downgrade owl api and reorganised src files

1 files changed, 129 insertions, 0 deletions

diff --git a/external/uk/ac/ox/cs/data/Fragment.java b/external/uk/ac/ox/cs/data/Fragment.java
new file mode 100644
index 0000000..1038a33
--- /dev/null
+++ b/external/uk/ac/ox/cs/data/Fragment.java
@@ -0,0 +1,129 @@
+package uk.ac.ox.cs.data;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.util.Random;
+
+import org.openrdf.model.Statement;
+import org.openrdf.rio.RDFHandler;
+import org.openrdf.rio.RDFHandlerException;
+import org.openrdf.rio.turtle.TurtleParser;
+import org.openrdf.rio.turtle.TurtleWriter;
+
+import uk.ac.ox.cs.pagoda.util.Utility;
+
+public class Fragment {
+        
+        private TurtleWriter m_writer;
+        private FragmentRDFHandler m_handler; 
+
+        public Fragment(int fragment, String outFile) {
+                try {
+                        m_writer = new TurtleWriter(new FileOutputStream(outFile));
+                } catch (FileNotFoundException e) {
+                        e.printStackTrace();
+                }
+                m_handler = new FragmentRDFHandler(fragment, m_writer); 
+        }
+        
+        public void process(String prefix, String fileName) {
+                FileInputStream istream; 
+                try {
+                        TurtleParser parser = new TurtleParser();
+                        parser.setRDFHandler(m_handler);
+                        
+                        File f = new File(fileName);
+                        if (f.isDirectory())
+                                for (String tFileName: f.list()) {
+                                        if (tFileName.endsWith(".ttl")) {
+                                                parser.parse(istream = new FileInputStream(fileName + Utility.FILE_SEPARATOR + tFileName), prefix);
+                                                istream.close(); 
+                                        }
+                                }
+                        else {
+                                parser.parse(istream = new FileInputStream(fileName), prefix);
+                                istream.close(); 
+                        }
+                } catch (Exception e) {
+                        e.printStackTrace();
+                        Utility.logError("aoaoaoao ~~~~~");
+                        return ;
+                }
+                Utility.logInfo("DONE");
+        }
+
+        public void dispose() {
+                try {
+                        m_writer.endRDF();
+                } catch (RDFHandlerException e) {
+                        e.printStackTrace();
+                } 
+        }
+        
+        public static void main(String[] args) {
+                /**
+                 * for ChEMBL
+                 */
+                Fragment f = new Fragment(100, "data_01.ttl");
+                f.process("http://rdf.ebi.ac.uk/terms/chembl#", "/media/krr-nas-share/Yujiao/ontologies/bio2rdf/chembl/data");
+                
+                /**
+                 * for Reactome
+                 *              "http://www.biopax.org/release/biopax-level3.owl#", 
+                                "/home/scratch/yzhou/ontologies/bio2rdf/reactome"
+                                "/home/scratch/yzhou/ontologies/bio2rdf/reactome/biopaxrdf", 
+                 */
+                
+//              Fragment f = new Fragment(1000, "data_001.ttl");
+//              f.process("http://www.biopax.org/release/biopax-level3.owl#", "/media/krr-nas-share/Yujiao/ontologies/bio2rdf/reactome/data.ttl");
+                
+                f.dispose();
+        }
+        
+}
+
+
+class FragmentRDFHandler implements RDFHandler {
+        
+        int m_mod;
+        TurtleWriter m_writer; 
+        Random m_rand = new Random(); 
+        
+        public FragmentRDFHandler(int mod, TurtleWriter writer) {
+                m_mod = mod;  
+                m_writer = writer; 
+        }
+
+        @Override
+        public void endRDF() throws RDFHandlerException {
+        }
+
+        @Override
+        public void handleComment(String arg0) throws RDFHandlerException {
+                m_writer.handleComment(arg0);
+                Utility.logDebug("handling comment: " + arg0);
+        }
+
+        @Override
+        public void handleNamespace(String arg0, String arg1) throws RDFHandlerException {
+                m_writer.handleNamespace(arg0, arg1);
+        }
+
+        @Override
+        public void handleStatement(Statement arg0) throws RDFHandlerException {
+                if (m_rand.nextInt() % m_mod == 0)
+                        m_writer.handleStatement(arg0);
+        }
+        
+        boolean m_started = false; 
+
+        @Override
+        public void startRDF() throws RDFHandlerException {
+                if (m_started) return ; 
+                m_started = true; 
+                m_writer.startRDF();
+        }
+        
+}
\ No newline at end of file