/*************************************************************************
* *
* This file is part of the 20n/act project. *
* 20n/act enables DNA prediction for synthetic biology/bioengineering. *
* Copyright (C) 2017 20n Labs, Inc. *
* *
* Please direct all queries to act@20n.com. *
* *
* This program is free software: you can redistribute it and/or modify *
* it under the terms of the GNU General Public License as published by *
* the Free Software Foundation, either version 3 of the License, or *
* (at your option) any later version. *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU General Public License for more details. *
* *
* You should have received a copy of the GNU General Public License *
* along with this program. If not, see <http://www.gnu.org/licenses/>. *
* *
*************************************************************************/
package act.server;
import act.shared.Chemical;
import act.shared.Cofactor;
import act.shared.Organism;
import act.shared.Reaction;
import act.shared.Seq;
import com.act.reachables.LoadAct;
import com.act.reachables.Network;
import com.mongodb.DBObject;
import org.json.JSONObject;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Set;
public class NoSQLAPI {
MongoDB readDB;
MongoDB writeDB;
public NoSQLAPI(String sourceDB, String destDB) {
// This API is expected to interact and interface between two
// versions of our knowledge graph (/ mongo dbs)
//
// Ref: https://github.com/20n/act/wiki/Naming-schemes
// Lucille: KG after data integration
// DrKnow: KG after data cleanup (bio-interpretation)
//
// Lucille is the readDB, expected to run on 27017
// DrKnow is the writeDB, expected to run on 37017
//
// There are separate read and write function in this API
// that transparently read and write to the right KG
if (sourceDB.equals("lucille")) {
sourceDB = "actv01";
}
this.readDB = new MongoDB("localhost", 27017, sourceDB);
this.writeDB = new MongoDB("localhost", 27017, destDB);
}
public static void dropDB(String destDB) {
MongoDB.dropDB("localhost", 27017, destDB);
}
public static void dropDB(String destDB, boolean force) {
MongoDB.dropDB("localhost", 27017, destDB, force);
}
public NoSQLAPI() {
this("lucille", "drknow");
}
// Thin wrapper around getIteratorOverReactions that returns actual Reaction objects.
public Iterator<Reaction> readRxnsFromInKnowledgeGraph() {
final DBIterator iter = this.readDB.getIteratorOverReactions();
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 readDB.convertDBObjectToReaction(o);
}
};
}
public Iterator<Chemical> readChemsFromInKnowledgeGraph() {
final DBIterator iter = this.readDB.getIteratorOverChemicals();
return new Iterator<Chemical>() {
@Override
public boolean hasNext() {
boolean hasNext = iter.hasNext();
if (!hasNext)
iter.close();
return hasNext;
}
@Override
public Chemical next() {
DBObject o = iter.next();
return readDB.convertDBObjectToChemical(o);
}
};
}
public Iterator<Seq> readSeqsFromInKnowledgeGraph() {
final DBIterator iter = this.readDB.getDbIteratorOverSeq();
return new Iterator<Seq>() {
@Override
public boolean hasNext() {
boolean hasNext = iter.hasNext();
if (!hasNext)
iter.close();
return hasNext;
}
@Override
public Seq next() {
DBObject o = iter.next();
return readDB.convertDBObjectToSeq(o);
}
};
}
public Iterator<Organism> readOrgsFromInKnowledgeGraph() {
final DBIterator iter = this.readDB.getDbIteratorOverOrgs();
return new Iterator<Organism> () {
@Override
public boolean hasNext() {
boolean hasNext = iter.hasNext();
if (!hasNext)
iter.close();
return hasNext;
}
@Override
public Organism next() {
DBObject o = iter.next();
return readDB.convertDBObjectToOrg(o);
}
};
}
public List<JSONObject> getObservations(Reaction rxn) {
List<JSONObject> results = new ArrayList<>();
for (JSONObject dbo : rxn.getProteinData()) {
results.add(dbo);
}
return results;
}
public Reaction readReactionFromInKnowledgeGraph(Long id) {
return this.readDB.getReactionFromUUID(id);
}
public Chemical readChemicalFromInKnowledgeGraph(Long id) {
return this.readDB.getChemicalFromChemicalUUID(id);
}
public Chemical readChemicalFromInKnowledgeGraph(String inchi) {
return this.readDB.getChemicalFromInChI(inchi);
}
public int writeToOutKnowlegeGraph(Reaction r) {
// set the UUID of the reaction to `-1` otherwise
// the write will fail. The mongo interface expects
// a -1 value so that it can assign whatever is
// the the next available dbid in the collection
r.clearUUID();
int writtenid = this.writeDB.submitToActReactionDB(r);
return writtenid;
}
public long writeToOutKnowlegeGraph(Chemical c) {
long installid = this.writeDB.getNextAvailableChemicalDBid();
return this.writeDB.submitToActChemicalDB(c, installid);
}
public Map<Long, String> reachables(String db, Set<String> natives, Set<String> cofactors, boolean restrictToSeq) {
Network l2tree = LoadAct.getReachablesTree(db, natives, cofactors, restrictToSeq);
Map<Long, String> l2 = new HashMap<Long, String>();
for (Long reachable_id : l2tree.nodesAndIds().values()) {
l2.put(reachable_id, LoadAct.toInChI(reachable_id));
}
System.out.println("L2 Total size = " + l2.size());
System.out.println("L2 (Ids, InChI) = " + l2);
return l2;
}
public long writeCofactorToOutKnowledgeGraph(Cofactor c) {
long id = this.writeDB.getNextAvailableCofactorDBid();
this.writeDB.submitToActCofactorsDB(c, id);
return id;
}
public Iterator<Cofactor> readCofactorsFromInKnowledgeGraph() {
final DBIterator iter = readDB.getIteratorOverCofactors();
return new Iterator<Cofactor>() {
@Override
public boolean hasNext() {
boolean hasNext = iter.hasNext();
if (!hasNext) {
iter.close();
}
return hasNext;
}
@Override
public Cofactor next() {
return readDB.getNextCofactor(iter);
}
};
}
public Cofactor getCofactorFromInKnowledgeGraphByUUID(Long uuid) {
return this.readDB.getCofactorFromUUID(uuid);
}
public MongoDB getReadDB() {
return this.readDB;
}
public MongoDB getWriteDB() {
return this.writeDB;
}
}