/*
* 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 org.erasmusmc.dataimport.tox;
import org.erasmusmc.ontology.Concept;
import org.erasmusmc.ontology.DefaultTypes;
import org.erasmusmc.ontology.OntologyManager;
import org.erasmusmc.ontology.OntologyStore;
import org.erasmusmc.ontology.Relation;
public class ReenumerateToxThesaurus {
public static void main(String[] args) {
OntologyStore newOntology = new OntologyStore();
newOntology.setName("toxGlossary_310811");
int semID = 169;
Concept semtype = new Concept(-semID);
semtype = new Concept(-semID);
semtype.setDefinition("A concept which is of interest because it pertains to the carrying out of a process or activity.");
semtype.setName("Functional Concept");
newOntology.setConcept(semtype);
int vocID = 1500;
Concept voc = new Concept(-vocID);
voc.setName("TOX");
newOntology.setConcept(voc);
OntologyManager manager = new OntologyManager();
OntologyStore ontology = manager.fetchStoreFromDatabase("toxGlossary_290509");
for (Concept concept: ontology){
if (concept.getID()>0){
Concept newConcept = new Concept(concept.getID()+99000);
newConcept.setName(concept.getName());
newConcept.setTerms(concept.getTerms());
newConcept.setDefinition(concept.getDefinition());
newOntology.setConcept(newConcept);
Relation vocrelation = new Relation(newConcept.getID(), DefaultTypes.fromVocabulary, -1500);
newOntology.setRelation(vocrelation);
Relation semrelation = new Relation(newConcept.getID(), DefaultTypes.isOfSemanticType, -semID);
newOntology.setRelation(semrelation);
}
}
manager.dumpStoreInDatabase(newOntology);
}
}