Example usage for com.mongodb DBObject put

Introduction

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

Prototype

Object put(String key, Object v);

Source Link

Document

Sets a name/value pair in this object.

Usage

From source file:act.server.MongoDB.java

License:Open Source License

public List<Chemical> getChemicalsThatHaveField(String field) {
    DBObject val = new BasicDBObject();
    val.put("$exists", "true");
    return constructAllChemicalsFromActData(field, val);
}

From source file:act.server.MongoDB.java

License:Open Source License

public List<Chemical> getDrugbankChemicals() {
    DBObject val = new BasicDBObject();
    val.put("$ne", null);
    String field = "xref.DRUGBANK";

    return constructAllChemicalsFromActData(field, val);
}

From source file:act.server.MongoDB.java

License:Open Source License

public List<Chemical> getSigmaChemicals() {
    DBObject val = new BasicDBObject();
    val.put("$ne", null);
    String field = "xref.SIGMA";

    return constructAllChemicalsFromActData(field, val);
}

From source file:act.server.MongoDB.java

License:Open Source License

public DBIterator getIdCursorForFakeChemicals() {
    DBObject fakeRegex = new BasicDBObject();
    DBObject abstractInchi = new BasicDBObject();
    fakeRegex.put(ChemicalKeywords.INCHI$.MODULE$.toString(),
            new BasicDBObject(MongoKeywords.REGEX$.MODULE$.toString(), "^InChI=/FAKE"));

    abstractInchi.put(ChemicalKeywords.INCHI$.MODULE$.toString(),
            new BasicDBObject(MongoKeywords.REGEX$.MODULE$.toString(), "^InChI=.*R.*"));

    BasicDBList conditionList = new BasicDBList();
    conditionList.add(fakeRegex);/*w  w  w .j  a v  a2 s.c om*/
    conditionList.add(abstractInchi);

    BasicDBObject conditions = new BasicDBObject(MongoKeywords.OR$.MODULE$.toString(), conditionList);

    return getIteratorOverChemicals(conditions,
            new BasicDBObject(ChemicalKeywords.ID$.MODULE$.toString(), true));
}

From source file:act.server.MongoDB.java

License:Open Source License

public Set<Long> getOrganismIDs(Long reactionID) {
    if (reactionID < 0) {
        reactionID = Reaction.reverseID(reactionID);
    }/*from w  w  w  . java2  s .co  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   w  w  w . j  ava2s  .co  m*/
    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);
            }/* w w  w  .  java  2 s . co  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);
            }/*from  w  w w . j a  v a2s . c  om*/
        }
    }
    return turnoverSet;
}

From source file:act.server.MongoDB.java

License:Open Source License

public void updateMetadata(Seq seq) {
    BasicDBObject query = new BasicDBObject().append("_id", seq.getUUID());
    DBObject obj = this.dbSeq.findOne(query);
    obj.put("metadata", MongoDBToJSON.conv(seq.getMetadata()));
    this.dbSeq.update(query, obj);
}

From source file:act.server.MongoDB.java

License:Open Source License

public void updateReferences(Seq seq) {
    BasicDBObject query = new BasicDBObject().append("_id", seq.getUUID());
    DBObject obj = this.dbSeq.findOne(query);
    BasicDBList refs = new BasicDBList();

    List<DBObject> newReferences = new ArrayList<>();
    for (JSONObject ref : seq.getReferences()) {
        newReferences.add(MongoDBToJSON.conv(ref));
    }/*from   w ww  .  jav  a  2 s.c  o  m*/

    refs.addAll(newReferences);
    obj.put("references", refs);
    this.dbSeq.update(query, obj);
}