--- /dev/null
+/*
+ * 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 Mar 15, 2006
+ *
+ */
+package org.biojava.dasobert.das2.io;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.biojava.dasobert.das2.Das2Capability;
+import org.biojava.dasobert.das2.Das2CapabilityImpl;
+import org.biojava.dasobert.das2.Das2Source;
+import org.biojava.dasobert.das2.Das2SourceImpl;
+import org.biojava.dasobert.dasregistry.DasCoordinateSystem;
+import org.biojava.dasobert.dasregistry.DasSource;
+import org.xml.sax.Attributes;
+import org.xml.sax.helpers.DefaultHandler;
+
+/** a parser for the DAS2 sources response
+ *
+ * @author Andreas Prlic
+ * @since 6:53:45 PM
+ * @version %I% %G%
+ */
+public class DAS2SourceHandler extends DefaultHandler{
+
+ List sources;
+ Das2Source currentSource;
+ List coordinates;
+ List capabilities;
+
+ public DAS2SourceHandler() {
+ super();
+
+ sources = new ArrayList();
+ currentSource = new Das2SourceImpl();
+ coordinates = new ArrayList();
+ capabilities = new ArrayList();
+ }
+
+ private void startSource (String uri, String name, String qName, Attributes atts){
+
+ String id = atts.getValue("uri");
+ String title = atts.getValue("title");
+ String doc_ref = atts.getValue("doc_href");
+ String description = atts.getValue("description");
+
+
+ currentSource.setId(id);
+ currentSource.setNickname(title);
+ currentSource.setHelperurl(doc_ref);
+ currentSource.setDescription(description);
+
+ }
+
+ private DasCoordinateSystem getCoordinateSystem(String uri, String name, String qname, Attributes atts){
+ // e.g. uri="http://das.sanger.ac.uk/dasregistry/coordsys/CS_LOCAL6"
+ // source="Protein Sequence" authority="UniProt" test_range="P06213" />
+ DasCoordinateSystem dcs = new DasCoordinateSystem();
+ String id = atts.getValue("uri");
+ dcs.setUniqueId(id);
+
+ String source = atts.getValue("source");
+ dcs.setCategory(source);
+
+ String authority = atts.getValue("authority");
+ dcs.setName(authority);
+
+ String test_range = atts.getValue("test_range");
+ dcs.setTestCode(test_range);
+
+ try {
+ String taxidstr = atts.getValue("taxid");
+ int taxid = Integer.parseInt(taxidstr);
+ dcs.setNCBITaxId(taxid);
+ } catch (Exception e){}
+
+ String version = atts.getValue("version");
+ if ( version != null)
+ dcs.setVersion(version);
+
+ return dcs;
+ }
+
+ public void startElement (String uri, String name, String qName, Attributes atts){
+ //System.out.println("new element "+qName);
+
+ if (qName.equals("SOURCE")) {
+ //System.out.println("new Source " + atts.getValue(uri));
+ currentSource = new Das2SourceImpl();
+ coordinates = new ArrayList();
+ capabilities = new ArrayList();
+
+ startSource(uri,name, qName, atts);
+
+ } else if ( qName.equals("MAINTAINER")){
+ String email = atts.getValue("email");
+ currentSource.setAdminemail(email);
+ } else if ( qName.equals("COORDINATES")){
+ DasCoordinateSystem dcs = getCoordinateSystem(uri,name,qName,atts);
+ coordinates.add(dcs);
+
+ } else if ( qName.equals("CAPABILITY")){
+ Das2Capability cap = getCapability(uri,name,qName,atts);
+ capabilities.add(cap);
+ }
+
+ //TODO: add support for "labels"
+
+ }
+
+ private Das2Capability getCapability(String uri, String name, String qName, Attributes atts){
+ // e.g <CAPABILITY type="features" query_id="http://das.biopackages.net/das/genome/yeast/S228C/feature" />
+ Das2Capability cap = new Das2CapabilityImpl();
+
+ String type = atts.getValue("type");
+ cap.setCapability(type);
+ String query_uri = atts.getValue("query_uri");
+ cap.setQueryUri(query_uri);
+ return cap;
+
+ }
+
+ public void startDocument(){
+ sources = new ArrayList();
+ coordinates = new ArrayList();
+ capabilities = new ArrayList();
+ }
+
+ public void endElement(String uri, String name, String qName) {
+ if ( qName.equals("SOURCE")) {
+ currentSource.setDas2Capabilities((Das2Capability[])capabilities.toArray(new Das2Capability[capabilities.size()]));
+ //System.out.println("got coordinates " + coordinates.size());
+ currentSource.setCoordinateSystem((DasCoordinateSystem[])coordinates.toArray(new DasCoordinateSystem[coordinates.size()]));
+ //System.out.println("Das2SourceHandler endElement name " + name + " uri " + uri + " qName " + qName);
+ //System.out.println("Das2SourceHandler adding to source: " + currentSource.getId());
+ sources.add(currentSource);
+ currentSource = new Das2SourceImpl();
+ }
+ }
+
+ public DasSource[] getSources(){
+ //System.out.println("Das2SourceHandler: source size: " + sources.size());
+ return (DasSource[])sources.toArray(new DasSource[sources.size()]);
+ }
+
+
+
+}
--- /dev/null
+/*
+ * 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();
+ }
+
+ }
+
+
+
+}
git://source.jalview.org / jalview.git / commitdiff