/*
* Concept profile generation tool suite
* Copyright (C) 2015 Biosemantics Group, Erasmus University Medical Center,
* Rotterdam, The Netherlands
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero 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 Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>
*/
package JochemBuilder.chemIDplus;
import java.util.Iterator;
import java.util.List;
import org.erasmusmc.ids.DatabaseID;
import org.erasmusmc.ontology.Concept;
import org.erasmusmc.ontology.OntologyStore;
import org.erasmusmc.utilities.StringUtilities;
import org.erasmusmc.utilities.WriteTextFile;
public class GetIDsfromChemIDplus {
public void run(OntologyStore ontology, String outfile){
System.out.println("Starting script: "+StringUtilities.now());
WriteTextFile write = new WriteTextFile(outfile);
Iterator<Concept> conceptIterator = ontology.getConceptIterator();
while (conceptIterator.hasNext()){
Concept concept = conceptIterator.next();
List<DatabaseID> databaseIDs = ontology.getDatabaseIDsForConcept(concept.getID());
for (DatabaseID databaseID: databaseIDs){
String db = databaseID.database;
if (db.equals("CHID")){
write.writeln(databaseID.ID);
}
}
}
write.close();
}
}