Example usage for com.mongodb DBObject get

List of usage examples for com.mongodb DBObject get

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Introduction

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

Prototype

Object get(String key);

Source Link

Document

Gets a field from this object by a given name.

Usage

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.c  o 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);
            }//from   w w w.j  a va  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);
            }//from  ww w.  j a v a 2s. c o 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));
    }/*from   w ww  .jav  a2  s .  c  o  m*/
    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;
}

From source file:act.server.MongoDB.java

License:Open Source License

/**
 * graphByOrganism() returns a list of all reactionIDs containing the given organismID.
 *
 * @param organismID/*from   ww w  . j a v  a  2  s. c  o  m*/
 * @return List<Long> List of reaction IDs for given organismID
 */
public List<Long> graphByOrganism(Long organismID) {

    DBObject query = new BasicDBObject();
    if (organismID == null || organismID > -1)
        query.put("organisms.id", organismID);
    List<Long> graphList = new ArrayList<Long>();

    DBCursor reactionCursor = this.dbReactions.find(query);
    for (DBObject i : reactionCursor) {
        graphList.add(((Integer) i.get("_id")).longValue()); // checked: db type IS int
    }
    return graphList;
}

From source file:act.server.MongoDB.java

License:Open Source License

/**
 * getOrganisms() returns a list of all unique species IDs in database
 * mapped to itself, its parents, and descendants
 *
 * @return//w  w  w .  j a  va 2s .  c om
 */
@SuppressWarnings("unchecked")
public Map<Long, Set<Long>> getOrganisms() {
    List<Long> ids = (List<Long>) this.dbReactions.distinct("organisms.id");
    //map species id to all ids associated with it
    Map<Long, Set<Long>> speciesIDs = new HashMap<Long, Set<Long>>();
    for (Long organismID : ids) {
        //check if organism id on species level
        List<Long> idsToAdd = new ArrayList<Long>();
        Long speciesID;
        DBObject orgQuery = new BasicDBObject();
        orgQuery.put("_id", organismID);
        DBObject org = dbOrganisms.findOne(orgQuery);
        String rank = (String) org.get("rank");
        Long parent = (Long) org.get("parent_id"); // checked: db type IS long
        speciesID = null;
        while (organismID != 1) {
            idsToAdd.add(organismID);
            if (rank.equals("species")) {
                speciesID = organismID;
                //break;
            }
            orgQuery.put("_id", parent);
            org = dbOrganisms.findOne(orgQuery);
            organismID = parent;
            rank = (String) org.get("rank");
            parent = (Long) org.get("parent_id"); // checked: db type IS long
        }
        if (speciesID == null)
            continue;
        if (!speciesIDs.containsKey(speciesID)) {
            speciesIDs.put(speciesID, new HashSet<Long>());
        }
        speciesIDs.get(speciesID).addAll(idsToAdd);
    }
    return speciesIDs;
}

From source file:act.server.MongoDB.java

License:Open Source License

public Map<String, Long> getKeggID_ActID(boolean useCached) {
    if (keggID_ActID == null || !useCached)
        keggID_ActID = new HashMap<String, Long>();
    else//from w w w  . j a  v  a2 s  .c o m
        return keggID_ActID;
    DBIterator it = getIteratorOverChemicals();
    while (it.hasNext()) {
        Chemical c = getNextChemical(it);
        DBObject o = (DBObject) c.getRef(Chemical.REFS.KEGG);
        if (o == null)
            continue;
        BasicDBList list = (BasicDBList) o.get("id");
        for (Object s : list) {
            keggID_ActID.put((String) s, c.getUuid());
        }
    }
    return keggID_ActID;
}

From source file:act.shared.helpers.MongoDBToJSON.java

License:Open Source License

public static JSONObject conv(DBObject o) {
    JSONObject result = new JSONObject();
    try {/* w  w w  .  j a  v  a  2s  .c  o  m*/
        for (String k : o.keySet()) {
            Object v = o.get(k);
            if (v instanceof BasicDBList) {
                result.put(k, conv((BasicDBList) v));
            } else if (v instanceof DBObject) {
                result.put(k, conv((DBObject) v));
            } else {
                result.put(k, v);
            }
        }
        return result;
    } catch (JSONException je) {
        return null;
    }
}

From source file:act.shared.helpers.XMLToImportantChemicals.java

License:Open Source License

private void process(XMLStreamReader xml) throws XMLStreamException {
    String tag;/*from   w  ww.j a  v  a2  s.c  o  m*/
    String root = null;
    Stack<DBObject> json = new Stack<DBObject>();
    DBObject js;
    while (xml.hasNext()) {
        int eventType = xml.next();
        while (xml.isWhiteSpace() || eventType == XMLEvent.SPACE)
            eventType = xml.next();

        switch (eventType) {
        case XMLEvent.START_ELEMENT:
            tag = xml.getLocalName();
            if (root == null) {
                root = tag;
            } else {
                json.push(new BasicDBObject());
            }
            break;
        case XMLEvent.END_ELEMENT:
            tag = xml.getLocalName();
            if (tag.equals(root)) {
                // will terminate in next iteration
            } else {
                js = json.pop();
                if (json.size() == 0) {
                    if (tag.equals(rowTag))
                        printEntry(js);
                    else
                        printUnwantedEntry(js);
                } else {
                    putListStrOrJSON(json.peek(), tag, js);
                }
            }
            break;

        case XMLEvent.CHARACTERS:
            String txt = xml.getText();
            js = json.peek();
            if (js.containsField(strTag)) {
                txt = js.get(strTag) + txt;
                js.removeField(strTag);
            }
            js.put(strTag, txt);
            break;

        case XMLEvent.START_DOCUMENT:
            break;
        case XMLEvent.END_DOCUMENT:
            break;
        case XMLEvent.COMMENT:
        case XMLEvent.ENTITY_REFERENCE:
        case XMLEvent.ATTRIBUTE:
        case XMLEvent.PROCESSING_INSTRUCTION:
        case XMLEvent.DTD:
        case XMLEvent.CDATA:
        case XMLEvent.SPACE:
            System.out.format("%s --\n", eventType);
            break;
        }
    }
}

From source file:act.shared.helpers.XMLToImportantChemicals.java

License:Open Source License

private void putListStrOrJSON(DBObject json, String tag, DBObject toAdd) {
    // if it is a string add it unencapsulated
    if (toAdd.keySet().size() == 1 && toAdd.containsField(strTag))
        putElemOrList(json, tag, toAdd.get(strTag));
    else/*from   w w w.  j  av  a  2s.  c  om*/
        putElemOrList(json, tag, toAdd);
}