[Gmod-apollo-cmts] SF.net SVN: gmod:[22510] apollo/trunk/src/java/apollo/analysis

[<gk...@us...>]

Revision: 22510
          http://gmod.svn.sourceforge.net/gmod/?rev=22510&view=rev
Author:   gk_fan
Date:     2010-01-08 17:12:13 +0000 (Fri, 08 Jan 2010)

Log Message:
-----------
Changed XML parsing of BLAST results to use URIs instead of InputStreams, as it was causing errors in Java Web Start mode.

Modified Paths:
--------------
    apollo/trunk/src/java/apollo/analysis/BlastXMLParser.java
    apollo/trunk/src/java/apollo/analysis/BlastXMLParserTest.java
    apollo/trunk/src/java/apollo/analysis/RemoteBlastNCBI.java

Modified: apollo/trunk/src/java/apollo/analysis/BlastXMLParser.java
===================================================================
--- apollo/trunk/src/java/apollo/analysis/BlastXMLParser.java	2010-01-08 16:53:07 UTC (rev 22509)
+++ apollo/trunk/src/java/apollo/analysis/BlastXMLParser.java	2010-01-08 17:12:13 UTC (rev 22510)
@@ -1,8 +1,6 @@
 package apollo.analysis;
 
 import java.io.IOException;
-import java.io.InputStream;
-import java.io.StringReader;
 
 import javax.xml.parsers.DocumentBuilder;
 import javax.xml.parsers.DocumentBuilderFactory;
@@ -12,8 +10,6 @@
 import org.w3c.dom.Element;
 import org.w3c.dom.Node;
 import org.w3c.dom.NodeList;
-import org.xml.sax.EntityResolver;
-import org.xml.sax.InputSource;
 import org.xml.sax.SAXException;
 
 import apollo.datamodel.FeaturePair;
@@ -44,23 +40,17 @@
   {
     DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
     db = dbf.newDocumentBuilder();
-    db.setEntityResolver(new EntityResolver() {
-      public InputSource resolveEntity(String publicId, String systemId)
-      {
-        return new InputSource(new StringReader(""));
-      }
-    });
   }
   
-  public String parse(InputStream is, StrandedFeatureSetI results) throws SAXException, IOException, BlastXMLParserException
+  public String parse(String uri, StrandedFeatureSetI results) throws SAXException, IOException, BlastXMLParserException
   {
-    return parse(is, results, 1, 0, 0);
+    return parse(uri, results, 1, 0, 0);
   }
   
-  public String parse(InputStream is, StrandedFeatureSetI results, int strand, int genomicLength, int offset) throws
+  public String parse(String uri, StrandedFeatureSetI results, int strand, int genomicLength, int offset) throws
   SAXException, IOException, BlastXMLParserException
   {
-    Document doc = db.parse(is);
+    Document doc = db.parse(uri);
     String blast = getTextContent(doc.getElementsByTagName("BlastOutput_program").item(0));
     String db = getTextContent(doc.getElementsByTagName("BlastOutput_db").item(0));
     String type = blast + ":" + db;

Modified: apollo/trunk/src/java/apollo/analysis/BlastXMLParserTest.java
===================================================================
--- apollo/trunk/src/java/apollo/analysis/BlastXMLParserTest.java	2010-01-08 16:53:07 UTC (rev 22509)
+++ apollo/trunk/src/java/apollo/analysis/BlastXMLParserTest.java	2010-01-08 17:12:13 UTC (rev 22510)
@@ -1,13 +1,7 @@
 package apollo.analysis;
 
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.IOException;
+import java.io.File;
 
-import javax.xml.parsers.ParserConfigurationException;
-
-import org.xml.sax.SAXException;
-
 import apollo.datamodel.StrandedFeatureSet;
 
 import junit.framework.TestCase;
@@ -16,10 +10,10 @@
 
   public void testParse() throws Exception
   {
-    FileInputStream fis = new FileInputStream("/Users/elee/blah/blast_3.xml");
+    File f = new File("/Users/elee/blah/blast_3.xml");
     BlastXMLParser parser = new BlastXMLParser();
     StrandedFeatureSet results = new StrandedFeatureSet();
-    parser.parse(fis, results);
+    parser.parse(f.toURL().toString(), results);
   }
   
 }

Modified: apollo/trunk/src/java/apollo/analysis/RemoteBlastNCBI.java
===================================================================
--- apollo/trunk/src/java/apollo/analysis/RemoteBlastNCBI.java	2010-01-08 16:53:07 UTC (rev 22509)
+++ apollo/trunk/src/java/apollo/analysis/RemoteBlastNCBI.java	2010-01-08 17:12:13 UTC (rev 22510)
@@ -30,6 +30,7 @@
 
   private static final String ENCODING = "UTF-8";
   private static final String BLAST_URL = "http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?";
+  //private static final String BLAST_URL = "http://130.14.29.110/blast/Blast.cgi?";
   private static final int SLEEP = 3000;
   private static final Pattern RID_PATTERN = Pattern.compile("^\\s*RID\\s*=\\s*(\\w+)$");
   private static final Pattern RTOE_PATTERN = Pattern.compile("^\\s*RTOE\\s*=\\s*(\\d+)$");
@@ -285,13 +286,14 @@
     }
     is.close();
     getUrl = new URL(createGetUrl(req, false));
-    is = getUrl.openStream();
+    
+    //is = getUrl.openStream();
 
     BlastXMLParser parser = new BlastXMLParser();
 
-    String type = parser.parse(is, cs.getResults(), strand, genomicLength, offset);
+    String type = parser.parse(getUrl.toString(), cs.getResults(), strand, genomicLength, offset);
     
-    is.close();
+    //is.close();
     
     if (cs.getResults().getForwardSet() != null) {
       System.out.println("forward hits: " + cs.getResults().getForwardSet().size());


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.