[MOBY-guts] biomoby commit

[Gary Schiltz]

gss
Mon Mar 21 16:32:38 EST 2005
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/parser
In directory pub.open-bio.org:/tmp/cvs-serv8465/src/org/semanticmoby/parser

Modified Files:
	Parser.java 
Log Message:
Fixed to use new org.semanticmoby.graph.* signatures

moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/parser Parser.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/parser/Parser.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/parser/Parser.java	2004/11/23 00:18:46	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/parser/Parser.java	2005/03/21 21:32:38	1.2
@@ -5,17 +5,16 @@
 import java.util.*;
 
 import org.semanticmoby.graph.*;
-import org.semanticmoby.parser.*;
-import org.semanticmoby.tools.ModelRetriever;
-import org.semanticmoby.tools.Util;
+import org.semanticmoby.tools.*;
 import org.semanticmoby.vocabulary.*;
 
 import com.hp.hpl.jena.rdf.model.*;
 import com.hp.hpl.jena.vocabulary.*;
 
 /**
- * This class is used to parse OWL models, stored as Jena2 models, into
- * objects that implement interfaces from the org.semanticmoby.graph package.
+ * This class is used to parse RDF models, stored as Jena2 models, into
+ * objects that implement interfaces from the org.semanticmoby.graph
+ * package.
  */
 public class Parser
 {
@@ -186,7 +185,7 @@
         
         // Create and return an unordered collection of the parsed providers
         //
-        return new MOBYUnorderedCollection(null, providers, null);
+        return new MOBYUnorderedCollection(providers, null, null);
     }
     
     /**
@@ -199,9 +198,9 @@
     	
         // First parse the scalar properties name, oneLineDescription, and aboutURI
         //
-        String name 	= getDataPropertyValue(provider, MOBY.name);
-        String oneLiner = getDataPropertyValue(provider, MOBY.oneLineDescription);
-        String aboutURI = getDataPropertyValue(provider, MOBY.aboutURI);
+        Statement nameStmt = model.getProperty(provider, MOBY.name);
+        Statement oneLineDescriptionStmt = model.getProperty(provider, MOBY.oneLineDescription);
+        Statement aboutURIStmt = model.getProperty(provider, MOBY.aboutURI);
         
         // A provider can have multiple operatesOn properties, each of
         // which leads to a subgraph. Parse each of these subgraphs.
@@ -219,8 +218,8 @@
         // oneLineDescription, aboutURI, and collection of operatesOn subgraphs
         //
         return new MOBYProvider(
-            provider, name, oneLiner, aboutURI,
-            new MOBYUnorderedCollection(provider, operatesOn, model),
+            provider, nameStmt, oneLineDescriptionStmt, aboutURIStmt,
+            new MOBYUnorderedCollection(operatesOn, provider, model),
             model);
     }
     
@@ -326,16 +325,16 @@
         // Create and return a Subject to describe this hasMapping subgraph
         //
         return new MOBYSubject(res,
-            new MOBYFixedCollection(res, statements, model),
-            new MOBYUnorderedCollection(res, directMappings, model),
+            new MOBYFixedCollection(statements, res, model),
+            new MOBYUnorderedCollection(directMappings, res, model),
             collectionFor(res, nestedMappings),
             model);
     }
 
     
     /**
-     * Parse the object of a mapsTo statement, which should be a
-     * Subject, a data structure, or both. If the object is a data
+     * Parse the object of a mapsTo statement, which should be an
+     * Object, a data structure, or both. If the object is a data
      * structure, then each element of the data structure should
      * be a mapped subgraph.
      */
@@ -370,7 +369,7 @@
         //
         Model model = res.getModel();
         return new MOBYObject(res,
-            new MOBYFixedCollection(res, statements, model),
+            new MOBYFixedCollection(statements, res, model),
             collectionFor(res, nested), model);
     }
     
@@ -462,12 +461,6 @@
 			model.contains(p, RDFS.subPropertyOf, MOBY.Property);
     }
     
-    private String getDataPropertyValue(Resource subject, Property property)
-    {
-        Statement s = subject.getModel().getProperty(subject, property);
-        return (s == null) ? null : s.getObject().toString();
-    }
-    
     private Resource getResourcePropertyValue(Resource subject, Property property)
     {
         Statement s = subject.getModel().getProperty(subject, property);
@@ -500,13 +493,13 @@
     private MOBYCollection collectionFor(Resource res, List elements)
     {
         if (isList(res)) {
-            return new MOBYFixedCollection(res, elements, res.getModel());
+            return new MOBYFixedCollection(elements, res, res.getModel());
         } else if (isBag(res)) {
-            return new MOBYUnorderedCollection(res, elements, res.getModel());
+            return new MOBYUnorderedCollection(elements, res, res.getModel());
         } else if (isSeq(res)) {
-            return new MOBYOrderedCollection(res, elements, res.getModel());
+            return new MOBYOrderedCollection(elements, res, res.getModel());
         } else if (isAlt(res)) {
-            return new MOBYEnumeration(res, elements, res.getModel());
+            return new MOBYEnumeration(elements, res, res.getModel());
         } else {
             return null;
         }