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[jalview.git] / src / org / biojava / dasobert / das2 / io / DasSourceReaderImpl.java

diff --git a/src/org/biojava/dasobert/das2/io/DasSourceReaderImpl.java b/src/org/biojava/dasobert/das2/io/DasSourceReaderImpl.java
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+/*
+ *                  BioJava development code
+ *
+ * This code may be freely distributed and modified under the
+ * terms of the GNU Lesser General Public Licence.  This should
+ * be distributed with the code.  If you do not have a copy,
+ * see:
+ *
+ *      http://www.gnu.org/copyleft/lesser.html
+ *
+ * Copyright for this code is held jointly by the individual
+ * authors.  These should be listed in @author doc comments.
+ *
+ * For more information on the BioJava project and its aims,
+ * or to join the biojava-l mailing list, visit the home page
+ * at:
+ *
+ *      http://www.biojava.org/
+ *
+ * Created on Feb 24, 2006
+ *
+ */
+package org.biojava.dasobert.das2.io;
+
+import java.io.InputStream;
+import java.net.HttpURLConnection;
+import java.net.URL;
+
+
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.parsers.SAXParser;
+import javax.xml.parsers.SAXParserFactory;
+
+import org.biojava.dasobert.dasregistry.DasSource;
+import org.xml.sax.InputSource;
+import org.xml.sax.SAXException;
+import org.xml.sax.SAXNotRecognizedException;
+import org.xml.sax.XMLReader;
+import org.biojava.dasobert.das.DAS_FeatureRetrieve;
+
+public class DasSourceReaderImpl implements DasSourceReader {
+
+    Exception loggedException;
+
+    public DasSourceReaderImpl() {
+        super();
+        loggedException = null;
+
+        // open the stream to a server and then parse the result ...
+    }
+
+    private InputStream open(URL url)
+    throws java.io.IOException, java.net.ConnectException
+    {
+        InputStream inStream = null;
+
+
+        HttpURLConnection huc = DAS_FeatureRetrieve.openHttpURLConnection(url);
+
+        inStream = huc.getInputStream();
+
+        return inStream;
+
+    }
+
+
+    public DasSource[] readDasSource(URL url){
+        DasSource[] sources = new DasSource[0];
+
+        try {
+            InputStream stream = open(url);
+
+            sources = readDasSource(stream);
+        } catch (Exception e){
+            e.printStackTrace();
+            loggedException = e;
+        }
+        return sources;
+    }
+
+    /** read a DAS2 sources response and return a list of DAS sources.
+     *
+     */
+    public DasSource[] readDasSource(InputStream stream)  {
+
+        DasSource[] sources = new DasSource[0];
+
+        try {
+        SAXParserFactory spfactory =
+            SAXParserFactory.newInstance();
+
+        spfactory.setValidating(false);
+
+        SAXParser saxParser = null ;
+
+        try{
+            saxParser =
+                spfactory.newSAXParser();
+        } catch (ParserConfigurationException e) {
+            e.printStackTrace();
+            loggedException = e;
+        }
+
+        String vali = System.getProperty("XMLVALIDATION");
+
+        boolean validation = false ;
+        if ( vali != null )
+            if ( vali.equals("true") )
+                validation = true ;
+
+
+        XMLReader xmlreader = saxParser.getXMLReader();
+
+        //XMLReader xmlreader = XMLReaderFactory.createXMLReader();
+        try {
+            xmlreader.setFeature("http://xml.org/sax/features/validation", validation);
+        } catch (SAXException e) {
+            //logger.log(Level.FINE,"Cannot set validation " + validation);
+        }
+
+        try {
+            xmlreader.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd",validation);
+        } catch (SAXNotRecognizedException e){
+            e.printStackTrace();
+            //logger.log(Level.FINE,"Cannot set load-external-dtd "+validation);
+
+        }
+
+        DAS2SourceHandler cont_handle = new DAS2SourceHandler() ;
+
+        xmlreader.setContentHandler(cont_handle);
+        xmlreader.setErrorHandler(new org.xml.sax.helpers.DefaultHandler());
+        InputSource insource = new InputSource() ;
+        insource.setByteStream(stream);
+
+
+        xmlreader.parse(insource);
+        sources = cont_handle.getSources();
+
+
+
+        } catch (Exception e) {
+            e.printStackTrace();
+            loggedException = e;
+        }
+        return sources;
+    }
+
+    public Exception getLoggedException(){
+        return loggedException;
+    }
+
+    public static void main (String[] args){
+        String url = "http://www.spice-3d.org/dasregistry/das2/sources/";
+        DasSourceReaderImpl reader = new DasSourceReaderImpl();
+        try {
+            URL u = new URL(url);
+            DasSource[] sources = reader.readDasSource(u);
+            for (int i=0; i< sources.length;i++){
+                DasSource ds = sources[i];
+                System.out.println(ds.toString());
+            }
+
+        } catch (Exception e){
+            e.printStackTrace();
+        }
+
+    }
+
+
+
+}