .jav  a 2  s .  c  o  m
        return (Long) cur.get("org_id"); // checked: db type IS long
    } else {
        //System.out.println("no organism names collection");
    }
    return -1;
}

From source file:act.server.MongoDB.java

License:Open Source License

public Set<Long> getOrganismIDs() {
    DBIterator iterator = getIteratorOverReactions(new BasicDBObject(), null);
    Set<Long> ids = new HashSet<Long>();
    while (iterator.hasNext()) {
        DBObject r = iterator.next();//from w ww. java  2 s. com
        BasicDBList orgs = (BasicDBList) r.get("organisms");
        for (Object o : orgs) {
            ids.add((Long) ((DBObject) o).get("id")); // checked: db type IS Long
        }
    }
    return ids;
}

From source file:act.server.MongoDB.java

License:Open Source License

public Set<Long> getOrganismIDs(Long reactionID) {
    if (reactionID < 0) {
        reactionID = Reaction.reverseID(reactionID);
    }/* w ww.  ja va 2  s  . c  o  m*/
    DBObject query = new BasicDBObject();
    query.put("_id", reactionID);
    Set<Long> ids = new HashSet<Long>();
    DBObject reaction = this.dbReactions.findOne(query);
    if (reaction != null) {
        BasicDBList orgs = (BasicDBList) reaction.get("organisms");
        for (Object o : orgs) {
            ids.add((Long) ((DBObject) o).get("id")); // checked: db type IS long
        }
    }
    return ids;
}

From source file:act.server.MongoDB.java

License:Open Source License

public List<P<Reaction.RefDataSource, String>> getReferences(Long reactionID) {
    if (reactionID < 0) {
        reactionID = Reaction.reverseID(reactionID);
    }//from  ww  w . j a v  a  2 s. c  om
    DBObject query = new BasicDBObject();
    query.put("_id", reactionID);
    List<P<Reaction.RefDataSource, String>> refs = new ArrayList<>();
    DBObject reaction = this.dbReactions.findOne(query);
    if (reaction != null) {
        BasicDBList dbrefs = (BasicDBList) reaction.get("references");
        if (dbrefs != null)
            for (Object oo : dbrefs) {
                DBObject ref = (DBObject) oo;
                Reaction.RefDataSource src = Reaction.RefDataSource.valueOf((String) ref.get("src"));
                String val = (String) ref.get("val");
                refs.add(new P<Reaction.RefDataSource, String>(src, val));
            }
    }
    return refs;
}

From source file:act.server.MongoDB.java

License:Open Source License

public Set<String> getKMValues(Long reactionID) {
    DBObject query = new BasicDBObject();
    query.put("_id", reactionID);
    Set<String> kmSet = new HashSet<String>();
    DBObject reaction = this.dbReactions.findOne(query);
    if (reaction != null) {
        BasicDBList kms = (BasicDBList) reaction.get("km_values");
        if (kms != null) {
            for (Object km : kms) {
                kmSet.add((String) km);
            }/*from w  w  w.  java  2s  .  c o m*/
        }
    }
    return kmSet;
}

From source file:act.server.MongoDB.java

License:Open Source License

public Set<String> getTurnoverNumbers(Long reactionID) {
    DBObject query = new BasicDBObject();
    query.put("_id", reactionID);
    Set<String> turnoverSet = new HashSet<String>();
    DBObject reaction = this.dbReactions.findOne(query);
    if (reaction != null) {
        BasicDBList turnovers = (BasicDBList) reaction.get("turnover_numbers");
        if (turnovers != null) {
            for (Object turnover : turnovers) {
                turnoverSet.add((String) turnover);
            }/* ww  w.  j  a v a  2 s  .  co  m*/
        }
    }
    return turnoverSet;
}

From source file:act.server.MongoDB.java

License:Open Source License

public int submitToActSeqDB(Seq.AccDB src, String ec, String org, Long org_id, String seq,
        List<JSONObject> references, Set<Long> rxns, DBObject meta) {
    BasicDBObject doc = new BasicDBObject();
    int id = new Long(this.dbSeq.count()).intValue();
    doc.put("_id", id);
    doc.put("src", src.name()); // genbank, uniprot, swissprot, trembl, embl
    doc.put("ecnum", ec);
    doc.put("org", org);
    doc.put("org_id", org_id); // this is the NCBI Taxonomy id, should correlate with db.organismnames{org_id} and db.organisms.{id}
    doc.put("seq", seq);

    BasicDBList refs = new BasicDBList();
    for (JSONObject ref : references) {
        refs.add(MongoDBToJSON.conv(ref));
    }//  w  w w  .j  ava 2  s . com
    doc.put("references", refs);

    doc.put("metadata", meta); // the metadata contains the uniprot acc#, name, uniprot catalytic activity,
    Object accession = meta.get("accession");

    doc.put("rxn_refs", to_dblist(rxns));

    this.dbSeq.insert(doc);

    if (org != null && seq != null)
        System.out.format("Inserted %s = [%s, %s] = %s %s\n", accession, ec,
                org.substring(0, Math.min(10, org.length())), seq.substring(0, Math.min(20, seq.length())),
                refs);

    return id;
}