/*
* 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.MergeOntologies;
import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Set;
import org.erasmusmc.ids.DatabaseID;
import org.erasmusmc.ontology.Concept;
import org.erasmusmc.ontology.Ontology;
import org.erasmusmc.ontology.OntologyStore;
import org.erasmusmc.ontology.TermStore;
import org.erasmusmc.ontology.ontologyutilities.OntologyUtilities;
import org.erasmusmc.utilities.WriteTextFile;
public class CompareThesauri {
public Integer numberOfTerms = 0;
public Integer numberOfSignificantTerms = 0;
public Integer numberOfConcepts = 0;
public Integer numberOfOverlappingIdentifiers = 0;
public Set<Integer> numberOfsignificantConcepts = new HashSet<Integer>();
public Map<String, Set<Integer>> allDatabaseIDsWithCuis(Ontology ontology){
Map<String, Set<Integer>> allDatabaseIds = new HashMap<String, Set<Integer>>();
Iterator<Concept> conceptIterator = ontology.getConceptIterator();
while (conceptIterator.hasNext()){
Concept concept = conceptIterator.next();
List<DatabaseID> dbIds = ontology.getDatabaseIDsForConcept(concept.getID());
Iterator<DatabaseID> idIterator = dbIds.iterator();
while (idIterator.hasNext()){
DatabaseID dbid = idIterator.next();
StringBuffer id = new StringBuffer();
id.append(dbid.database+"_");
id.append(dbid.ID);
String idString = id.toString();
if (allDatabaseIds.containsKey(idString)){
Set<Integer> cuis = allDatabaseIds.get(idString);
cuis.add(concept.getID());
allDatabaseIds.put(idString, cuis);
}else {
Set<Integer> cuis = new HashSet<Integer>();
cuis.add(concept.getID());
allDatabaseIds.put(idString, cuis);
}
}
}
return allDatabaseIds;
}
public OntologyStore compareConceptsInOneThesaurusBasedOnIdentifiers(Concept conceptToCompare, OntologyStore ontology, Map<String, Set<Integer>> allDbIds, Integer startID, WriteTextFile writeFile) {
boolean match = false;
List<DatabaseID> databaseIDsToCompare = ontology.getDatabaseIDsForConcept(conceptToCompare.getID());
Set<String> databaseStringsToCompare = new HashSet<String>();
for (DatabaseID id: databaseIDsToCompare){
StringBuffer idString = new StringBuffer();
idString.append(id.database+"_");
idString.append(id.ID);
databaseStringsToCompare.add(idString.toString());
}
Set<Integer> cuis = getCuisForDatabaseIDsToCompare(databaseStringsToCompare, allDbIds, ontology);
Map<Integer,Concept> concepts = ontology.getConcepts(cuis);
Collection<Concept> conceptList = concepts.values();
Iterator<Concept> conceptListIterator = conceptList.iterator();
while (conceptListIterator.hasNext()){
Concept concept = conceptListIterator.next();
if (concept!=null && concept.getID()>startID && !(concept.getID().equals(conceptToCompare.getID()))){
List<DatabaseID> databaseIDsForConcept = ontology.getDatabaseIDsForConcept(concept.getID());
Set<String> databaseStringsForConcept = new HashSet<String>();
for (DatabaseID id: databaseIDsForConcept){
StringBuffer idString = new StringBuffer();
idString.append(id.database+"_");
idString.append(id.ID);
databaseStringsForConcept.add(idString.toString());
}
Iterator<String> idIterator = databaseStringsForConcept.iterator();
while (idIterator.hasNext()){
String id = idIterator.next();
if (databaseStringsToCompare.contains(id)){
match = true;
}
}
}
if (match){
numberOfConcepts++;
OntologyUtilities.mergeConcepts(ontology, conceptToCompare.getID(), concept.getID());
List<TermStore> terms = concept.getTerms();
OntologyUtilities.removeDuplicateTerms(terms);
concept.setTerms(terms);
String definition = concept.getDefinition();
if (definition.length()!=0){
if (!definition.endsWith(".") && definition.length()<=1024){
definition = definition+".";
} else if (!definition.endsWith(".") && definition.length()>1024){
definition = definition.substring(0, 1023)+".";
} else if (definition.length()>1024){
definition = definition.substring(0, 1023)+".";
}
concept.setDefinition(definition);
}
writeFile.writeln(concept.getID()+"\t"+concept.getName()+"\t"+conceptToCompare.getID()+"\t"+conceptToCompare.getName());
}
match = false;
}
return ontology;
}
public Set<Integer> getCuisForDatabaseIDsToCompare(Set<String> dbIDsToCompare, Map<String, Set<Integer>> allDatabaseIDs, Ontology ontology){
Set<Integer> cuis = new HashSet<Integer>();
for (String dbid: dbIDsToCompare){
Set<Integer> cuisPerDbId = new HashSet<Integer>();
cuisPerDbId = allDatabaseIDs.get(dbid);
if (cuisPerDbId!=null){
cuis.addAll(cuisPerDbId);
}
}
return cuis;
}
}