3 files changed, 26 insertions, 17 deletions

diff --git a/src/org/semanticweb/simpleETL/SimpleETL.java b/src/org/semanticweb/simpleETL/SimpleETL.java
index 4d4a193..8dcd87a 100644
--- a/src/org/semanticweb/simpleETL/SimpleETL.java
+++ b/src/org/semanticweb/simpleETL/SimpleETL.java
@@ -42,25 +42,31 @@ public class SimpleETL {
 //              RDFParser parser = new TurtleParser();
                 RDFParser parser = new RDFXMLParser(); 
                 
-                RDFWriter writer = new TurtleWriter(new FileOutputStream(m_fileToExport));
+                FileOutputStream fos = new FileOutputStream(m_fileToExport); 
+                try {
+                        RDFWriter writer = new TurtleWriter(fos);
                 
-//              String m_fileToExport = m_fileToImport.replace(".owl", ".ntriple"); 
-//              RDFWriter writer = new NTriplesWriter(new FileOutputStream(m_fileToExport));
+//                      String m_fileToExport = m_fileToImport.replace(".owl", ".ntriple"); 
+//                      RDFWriter writer = new NTriplesWriter(new FileOutputStream(m_fileToExport));
                 
-                RDFHandlerWriter multiHandler = new RDFHandlerWriter(writer);
-                parser.setRDFHandler(multiHandler);
-                File fileToImport = new File(m_fileToImport);
-                if(fileToImport.isDirectory()) {
-                        for(File file : fileToImport.listFiles()) {
-                                if(file.isFile() && (Pattern.matches(".*.owl", file.getName()) || Pattern.matches(".*.rdf", file.getName()))) {
-                                        Utility.logDebug("Parsing " + file.getName());
-                                        parser.parse(new FileInputStream(file), m_prefix);
+                        RDFHandlerWriter multiHandler = new RDFHandlerWriter(writer);
+                        parser.setRDFHandler(multiHandler);
+                        File fileToImport = new File(m_fileToImport);
+                        if(fileToImport.isDirectory()) {
+                                for(File file : fileToImport.listFiles()) {
+                                        if(file.isFile() && (Pattern.matches(".*.owl", file.getName()) || Pattern.matches(".*.rdf", file.getName()))) {
+                                                Utility.logDebug("Parsing " + file.getName());
+                                                parser.parse(new FileInputStream(file), m_prefix);
+                                        }
                                 }
                         }
+                        else
+                                parser.parse(new FileInputStream(fileToImport), m_prefix);
+                        writer.endRDF();
+                }
+                finally {
+                        fos.close();
                 }
-                else
-                        parser.parse(new FileInputStream(fileToImport), m_prefix);
-                writer.endRDF();
                 Utility.logInfo("SimpleETL rewriting DONE", 
                                 "additional ontology data is saved in " + m_fileToExport + "."); 
         }
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxQueryEngine.java b/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxQueryEngine.java
index 30771ab..70d0cc9 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxQueryEngine.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxQueryEngine.java
@@ -36,8 +36,9 @@ public abstract class RDFoxQueryEngine implements QueryEngine {
                 DataStore store = getDataStore(); 
                 try {
                         long oldTripleCount = store.getTriplesCount(), tripleCount;
-                        for (String file: importedFile.split(QueryReasoner.ImportDataFileSeparator))
+                        for (String file: importedFile.split(QueryReasoner.ImportDataFileSeparator)) {
                                 store.importTurtleFile(new File(file), prefixes);
+                        }
                         tripleCount = store.getTriplesCount(); 
                         Utility.logDebug(name + " store after importing " + fileName + ": " + tripleCount + " (" + (tripleCount - oldTripleCount) + " new)");
                         store.clearRulesAndMakeFactsExplicit();
diff --git a/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java b/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java
index e040c18..d754a70 100644
--- a/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java
+++ b/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java
@@ -107,8 +107,10 @@ public class PagodaTester {
 //                      args = new String[] {npd_tbox, npd_abox, npd_query};
 //                      args = new String[] {npd_bench_tbox, npd_bench_abox, npd_bench_query};
 //                      args = new String[] {"../SemFacet/WebContent/WEB-INF/data/dbpedia.owl", "../SemFacet/WebContent/WEB-INF/data/dbpediaA.nt", null}; 
-//                      args = new String[] {"../SemFacet/WebContent/WEB-INF/data/isg.owl", "../SemFacet/WebContent/WEB-INF/data/isg.nt", null}; 
-                        args = new String[] {"..\\core\\WebContent\\WEB-INF\\data\\fly.owl", "..\\core\\WebContent\\WEB-INF\\data\\fly-data.nt", null}; 
+//                      args = new String[] {"../core/WebContent/WEB-INF/data/fly.owl", "../core/WebContent/WEB-INF/data/fly-data.nt", null}; 
+//                      args = new String[] {"data/lubm/univ-bench.owl", "data/lubm/lubm1.ttl", "data/lubm/lubm.sparql", "lubm.ans"}; 
+                        args = new String[] {"data/uobm/univ-bench-dl.owl", "data/uobm/uobm1.ttl", "data/uobm/uobm.sparql", "uobm.ans"}; 
+//                      args = new String[] {"data/fly/fly_anatomy_XP_with_GJ_FC_individuals.owl", "data/fly/fly.sparql", "fly.ans"}; 
 //                      args = new String[] {bioModels_tbox, bioModels_abox, bioModels_queries}; 
 //                      args = new String[] {chembl_tbox, chembl_abox, chembl_queries};
 //                      args = new String[] {reactome_tbox, reactome_abox, reactome_queries};