[MOBY-guts] biomoby commit

[Paul Gordon]

gordonp
Tue Jun  9 15:01:19 EDT 2009
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared
In directory dev.open-bio.org:/tmp/cvs-serv19780/src/main/org/biomoby/shared

Modified Files:
	LSIDResolver.java 
Log Message:
Logging support, fallback in case DNS not accessible, and temporary reliance on Apache XPath rather than JAX-T due to Google App Engine bug
moby-live/Java/src/main/org/biomoby/shared LSIDResolver.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/LSIDResolver.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/LSIDResolver.java	2008/06/30 21:22:08	1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/LSIDResolver.java	2009/06/09 19:01:19	1.3
@@ -14,6 +14,7 @@
 import java.io.*;
 import java.net.URL;
 import java.util.*;
+import java.util.logging.*;
 import java.util.regex.*;
 
 /**
@@ -47,12 +48,17 @@
     public static final String LSID_HTTP_NAMESPACE = "http://www.omg.org/LSID/2003/AuthorityServiceHTTPBindings";
     public static final String LSID_SOAP_NAMESPACE = "http://www.omg.org/LSID/2003/AuthorityServiceSOAPBindings";
     public static final String LSID_WSDL_NAMESPACE = "http://www.omg.org/LSID/2003/Standard/WSDL";
+    private boolean warnedOfDNSAccess = false;
+
+    private static Logger logger = Logger.getLogger(LSIDResolver.class.getName());    
 
     private XPath xPath;
     private DocumentBuilder docBuilder;
 
     public LSIDResolver(){
-        XPathFactory xPathFactory = XPathFactory.newInstance();
+        //PG Temporarily use xalan while Google App Engine XPath bug exists
+        //XPathFactory xPathFactory = XPathFactory.newInstance();
+        XPathFactory xPathFactory = new org.apache.xpath.jaxp.XPathFactoryImpl();
 	try{
 	    xPath = xPathFactory.newXPath();
 	    xPath.setNamespaceContext(new NamespaceContextImpl());
@@ -81,7 +87,22 @@
 				"cannot extract the lookup authority.");
 	}
 
-	Record[] records = new Lookup(SRV_PREFIX + lsidAuthority, Type.SRV).run();
+	Record[] records = null;
+	try{
+	    records = new Lookup(SRV_PREFIX + lsidAuthority, Type.SRV).run();
+	} catch(Throwable t){
+	    // If we can't access DNA resources (e.g. in a restricted environment 
+	    // such as an applet or Google App Engine), do a last ditch guess
+	    // as to the location of the server rather than using the second well-known rule
+	    if(!warnedOfDNSAccess){
+		warnedOfDNSAccess = true;
+		logger.log(Level.WARNING, "Cannot access DNS SRV records for LSID resolution, will use hostname directly", t);
+	    }
+	    return new URL("http", 
+			   lsidAuthority, 
+			   80, 
+			   AUTHORITY_WSDL_LOCATION);
+	}
 	if(records == null || records.length == 0){
 	    throw new Exception("While trying to use LSID resolution's Second Well-Known Rule: " +
 				" The authority for the lsid (" + lsidAuthority + 
@@ -281,7 +302,7 @@
 	NodeList addrs = es[0].getElementsByTagNameNS(MobyPrefixResolver.HTTP_NAMESPACE, "address");
 	if(addrs == null || addrs.getLength() == 0){
 	    throw new Exception("Could not find the definition of the HTTP address within " +
-				"the WSDL's LSIDMetadataHTTPBinding spec");
+				"the WSDL's LSIDMetadataHTTPBinding spec, maybe a non-existant LSID? (" + lsid + ")");
 	}
 	else{
 	    // baseURL is a bad assumption, as the node may be from an import in another location