[MOBY-guts] biomoby commit

[Paul Gordon]

gordonp
Mon Dec 17 13:39:30 EST 2007
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services
In directory dev.open-bio.org:/tmp/cvs-serv6107/src/main/ca/ucalgary/seahawk/services

Modified Files:
	MobyComplexBuilder.java 
Log Message:
Changed registry spec source from SeahawkOptions to parent MobyClient
moby-live/Java/src/main/ca/ucalgary/seahawk/services MobyComplexBuilder.java,1.13,1.14
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/MobyComplexBuilder.java,v
retrieving revision 1.13
retrieving revision 1.14
diff -u -r1.13 -r1.14
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/MobyComplexBuilder.java	2007/12/06 23:46:34	1.13
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/MobyComplexBuilder.java	2007/12/17 18:39:30	1.14
@@ -1,7 +1,5 @@
 package ca.ucalgary.seahawk.services;
 
-import ca.ucalgary.seahawk.util.SeahawkOptions;
-
 import org.biomoby.shared.*;
 import org.biomoby.shared.data.MobyDataBytes;
 import org.biomoby.shared.data.MobyDataComposite;
@@ -50,7 +48,7 @@
     }
 
     public MobyComplexBuilder(String dataType, Map<String,String[]> members, Map<String,String> nameSpaces, MobyClient cl, String articleName) throws Exception{
-	mobyDataType = MobyDataType.getDataType(dataType, SeahawkOptions.getRegistry());
+	mobyDataType = MobyDataType.getDataType(dataType, cl.getRegistry());
 	// Not an existing Ontology data type
 	if(mobyDataType == null){
 	    mobyDataType = new MobyDataType(dataType);
@@ -114,9 +112,9 @@
 		    MobyRelationship child = mobyDataType.getChild(member.getKey());
 		    String defaultDataTypeName = child.getDataTypeName();
 		    MobyDataType castType = MobyDataType.getDataType(memberDataTypeSetting, 
-								     SeahawkOptions.getRegistry());
+								     client.getRegistry());
 		    MobyDataType origType = MobyDataType.getDataType(defaultDataTypeName, 
-								     SeahawkOptions.getRegistry());
+								     client.getRegistry());
 		    if(castType == null){
 			System.err.println("Could not find the data type "+memberDataTypeSetting+
 					   " in the ontology, ignoring the data type cast"+
@@ -152,7 +150,7 @@
 		String ns = (String) iter.next();
 
 		// Give the namespace a meaningful description from the MOBY registry
-		mobyNS[i] = MobyNamespace.getNamespace(ns, SeahawkOptions.getRegistry());
+		mobyNS[i] = MobyNamespace.getNamespace(ns, client.getRegistry());
 		if(mobyNS[i] == null){
 		    System.err.println("Namespace '"+ns+"' is not registered in MOBY Central");
 		    // Not a registered namespace in MOBY Central's ontology
@@ -170,9 +168,9 @@
 	MobyDataObject mobyObj = null;
 	
 	if(mobyDataType.getName().equals("Object")){
-	    mobyObj = new MobyDataObject("", SeahawkOptions.getRegistry());
+	    mobyObj = new MobyDataObject("", client.getRegistry());
 	}
-	else if(mobyDataType.inheritsFrom(MobyDataType.getDataType(MobyDataBytes.BASE64_DATATYPE, SeahawkOptions.getRegistry()))){
+	else if(mobyDataType.inheritsFrom(MobyDataType.getDataType(MobyDataBytes.BASE64_DATATYPE, client.getRegistry()))){
 	    mobyObj = new MobyDataBytes("", (String) null);
 	    mobyObj.setDataType(mobyDataType);
 	}
@@ -212,7 +210,7 @@
 		    }
 		    else{
 			// ... the subsequent ones are saved as cross-references
-			mobyObj.addCrossReference(new MobyDataObject(mobyNS[i].getName(), result, SeahawkOptions.getRegistry()));
+			mobyObj.addCrossReference(new MobyDataObject(mobyNS[i].getName(), result, client.getRegistry()));
 		    }
 		}
 	    }
@@ -286,9 +284,9 @@
 	    for(String result: results){
 		
 		if(PrimitiveTypes.isPrimitive(dataTypeName) ||
-		   MobyDataType.getDataType(dataTypeName, SeahawkOptions.getRegistry()).inheritsFrom(MobyDataType.getDataType(MobyDataBytes.BASE64_DATATYPE, SeahawkOptions.getRegistry()))){
+		   MobyDataType.getDataType(dataTypeName, client.getRegistry()).inheritsFrom(MobyDataType.getDataType(MobyDataBytes.BASE64_DATATYPE, client.getRegistry()))){
 		    ((MobyDataComposite) mobyObj).put(memberName, 
-						      MobyDataObject.createInstanceFromString(dataTypeName, result, SeahawkOptions.getRegistry()));
+						      MobyDataObject.createInstanceFromString(dataTypeName, result, client.getRegistry()));
 		}
 		else{
 		    // Recursively call the object creator for complex members
@@ -501,7 +499,7 @@
 	MobyDataObject mobyObj = null;
 	
 	if(mobyDataType.getName().equals("Object")){
-	    mobyObj = new MobyDataObject("", SeahawkOptions.getRegistry());
+	    mobyObj = new MobyDataObject("", client.getRegistry());
 	}
 	// else ifs for other primitives in the future maybe?
 	else{
@@ -526,7 +524,7 @@
 		    }
 		    else{
 			// ... the subsequent ones are saved as cross-references
-			mobyObj.addCrossReference(new MobyDataObject(mobyNS[i].getName(), value, SeahawkOptions.getRegistry()));
+			mobyObj.addCrossReference(new MobyDataObject(mobyNS[i].getName(), value, client.getRegistry()));
 		    }
 		}
 	    }
@@ -541,7 +539,7 @@
 		    String value = xpath.evaluate(expr, result);
 
 		    ((MobyDataComposite) mobyObj).put(memberName, 
-						      MobyDataObject.createInstanceFromString(children[i].getDataTypeName(), value, SeahawkOptions.getRegistry()));
+						      MobyDataObject.createInstanceFromString(children[i].getDataTypeName(), value, client.getRegistry()));
 		}
 	    }
 	}