[pagoda] Move project to Scala

This commit includes a few changes:
- The repository still uses Maven to manage dependency but it is now a
  Scala project.
- The code has been ported from OWLAPI 3.4.10 to 5.1.20
- A proof of concept program using both RSAComb and PAGOdA has been
  added.

1 files changed, 76 insertions, 0 deletions

diff --git a/src/main/java/org/semanticweb/simpleETL/SimpleETL.java b/src/main/java/org/semanticweb/simpleETL/SimpleETL.java
new file mode 100644
index 0000000..cc91e1f
--- /dev/null
+++ b/src/main/java/org/semanticweb/simpleETL/SimpleETL.java
@@ -0,0 +1,76 @@
+package org.semanticweb.simpleETL;
+
+import org.openrdf.rio.RDFParser;
+import org.openrdf.rio.RDFWriter;
+import org.openrdf.rio.rdfxml.RDFXMLParser;
+import org.openrdf.rio.turtle.TurtleWriter;
+import uk.ac.ox.cs.pagoda.util.Utility;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.util.regex.Pattern;
+
+public class SimpleETL {
+        
+        protected final static String m_prefix_LUBM = "http://www.lehigh.edu/~zhp2/2004/0401/univ-bench.owl#";
+        protected final static String m_prefix_UOBM = "http://semantics.crl.ibm.com/univ-bench-dl.owl#";
+        protected final static String m_prefix_FLY= "http://www.virtualflybrain.org/ontologies/individual_neurons/FC_neuron_GF_an.owl#";
+
+        String m_prefix; 
+        String m_fileToImport;
+        String m_fileToExport; 
+        
+        public SimpleETL(String prefix, String fileToImport) {
+                m_prefix = prefix; 
+                m_fileToImport = fileToImport; 
+                m_fileToExport = m_fileToImport.replace(".owl", ".ttl"); 
+        }
+        
+        public SimpleETL(String prefix, String fileToImport, String outPath) {
+                m_prefix = prefix; 
+                m_fileToImport = fileToImport;
+                File file = new File(outPath); 
+                if (file.exists() && file.isDirectory())
+                        m_fileToExport = outPath + Utility.FILE_SEPARATOR + "data.ttl"; 
+                else 
+                        m_fileToExport = outPath; 
+//                              + Utility.FILE_SEPARATOR + m_fileToImport.substring(m_fileToImport.lastIndexOf(Utility.FILE_SEPARATOR), m_fileToImport.lastIndexOf(".")) + ".ttl"; 
+        }
+        
+        public void rewrite() throws Exception {
+//              RDFParser parser = new TurtleParser();
+                RDFParser parser = new RDFXMLParser(); 
+                
+                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));
+                
+                        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();
+                }
+                Utility.logDebug("SimpleETL rewriting DONE: additional ontology data is saved in " + m_fileToExport + ".");
+        }
+        
+        public String getExportedFile() {
+                return m_fileToExport; 
+        }
+}