Example usage for com.mongodb BasicDBList BasicDBList

Introduction

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

Prototype

BasicDBList

Source Link

Usage

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);/*from   ww w . ja  v  a2s  . c  o  m*/
    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 Iterator<Chemical> getChemicalsbyIds(List<Long> ids, boolean notimeout) {
    BasicDBList queryList = new BasicDBList();
    for (Long id : ids) {
        queryList.add(new BasicDBObject(ChemicalKeywords.ID$.MODULE$.toString(), id));
    }/*from   w  ww . ja  v  a  2  s  .  c  o  m*/

    return getJavaIteratorOverChemicals(new BasicDBObject(MongoKeywords.OR$.MODULE$.toString(), queryList));
}

From source file:act.server.MongoDB.java

License:Open Source License

public Set<Reaction> getReactionsConstrained(Map<String, Object> equalityCriteria) {
    BasicDBList andList = new BasicDBList();
    for (String k : equalityCriteria.keySet()) {
        BasicDBObject query = new BasicDBObject();
        query.put(k, equalityCriteria.get(k));
        andList.add(query);/*from  w w  w  . j a  v  a2 s.co  m*/
    }
    BasicDBObject query = new BasicDBObject();
    query.put("$and", andList);
    DBCursor cur = this.dbReactions.find(query);

    Set<Reaction> results = new HashSet<Reaction>();
    while (cur.hasNext()) {
        results.add(convertDBObjectToReaction(cur.next()));
    }
    return results;
}

From source file:act.server.MongoDB.java

License:Open Source License

public Iterator<Reaction> getReactionsIteratorById(List<Long> ids, boolean notimeout) {
    BasicDBList reactionList = new BasicDBList();

    for (Long id : ids) {
        reactionList.add(new BasicDBObject(ChemicalKeywords.ID$.MODULE$.toString(), id));
    }/*from   w  w  w  .  j av a 2s.  com*/

    BasicDBObject query = new BasicDBObject(MongoKeywords.OR$.MODULE$.toString(), reactionList);

    final DBIterator iter = getIteratorOverReactions(query, null);

    return new Iterator<Reaction>() {
        @Override
        public boolean hasNext() {
            boolean hasNext = iter.hasNext();
            if (!hasNext)
                iter.close();
            return hasNext;
        }

        @Override
        public Reaction next() {
            DBObject o = iter.next();
            return convertDBObjectToReaction(o);
        }
    };
}

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  w  w  . j  a  va2  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

<X> BasicDBList to_dblist(Set<X> set) {
    BasicDBList dblist = new BasicDBList();
    if (set != null)
        dblist.addAll(set);
    return dblist;
}

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  ww w.  j a v  a 2  s. c o m*/

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

From source file:act.server.MongoDB.java

License:Open Source License

/**
 * Following methods are related to Bing cross-references installation in the Installer DB along with various
 * queries to obtain names (aka synonyms)
 */// ww  w  .j  a va2 s.  co  m

public BasicDBObject createBingMetadataDoc(Set<UsageTermUrlSet> usageTerms, Long totalCountSearchResults,
        String bestName) {
    BasicDBObject metadata = new BasicDBObject();
    if (usageTerms != null) {
        BasicDBList usageTermsDBObject = new BasicDBList();
        for (UsageTermUrlSet usageTerm : usageTerms) {
            // What happens if you don't translate to basic db obj in the next line?
            usageTermsDBObject.add(usageTerm.getBasicDBObject());
        }
        metadata.put("usage_terms", usageTermsDBObject);
    }
    if (totalCountSearchResults >= 0) {
        metadata.put("total_count_search_results", totalCountSearchResults);
    }
    if (!bestName.equals("")) {
        metadata.put("best_name", bestName);
    }
    return metadata;
}

From source file:act.server.MongoDB.java

License:Open Source License

public DBCursor fetchNamesAndUsageForInchis(Set<String> inchis) {
    BasicDBList inchiList = new BasicDBList();
    inchiList.addAll(inchis);//from  www. j  ava  2s.  co m
    BasicDBObject inClause = new BasicDBObject("$in", inchiList);
    BasicDBObject whereQuery = new BasicDBObject("InChI", inClause);
    whereQuery.put("xref.BING", new BasicDBObject("$exists", true));
    BasicDBObject fields = new BasicDBObject();
    fields.put("InChI", true);
    fields.put("names.brenda", true);
    fields.put("xref", true);
    DBCursor cursor = dbChemicals.find(whereQuery, fields);
    return cursor;
}

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

License:Open Source License

public static DBObject conv(JSONArray a) {
    BasicDBList result = new BasicDBList();
    try {//w  w  w.jav  a  2s. c om
        for (int i = 0; i < a.length(); ++i) {
            Object o = a.get(i);
            if (o instanceof JSONObject) {
                result.add(conv((JSONObject) o));
            } else if (o instanceof JSONArray) {
                result.add(conv((JSONArray) o));
            } else {
                result.add(o);
            }
        }
        return result;
    } catch (JSONException je) {
        return null;
    }
}