From 9ce65c5a963b03ee97fe9cb6c5aa65a3c04a80a8 Mon Sep 17 00:00:00 2001
From: yzhou <yujiao.zhou@gmail.com>
Date: Tue, 21 Apr 2015 10:34:27 +0100
Subject: initial version

---
 test/uk/ac/ox/cs/data/Fragment.java | 129 ++++++++++++++++++++++++++++++++++++
 1 file changed, 129 insertions(+)
 create mode 100644 test/uk/ac/ox/cs/data/Fragment.java

(limited to 'test/uk/ac/ox/cs/data/Fragment.java')

diff --git a/test/uk/ac/ox/cs/data/Fragment.java b/test/uk/ac/ox/cs/data/Fragment.java
new file mode 100644
index 0000000..1038a33
--- /dev/null
+++ b/test/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();
+	}
+	
+}
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