[MOBY-guts] biomoby commit

[Paul Gordon]

gordonp
Mon Apr  2 22:29:54 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services
In directory dev.open-bio.org:/tmp/cvs-serv6718/src/main/ca/ucalgary/seahawk/services

Modified Files:
	MobyClient.java 
Log Message:
Flanking whitespace processing for rules, plus disabled isAlive() check until we can do it more efficiently
moby-live/Java/src/main/ca/ucalgary/seahawk/services MobyClient.java,1.7,1.8
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/MobyClient.java,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/MobyClient.java	2007/03/21 16:23:43	1.7
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/MobyClient.java	2007/04/03 02:29:54	1.8
@@ -54,6 +54,7 @@
     public static final String WHITESPACE_ATTR = "whitespace";
     public static final String WHITESPACE_ATTR_STRIP_VAL = "strip";
     public static final String WHITESPACE_ATTR_NORMALIZE_VAL = "normalize";
+    public static final String WHITESPACE_ATTR_STRIP_FLANKING_VAL = "flanking";
     public static final String WHITESPACE_ATTR_KEEP_VAL = "keep";
     public static final String ENCODING_ATTR = "encoding";
     public static final String ENCODING_ATTR_BASE64_VAL = "Base64";
@@ -395,10 +396,12 @@
 	}
 	else if(!memberWhitespaceSetting.equals(WHITESPACE_ATTR_KEEP_VAL) &&
 		!memberWhitespaceSetting.equals(WHITESPACE_ATTR_NORMALIZE_VAL) &&
+		!memberWhitespaceSetting.equals(WHITESPACE_ATTR_STRIP_FLANKING_VAL) &&
 		!memberWhitespaceSetting.equals(WHITESPACE_ATTR_STRIP_VAL)){
 	    System.err.println("Object member " + memberNameKey + 
 			       " has an unrecognized value for the " + WHITESPACE_ATTR +
-			       " attribute, overriding with default of " + WHITESPACE_ATTR_KEEP_VAL);
+			       " attribute (" + memberWhitespaceSetting + 
+			       "), overriding with default of " + WHITESPACE_ATTR_KEEP_VAL);
 	    memberWhitespaceSetting = WHITESPACE_ATTR_KEEP_VAL;
 	}
 	String memberEncodingSetting = memTag.getAttribute(ENCODING_ATTR);
@@ -890,16 +893,20 @@
 	for(int i = 0; i < mdos.length; i++){
 	    MobyService templateServices = new MobyService("");
 	    templateServices.addInput(mdos[i]);
+	    // Normally category is "moby", which excludes async services. 
+	    // Turn it into a wildcard instead by making the template category blank
+	    templateServices.setCategory(""); 
 	    MobyService[] mService = c.findService(templateServices);
 
 	    Vector<MobyService> filteredServices = new Vector();
 	    // Let's make sure all of the services have their service type properly instantiated
 	    // for ontology checks later on
 	    for(int j = 0; j < mService.length; j++){
-		MobyService service = MobyService.getService(mService[j].getName(), mService[j].getAuthority());
-		if(service != null){
-		    mService[j] = service;
-		}
+ 		// Paul: commenting out is temporary until we can fetch the services more quickly
+		//MobyService service = MobyService.getService(mService[j].getName(), mService[j].getAuthority());
+ 		//if(service != null){
+		//mService[j] = service;
+ 		//}
 
 		mService[j].setServiceType(MobyServiceType.getServiceType(mService[j].getServiceType().getName()));
 		if(serviceLevel != MobyService.UNCHECKED){
@@ -911,7 +918,8 @@
 		}
 	    }
 
-	    if(serviceLevel != MobyService.UNCHECKED){
+	    // Paul: false is temporary until we can fetch the services more quickly (and check isAlive)
+	    if(false && serviceLevel != MobyService.UNCHECKED){
 		mService = (MobyService []) filteredServices.toArray(new MobyService[filteredServices.size()]);
 	    }