[MOBY-guts] biomoby commit

[Gary Schlitz]

gss
Wed May 19 19:33:05 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets
In directory pub.open-bio.org:/tmp/cvs-serv2250/src/com/acmepubs/servlets

Modified Files:
	CitationSearchServlet.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets CitationSearchServlet.java,1.8,1.9
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java	2004/05/19 18:26:52	1.8
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java	2004/05/19 23:33:05	1.9
@@ -7,6 +7,7 @@
 import org.go.vocabulary.*;
 import org.smoby.servlet.*;
 import org.smoby.graph.*;
+import org.smoby.graph.impl.MOBYObjectFactory;
 import org.smoby.vocabulary.*;
 import com.acmepubs.vocabulary.*;
 
@@ -35,47 +36,54 @@
      * a gene symbol and returning a URL for querying the
      * SGD database for literature pertaining to that URL.
      */
-    protected void handleRequest(MOBYProvider graph)
+    protected void handleRequest(MOBYProvider provider)
     {
-        // Retrieve the subject of the moby:operatesOn statement (there is only
-    	// one operatesOn statement in a valid MOBY graph)
-        //
-//        Resource mobyGraphSubject = (Resource) graph.getOperatesOnStmt().getObject();
-//        
-//        // There may be multiple moby:hasMapping statements. For each one,
-//        // map its geneSymbol to a literatureGuideURL
-//        //
-//        StmtIterator it = graph.getModel().listStatements(
-//        		mobyGraphSubject, MOBY.hasMapping, (RDFNode) null);
-//        
-//        while (it.hasNext())
-//        {
-//    		try
-//			{
-//	        	Statement hasMappingStmt = it.nextStatement();
-//	        	Resource mobySubject = (Resource) hasMappingStmt.getObject();
-//	        	
-//	        	Statement geneSymbolStmt =
-//	        		getFirstStatement(graph, mobySubject, AcmePubs.geneSymbol, null);
-//	        	
-//    			String geneSymbol = geneSymbolStmt.getString();
-//    			
-//    			Statement mapsToStmt = 
-//    				getFirstStatement(graph, mobySubject, MOBY.mapsTo, null);
-//    			
-//				Resource mobyObject = (Resource) mapsToStmt.getObject();
-//				
-//				Statement literatureGuideURLStmt =
-//					getFirstStatement(graph, mobyObject, AcmePubs.literatureGuideURL, null);
-//				
-//				String baseURI = "http://db.yeastgenome.org/cgi-bin/SGD/reference/geneinfo.pl?locus=";
-//				literatureGuideURLStmt.changeObject(baseURI + geneSymbol);
-//        	}
-//    		catch (Throwable t)
-//			{
-//    			// Something went wrong, so proceed to next hasMapping statement
-//    		}
-//        }
+        try
+        {
+            // There should be only one operatesOn subgraph, which should be
+            // a collection of MOBYGraph objects.
+            //
+            MOBYCollection coll = (MOBYCollection)
+            	provider.getOperatesOn().iterator().next();
+            
+            // Iterate over the MOBYGraph objects
+            //
+            Iterator it = coll.iterator();
+            while (it.hasNext())
+            {
+                MOBYGraph graph = (MOBYGraph) it.next();
+                
+                // The subject of the graph should be a MOBYSubject
+                //
+                MOBYSubject subject = (MOBYSubject) graph.gethasMapping();
+                
+                // That object should have a single subproperty of moby:Property,
+                // namely geneSymbol; its value should be a literal
+                //
+                MOBYPropertyValueStatement stmt = (MOBYPropertyValueStatement)
+                    subject.getPropertyValueStatements().iterator().next();
+                MOBYLiteral literal = (MOBYLiteral) stmt.getValue();
+                String geneSymbol = literal.getStringValue();
+                
+                // The object of the MOBYSubject should be a MOBYObject. That
+                // object should have a single subproperty of moby:Property,
+                // namely literatureGuideURL
+                //
+                MOBYObject object = (MOBYObject)
+                	subject.getDirectMappings().iterator().next();
+                stmt = (MOBYPropertyValueStatement)
+                	object.getPropertyValueStatements().iterator().next();
+                
+                // Set the value of the literatureGuideURL to a literal value
+                // based on a base URI string and the geneSymbol that was passed
+                //
+                String baseURI = "http://db.yeastgenome.org/cgi-bin/SGD/reference/geneinfo.pl?locus=";
+                literal = MOBYObjectFactory.newLiteralValue(
+                        baseURI + geneSymbol);
+                stmt.setPropertyValue(literal);
+            }
+        }
+        catch (Throwable t) {System.out.println(t);} // No feedback on failure...
     }
     
     /**