From gordonp at dev.open-bio.org  Thu Apr  8 22:23:15 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Thu, 8 Apr 2010 22:23:15 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004090223.o392NFDP006711@dev.open-bio.org>


gordonp
Thu Apr  8 22:23:15 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources/images
In directory dev.open-bio.org:/tmp/cvs-serv6679/src/main/ca/ucalgary/seahawk/resources/images

Added Files:
	case_insensitive.png case_sensitive.png 
Log Message:
Icon for search filter's case sensitivity
moby-live/Java/src/main/ca/ucalgary/seahawk/resources/images case_insensitive.png,NONE,1.1 case_sensitive.png,NONE,1.1

From gordonp at dev.open-bio.org  Fri Apr  9 11:47:04 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 9 Apr 2010 11:47:04 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004091547.o39Fl4m3001186@dev.open-bio.org>


gordonp
Fri Apr  9 11:47:03 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources
In directory dev.open-bio.org:/tmp/cvs-serv1154/src/main/ca/ucalgary/seahawk/resources

Added Files:
	PassFilterBeanShell FlattenListBeanShell 
Log Message:
Taverna beanshells used in Seahawk's programming-by-example system
moby-live/Java/src/main/ca/ucalgary/seahawk/resources PassFilterBeanShell,NONE,1.1 FlattenListBeanShell,NONE,1.1

From gordonp at dev.open-bio.org  Fri Apr  9 11:48:19 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 9 Apr 2010 11:48:19 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004091548.o39FmJJf001286@dev.open-bio.org>


gordonp
Fri Apr  9 11:48:19 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util
In directory dev.open-bio.org:/tmp/cvs-serv1250/src/main/ca/ucalgary/seahawk/util

Modified Files:
	FilterSearch.java 
Log Message:
Added case sensitivity, constant for select-all xpath
moby-live/Java/src/main/ca/ucalgary/seahawk/util FilterSearch.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/FilterSearch.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/FilterSearch.java	2010/03/29 19:49:52	1.2
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/FilterSearch.java	2010/04/09 15:48:19	1.3
@@ -20,9 +20,11 @@
 public class FilterSearch{
 
     private URL docURL;
+    private boolean caseSensitivity = false;
     private StringBuffer filterRegex;
     private Vector<XPathOption> xpathOptions;
     private int xpathSelected = 0;
+    public static final String SELECT_ALL_XPATH = "//* | //*/@*";
 
     /**
      * @param docToFilter the document that will be used to determine what XPaths can be suggested
@@ -34,7 +36,7 @@
 	docURL = docToFilter;
 	filterRegex = new StringBuffer();
 	xpathOptions = new Vector<XPathOption>();
-	xpathOptions.add(new XPathOption("//*", "entire document"));
+	xpathOptions.add(new XPathOption(SELECT_ALL_XPATH, "entire response"));
 	Document domDoc = docBuilder.parse(docURL.openStream());
 	// Get the moby jobs
 	NodeList jobs = domDoc.getDocumentElement().getElementsByTagNameNS(MobyPrefixResolver.MOBY_XML_NAMESPACE, MobyTags.MOBYDATA);
@@ -72,6 +74,14 @@
 	}
     }
 
+    public boolean getCaseSensitivity(){
+	return caseSensitivity;
+    }
+
+    public void setCaseSensitivity(boolean sensitivity){
+	caseSensitivity = sensitivity;
+    }
+
     public void setSelectedXPath(int cursor){
 	xpathSelected = cursor;
     }


From gordonp at dev.open-bio.org  Fri Apr  9 11:49:18 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 9 Apr 2010 11:49:18 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004091549.o39FnI8b001330@dev.open-bio.org>


gordonp
Fri Apr  9 11:49:18 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources
In directory dev.open-bio.org:/tmp/cvs-serv1294/src/main/ca/ucalgary/seahawk/resources

Modified Files:
	RegexFilterBeanShell 
Log Message:
Added case sensitivity, eliminated auto-attr matching since select-all xpath has been fixed
moby-live/Java/src/main/ca/ucalgary/seahawk/resources RegexFilterBeanShell,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources/RegexFilterBeanShell,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources/RegexFilterBeanShell	2010/03/17 20:03:06	1.1
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources/RegexFilterBeanShell	2010/04/09 15:49:18	1.2
@@ -1,4 +1,5 @@
 import java.util.*;
+import java.util.regex.Pattern;
 import org.dom4j.*;
 import org.dom4j.io.SAXReader;
 
@@ -13,24 +14,18 @@
 int i = 1;
 Map collections = new LinkedHashMap();
 Map collectionsEnd = new HashMap();
-select: for (Iterator iter = nodelist.iterator(); iter.hasNext();) {
+Pattern pattern = Pattern.compile(regex, Pattern.MULTILINE | Pattern.DOTALL | (Boolean.parseBoolean(case_sensitive) ? 0 : Pattern.CASE_INSENSITIVE));
+for (Iterator iter = nodelist.iterator(); iter.hasNext();) {
         Node node = (Node) iter.next();
         boolean match = false;
         switch(node.getNodeType()){
                 case Node.ELEMENT_NODE:
-                        if(node.getText().matches(".*?"+regex+".*")){
+                        if(pattern.matcher(node.getText()).find()){
                                 match = true;
                         }
-                        else{
-                                for(Object attr: ((Element) node).attributeIterator()){
-                                        if(((Attribute) attr).getValue().matches(".*?"+regex+".*")){
-                                                match = true; break;
-                                        }
-                                }
-                        }
                         break;
                 case Node.ATTRIBUTE_NODE:
-                        if(node.getValue().matches(".*?"+regex+".*")){
+                        if(pattern.matcher(node.getValue()).find()){
                                 match = true;
                         }
                         break;


From gordonp at dev.open-bio.org  Fri Apr  9 11:50:09 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 9 Apr 2010 11:50:09 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004091550.o39Fo903001396@dev.open-bio.org>


gordonp
Fri Apr  9 11:50:09 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv1360/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	FilterSearchWidget.java 
Log Message:
Added case sensitivity
moby-live/Java/src/main/ca/ucalgary/seahawk/gui FilterSearchWidget.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/FilterSearchWidget.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/FilterSearchWidget.java	2010/03/17 20:20:47	1.1
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/FilterSearchWidget.java	2010/04/09 15:50:09	1.2
@@ -17,9 +17,13 @@
 
     private FilterSearch currentFilterSearch;
     private JLabel closeIcon;
+    private JToggleButton caseButton;
     private JTextField searchField;
     private JComboBox docPartOptions;
     private MobyContentPane contentPane;
+    public static final String CASE_SENSITIVE_ICON_RESOURCE = "ca/ucalgary/seahawk/resources/images/case_sensitive.png";
+    public static final String CASE_INSENSITIVE_ICON_RESOURCE = "ca/ucalgary/seahawk/resources/images/case_insensitive.png";
+    private static final String CASE_BUTTON_NAME = "case_sensitivity_button"; 
 
     private static Logger logger = Logger.getLogger(FilterSearchWidget.class.getName());
 
@@ -27,7 +31,8 @@
 	super();
 
 	contentPane = mcp;
-	URL u = Thread.currentThread().getContextClassLoader().getResource(CloseTabIcon.CLOSE_TAB_ICON_RESOURCE);
+	ClassLoader cl = Thread.currentThread().getContextClassLoader();
+	URL u = cl.getResource(CloseTabIcon.CLOSE_TAB_ICON_RESOURCE);
 	if(u == null){
 	    throw new Exception("Could not find icon resource " + CloseTabIcon.CLOSE_TAB_ICON_RESOURCE);
 	}
@@ -37,9 +42,22 @@
 	closeIcon.addMouseListener(new Closer(this));
 	closeIcon.setToolTipText("Remove filter criteria");
 
+	Dimension buttonSize = new Dimension(24,24);
+	caseButton = new JToggleButton(new ImageIcon(cl.getResource(CASE_SENSITIVE_ICON_RESOURCE)));
+	caseButton.setDisabledIcon(new ImageIcon(cl.getResource(CASE_INSENSITIVE_ICON_RESOURCE)));
+	caseButton.setToolTipText("Toggles the case sensitivity of the filter");
+	caseButton.setPreferredSize(buttonSize);
+	caseButton.setEnabled(true);
+	caseButton.setSelected(false);
+	caseButton.addActionListener(this);
+	caseButton.setMargin(new java.awt.Insets(2,2,2,2));
+        caseButton.setName(CASE_BUTTON_NAME); // so test cases can find the component
+
 	setLayout(new BoxLayout(this, BoxLayout.LINE_AXIS));
 	add(closeIcon);
 	add(Box.createRigidArea(new Dimension(5,0)));
+	add(caseButton);
+	add(Box.createRigidArea(new Dimension(5,0)));
 	add(new JLabel("Show data if "));
 	add(Box.createRigidArea(new Dimension(5,0)));
 	searchField = new JTextField(25);
@@ -62,11 +80,15 @@
     public void setFilter(FilterSearch fs){
 	currentFilterSearch = null;
 	if(fs == null){
+	    caseButton.setEnabled(false);
 	    searchField.setEnabled(false);
 	    docPartOptions.setEnabled(false);
 	    return;
 	}
 
+	caseButton.setEnabled(true);
+	caseButton.setSelected(fs.getCaseSensitivity());
+
 	searchField.setEnabled(true);
 	searchField.setText(fs.getFilterRegex().toString());
 
@@ -79,7 +101,15 @@
      * Called when the user has changed the xpath
      */
     public void actionPerformed(ActionEvent e){
-	if(currentFilterSearch == null || e.getSource() != docPartOptions){
+	if(e.getSource() == caseButton){
+	    if(currentFilterSearch == null){
+	        return;
+            }
+            currentFilterSearch.setCaseSensitivity(caseButton.isSelected());
+	    contentPane.applyFilter(true);
+	    return;
+        }
+	else if(currentFilterSearch == null || e.getSource() != docPartOptions){
 	    return;
 	}
 	currentFilterSearch.setSelectedXPath(docPartOptions.getSelectedIndex());


From gordonp at dev.open-bio.org  Fri Apr  9 11:51:53 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 9 Apr 2010 11:51:53 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004091551.o39FprFb001496@dev.open-bio.org>


gordonp
Fri Apr  9 11:51:53 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv1460/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	MobyContentClipboard.java 
Log Message:
data xml src passthrough to enable 'previous input' services
moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyContentClipboard.java,1.8,1.9
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentClipboard.java,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentClipboard.java	2010/03/29 19:47:02	1.8
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentClipboard.java	2010/04/09 15:51:53	1.9
@@ -113,8 +113,8 @@
 	return false;
     }
 
-    protected void addExtraMobyOptions(JPopupMenu popup, MobyDataInstance mdi){
-	super.addExtraMobyOptions(popup, mdi);
+    protected void addExtraMobyOptions(JPopupMenu popup, MobyDataInstance mdi, URL srcURL){
+	super.addExtraMobyOptions(popup, mdi, srcURL);
 
 	// Only process if the passed in data is one of the top level collection elements
 	// (i.e. don't delete subparts of object)


From gordonp at dev.open-bio.org  Fri Apr  9 11:54:17 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 9 Apr 2010 11:54:17 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004091554.o39FsHP8001666@dev.open-bio.org>


gordonp
Fri Apr  9 11:54:16 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv1630/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	MobyContentPane.java 
Log Message:
Fixes to highlighting, added case sensitive search, added 'previous input' service options (equivalent to an if condition in PbE)
moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyContentPane.java,1.23,1.24
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java,v
retrieving revision 1.23
retrieving revision 1.24
diff -u -r1.23 -r1.24
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java	2010/03/29 19:54:36	1.23
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java	2010/04/09 15:54:16	1.24
@@ -107,6 +107,7 @@
     private Document currentDoc; //the doc DOM being actively filtered
     private NodeList currentSelectedData = null;
     private String currentSelectionXPath = null;
+    private Map<String,Boolean> jobXPtrs = null;  // Map<xptr,has a HAS member>
     private List<String> filterableNodes = null;  // List<xptr>
     private List<AttributeSet> origStyles = null;
     private boolean firstDocRendering = true;
@@ -442,9 +443,6 @@
 	    srv.addServlet(servletPath, servlet); // our deployment
 	}
 	else if(contentGUI.getServletContainer().getServlet(servletPath) == null){
-	    PBERecorder recorder = new PBERecorder();
-	    recorder.setGUIMap(id2GuiMap);
-	    servlet.setRecorder(recorder);
 	    contentGUI.getServletContainer().addServlet(servletPath, servlet); 
 	}
 
@@ -742,6 +740,7 @@
 	    currentDoc = null;  // get rid of previous in-memory doc use for interactive filtering, if any
 	    currentSelectedData = null;
 	    currentSelectionXPath = null;
+	    jobXPtrs = null;
 	    filterableNodes = null;
 	    origStyles = null;
 	    firstDocRendering = true;
@@ -774,6 +773,13 @@
 	return history.elementAt(historyIndex);
     }
 
+    protected URL getPreviousURL(){
+	if(historyIndex < 1 || historyIndex > history.size()){
+	    return null;
+	}
+	return history.elementAt(historyIndex-1);
+    }
+
     public boolean canFilter(){
 	return hasXMLSource();
     }
@@ -809,6 +815,7 @@
 		xPtrsReferencedInNextService = DataUtils.getInputXPtrs(history.elementAt(historyIndex+1), history.elementAt(historyIndex));
 	    } catch(Exception e){
 		logger.error("Cannot get the provenance data from "+history.elementAt(historyIndex+1), e);
+                return false;
 	    }
 	    
 	}
@@ -1187,7 +1194,8 @@
 	    return DataUtils.loadMobyDataFromXPointer(targetURL, filterHistory.get(getCurrentURL()));
 	}
 
-	// Simple case, build the object using the values encoded in the URL itself
+	// Simple case, build the object using the values encoded in the URL itself.
+	// Currently this is not used because it messes up provenance tracking for PbE
 	else{
 	    return loadMobyDataFromURLQuery(targetURL);
 	}
@@ -1204,7 +1212,7 @@
 
 	JPopupMenu popup = new DynamicJPopupMenu();
 	popup.setName(MOBY_SERVICE_POPUP_NAME);
-	addExtraMobyOptions(popup, mobyData);
+	addExtraMobyOptions(popup, mobyData, targetURL);
 	JMenuItem checkingLinksPopupItem = new JMenuItem("Check for services...");
 	popup.add(checkingLinksPopupItem);
 	popup.show(this, lastClickX+editorPane.getX(), lastClickY+editorPane.getY());
@@ -1223,7 +1231,7 @@
     /**
      * Subclasses can use this method to expand the popup menu.  Be sure to call super.addExtraMobyOptions()
      */
-    protected void addExtraMobyOptions(JPopupMenu popup, MobyDataInstance mdi){
+    protected void addExtraMobyOptions(JPopupMenu popup, MobyDataInstance mdi, URL srcURL){
 	// If we are wrapping a service, and you're getting the context menu, you must be 
 	// looking at service results, in which case let's give the option to create a service.
 	if(isWrapping){
@@ -1231,7 +1239,34 @@
 	    popup.add(createServicePopupItem);
 	    popup.setVisible(true);	    
 	}
+	// todo: 
+	// The item below is mainly to allow X to be used in service Y if running service Z on X meets some filter criteria.
+	// This is a common task in bioinformatics workflows.
+	// Backtrack from data to input used for service that generated the data.
+
+	// Here's an important point: if there is no filter on the current doc, we shouldn't be offering
+	// a "previous input" option, because the current doc's service contributed nothing to deciding 
+	// on how to proceed (no "if" conditon).
+	if(getFilter() == null){
+	    return;
+	}
+
+	//System.err.println("Should create a previous input menu item for " + mdi.getUserData());
+	try{
+	    Document srcDoc = docBuilder.parse(srcURL.openStream());
 
+	    // Get the input data for the *previous* service
+	    MobyDataJob inputData = DataUtils.getInputSample(srcDoc, SeahawkOptions.getRegistry());
+	    for(MobyDataInstance previousMDI: inputData.getPrimaryData()){		
+		// add conditional of the current service as a criteria in user data for each previousMDI, 
+		// so PbE will properly reflect the logic of if(f1(x) matches filter){f2(x)}
+		DataUtils.addUserData(previousMDI, srcURL, getFilter());
+
+		servicesGUI.addPopupOptions(previousMDI, popup, true, null, "previous input");
+	    }
+	} catch(Exception e){
+	    logger.warn("Could not load previous service info, 'previous input' option will not be displayed", e);
+	}
     }
 
     /**
@@ -1372,11 +1407,13 @@
 	}
 	// Filter out any moby jobs, parameters, collection members or HAS members that aren't in the matchingNodes
 	if(filterableNodes == null){
+	    jobXPtrs = new HashMap<String,Boolean>();
 	    filterableNodes = new Vector<String>();
 	    NodeList nodes = currentDoc.getElementsByTagNameNS(MobyTags.MOBY_XML_NS, MobyTags.MOBYDATA);
 	    for(int i = 0; i < nodes.getLength(); i++){
-		filterableNodes.add(getXPtr(nodes.item(i)));
-		addHASXPtrs(filterableNodes, (Element) nodes.item(i));
+		String jobXPtr = getXPtr(nodes.item(i));		
+		filterableNodes.add(jobXPtr);
+		jobXPtrs.put(jobXPtr, addHASXPtrs(filterableNodes, (Element) nodes.item(i)));
 	    }
 		
 	    // Collections
@@ -1429,26 +1466,43 @@
 	// Find just the data subset also matching the regex
 	Map<String,Boolean> matchingXPtrs = new LinkedHashMap<String,Boolean>();
 	// Build the FSA only once, for efficiency
-	Pattern regex = Pattern.compile(fs.getFilterRegex().toString(), Pattern.MULTILINE);
+	Pattern regex = Pattern.compile(fs.getFilterRegex().toString(), 
+                                        Pattern.MULTILINE | Pattern.DOTALL | 
+                                         (fs.getCaseSensitivity() ? 0 : Pattern.CASE_INSENSITIVE));
 	for(int i = 0; i < currentSelectedData.getLength(); i++){
 	    Node node = currentSelectedData.item(i);	    
 	    if(node instanceof Element){
-		if(regex.matcher(((Element) node).getTextContent()).find()){
-		    matchingXPtrs.put(getXPtr(node), Boolean.TRUE);
+		String elementXPtr = getXPtr(node);
+		if(matchingXPtrs.containsKey(elementXPtr) &&
+		   matchingXPtrs.get(elementXPtr).booleanValue()){
+		    	continue;  // already true, no 
+                    }
+		else if(regex.matcher(((Element) node).getTextContent()).find()){
+		    matchingXPtrs.put(elementXPtr, Boolean.TRUE);
+		    System.err.println("Adding " + elementXPtr + " as " + matchingXPtrs.get(elementXPtr));
 		}
 		else{
-		    matchingXPtrs.put(getXPtr(node), Boolean.FALSE);
+		    matchingXPtrs.put(elementXPtr, Boolean.FALSE);
+		    System.err.println("Adding " + elementXPtr + " as " + matchingXPtrs.get(elementXPtr));
 		}
-		//System.err.println("Adding " + getXPtr(node) + " as " + matchingXPtrs.get(getXPtr(node)));
 	    }
 	    else if(node instanceof Attr){
-		if(regex.matcher(((Attr) node).getValue()).find()){
+		String attrParentXPtr = getXPtr(((Attr) node).getOwnerElement());
+		if(matchingXPtrs.containsKey(attrParentXPtr) &&
+	 	   matchingXPtrs.get(attrParentXPtr).booleanValue()){
+		    continue;
+                }
+		else if(regex.matcher(((Attr) node).getValue()).find()){
 		    // Mark the element to which the attribute belongs
-		    matchingXPtrs.put(getXPtr(((Attr) node).getOwnerElement()), Boolean.TRUE);
+		    matchingXPtrs.put(attrParentXPtr, Boolean.TRUE);
+		    System.err.println("Adding " + attrParentXPtr + " attr parent as " + matchingXPtrs.get(attrParentXPtr));
 		}
-		else{
-		    matchingXPtrs.put(getXPtr(((Attr) node).getOwnerElement()), Boolean.FALSE);
+		// so false doesn't override true for multi-attr elements
+		else if(!matchingXPtrs.containsKey(attrParentXPtr)){ 
+		    matchingXPtrs.put(attrParentXPtr, Boolean.FALSE);
+		    System.err.println("Adding " + attrParentXPtr + " attr parent as " + matchingXPtrs.get(attrParentXPtr));
 		}
+		
 	    }
 	    else{
 		logger.warn("Found filter xpath result item that was not an Element or Attribute as expected ("+
@@ -1462,7 +1516,7 @@
 		if(matchingXPtr.getKey().startsWith(currXPtr+"/")){ // a parent of the matching data
 		    // No positive example yet?
 		    if(!parentMatchingXPtrs.containsKey(currXPtr) || !parentMatchingXPtrs.get(currXPtr).booleanValue()){
-			//System.err.println("Adding "+ matchingXPtr.getValue() + " for " + currXPtr);
+			System.err.println("Adding "+ matchingXPtr.getValue() + " for " + currXPtr);
 			parentMatchingXPtrs.put(currXPtr, matchingXPtr.getValue());
 		    }
 		}
@@ -1472,7 +1526,9 @@
 	matchingXPtrs.putAll(parentMatchingXPtrs);
 	for(String currXPtr: matchingXPtrs.keySet()){
 	    // Is part of the selection criteria, but doesn't match the regex
-	    if(!matchingXPtrs.get(currXPtr).booleanValue()){
+	    if(!matchingXPtrs.get(currXPtr).booleanValue() &&
+	       // special condition: if "entire document" xpath is given, filter only at the job level
+	       (!currentSelectionXPath.equals(FilterSearch.SELECT_ALL_XPATH) || jobXPtrs.containsKey(currXPtr))){
 		filteredData.put(currXPtr, "todo");
 	    }
 	}
@@ -1484,7 +1540,7 @@
     }
 
     // If any moby object member is in a HAS relationship, add it to the list of filterable items
-    private void addHASXPtrs(List<String> filterList, Element object){
+    private Boolean addHASXPtrs(List<String> filterList, Element object){
 	String tagName = object.getLocalName();
 	boolean isContainer = false;
 	MobyDataType mobyDataType = null;	
@@ -1496,10 +1552,11 @@
 	    mobyDataType = MobyDataType.getDataType(tagName, SeahawkOptions.getRegistry());
 	    if(mobyDataType == null){
 		logger.warn("Found datatype unknown to the registry ("+object.getLocalName()+")");
-		return;
+		return Boolean.FALSE;
 	    }
 	}
 
+	Boolean hasHAS = Boolean.FALSE; // does the object have a member with a HAS relationship?
 	NodeList members = object.getChildNodes();
 	for(int i = 0; i < members.getLength(); i++){
 	    if(!(members.item(i) instanceof Element)){
@@ -1516,9 +1573,13 @@
 		//		   " is " + (membership == null ? null : membership.getRelationshipType()));
 		if(membership != null && membership.getRelationshipType() == Central.iHAS){
 		    filterList.add(getXPtr(member));
+		    if(!hasHAS){
+			hasHAS = Boolean.TRUE;
+		    }
 		}
 	    }
 	}
+	return hasHAS;
     }
 
     // Recursively ascend the DOM tree and find out our place in its branching structure
@@ -1527,6 +1588,9 @@
 	    return "";
 	}
 	Node parent = n.getParentNode();
+        if(parent == null && n instanceof Attr){
+	    parent = ((Attr) n).getOwnerElement();
+	}
 
 	NodeList children = parent.getChildNodes();
 	int nonElementCnt = 0;
@@ -1624,19 +1688,27 @@
 	int matchCount = 0;
 	if(fs != null && fs.getFilterRegex().length() > 0){
 	    try{
+                Map<String,Boolean> highlights = new HashMap<String,Boolean>();
 		javax.swing.text.LayeredHighlighter.LayerPainter painter = 
 		    new DefaultHighlighter.DefaultHighlightPainter(Color.yellow);
-		Pattern p = Pattern.compile(fs.getFilterRegex().toString(), Pattern.MULTILINE);
+		Pattern p = Pattern.compile(fs.getFilterRegex().toString(), 
+				            Pattern.MULTILINE | Pattern.DOTALL | 
+                                             (fs.getCaseSensitivity() ? 0 : Pattern.CASE_INSENSITIVE));
 		for(String filterable: filterableNodes){
 		    javax.swing.text.Element el = d.getElement(filterable);
 		    String fragment = d.getText(el.getStartOffset(),
 						el.getEndOffset() - el.getStartOffset());
 		    Matcher matcher = p.matcher(fragment);
 		    while (matcher.find()) {
-			h.addHighlight(el.getStartOffset() + matcher.start(),
-				       el.getStartOffset() + matcher.end(),
-				       painter);
-			matchCount++;
+			// Only count match if not already highlighted in a containing filterable node
+			// todo: in future, avoid looking in text bits already checked, for efficiency
+			int hstart = el.getStartOffset() + matcher.start();
+                        int hend = el.getStartOffset() + matcher.end();
+			if(!highlights.containsKey(""+hstart+","+hend)){
+			    h.addHighlight(hstart, hend, painter);
+			    matchCount++;
+			    highlights.put(""+hstart+","+hend, Boolean.TRUE);
+                        }	
 		    }
 		}
 	    } catch(Exception e){
@@ -1687,6 +1759,7 @@
 	    searchPanel.add(filterSearchWidget);
 	    searchPanel.revalidate();
 	    revalidate(); // redo the panel layout
+	    applyFilter(true);
 	}
 	else{
 	    // have a backup, so if re-enabled the old search is restored
@@ -1768,6 +1841,11 @@
 		    }
 		}
 	    }
+	    // todo: If the selection was over the Moby XML display, harvest the set of data and show options for those
+	    // from experience, users try to highlight the whole data and send forward to the next service rather than
+	    // just picking an example value.
+
+	    // If display was not moby data links, but rather just text of some sort, do data recognition over it.
 	    MobyDataInstance[] mobyData = loadMobyDataFromString(selectedTextData);
 	    if(mobyData == null || mobyData.length == 0){
 		logger.warn("No MobyData could be made from the selected text");


From gordonp at dev.open-bio.org  Fri Apr  9 11:55:49 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 9 Apr 2010 11:55:49 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004091555.o39FtnLh001766@dev.open-bio.org>


gordonp
Fri Apr  9 11:55:48 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv1730/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	MobyServicesGUI.java 
Log Message:
Added ability to customize top level menu items with extra text (used initially by 'previous input' feature)
moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyServicesGUI.java,1.16,1.17
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java,v
retrieving revision 1.16
retrieving revision 1.17
diff -u -r1.16 -r1.17
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java	2009/06/09 19:27:56	1.16
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java	2010/04/09 15:55:48	1.17
@@ -442,7 +442,7 @@
 	    // Create the top level menu items for these moby objects right away
 	    submenus = new JMenu[mobyObjects.length];
 	    for(int i = 0; i < mobyObjects.length; i++){
-		JMenu submenu = createObjectSubMenu(mobyObjects[i]);
+		JMenu submenu = createObjectSubMenu(mobyObjects[i], null);
 		if(submenu == null){
 		    continue;
 		}
@@ -503,6 +503,7 @@
 	Node targetNode = null;
 	MobyRequestEventHandler handler = null;
 	MobyDataInstance mobyData = null;
+	String extraMenuText = null;
 	JPopupMenu popupList;
 
 	public OptionLoaderThread(Node targetNode, JPopupMenu popupList, MobyRequestEventHandler handler){
@@ -512,11 +513,12 @@
 	    this.handler = handler;
 	}
 
-	public OptionLoaderThread(MobyDataInstance mobyData, JPopupMenu popupList, MobyRequestEventHandler handler){
+	public OptionLoaderThread(MobyDataInstance mobyData, JPopupMenu popupList, MobyRequestEventHandler handler, String extraMenuText){
 	    super();
 	    this.mobyData = mobyData;
 	    this.popupList = popupList;
 	    this.handler = handler;
+	    this.extraMenuText = extraMenuText;
 	}
 
 	public void run(){
@@ -524,7 +526,7 @@
 		addPopupOptions(targetNode, popupList, false, handler);
 	    }
 	    else if(mobyData != null){
-		addPopupOptions(mobyData, popupList, false, handler);
+		addPopupOptions(mobyData, popupList, false, handler, extraMenuText);
 	    }
 	    else{
 		logger.warn("Warning: OptionLoaderThread has no data to work with");
@@ -584,6 +586,13 @@
      * Find the list of available services querying MobyCentral directly with a piece of data.
      */
     public void addPopupOptions(MobyDataInstance mobyData, JPopupMenu popupList, boolean asynchronous, MobyRequestEventHandler handler){
+	addPopupOptions(mobyData, popupList, asynchronous, handler, null);
+    }
+
+    /**
+     * Find the list of available services querying MobyCentral directly with a piece of data.
+     */
+    public void addPopupOptions(MobyDataInstance mobyData, JPopupMenu popupList, boolean asynchronous, MobyRequestEventHandler handler, String extraMenuText){
 
 	if(asynchronous){
 	    //Show the user that we're doing something...
@@ -596,13 +605,13 @@
 	    }
 
 	    // Call this method synchronously in a different thread
-	    OptionLoaderThread lt = new OptionLoaderThread(mobyData, popupList, handler);
+	    OptionLoaderThread lt = new OptionLoaderThread(mobyData, popupList, handler, extraMenuText);
 	    lt.start();
 	    return;
 	}
 
 	// Create submenu for this object
-	JMenu submenu = createObjectSubMenu(mobyData);
+	JMenu submenu = createObjectSubMenu(mobyData, extraMenuText);
 	// Add option to copy object to clipboard.  We don't need to wait until services are found.
 	if(submenu == null){
 	    return;
@@ -1127,7 +1136,7 @@
 	return menu;
     }
 
-    public JMenu createObjectSubMenu(MobyDataInstance mdi){
+    public JMenu createObjectSubMenu(MobyDataInstance mdi, String extraMenuText){
 	if(!(mdi instanceof MobyPrimaryData)){
 	    logger.warn("Ignoring non-primary data object submitted to menu creation: " + mdi);
 	    return null;
@@ -1205,7 +1214,7 @@
 		}
 	    }
 	    desc = "Record Identifier - " + mobydesc;
-	    submenu = new JMenu("Services for " + datatype + ":" + id);
+	    submenu = new JMenu("Services for " + (extraMenuText == null ? "" : extraMenuText+" ")+datatype + ":" + id);
 	    assignMenuDataIndex(submenu);
 	}
 	else if("String".equals(mobyDataType.getName())){
@@ -1217,7 +1226,8 @@
 		sample = sample.substring(0, MAX_ID_LEN)+"...";
 	    }
 	    desc = "A piece of text";
-	    submenu = new JMenu("Services for String \"" + sample + "\"");
+	    submenu = new JMenu("Services for "+(extraMenuText == null ? "" : extraMenuText+" ")+
+				"String \"" + sample + "\"");
 	    assignMenuDataIndex(submenu);
 	}
 	// Complex object
@@ -1236,7 +1246,7 @@
 	    else if(targetData instanceof MobyDataObjectSet){
 		objectLabel += " collection";
 	    }
-	    submenu = new JMenu("Services for " + objectLabel);
+	    submenu = new JMenu("Services for " + (extraMenuText == null ? "" : extraMenuText+" ")+objectLabel);
 	    assignMenuDataIndex(submenu);
 	}
 	desc = "Input data: " + desc;


From gordonp at dev.open-bio.org  Fri Apr  9 11:57:46 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 9 Apr 2010 11:57:46 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004091557.o39FvkSp001872@dev.open-bio.org>


gordonp
Fri Apr  9 11:57:46 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util
In directory dev.open-bio.org:/tmp/cvs-serv1836/src/main/ca/ucalgary/seahawk/util

Modified Files:
	DataUtils.java 
Log Message:
Added support for case sensitive searches, and 'previous input' conditional service execution
moby-live/Java/src/main/ca/ucalgary/seahawk/util DataUtils.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataUtils.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataUtils.java	2010/03/29 19:58:17	1.1
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataUtils.java	2010/04/09 15:57:46	1.2
@@ -117,7 +117,7 @@
 		    if(newFilter != null){
 			XPathOption xsel = newFilter.getSelectedXPath();
 			newProvenanceData += "\t"+newFilter.getFilterRegex()+
-			    "\t"+xsel.getXPath()+"\t"+xsel.getDesc();
+			    "\t"+xsel.getXPath()+"\t"+xsel.getDesc()+"\t"+newFilter.getCaseSensitivity();
 		    }
 		    pi.setData(attr_val[0]+"=\""+newProvenanceData+"\"");
 		}
@@ -300,7 +300,7 @@
 	return temp.toURI().toURL();
     }
 
-    private static URL getInputURL(Document responseDom) throws Exception{
+    public static URL getInputURL(Document responseDom) throws Exception{
 	String inputAddr = getSeahawkAttrFromDoc(responseDom, SERVICEINPUT_ATTR);
 	if(inputAddr == null){
 	    return null;
@@ -315,7 +315,11 @@
 	}
     }
 
-    private static Document getInputDoc(Document responseDom) throws Exception{
+    public static Document getInputDoc(Document responseDom) throws Exception{
+	URL inputURL = getInputURL(responseDom);
+	if(inputURL == null){
+	    return null;
+	}
 	try{
 	    return docBuilder.parse(getInputURL(responseDom).openStream());
 	} catch(org.xml.sax.SAXException saxe){
@@ -332,6 +336,9 @@
      */
     public static MobyDataJob getInputSample(Document responseDom, Registry registry) throws Exception{
 	Document inputDoc = getInputDoc(responseDom);
+	if(inputDoc == null){
+	    return null;
+	}
 	MobyContentInstance inputPayload = MobyDataUtils.fromXMLDocument(inputDoc.getDocumentElement(),
 									 registry);
 	if(inputPayload == null || inputPayload.size() == 0){
@@ -633,12 +640,30 @@
 	
 	if(fs != null && fs.getFilterRegex().length() > 0){
 	    XPathOption xsel = fs.getSelectedXPath();
-	    userData.append("\t"+fs.getFilterRegex()+"\t"+xsel.getXPath()+"\t"+xsel.getDesc());
+	    userData.append("\t"+fs.getFilterRegex()+"\t"+xsel.getXPath()+"\t"+xsel.getDesc()+"\t"+fs.getCaseSensitivity());
 	}
 	mobyData.setUserData(userData.toString());
     }
 
     /**
+     * Record a condition for data acceptability, 
+     * another service call with an output filter criteria. i.e. records if(f1(x) matches f1's output filter){...}
+     */
+    public static void addUserData(MobyDataInstance mdi, URL conditionalOutputURL, FilterSearch filter){
+	String filterSpec = "";
+	if(filter != null && filter.getFilterRegex().length() > 0){
+	    XPathOption xsel = filter.getSelectedXPath();
+	    filterSpec = "\t"+filter.getFilterRegex()+"\t"+xsel.getXPath()+"\t"+xsel.getDesc()+"\t"+filter.getCaseSensitivity();
+	}
+	if(mdi.getUserData() != null){
+	    mdi.setUserData(mdi.getUserData().toString()+"\t"+conditionalOutputURL+filterSpec);
+	}
+	else{
+	    mdi.setUserData(conditionalOutputURL.toString()+filterSpec);
+	}
+    }
+
+    /**
      * Retrieves processing instructions embedded in Moby XML docs if they have the for <?seahawk attr="val"?>
      */
     public static String getSeahawkAttrFromDoc(URL docURL, String attrName) throws Exception{ 


From gordonp at dev.open-bio.org  Fri Apr  9 11:58:23 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 9 Apr 2010 11:58:23 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004091558.o39FwMVA001941@dev.open-bio.org>


gordonp
Fri Apr  9 11:58:22 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util
In directory dev.open-bio.org:/tmp/cvs-serv1902/src/main/ca/ucalgary/seahawk/util

Modified Files:
	DataFlowRecorder.java 
Log Message:
Added support for case sensitive searches, and 'previous input' conditional service execution
moby-live/Java/src/main/ca/ucalgary/seahawk/util DataFlowRecorder.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataFlowRecorder.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataFlowRecorder.java	2010/03/29 20:53:04	1.2
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataFlowRecorder.java	2010/04/09 15:58:22	1.3
@@ -31,6 +31,8 @@
     public static final String T2FLOW_DISPATCHXML = "ca/ucalgary/seahawk/resources/t2flowDispatchStack.xml";
     public static final String T2FLOW_REGEXFILTER_BEANSHELL = "ca/ucalgary/seahawk/resources/RegexFilterBeanShell";
     public static final String T2FLOW_XPATHFILTER_BEANSHELL = "ca/ucalgary/seahawk/resources/XPathFilterBeanShell";
+    public static final String T2FLOW_PASSFILTER_BEANSHELL = "ca/ucalgary/seahawk/resources/PassFilterBeanShell"; // = if condition
+    public static final String T2FLOW_LISTFLATTEN_BEANSHELL = "ca/ucalgary/seahawk/resources/FlattenListBeanShell";
 
     private Central mobyCentral;
     private Map<String,Integer> namesUsed;  // keep count of workflow element name usage so as not to duplicate an ID
@@ -39,9 +41,12 @@
     // Value is processor and port names
     private Map<String,String[]> filter2Processor;
     private Map<String,String[]> decomp2Processor; // reuse decomposition processors if same decomp done more than once on a given doc
+    private Map<String,String[]> input2Processor; // if same input use more than once, create only one input port
     private DocumentBuilder docBuilder;
     private static String regexFilterScript = null;
     private static String xpathFilterScript = null;
+    private static String passFilterScript = null;
+    private static String listFlattenScript = null;
     private static Element dispatchStack = null;
     private static Transformer nullTransformer = null;
     private static Logger logger = Logger.getLogger(DataFlowRecorder.class.getName());
@@ -57,8 +62,9 @@
 
 	namesUsed = new HashMap<String,Integer>();
 	url2Processor = new HashMap<String,String>();
-	filter2Processor = new HashMap<String,String[]>(); // key is compound:  url \n regex \n xpath
+	filter2Processor = new HashMap<String,String[]>(); // key is compound:  url \n regex \n xpath \n caseSensitivity
 	decomp2Processor = new HashMap<String,String[]>(); // key is url with xpath attached as ref (the way Seahawk generates them)
+	input2Processor = new HashMap<String,String[]>(); // key is input instance XML 
     }
 
     /**
@@ -154,6 +160,7 @@
 	url2Processor.clear();  // clear map of results already produced in backtracking (handling workflow forks)
 	filter2Processor.clear(); // ditto
 	decomp2Processor.clear(); // ditto
+	input2Processor.clear(); // ditto
 
 	// Generate all of the outputs requested by the call.  None should be intermediaries 
 	// of another (the backtracking done by addWorkflowElements will capture these).
@@ -162,7 +169,7 @@
 	    // Create the inputs, processors and data links required for the workflow to create the result doc
 	    String ultimateProcessorName = addWorkflowElements(result.getKey(), doc, inputPorts, processors, datalinks);
 	    
-	    // If there is a filter active on the currently displyed doc, we need to apply it here
+	    // If there is a filter active on the currently displayed doc, we need to apply it here
 	    FilterSearch filter = result.getValue();
 	    String[] regexProcessorAndPorts = null;
 	    String filterKey = null;
@@ -190,9 +197,11 @@
 		    }
 		    else{
 			regexProcessorAndPorts = createRegexFilter(filter.getFilterRegex().toString(), 
-								   filter.getSelectedXPath(), 
+								   filter.getSelectedXPath(),
+								   filter.getCaseSensitivity(),
 								   ultimateProcessorName,
-								   getPortName(outputParam, true), 
+								   getPortName(outputParam, true),
+								   1, // desired list dpeth
 								   processors, datalinks, doc);
 			filter2Processor.put(filterKey, regexProcessorAndPorts);
 		    }
@@ -275,6 +284,9 @@
 	MobyService service = DataUtils.getService(resultDom);
 	Registry registry = DataUtils.getRegistry(resultDom);
 	MobyDataJob sampleJob = DataUtils.getInputSample(resultDom, registry);
+	if(sampleJob == null){
+	    return "foo";  //todo: doc was a loaded Moby XML, not a service output or recognized data
+	}
 
 	Element processorElement = createProcessorElement(service, sampleJob, doc);
 	// add processor to workflow
@@ -297,111 +309,181 @@
 	    MobyPrimaryData sampleData = (MobyPrimaryData) sd;
 
 	    // has provenance info?
+	    String[] data = null;
+	    String[] condPassProcessorAndPorts = null;  //[procname, input port, outputport]
 	    if(sampleData.getUserData() != null){
-		// User data has the form srcURL#generalSelectionXPath <tab> actualInputDataXptr <tab> regexFilter 
-		// where the filter is optional 
-		String[] data = sampleData.getUserData().toString().split("\t");
+		// User data has the form 
+		// srcURL#generalSelectionXPath <tab> actualInputDataXptr <tab> regexFilter <tab> conditionalURL
+		// where the filter and conditionalURL are optional 
+		data = sampleData.getUserData().toString().split("\t");
+		//options: selection + filter + cond, selection + cond, or cond only
+		if(data.length == 11 || data.length == 7 || data.length == 5){
+		    System.err.println("Adding conditional for " + resultURLString);
+		    String conditionURL = data[data.length-5];
+		    String conditionRegex = data[data.length-4];
+		    XPathOption conditionXPath = new XPathOption(data[data.length-3], data[data.length-2]);
+		    boolean caseSensitivity = Boolean.parseBoolean(data[data.length-1]);
+		    condPassProcessorAndPorts = createServiceConditionFilter(new URL(conditionURL), conditionRegex, conditionXPath, caseSensitivity,
+									     doc, inputPorts, processors, datalinks);
+		    String[] conditionlessData = new String[data.length-5];
+		    System.arraycopy(data, 0, conditionlessData, 0, data.length-5);
+		    data = conditionlessData;
+		}
+		else{
+		    System.err.println("Skipping conditional, only " + data.length + 
+				       "members in provenance data for " + resultURLString);
+		}
+	    }
+
+	    // true means treat as a collection if that's what the sample data is
+	    String sinkPortName = getPortName(sampleData, true);
+	    if(data != null && data.length != 0){
 		URL dataSrcURL = null;
 		try{
 		    dataSrcURL = new URL(data[0]);
 		} catch(Exception e){
 		    logger.log(Level.WARNING, "Ignoring unexpected UserData in Moby DOM, was not " +
 			       "a provenance URL as expected URL (" + sampleData.getUserData().toString() + ")");
+		    continue;
 		}
-		if(dataSrcURL != null){
-		    // recursion for workflow creation by backtracking service input provenance
-		    String feedingProcessorName = null;
-		    String feedingProcessorPort = null;
-		    String dataSrcURLString = dataSrcURL.toString().replaceFirst("#.*$", ""); //get rid of ref part
-		    if(url2Processor.containsKey(dataSrcURLString)){
-			feedingProcessorName = url2Processor.get(dataSrcURLString);
+		// recursion for workflow creation by backtracking service input provenance
+		String feedingProcessorName = null;
+		String feedingProcessorPort = null;
+		String dataSrcURLString = dataSrcURL.toString().replaceFirst("#.*$", ""); //get rid of ref part
+		if(url2Processor.containsKey(dataSrcURLString)){
+		    feedingProcessorName = url2Processor.get(dataSrcURLString);
+		}
+		else{
+		    feedingProcessorName = addWorkflowElements(dataSrcURL, doc, inputPorts, processors, datalinks);
+		}
+		
+		// Take into account data[2..5] if they are present, 
+		// which filter the data by a regex before any other activities happen
+		// Format of spec is regex <tab> xpath <tab> xpathTextDesc <tab> booleanForCaseSensitivity
+		if(data.length == 6){
+		    String[] origFeederProcessorAndPort = getPortFromURLRef(dataSrcURL,
+									    sampleData,
+									    feedingProcessorName,
+									    null,
+									    processors, 
+									    datalinks,
+									    doc,
+									    false);
+		    
+		    // Lookup key is url \n regex \n xpath \n caseSensitivity
+		    String[] regexProcessorAndPorts = null;
+		    String filterKey = dataSrcURLString+"\n"+data[2]+"\n"+data[3]+"\n"+data[5];
+		    if(filter2Processor.containsKey(filterKey)){ // filter already exists from another branch
+			regexProcessorAndPorts = filter2Processor.get(filterKey);
 		    }
 		    else{
-			feedingProcessorName = addWorkflowElements(dataSrcURL, doc, inputPorts, processors, datalinks);
-		    }
-
-		    // true means treat as a collection if that's what the sample data is
-		    String sinkPortName = getPortName(sampleData, true);
-
-		    // Take into account data[2..4] if they are present, 
-		    // which filter the data by a regex before any other activities happen
-		    // Format of spec is regex <tab> xpath <tab> xpathTextDesc, so the earlier split gives use indices 1..3
-		    if(data.length == 5){
-			String[] origFeederProcessorAndPort = getPortFromURLRef(dataSrcURL,
-										sampleData,
-										feedingProcessorName,
-										null,
-										processors, 
-										datalinks,
-										doc,
-										false);
-
-			// Lookup key is url \n regex \n xpath
-			String[] regexProcessorAndPorts = null;
-			String filterKey = dataSrcURLString+"\n"+data[2]+"\n"+data[3];
-			if(filter2Processor.containsKey(filterKey)){ // filter already exists from another branch
-			    regexProcessorAndPorts = filter2Processor.get(filterKey);
-			}
-			else{
-			    regexProcessorAndPorts = createRegexFilter(data[2], 
-								       new XPathOption(data[3], data[4]), 
-								       origFeederProcessorAndPort[0], 
-								       origFeederProcessorAndPort[1], 
-								       processors, datalinks, doc);
-			    // New filter is applied to just this branch from a service for the moment...record the filter
-			    // so that if same filter criteria are applied to more than one branch, we only make one filter
-			    filter2Processor.put(dataSrcURLString+"\n"+data[2]+"\n"+data[3], regexProcessorAndPorts);
-			}
-			feedingProcessorName = regexProcessorAndPorts[0];
-			feedingProcessorPort = regexProcessorAndPorts[regexProcessorAndPorts.length-1];  //last one is output
+			regexProcessorAndPorts = createRegexFilter(data[2], 
+								   new XPathOption(data[3], data[4]),
+								   Boolean.parseBoolean(data[5]),
+								   origFeederProcessorAndPort[0], 
+								   origFeederProcessorAndPort[1],
+								   1, // desired list depth 
+								   processors, datalinks, doc);
+			// New filter is applied to just this branch from a service for the moment...record the filter
+			// so that if same filter criteria are applied to more than one branch, we only make one filter
+			filter2Processor.put(filterKey, regexProcessorAndPorts);
 		    }
-
-		    // getPortFromURLRef() may inject extra processors between the processorName and feedingProcessorName
-		    // in order to maintain type safety, etc. so the data link may change (based on last arg being set to true).
-		    String[] feederProcessorAndPort = getPortFromURLRef(dataSrcURL,
-									sampleData,
-									feedingProcessorName,
-									feedingProcessorPort, //if null, determined from urlref
-									processors, 
-									datalinks,
-									doc,
-									true); 
-		    datalinks.appendChild(createDataLinkElement(feederProcessorAndPort[0], feederProcessorAndPort[1],
-								processorName, sinkPortName, 
+		    feedingProcessorName = regexProcessorAndPorts[0];
+		    feedingProcessorPort = regexProcessorAndPorts[regexProcessorAndPorts.length-1];  //last one is output
+		}
+		
+		// getPortFromURLRef() may inject extra processors between the processorName and feedingProcessorName
+		// in order to maintain type safety, etc. so the data link may change (based on last arg being set to true).
+		String[] feederProcessorAndPort = getPortFromURLRef(dataSrcURL,
+								    sampleData,
+								    feedingProcessorName,
+								    feedingProcessorPort, //if null, determined from urlref
+								    processors, 
+								    datalinks,
+								    doc,
+								    true); 
+		if(condPassProcessorAndPorts != null){
+		    // inject condition filter between feeder service and current service 
+		    datalinks.appendChild(createDataLinkElement(feederProcessorAndPort[0],
+								feederProcessorAndPort[1],
+								condPassProcessorAndPorts[0], 
+								condPassProcessorAndPorts[1],
 								doc));
-		    
+		    feederProcessorAndPort[0] = condPassProcessorAndPorts[0];
+		    feederProcessorAndPort[1] = condPassProcessorAndPorts[2];
 		}
+
+		datalinks.appendChild(createDataLinkElement(feederProcessorAndPort[0], feederProcessorAndPort[1],
+							    processorName, sinkPortName, 
+							    doc));
+		
 	    }
 	    // Otherwise it's a workflow input the user will need to specify
 	    else{
-		String uniqueInputName = createUniqueName(getInputName(sampleData));
-		// todo: sample data may be of more specific type than service requires
-		inputPorts.appendChild(createWorkflowInputElement(uniqueInputName, sampleData, doc));
-		if(sampleData.getDataType().getName().equals(MobyTags.MOBYOBJECT)){
-		    String mobifyingProcessorName = addIdMobifyingProcessor(processors, datalinks, 
-									    sampleData, processorName, 
-									    inputName, doc);
-		    datalinks.appendChild(createWorkflowInputLinkElement(uniqueInputName, 
-									 mobifyingProcessorName, 
-									 "fileurl", 
-									 sampleData, 
-									 doc));
+		// pName is editable name for input processor target...
+		// allows injection of condition without affecting method's return value
+		String pName = processorName; 
+		if(condPassProcessorAndPorts != null){
+		    // inject condition filter between data creator and current service 
+		    datalinks.appendChild(createDataLinkElement(condPassProcessorAndPorts[0],
+								condPassProcessorAndPorts[2],
+								pName,
+								sinkPortName,
+								doc));
+		    pName = condPassProcessorAndPorts[0];
+		    sinkPortName = condPassProcessorAndPorts[1];
+		}
+		// The sample data may be used in more than one branch of the flow...avoid duplication
+		// Get the real data XML, to see if we've encountered it before as input (it'd be in the hash)
+		// Remember that sd is the loop's original MobyDataInstance before it's been coerced into a MobyPrimaryData, 
+		// which doesn't have XML modes, etc.
+		String inputKey = getInputKey(sd);
+		System.err.println("Input key for " + processorName + " is " + inputKey);
+
+		String[] mobifyingProcessorNameAndPorts = null;
+		if(input2Processor.containsKey(inputKey)){
+		    mobifyingProcessorNameAndPorts = input2Processor.get(inputKey);		    
 		}
 		else{
-		    // TODO: Need to build complex input from MOB rule or spreadsheet fields?
+		    if(sampleData.getDataType().getName().equals(MobyTags.MOBYOBJECT)){
+			mobifyingProcessorNameAndPorts = addIdMobifyingProcessor(processors, datalinks, inputPorts,
+										 sampleData, doc);
+			input2Processor.put(inputKey, mobifyingProcessorNameAndPorts);
+		    }
+		    else{
+			// TODO: Need to build complex input from MOB rule or spreadsheet fields?
+		    }
 		}
+		// link the created data to the workflow service
+		datalinks.appendChild(createDataLinkElement(mobifyingProcessorNameAndPorts[0], 
+							    mobifyingProcessorNameAndPorts[1], 
+							    pName, sinkPortName, 
+							    doc));
 	    }
+
 	}
 
 	return processorName;
     }
 
+    // returns the same value for moby sample data instances containing the same data in XML form
+    private String getInputKey(MobyDataInstance sd){
+	int oldXmlMode = sd.getXmlMode();
+	sd.setXmlMode(MobyDataInstance.SERVICE_XML_MODE);
+	String inputKey = sd.toXML();
+	sd.setXmlMode(oldXmlMode);
+
+	// get rid of the top-level article name, as this is immaterial to the 
+	// value equivalence of objects (only matters to the actual service call mechanism)
+	return inputKey.replaceFirst(MobyTags.ARTICLENAME+"\\s*=\\s*(['\"]).*?\\1", "");
+    }
+
     // Actually adds a few processors, but only one needs to be returned and connected to an input port.
     // The others are constant values.  By default we assume that you want to run a bunch of IDs 
     // in a file, we also link in a Taverna spreadsheet importer.
-    private String addIdMobifyingProcessor(Element processors, Element datalinks, 
-					   MobyPrimaryData sampleData, String targetProcessorName, 
-					   String targetProcessorPort, Document doc) throws Exception{
+    // Returns [spreadsheetReadingProcName, outputPort]
+    private String[] addIdMobifyingProcessor(Element processors, Element datalinks, Element dataFlowInputPorts,
+					     MobyPrimaryData sampleData, Document doc) throws Exception{
 	String processorName = "Create-" + sampleData.getDataType().getName();
 	MobyNamespace ns = null;
 	MobyNamespace[] nss = ((MobyPrimaryData) sampleData).getNamespaces();
@@ -518,7 +600,7 @@
 	Map<String,String> feeds = new HashMap<String,String>();  //what port on data creator it maps to
 	constants.put(ns.getName()+"-namespace-constant", ns.getName());
 	feeds.put(ns.getName()+"-namespace-constant", "namespace");
-	constants.put("article_name-constant", targetProcessorPort);
+	constants.put("article_name-constant", "unimportant");
 	feeds.put("article_name-constant", "article name");
 
 	for(Map.Entry<String,String> constant: constants.entrySet()){
@@ -632,19 +714,23 @@
 	port.setAttribute("name", "fileurl");
 	port.setAttribute("depth", "0");
 
+	String uniqueInputName = createUniqueName(getInputName(sampleData));
+	// todo: sample data may be of more specific type than service requires
+	dataFlowInputPorts.appendChild(createWorkflowInputElement(uniqueInputName, sampleData, doc));
+	datalinks.appendChild(createWorkflowInputLinkElement(uniqueInputName, 
+							     importerName, 
+							     "fileurl", 
+							     sampleData, 
+							     doc));
+
 	// link the spreadsheet reader to the Moby data creator 
 	datalinks.appendChild(createDataLinkElement(importerName, outputUniqueName,
 						    processorName, "id",
 						    doc));
 
-	// link the created data to the first workflow service, which takes an id
-	datalinks.appendChild(createDataLinkElement(processorName, "mobyData", 
-						    targetProcessorName, "Object("+targetProcessorPort+")", 
-						    doc));
-
-	// return the name of the spreadsheet reading processor so it can be hooked up
-	// to an input port for a Moby service
-	return importerName;
+	// return the name of the spreadsheet reading processor and output port so it can be hooked up
+	// to input ports for Moby services
+	return new String[]{processorName, portNames[portNames.length-1]};
     }
 
     private Element createConstantProcessor(String constantName, String constantValue, Document doc)
@@ -884,15 +970,86 @@
 				 processors, datalinks, doc);
     }
 
-    private String[] createRegexFilter(String regex, XPathOption xpath, String srcProcessor, String srcPort, 
+    // Make the continued use of data X in the workflow conditional on the results of running X through service f
+    // and passing the filter condition set on f.  Equivalent to if(f(X) matches f_filter){...}
+    // returns [proc name, input port, output port]
+    private String[] createServiceConditionFilter(URL conditionURL, String filterRegex, XPathOption filterXPath,
+						  boolean caseSensitive, Document doc,
+						  Element inputPorts, Element processors, Element datalinks)
+	throws Exception{
+
+	// Open the conditionURL, and find out what service result is used, and what filter applied
+ 	Document conditionDoc = docBuilder.parse(conditionURL.openStream());
+ 	MobyService service = DataUtils.getService(conditionDoc);
+ 	Document condServiceOutputDoc = DataUtils.getInputDoc(conditionDoc);
+
+	// The bits to run the service "f"
+
+ 	String dataSrcURLString = conditionURL.toString().replaceFirst("#.*$", ""); //get rid of ref part
+ 	String processorName = null;
+ 	// See if the service creating the input for the conditional service has already been added to the workflow
+ 	if(url2Processor.containsKey(dataSrcURLString)){
+ 	    processorName = url2Processor.get(dataSrcURLString);
+ 	}
+ 	else{
+	    processorName = addWorkflowElements(conditionURL, doc, inputPorts, processors, datalinks);
+ 	}
+
+ 	String filterKey = dataSrcURLString+"\n"+filterRegex+"\n"+filterXPath.getXPath()+"\n"+caseSensitive;
+ 	String[] regexFilterProcNameAndPort = null;
+ 	//todo: gimpy loop below, as more than one service output would cause a trampling of regex output ports
+ 	for(MobyPrimaryData outputParam: service.getPrimaryOutputs()){
+ 	    // See if the filter on the conditional service has already been used in the workflow
+ 	    if(filter2Processor.containsKey(filterKey)){
+ 		regexFilterProcNameAndPort = filter2Processor.get(filterKey);
+ 	    }
+ 	    else{
+ 		regexFilterProcNameAndPort = createRegexFilter(filterRegex, 
+ 							       filterXPath,
+							       caseSensitive, 
+ 							       processorName,
+ 							       getPortName(outputParam, true),
+							       0, //depth of list desired (will return match count)
+ 							       processors, datalinks, doc);
+ 		filter2Processor.put(filterKey, regexFilterProcNameAndPort);
+ 	    }
+ 	}
+
+	// We need to flatten the 2-deep list generated by the regex filter's cross product
+	String[] beanShellFlattenerProcNameAndPorts = addListFlattenBeanShell(processors, doc);
+
+	datalinks.appendChild(createDataLinkElement(regexFilterProcNameAndPort[0],
+						    regexFilterProcNameAndPort[1],
+						    beanShellFlattenerProcNameAndPorts[0], 
+						    beanShellFlattenerProcNameAndPorts[1],
+						    doc));
+
+	// Essentially an "if" condition, error if incoming value is empty, missing, or zero
+	String[] beanShellFilterProcNameAndPorts = addPassFilterBeanShell(processors, doc);
+
+	datalinks.appendChild(createDataLinkElement(beanShellFlattenerProcNameAndPorts[0],
+						    beanShellFlattenerProcNameAndPorts[2],
+						    beanShellFilterProcNameAndPorts[0], 
+						    beanShellFilterProcNameAndPorts[2],
+						    doc));
+
+	return new String[]{beanShellFilterProcNameAndPorts[0], 
+                            beanShellFilterProcNameAndPorts[1], 
+                            beanShellFilterProcNameAndPorts[3]};
+    }
+
+    private String[] createRegexFilter(String regex, XPathOption xpath, boolean caseSensitive, 
+				       String srcProcessor, String srcPort, int listDepth, 
  				       Element processors, Element datalinks, Document doc)
  	throws Exception{
 	String constantXPathName = createUniqueName(xpath.toString());
 	processors.appendChild(createConstantProcessor(constantXPathName, xpath.getXPath(), doc));
 	String constantRegexName = createUniqueName(regex);
 	processors.appendChild(createConstantProcessor(constantRegexName, regex, doc));
+	String constantCaseSensitivityName = createUniqueName("cs_"+caseSensitive);
+	processors.appendChild(createConstantProcessor(constantCaseSensitivityName, ""+caseSensitive, doc));
 
-	String[] beanShellFilterProcNameAndPorts = addRegexFilterBeanShell(processors, doc);
+	String[] beanShellFilterProcNameAndPorts = addRegexFilterBeanShell(listDepth, processors, doc);
 	
 	datalinks.appendChild(createDataLinkElement(srcProcessor,
 						    srcPort,
@@ -903,11 +1060,15 @@
 						    beanShellFilterProcNameAndPorts[0], 
 						    beanShellFilterProcNameAndPorts[2],
 						    doc)); 
-	datalinks.appendChild(createDataLinkElement(constantXPathName, "value",
+	datalinks.appendChild(createDataLinkElement(constantCaseSensitivityName, "value",
 						    beanShellFilterProcNameAndPorts[0], 
 						    beanShellFilterProcNameAndPorts[3],
 						    doc)); 
-	return new String[]{beanShellFilterProcNameAndPorts[0], beanShellFilterProcNameAndPorts[4]};	
+	datalinks.appendChild(createDataLinkElement(constantXPathName, "value",
+						    beanShellFilterProcNameAndPorts[0], 
+						    beanShellFilterProcNameAndPorts[4],
+						    doc)); 
+	return new String[]{beanShellFilterProcNameAndPorts[0], beanShellFilterProcNameAndPorts[5]};	
     }
     
     private String[] createXrefParser(MobyNamespace nsObj, String srcProcessor, String srcPort, 
@@ -1231,29 +1392,76 @@
 	}
     }
 
+   private String[] addListFlattenBeanShell(Element processors, Document doc) 
+	throws Exception{
+	String beanShellProcName = createUniqueName("Create_Pass_Fail_List");
+	
+	// Now do all the param-specific stuff below (inserts into various parts of the elements defined above)
+	Map<String,String> inputsMap = new LinkedHashMap<String,String>();  
+	// linked because order is important to line up port connections
+	Map<String,String> inputTypes = new LinkedHashMap<String,String>();
+	inputsMap.put("inputlist", "2");
+	inputTypes.put("inputlist", "text/plain");
+	Map<String,String> outputsMap = new LinkedHashMap<String,String>();
+	outputsMap.put("outputlist", "1");
+
+	return addBeanShell(beanShellProcName, "dot",
+			    inputsMap, inputTypes, outputsMap, 
+			    getListFlattenScript(), new String[]{}, 
+			    processors, doc);	
+    }    
+
+    private String[] addPassFilterBeanShell(Element processors, Document doc) 
+	throws Exception{
+	String beanShellProcName = createUniqueName("IfPassesContentFilter");
+	
+	// Now do all the param-specific stuff below (inserts into various parts of the elements defined above)
+	Map<String,String> inputsMap = new LinkedHashMap<String,String>();  
+	// linked because order is important to line up port connections
+	Map<String,String> inputTypes = new LinkedHashMap<String,String>();
+	inputsMap.put("dataToPassThrough", "1");
+	inputsMap.put("conditionResults", "1");
+	inputTypes.put("dataToPassThrough", "text/xml");
+	inputTypes.put("conditionResults", "text/plain");
+	Map<String,String> outputsMap = new LinkedHashMap<String,String>();
+	outputsMap.put("dataPassed", "1");
+
+	return addBeanShell(beanShellProcName, "cross",
+			    inputsMap, inputTypes, outputsMap, 
+			    getPassFilterScript(), new String[]{}, 
+			    processors, doc);	
+    }    
+
     // Returns the name of the bean shell processor and its ports, so we can create the data links in the caller
     // The input is the original moby xml, and the xpath to extract, and the regex to apply to the text contents of the xpath results.
     // The output is a list of moby xml docs, one for each mobyData that fit the xpath and regex criteria.
-    private String[] addRegexFilterBeanShell(Element processors, Document doc) 
+    private String[] addRegexFilterBeanShell(int listDepth, Element processors, Document doc) 
 	throws Exception{
-	String beanShellProcName = createUniqueName("Filter_By_Content");
+	String beanShellProcName = createUniqueName("Filter"+(listDepth == 0 ? "_Match_Count" : "_By_Content"));
 	
 	// Now do all the param-specific stuff below (inserts into various parts of the elements defined above)
 	Map<String,String> inputsMap = new LinkedHashMap<String,String>();  
-	// linked because order is importtant to line up port connections
+	// linked because order is important to line up port connections
 	Map<String,String> inputTypes = new LinkedHashMap<String,String>();
 	inputsMap.put("xml_text", "0");
 	inputsMap.put("regex", "0");
+        inputsMap.put("case_sensitive", "0");
 	inputsMap.put("xpath", "0");
 	inputTypes.put("xml_text", "text/xml");
 	inputTypes.put("xpath", "text/plain");
 	inputTypes.put("regex", "text/plain");
+	inputTypes.put("case_sensitive", "text/plain");
 	Map<String,String> outputsMap = new LinkedHashMap<String,String>();
-	outputsMap.put("nodelistAsXML", "1");
+	if(listDepth == 0){
+	    outputsMap.put("matchCount", "0");
+        }
+        else{
+            outputsMap.put("nodelistAsXML", ""+listDepth);
+        }
 
-	return addBeanShell(beanShellProcName,
+	return addBeanShell(beanShellProcName, "cross",
 			    inputsMap, inputTypes, outputsMap, 
-			    getRegexFilterScript(), new String[]{"dom4j:dom4j:1.6"}, 
+			    getRegexFilterScript(listDepth), new String[]{"dom4j:dom4j:1.6"}, 
 			    processors, doc);	
     }
 
@@ -1274,13 +1482,13 @@
 	Map<String,String> outputsMap = new HashMap<String,String>();
 	outputsMap.put("nodelistAsXML", "1");
 
-	return addBeanShell(beanShellProcName,
+	return addBeanShell(beanShellProcName, "cross",
 			    inputsMap, inputTypes, outputsMap, 
 			    getXPathFilterScript(), new String[]{"dom4j:dom4j:1.6"}, 
 			    processors, doc);
     }
 
-    private String[] addBeanShell(String beanShellProcName,
+    private String[] addBeanShell(String beanShellProcName, String vectorComboOp,
 				  Map<String,String> inputsMap, Map<String,String> inputTypes, 
 				  Map<String,String> outputsMap, String script, String[] dependencySpecs,
 				  Element processors, Document doc) throws Exception{
@@ -1345,8 +1553,11 @@
 	iterationStrategyStack.appendChild(iteration);
 	Element strategy = doc.createElementNS(T2FLOW_NS, "strategy");
 	iteration.appendChild(strategy);
-	Element cross = doc.createElementNS(T2FLOW_NS, "cross");
-	strategy.appendChild(cross);
+	Element vectorOp = null;
+        if(vectorComboOp != null){
+            vectorOp = doc.createElementNS(T2FLOW_NS, vectorComboOp);
+	    strategy.appendChild(vectorOp); // either cross or dot
+        }
 
 	// Lst processor name, input ports and output ports, in that order.
 	Vector<String> returnSpec = new Vector<String>();
@@ -1370,7 +1581,9 @@
 	    mimeTypes.appendChild(createElWithText(doc, "", "string", inputTypes.get(input.getKey())));
 
 	    Element port = doc.createElementNS(T2FLOW_NS, "port");
-	    cross.appendChild(port);
+	    if(vectorOp != null){
+                vectorOp.appendChild(port);
+            }
 	    port.setAttribute("depth", input.getValue());
 	    port.setAttribute("name", input.getKey());
 	}
@@ -1517,7 +1730,7 @@
     private String createUniqueName(String preferredName){
 	if(namesUsed.containsKey(preferredName)){
 	    namesUsed.put(preferredName, namesUsed.get(preferredName).intValue()+1); //increment
-	    preferredName += namesUsed.get(preferredName);
+	    preferredName += "_"+namesUsed.get(preferredName);
 	}
 	else{
 	    namesUsed.put(preferredName, 1); // will be auto-boxed to Integer
@@ -1528,8 +1741,6 @@
     // dataType(articleName) as required by the Taverna Moby plugin
     private String getPortName(MobyPrimaryData data, boolean asCollection){
 	if(data instanceof MobyPrimaryDataSet){
-	    // todo: Hmm...don't yet handle case where collections are passed from one service to another...
-	    // here we assume iterating over the collection
 	    if(asCollection){
 		return data.getDataType().getName()+"(Collection - '"+data.getName()+"')";
 	    }
@@ -1680,7 +1891,7 @@
 
 	    // Did we override the default value for the secondary param in the example input?
 	    Element stringValue = doc.createElementNS("", "string");
-	    if(sampleInput.containsKey(secParam.getName())){
+	    if(sampleInput != null && sampleInput.containsKey(secParam.getName())){
 		stringValue.appendChild(doc.createTextNode(((MobyDataSecondaryInstance) sampleInput.get(secParam.getName())).getValue()));
 	    }
 	    else{  // use the default defined in Moby Central
@@ -1739,6 +1950,28 @@
 	return central;
     }
 
+    private synchronized String getListFlattenScript() throws Exception{
+	if(listFlattenScript == null){
+	    URL scriptURL = getClass().getClassLoader().getResource(T2FLOW_LISTFLATTEN_BEANSHELL);
+	    if(scriptURL == null){
+		throw new Exception("Cannot find resource " + T2FLOW_LISTFLATTEN_BEANSHELL);
+	    }
+	    listFlattenScript = HTMLUtils.getURLContents(scriptURL);
+	}
+	return listFlattenScript;
+    }
+
+    private synchronized String getPassFilterScript() throws Exception{
+	if(passFilterScript == null){
+	    URL scriptURL = getClass().getClassLoader().getResource(T2FLOW_PASSFILTER_BEANSHELL);
+	    if(scriptURL == null){
+		throw new Exception("Cannot find resource " + T2FLOW_PASSFILTER_BEANSHELL);
+	    }
+	    passFilterScript = HTMLUtils.getURLContents(scriptURL);
+	}
+	return passFilterScript;
+    }
+
     private synchronized String getXPathFilterScript() throws Exception{
 	if(xpathFilterScript == null){
 	    URL scriptURL = getClass().getClassLoader().getResource(T2FLOW_XPATHFILTER_BEANSHELL);
@@ -1750,7 +1983,7 @@
 	return xpathFilterScript;
     }
 
-    private synchronized String getRegexFilterScript() throws Exception{
+    private synchronized String getRegexFilterScript(int listDepth) throws Exception{
 	if(regexFilterScript == null){
 	    URL scriptURL = getClass().getClassLoader().getResource(T2FLOW_REGEXFILTER_BEANSHELL);
 	    if(scriptURL == null){
@@ -1758,7 +1991,12 @@
 	    }
 	    regexFilterScript = HTMLUtils.getURLContents(scriptURL);
 	}
-	return regexFilterScript;
+	if(listDepth == 0){// list to scalar conversion
+	    return regexFilterScript+"\nString matchCount = \"\"+nodelistAsXML.size();";
+        }
+        else{
+ 	    return regexFilterScript;
+        }
     }
 
     private synchronized Element getDispatchStack(Document newOwnerDoc) throws Exception{


From gordonp at dev.open-bio.org  Fri Apr  9 12:58:14 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 9 Apr 2010 12:58:14 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004091658.o39GwEOB003781@dev.open-bio.org>


gordonp
Fri Apr  9 12:58:13 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/minnow
In directory dev.open-bio.org:/tmp/cvs-serv3745/src/main/ca/ucalgary/minnow

Modified Files:
	MinJarMaker.java 
Log Message:
got rid of annoying cvs-related files in secondary jars
moby-live/Java/src/main/ca/ucalgary/minnow MinJarMaker.java,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/minnow/MinJarMaker.java,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/minnow/MinJarMaker.java	2010/03/30 19:14:04	1.6
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/minnow/MinJarMaker.java	2010/04/09 16:58:13	1.7
@@ -812,7 +812,7 @@
 	       relativePath.equals("META-INF") || //this one causes null pointers in jarsigner 
 	       relativePath.equals("testdata") || 
 	       relativePath.equals("deployment") || 
-	       relativePath.equals("CVS")){
+	       relativePath.endsWith("CVS")){
 		//System.err.println("Skipping " + relativePath);
 		continue;
 	    }


From gordonp at dev.open-bio.org  Fri Apr  9 20:40:17 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 9 Apr 2010 20:40:17 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004100040.o3A0eH2E014912@dev.open-bio.org>


gordonp
Fri Apr  9 20:40:17 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources
In directory dev.open-bio.org:/tmp/cvs-serv14854/src/main/ca/ucalgary/seahawk/resources

Modified Files:
	RegexFilterBeanShell 
Log Message:
Added support for filter inversion (boolean negation)
moby-live/Java/src/main/ca/ucalgary/seahawk/resources RegexFilterBeanShell,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources/RegexFilterBeanShell,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources/RegexFilterBeanShell	2010/04/09 15:49:18	1.2
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources/RegexFilterBeanShell	2010/04/10 00:40:17	1.3
@@ -11,9 +11,12 @@
 List nodelist = document.selectNodes(xpath);
 
 ArrayList outputXmlList = new ArrayList();
+ArrayList outputXmlList_false = new ArrayList();
 int i = 1;
 Map collections = new LinkedHashMap();
 Map collectionsEnd = new HashMap();
+Map collections_false = new LinkedHashMap();
+Map collectionsEnd_false = new HashMap();
 Pattern pattern = Pattern.compile(regex, Pattern.MULTILINE | Pattern.DOTALL | (Boolean.parseBoolean(case_sensitive) ? 0 : Pattern.CASE_INSENSITIVE));
 for (Iterator iter = nodelist.iterator(); iter.hasNext();) {
         Node node = (Node) iter.next();
@@ -31,10 +34,17 @@
                         break;
                 default: break;
         }
-        if(!match){
-                continue;
-        }
 
+	Map cs = null;
+	Map csEnd = null;
+        if(match){
+		cs = collections;
+		csEnd = collectionsEnd;
+	}
+	else{
+		cs = collections_false;
+		csEnd = collectionsEnd_false;
+        }
         //go up the tree until we hit a mobyData...this is the unit we can forward
         StringBuilder collection = null;
         StringBuilder collectionEnd = null;
@@ -43,11 +53,11 @@
                    node.getParent().getName().equals("Collection")){
                         collection = new StringBuilder();  //start tracking parents
                         collectionEnd = new StringBuilder();
-                        if(!collections.containsKey(collection)){
-                                collections.put(collection, new Vector());
-                                collectionsEnd.put(collection, collectionEnd);
+                        if(!cs.containsKey(collection)){
+                                cs.put(collection, new Vector());
+                                csEnd.put(collection, collectionEnd);
                         }
-                        ((Vector)collections.get(collection)).add(node.asXML());
+                        ((Vector)cs.get(collection)).add(node.asXML());
                 }
                 node = node.getParent();
                 if(node != null && collection != null){
@@ -61,14 +71,17 @@
                         collectionEnd.append("</"+((Element) node).getQualifiedName()+">");
                 }
         }
-        if(node == null){
+        if(node == null){ // wasn't part of a mobyData block
                 continue;
         }
-        // At mobyData level if we got here
+        // At mobyData level if we got here, add if job not already present
         if(collection == null){
-                outputXmlList.add(
-                "<moby:MOBY xmlns:moby='http://www.biomoby.org/moby' xmlns='http://www.biomoby.org/moby'>"+
-                "<moby:mobyContent>"+node.asXML()+"</moby:mobyContent></moby:MOBY>");
+		String jobData = "<moby:MOBY xmlns:moby='http://www.biomoby.org/moby' xmlns='http://www.biomoby.org/moby'>"+
+                		 "<moby:mobyContent>"+node.asXML()+"</moby:mobyContent></moby:MOBY>";
+                List list = (match ? outputXmlList : outputXmlList_false);
+		if(!list.contains(jobData)){
+			list.add(jobData);
+		}
         }
 }
 
@@ -83,6 +96,16 @@
         }
         ((List) uniqueCollections.get(keyString)).addAll((List) collection.getValue());
 }
+Map uniqueCollections_false = new LinkedHashMap();
+Map uniqueCollectionsEnd_false = new LinkedHashMap();
+for(Map.Entry collection: collections_false.entrySet()){
+        String keyString = collection.getKey().toString();
+        if(!uniqueCollections_false.containsKey(keyString)){
+                uniqueCollections_false.put(keyString, new Vector());
+                uniqueCollectionsEnd_false.put(keyString, collectionsEnd_false.get(collection.getKey()));
+        }
+        ((List) uniqueCollections_false.get(keyString)).addAll((List) collection.getValue());
+}
 
 //Now concat the collection members that pass the filter
 for(Map.Entry collection: uniqueCollections.entrySet()){
@@ -99,6 +122,21 @@
 
         outputXmlList.add(block.toString());
 }
+for(Map.Entry collection: uniqueCollections_false.entrySet()){
+        StringBuilder block = new StringBuilder();
+        block.append("<moby:MOBY xmlns:moby='http://www.biomoby.org/moby' xmlns='http://www.biomoby.org/moby'>\n");
+        block.append("<moby:mobyContent>\n");
+        block.append(collection.getKey().toString());
+        for(String val: (List) collection.getValue()){
+                block.append(val);
+        }
+        block.append(uniqueCollectionsEnd_false.get(collection.getKey().toString()));  // closing tags
+        block.append("</moby:mobyContent>\n");
+        block.append("</moby:MOBY>\n");
+
+        outputXmlList_false.add(block.toString());
+}
 
-List nodelistAsXML=outputXmlList;
+List TRUE_nodelistAsXML=outputXmlList;
+List FALSE_nodelistAsXML=outputXmlList_false;
 


From gordonp at dev.open-bio.org  Fri Apr  9 20:40:17 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 9 Apr 2010 20:40:17 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004100040.o3A0eHik014894@dev.open-bio.org>


gordonp
Fri Apr  9 20:40:17 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv14854/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	FilterSearchWidget.java MobyContentPane.java 
Log Message:
Added support for filter inversion (boolean negation)
moby-live/Java/src/main/ca/ucalgary/seahawk/gui FilterSearchWidget.java,1.2,1.3 MobyContentPane.java,1.24,1.25
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/FilterSearchWidget.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/FilterSearchWidget.java	2010/04/09 15:50:09	1.2
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/FilterSearchWidget.java	2010/04/10 00:40:17	1.3
@@ -18,12 +18,18 @@
     private FilterSearch currentFilterSearch;
     private JLabel closeIcon;
     private JToggleButton caseButton;
+    private JButton inverseButton; // decides whether filter is "if" or "unless"
     private JTextField searchField;
     private JComboBox docPartOptions;
     private MobyContentPane contentPane;
     public static final String CASE_SENSITIVE_ICON_RESOURCE = "ca/ucalgary/seahawk/resources/images/case_sensitive.png";
     public static final String CASE_INSENSITIVE_ICON_RESOURCE = "ca/ucalgary/seahawk/resources/images/case_insensitive.png";
+    private static final String IF_TEXT = "<html><u>if</u></html>";
+    private static final String UNLESS_TEXT = "<html><u>unless</u></html>";
+    private static final String CASE_INSENSITIVE_MSG = "<html>The filter is case insensitive,<br>click to make case sensitive</html>";
+    private static final String CASE_SENSITIVE_MSG = "<html>The filter is case sensitive,<br>click to make case insensitive</html>";
     private static final String CASE_BUTTON_NAME = "case_sensitivity_button"; 
+    private static final String INVERSE_BUTTON_NAME = "boolean_button"; 
 
     private static Logger logger = Logger.getLogger(FilterSearchWidget.class.getName());
 
@@ -45,7 +51,7 @@
 	Dimension buttonSize = new Dimension(24,24);
 	caseButton = new JToggleButton(new ImageIcon(cl.getResource(CASE_SENSITIVE_ICON_RESOURCE)));
 	caseButton.setDisabledIcon(new ImageIcon(cl.getResource(CASE_INSENSITIVE_ICON_RESOURCE)));
-	caseButton.setToolTipText("Toggles the case sensitivity of the filter");
+	caseButton.setToolTipText(CASE_INSENSITIVE_MSG);
 	caseButton.setPreferredSize(buttonSize);
 	caseButton.setEnabled(true);
 	caseButton.setSelected(false);
@@ -53,12 +59,20 @@
 	caseButton.setMargin(new java.awt.Insets(2,2,2,2));
         caseButton.setName(CASE_BUTTON_NAME); // so test cases can find the component
 
+	inverseButton = new JButton(IF_TEXT);
+	inverseButton.setToolTipText("<html>Click to invert the selection between \"if\" and \"unless\"</html>");
+	inverseButton.setEnabled(true);
+	inverseButton.addActionListener(this);
+	inverseButton.setBorderPainted(false); // underline is hint enough that we can press it...looks cleaner
+        inverseButton.setName(INVERSE_BUTTON_NAME); // so test cases can find the component	
+
 	setLayout(new BoxLayout(this, BoxLayout.LINE_AXIS));
 	add(closeIcon);
 	add(Box.createRigidArea(new Dimension(5,0)));
 	add(caseButton);
 	add(Box.createRigidArea(new Dimension(5,0)));
-	add(new JLabel("Show data if "));
+	add(new JLabel("Show data "));
+	add(inverseButton);
 	add(Box.createRigidArea(new Dimension(5,0)));
 	searchField = new JTextField(25);
 	searchField.setToolTipText("A literal string, or a regular expression");
@@ -81,11 +95,15 @@
 	currentFilterSearch = null;
 	if(fs == null){
 	    caseButton.setEnabled(false);
+	    inverseButton.setEnabled(false);
 	    searchField.setEnabled(false);
 	    docPartOptions.setEnabled(false);
 	    return;
 	}
 
+	inverseButton.setEnabled(true);
+	inverseButton.setText(fs.getSelectionInversed() ? UNLESS_TEXT : IF_TEXT);
+
 	caseButton.setEnabled(true);
 	caseButton.setSelected(fs.getCaseSensitivity());
 
@@ -101,11 +119,30 @@
      * Called when the user has changed the xpath
      */
     public void actionPerformed(ActionEvent e){
-	if(e.getSource() == caseButton){
+	if(e.getSource() == inverseButton){
+	    // Toggle the label for the if/unless button
+	    if(inverseButton.getText().equals(IF_TEXT)){
+		inverseButton.setText(UNLESS_TEXT);
+		currentFilterSearch.setSelectionInversed(true);
+	    }
+	    else{
+		inverseButton.setText(IF_TEXT);
+		currentFilterSearch.setSelectionInversed(false);
+	    }
+	    contentPane.applyFilter(true);
+	    return;
+        }
+	else if(e.getSource() == caseButton){
 	    if(currentFilterSearch == null){
 	        return;
             }
             currentFilterSearch.setCaseSensitivity(caseButton.isSelected());
+	    if(caseButton.isSelected()){
+		caseButton.setToolTipText(CASE_SENSITIVE_MSG);
+	    }
+	    else{
+		caseButton.setToolTipText(CASE_INSENSITIVE_MSG);
+	    }
 	    contentPane.applyFilter(true);
 	    return;
         }
@@ -127,6 +164,7 @@
 	sb.replace(0, sb.length(), searchField.getText());
 	contentPane.applyFilter(true);
     }
+
     public void insertUpdate(DocumentEvent e){
 	if(currentFilterSearch == null){
 	    return;

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java,v
retrieving revision 1.24
retrieving revision 1.25
diff -u -r1.24 -r1.25
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java	2010/04/09 15:54:16	1.24
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java	2010/04/10 00:40:17	1.25
@@ -1239,7 +1239,6 @@
 	    popup.add(createServicePopupItem);
 	    popup.setVisible(true);	    
 	}
-	// todo: 
 	// The item below is mainly to allow X to be used in service Y if running service Z on X meets some filter criteria.
 	// This is a common task in bioinformatics workflows.
 	// Backtrack from data to input used for service that generated the data.
@@ -1510,12 +1509,15 @@
 	    }
 	}
 	
+	boolean inversed = fs.getSelectionInversed();
 	Map<String,Boolean> parentMatchingXPtrs = new LinkedHashMap<String,Boolean>();
 	for(String currXPtr: filterableNodes){
 	    for(Map.Entry<String,Boolean> matchingXPtr: matchingXPtrs.entrySet()){
 		if(matchingXPtr.getKey().startsWith(currXPtr+"/")){ // a parent of the matching data
 		    // No positive example yet?
-		    if(!parentMatchingXPtrs.containsKey(currXPtr) || !parentMatchingXPtrs.get(currXPtr).booleanValue()){
+		    if(!parentMatchingXPtrs.containsKey(currXPtr) || 
+		       !inversed && !parentMatchingXPtrs.get(currXPtr).booleanValue() ||
+		       inversed && parentMatchingXPtrs.get(currXPtr).booleanValue()){
 			System.err.println("Adding "+ matchingXPtr.getValue() + " for " + currXPtr);
 			parentMatchingXPtrs.put(currXPtr, matchingXPtr.getValue());
 		    }
@@ -1526,11 +1528,16 @@
 	matchingXPtrs.putAll(parentMatchingXPtrs);
 	for(String currXPtr: matchingXPtrs.keySet()){
 	    // Is part of the selection criteria, but doesn't match the regex
+	    boolean shouldFilter = false;
 	    if(!matchingXPtrs.get(currXPtr).booleanValue() &&
-	       // special condition: if "entire document" xpath is given, filter only at the job level
+	       // special condition: if "entire response" xpath is given, filter only at the job level
 	       (!currentSelectionXPath.equals(FilterSearch.SELECT_ALL_XPATH) || jobXPtrs.containsKey(currXPtr))){
-		filteredData.put(currXPtr, "todo");
+		shouldFilter = true;
 	    }
+	    if(!inversed && shouldFilter ||
+	       inversed && !shouldFilter){ 
+		filteredData.put(currXPtr, "todo");
+	    }	    
 	}
 
 	//todo: filter objects without the HAS field at all...


From gordonp at dev.open-bio.org  Fri Apr  9 20:40:18 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 9 Apr 2010 20:40:18 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004100040.o3A0eIZb014938@dev.open-bio.org>


gordonp
Fri Apr  9 20:40:17 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util
In directory dev.open-bio.org:/tmp/cvs-serv14854/src/main/ca/ucalgary/seahawk/util

Modified Files:
	DataFlowRecorder.java DataUtils.java FilterSearch.java 
Log Message:
Added support for filter inversion (boolean negation)
moby-live/Java/src/main/ca/ucalgary/seahawk/util DataFlowRecorder.java,1.3,1.4 DataUtils.java,1.2,1.3 FilterSearch.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataFlowRecorder.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataFlowRecorder.java	2010/04/09 15:58:22	1.3
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataFlowRecorder.java	2010/04/10 00:40:17	1.4
@@ -174,7 +174,8 @@
 	    String[] regexProcessorAndPorts = null;
 	    String filterKey = null;
 	    if(filter != null && filter.getFilterRegex().length() > 0){
-		filterKey = result.getKey()+"\n"+filter.getFilterRegex()+"\n"+filter.getSelectedXPath().getXPath();
+		filterKey = result.getKey()+"\n"+filter.getFilterRegex()+"\n"+
+		    filter.getSelectedXPath().getXPath()+"\n"+filter.getCaseSensitivity();
 	    }
 
 	    // Create the workflow output and data links
@@ -206,8 +207,10 @@
 			filter2Processor.put(filterKey, regexProcessorAndPorts);
 		    }
 
+		    // The proc has an output port for non-matches (penultimate index) and matches (ultimate index)
+		    int regexOutPort = regexProcessorAndPorts.length-(filter.getSelectionInversed() ? 2 : 1);
 		    datalinks.appendChild(createWorkflowOutputLinkElement(regexProcessorAndPorts[0],
-									  regexProcessorAndPorts[regexProcessorAndPorts.length-1],
+									  regexProcessorAndPorts[regexOutPort],
 									  uniqueOutputName,
 									  doc));
 		    break; // only one output when filter is attached: the XML doc
@@ -317,16 +320,18 @@
 		// where the filter and conditionalURL are optional 
 		data = sampleData.getUserData().toString().split("\t");
 		//options: selection + filter + cond, selection + cond, or cond only
-		if(data.length == 11 || data.length == 7 || data.length == 5){
+		if(data.length == 14 || data.length == 8 || data.length == 6){
 		    System.err.println("Adding conditional for " + resultURLString);
-		    String conditionURL = data[data.length-5];
-		    String conditionRegex = data[data.length-4];
-		    XPathOption conditionXPath = new XPathOption(data[data.length-3], data[data.length-2]);
-		    boolean caseSensitivity = Boolean.parseBoolean(data[data.length-1]);
-		    condPassProcessorAndPorts = createServiceConditionFilter(new URL(conditionURL), conditionRegex, conditionXPath, caseSensitivity,
+		    String conditionURL = data[data.length-6];
+		    String conditionRegex = data[data.length-5];
+		    XPathOption conditionXPath = new XPathOption(data[data.length-4], data[data.length-3]);
+		    boolean caseSensitivity = Boolean.parseBoolean(data[data.length-2]);
+		    boolean inverse = Boolean.parseBoolean(data[data.length-1]);
+		    condPassProcessorAndPorts = createServiceConditionFilter(new URL(conditionURL), conditionRegex, 
+									     conditionXPath, caseSensitivity, inverse,
 									     doc, inputPorts, processors, datalinks);
-		    String[] conditionlessData = new String[data.length-5];
-		    System.arraycopy(data, 0, conditionlessData, 0, data.length-5);
+		    String[] conditionlessData = new String[data.length-6];
+		    System.arraycopy(data, 0, conditionlessData, 0, data.length-6);
 		    data = conditionlessData;
 		}
 		else{
@@ -357,10 +362,10 @@
 		    feedingProcessorName = addWorkflowElements(dataSrcURL, doc, inputPorts, processors, datalinks);
 		}
 		
-		// Take into account data[2..5] if they are present, 
+		// Take into account data[2..6] if they are present, 
 		// which filter the data by a regex before any other activities happen
 		// Format of spec is regex <tab> xpath <tab> xpathTextDesc <tab> booleanForCaseSensitivity
-		if(data.length == 6){
+		if(data.length == 7){
 		    String[] origFeederProcessorAndPort = getPortFromURLRef(dataSrcURL,
 									    sampleData,
 									    feedingProcessorName,
@@ -370,9 +375,11 @@
 									    doc,
 									    false);
 		    
-		    // Lookup key is url \n regex \n xpath \n caseSensitivity
+		    // Lookup key is url \n regex \n xpath \n caseSensitivity 
+		    // (inverse selection uses same processor, different output port, so not part of the key)
 		    String[] regexProcessorAndPorts = null;
 		    String filterKey = dataSrcURLString+"\n"+data[2]+"\n"+data[3]+"\n"+data[5];
+		    boolean inversed = Boolean.parseBoolean(data[6]);
 		    if(filter2Processor.containsKey(filterKey)){ // filter already exists from another branch
 			regexProcessorAndPorts = filter2Processor.get(filterKey);
 		    }
@@ -389,7 +396,9 @@
 			filter2Processor.put(filterKey, regexProcessorAndPorts);
 		    }
 		    feedingProcessorName = regexProcessorAndPorts[0];
-		    feedingProcessorPort = regexProcessorAndPorts[regexProcessorAndPorts.length-1];  //last one is output
+		    // The proc has an output port for non-matches (penultimate index) and matches (ultimate index)
+		    int regexOutPort = regexProcessorAndPorts.length-(inversed ? 2 : 1);
+		    feedingProcessorPort = regexProcessorAndPorts[regexOutPort];  
 		}
 		
 		// getPortFromURLRef() may inject extra processors between the processorName and feedingProcessorName
@@ -921,6 +930,7 @@
 		// supertype of the output from the other service!		
 		if(namespace != null){
 		    MobyNamespace nsObj = MobyNamespace.getNamespace(namespace, getRegistryFromService(srcService));
+		    System.err.println("About to create namespace filter for "+ srcProcessor + " port " + portName + " when srcPort was " + srcPort);
 		    return createNamespaceFilter(nsObj, srcProcessor, portName, processors, datalinks, doc);
 		}
 		else if(xrefNs != null){
@@ -974,7 +984,7 @@
     // and passing the filter condition set on f.  Equivalent to if(f(X) matches f_filter){...}
     // returns [proc name, input port, output port]
     private String[] createServiceConditionFilter(URL conditionURL, String filterRegex, XPathOption filterXPath,
-						  boolean caseSensitive, Document doc,
+						  boolean caseSensitive, boolean inverse, Document doc,
 						  Element inputPorts, Element processors, Element datalinks)
 	throws Exception{
 
@@ -996,30 +1006,31 @@
  	}
 
  	String filterKey = dataSrcURLString+"\n"+filterRegex+"\n"+filterXPath.getXPath()+"\n"+caseSensitive;
- 	String[] regexFilterProcNameAndPort = null;
+ 	String[] regexFilterProcNameAndPorts = null;
  	//todo: gimpy loop below, as more than one service output would cause a trampling of regex output ports
  	for(MobyPrimaryData outputParam: service.getPrimaryOutputs()){
  	    // See if the filter on the conditional service has already been used in the workflow
  	    if(filter2Processor.containsKey(filterKey)){
- 		regexFilterProcNameAndPort = filter2Processor.get(filterKey);
+ 		regexFilterProcNameAndPorts = filter2Processor.get(filterKey);
  	    }
  	    else{
- 		regexFilterProcNameAndPort = createRegexFilter(filterRegex, 
+ 		regexFilterProcNameAndPorts = createRegexFilter(filterRegex, 
  							       filterXPath,
 							       caseSensitive, 
  							       processorName,
  							       getPortName(outputParam, true),
 							       0, //depth of list desired (will return match count)
  							       processors, datalinks, doc);
- 		filter2Processor.put(filterKey, regexFilterProcNameAndPort);
+ 		filter2Processor.put(filterKey, regexFilterProcNameAndPorts);
  	    }
  	}
 
 	// We need to flatten the 2-deep list generated by the regex filter's cross product
 	String[] beanShellFlattenerProcNameAndPorts = addListFlattenBeanShell(processors, doc);
 
-	datalinks.appendChild(createDataLinkElement(regexFilterProcNameAndPort[0],
-						    regexFilterProcNameAndPort[1],
+	int regexOutPort = regexFilterProcNameAndPorts.length-(inverse ? 2 : 1);
+	datalinks.appendChild(createDataLinkElement(regexFilterProcNameAndPorts[0],
+						    regexFilterProcNameAndPorts[regexOutPort],
 						    beanShellFlattenerProcNameAndPorts[0], 
 						    beanShellFlattenerProcNameAndPorts[1],
 						    doc));
@@ -1068,7 +1079,9 @@
 						    beanShellFilterProcNameAndPorts[0], 
 						    beanShellFilterProcNameAndPorts[4],
 						    doc)); 
-	return new String[]{beanShellFilterProcNameAndPorts[0], beanShellFilterProcNameAndPorts[5]};	
+	return new String[]{beanShellFilterProcNameAndPorts[0], 
+			    beanShellFilterProcNameAndPorts[5], // false (non-matching) output
+			    beanShellFilterProcNameAndPorts[6]}; // true (matching) output
     }
     
     private String[] createXrefParser(MobyNamespace nsObj, String srcProcessor, String srcPort, 
@@ -1090,6 +1103,7 @@
 	throws Exception{
 
 	String decompKey = srcProcessor+"\n"+srcPort+"\n"+xpath;
+	System.err.println("Decomp key is " + decompKey);
 	// Has this decomp already been created in another branch?
 	if(decomp2Processor.containsKey(decompKey)){
 	    return decomp2Processor.get(decompKey);
@@ -1108,7 +1122,7 @@
 						    beanShellFilterProcNameAndPorts[0], 
 						    beanShellFilterProcNameAndPorts[2],
 						    doc)); 
-	String[] procSpec =  new String[]{beanShellFilterProcNameAndPorts[0], beanShellFilterProcNameAndPorts[3]};
+	String[] procSpec = new String[]{beanShellFilterProcNameAndPorts[0], beanShellFilterProcNameAndPorts[3]};
 	decomp2Processor.put(decompKey, procSpec); //in case we need to reuse it in another branch
 	return procSpec;
     }
@@ -1453,10 +1467,12 @@
 	inputTypes.put("case_sensitive", "text/plain");
 	Map<String,String> outputsMap = new LinkedHashMap<String,String>();
 	if(listDepth == 0){
-	    outputsMap.put("matchCount", "0");
+	    outputsMap.put("FALSE_matchCount", "0");
+	    outputsMap.put("TRUE_matchCount", "0");
         }
         else{
-            outputsMap.put("nodelistAsXML", ""+listDepth);
+            outputsMap.put("FALSE_nodelistAsXML", ""+listDepth);
+            outputsMap.put("TRUE_nodelistAsXML", ""+listDepth);
         }
 
 	return addBeanShell(beanShellProcName, "cross",
@@ -1991,8 +2007,9 @@
 	    }
 	    regexFilterScript = HTMLUtils.getURLContents(scriptURL);
 	}
-	if(listDepth == 0){// list to scalar conversion
-	    return regexFilterScript+"\nString matchCount = \"\"+nodelistAsXML.size();";
+	if(listDepth == 0){// list to scalar conversions
+	    return regexFilterScript+"\nString TRUE_matchCount = \"\"+TRUE_nodelistAsXML.size();\n"+
+		                     "\nString FALSE_matchCount = \"\"+FALSE_nodelistAsXML.size();\n";
         }
         else{
  	    return regexFilterScript;

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataUtils.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataUtils.java	2010/04/09 15:57:46	1.2
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataUtils.java	2010/04/10 00:40:17	1.3
@@ -117,7 +117,8 @@
 		    if(newFilter != null){
 			XPathOption xsel = newFilter.getSelectedXPath();
 			newProvenanceData += "\t"+newFilter.getFilterRegex()+
-			    "\t"+xsel.getXPath()+"\t"+xsel.getDesc()+"\t"+newFilter.getCaseSensitivity();
+			    "\t"+xsel.getXPath()+"\t"+xsel.getDesc()+"\t"+
+			    newFilter.getCaseSensitivity()+"\t"+newFilter.getSelectionInversed();
 		    }
 		    pi.setData(attr_val[0]+"=\""+newProvenanceData+"\"");
 		}
@@ -640,7 +641,8 @@
 	
 	if(fs != null && fs.getFilterRegex().length() > 0){
 	    XPathOption xsel = fs.getSelectedXPath();
-	    userData.append("\t"+fs.getFilterRegex()+"\t"+xsel.getXPath()+"\t"+xsel.getDesc()+"\t"+fs.getCaseSensitivity());
+	    userData.append("\t"+fs.getFilterRegex()+"\t"+xsel.getXPath()+"\t"+xsel.getDesc()+"\t"+
+			    fs.getCaseSensitivity()+"\t"+fs.getSelectionInversed());
 	}
 	mobyData.setUserData(userData.toString());
     }
@@ -653,7 +655,8 @@
 	String filterSpec = "";
 	if(filter != null && filter.getFilterRegex().length() > 0){
 	    XPathOption xsel = filter.getSelectedXPath();
-	    filterSpec = "\t"+filter.getFilterRegex()+"\t"+xsel.getXPath()+"\t"+xsel.getDesc()+"\t"+filter.getCaseSensitivity();
+	    filterSpec = "\t"+filter.getFilterRegex()+"\t"+xsel.getXPath()+"\t"+xsel.getDesc()+"\t"+
+		filter.getCaseSensitivity()+"\t"+filter.getSelectionInversed();
 	}
 	if(mdi.getUserData() != null){
 	    mdi.setUserData(mdi.getUserData().toString()+"\t"+conditionalOutputURL+filterSpec);

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/FilterSearch.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/FilterSearch.java	2010/04/09 15:48:19	1.3
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/FilterSearch.java	2010/04/10 00:40:17	1.4
@@ -21,6 +21,7 @@
 
     private URL docURL;
     private boolean caseSensitivity = false;
+    private boolean inverseSelection = false;
     private StringBuffer filterRegex;
     private Vector<XPathOption> xpathOptions;
     private int xpathSelected = 0;
@@ -74,6 +75,14 @@
 	}
     }
 
+    public boolean getSelectionInversed(){
+	return inverseSelection;
+    }
+
+    public void setSelectionInversed(boolean inversed){
+	inverseSelection = inversed;
+    }
+
     public boolean getCaseSensitivity(){
 	return caseSensitivity;
     }


From gordonp at dev.open-bio.org  Sat Apr 10 18:42:09 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Sat, 10 Apr 2010 18:42:09 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004102242.o3AMg9nE014502@dev.open-bio.org>


gordonp
Sat Apr 10 18:42:09 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data
In directory dev.open-bio.org:/tmp/cvs-serv14466/src/main/org/biomoby/shared/data

Modified Files:
	MobyDataObject.java 
Log Message:
Improved equals() for base object equivalency...value not instance based
moby-live/Java/src/main/org/biomoby/shared/data MobyDataObject.java,1.26,1.27
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataObject.java,v
retrieving revision 1.26
retrieving revision 1.27
diff -u -r1.26 -r1.27
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataObject.java	2008/01/07 22:11:36	1.26
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataObject.java	2010/04/10 22:42:09	1.27
@@ -302,7 +302,7 @@
     public boolean equals(Object passedInObject) throws ClassCastException{
       Object ourObject = getObject();
       if(passedInObject != null && passedInObject instanceof MobyDataObject){
-	  if(((MobyDataObject) passedInObject).getDataType() == getDataType()){
+	  if(((MobyDataObject) passedInObject).getDataType().equals(getDataType())){
 	      // An object of the same class.  See if their XMLs are equivalent.
 	      int ourOldXMLMode = getXmlMode();
 	      int itsOldXMLMode = ((MobyDataObject) passedInObject).getXmlMode();


From gordonp at dev.open-bio.org  Sat Apr 10 21:58:05 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Sat, 10 Apr 2010 21:58:05 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004110158.o3B1w59N019017@dev.open-bio.org>


gordonp
Sat Apr 10 21:58:05 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services
In directory dev.open-bio.org:/tmp/cvs-serv18981/src/main/ca/ucalgary/seahawk/services

Modified Files:
	MobyClient.java 
Log Message:
Added regex support for IUPAC monosacchride residues (\M)
moby-live/Java/src/main/ca/ucalgary/seahawk/services MobyClient.java,1.25,1.26
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/MobyClient.java,v
retrieving revision 1.25
retrieving revision 1.26
diff -u -r1.25 -r1.26
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/MobyClient.java	2010/03/17 20:21:55	1.25
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/MobyClient.java	2010/04/11 01:58:05	1.26
@@ -1391,14 +1391,15 @@
 
     /**
      * Converts seahawk-specific regex syntax into generic Java syntax (e.g \N becomes a
-     * match for any IUPAC DNA character, \P any amino acid).  We pass in the member map so that
+     * match for any IUPAC DNA character, \P any amino acid, \M for any monosacchiride abbreviation).  
+     * We pass in the member map so that
      * this method can populate the last field of rules that inherit complex members (by virtue 
      * of using the capture group whose values is derived from \p{ruleName}), with ruleName 
      */
     protected String processRegExp(String regex, Map<String,String[]> membersMap) throws Exception{
 	String returnValue = regex.replaceAll("\\\\N", "[acgtunxACGTUNX]")
-	    .replaceAll("\\\\P", "[ARNDCQEGHILKMFPSTWYVBZXarndcqeghilkmfpstwyvbz*]");
-	
+	    .replaceAll("\\\\P", "[ARNDCQEGHILKMFPSTWYVBZXarndcqeghilkmfpstwyvbz*]")
+	    .replaceAll("\\\\M", "(?:Abe|IdoA|All|Lyx|Alt|Man|Api|Mur|Ara|Neu|Ara-ol|Neu5Ac|dRib|Neu2en5Ac|Fru|Neu5Gc|Fuc|Kdo|Fuc-ol|Rha|Gal|Rha3,4Me2|GalN|Psi|GalNAc|Qui|B-D-Galp4S|Rib|Glc|Rib5P|GlcN|Ribulo|Rul|GlcN3N|Sor|Glc-ol|Tag|GlcNAc|Tal|GlcA|Xyl|GlcpA6Et|Xylulo|Xul|Gul|Xyl2CMe|Ido)");
 	// Now see if there are any references to other patterns (by rule name) 
 	// with the \p{} syntax specific to Seahawk
 	Pattern charClassPattern = Pattern.compile("\\\\p\\{([A-Za-z0-9]+)\\}");


From gordonp at dev.open-bio.org  Sat Apr 10 22:00:02 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Sat, 10 Apr 2010 22:00:02 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004110200.o3B202wI019153@dev.open-bio.org>


gordonp
Sat Apr 10 22:00:02 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv19034/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	MobyObjectTransferHandler.java 
Log Message:
Added native support for primitive datatype recognition in text transfers
moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyObjectTransferHandler.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyObjectTransferHandler.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyObjectTransferHandler.java	2007/12/17 18:44:13	1.3
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyObjectTransferHandler.java	2010/04/11 02:00:02	1.4
@@ -218,7 +218,30 @@
 	for(String fieldName: acceptableData.keySet()){
 	    int itemCount = 1;
 	    MobyDataType desiredDataType = acceptableData.get(fieldName).getDataType();
+	    String dataTypeName = desiredDataType.getName();
 	    System.err.println("Checking text for field " + fieldName+ ", data type " + desiredDataType.getName());
+
+	    // trivial data creations first ...
+	    if(dataTypeName.equals(MobyTags.MOBYSTRING)){
+		foundData.put(fieldName+"#"+itemCount++, new MobyDataString(text));
+	    }
+	    else if(dataTypeName.equals(MobyTags.MOBYBOOLEAN) && 
+		    text.matches("(true|True|TRUE|1|yes|Yes|YES|false|False|FALSE|0|no|No|NO)")){
+		foundData.put(fieldName+"#"+itemCount++, 
+			      new MobyDataBoolean(text.matches("(true|True|TRUE|1|yes|Yes|YES)")));
+	    }
+	    else if(dataTypeName.equals(MobyTags.MOBYINTEGER) && 
+		    text.matches("\\d+")){
+		foundData.put(fieldName+"#"+itemCount++, new MobyDataInt("", text));
+	    }
+	    else if(dataTypeName.equals(MobyTags.MOBYFLOAT) && 
+		    text.matches("\\d+(?:\\.\\d*)?(?:[eE][\\-\\+]?\\d+)?")){
+		foundData.put(fieldName+"#"+itemCount++, new MobyDataFloat(text));
+	    }
+	    else if(dataTypeName.equals(MobyTags.MOBYFLOAT) && 
+		    text.matches("(?:19|20)\\d\\d-(?:0[1-9]|1[012])-([012][1-9]|3[01])")){
+		foundData.put(fieldName+"#"+itemCount++, new MobyDataDateTime(text));
+	    }
 	    MobyDataObject[] textData = client.getMobyObjects(text, desiredDataType);
 	    if(textData != null){
 		System.err.println("Found " + textData.length + " matches");


From gordonp at dev.open-bio.org  Sat Apr 10 22:20:46 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Sat, 10 Apr 2010 22:20:46 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004110220.o3B2Kkwu020079@dev.open-bio.org>


gordonp
Sat Apr 10 22:20:46 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources
In directory dev.open-bio.org:/tmp/cvs-serv20043/src/main/ca/ucalgary/seahawk/resources

Modified Files:
	mobyBuilderRules.xml 
Log Message:
Added LINUCS carbohydrate sequence recognition, for fun
moby-live/Java/src/main/ca/ucalgary/seahawk/resources mobyBuilderRules.xml,1.10,1.11
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources/mobyBuilderRules.xml,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources/mobyBuilderRules.xml	2010/03/17 20:21:55	1.10
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources/mobyBuilderRules.xml	2010/04/11 02:20:46	1.11
@@ -66,6 +66,16 @@
   <member value="Length" whitespace="strip">string-length('$1')</member>
 </object>
 
+<!-- \M is IUPAC monosaccharide residue shorthand -->
+<object>
+  <regex>\[\]\[\\S+\]\{.*?(?:([ab]-D-)?\M.?[\x20\(\)\[\]\-\+0-9\{\}]+){3,}</regex>
+  <datatype value="LINUCS"/>
+  <namespace>
+    <ns value="unknown">''</ns>
+  </namespace>
+  <member value="sequence" whitespace="strip">$0</member>
+</object>
+
 <!-- ABI sequence trace's magic signature at start of file -->
 <object>
   <regex>\AABIF.*\z</regex>


From gordonp at dev.open-bio.org  Sat Apr 10 22:22:07 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Sat, 10 Apr 2010 22:22:07 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004110222.o3B2M7Dc020123@dev.open-bio.org>


gordonp
Sat Apr 10 22:22:06 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv20087/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	MobyDataObjectWidget.java 
Log Message:
Better populated data field description
moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyDataObjectWidget.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyDataObjectWidget.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyDataObjectWidget.java	2007/12/06 17:26:26	1.3
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyDataObjectWidget.java	2010/04/11 02:22:06	1.4
@@ -18,6 +18,7 @@
  */
 public class MobyDataObjectWidget extends JLabel implements MobyObjectReceiver, MobyContentProducer{
     public static final int PARAM_TOOLTIP_WIDTH = 50;
+    public static final int MAX_DATA_DESC = 30;
     public static final Color INSTANTIATED_FG_COLOUR = Color.DARK_GRAY;
     public static final Color UNINSTANTIATED_FG_COLOUR = Color.RED;
     public static final String INSTANTIATED_ICON_RESOURCE = "ca/ucalgary/seahawk/resources/images/checkmark.gif";
@@ -150,7 +151,14 @@
 		labelText = name+": Collection("+dataType.getName()+") -- "+actualData.getName();
 	    }
 	    else{
-		labelText = name+": "+dataType.getName()+" -- "+actualData.getName();
+		String display = actualData.getName();
+		if(display == null || display.trim().length() == 0){
+		    display = ((MobyDataInstance) actualData).getObject().toString();
+		}
+		if(display.length() > MAX_DATA_DESC){
+		    display = display.substring(0, MAX_DATA_DESC-3)+"...";
+		}
+		labelText = name+": "+dataType.getName()+" -- "+display;
 	    }
 	    tipText = dataType.getDescription();
 	    if(tipText == null || tipText.length() == 0){


From gordonp at dev.open-bio.org  Sat Apr 10 22:25:03 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Sat, 10 Apr 2010 22:25:03 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004110225.o3B2P3eJ020209@dev.open-bio.org>


gordonp
Sat Apr 10 22:25:03 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv20173/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	MobyContentClipboard.java 
Added Files:
	DataImportChoiceDialog.java DataImportChoiceListener.java 
Log Message:
Improved data import to clipboard UI
moby-live/Java/src/main/ca/ucalgary/seahawk/gui DataImportChoiceDialog.java,NONE,1.1 DataImportChoiceListener.java,NONE,1.1 MobyContentClipboard.java,1.9,1.10
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentClipboard.java,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentClipboard.java	2010/04/09 15:51:53	1.9
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentClipboard.java	2010/04/11 02:25:03	1.10
@@ -6,6 +6,7 @@
 
 import org.biomoby.client.MobyRequestEventHandler;
 import org.biomoby.shared.MobyDataType;
+import org.biomoby.shared.MobyNamespace;
 import org.biomoby.shared.data.*;
 import org.biomoby.shared.parser.MobyTags;
 
@@ -20,12 +21,13 @@
 import java.io.FileOutputStream;
 import java.net.URL;
 import java.util.*;
+import java.util.regex.Pattern;
 
 /**
  * The clipboard is a special tab that holds a query with a MOBY Collection
  * that the user can add and subtract MobyDataInstances from.
  */
-public class MobyContentClipboard extends MobyContentPane{
+public class MobyContentClipboard extends MobyContentPane implements DataImportChoiceListener{
     public final static String CLEAR_CLIPBOARD_OPTION = "Clear Clipboard";
     public final static String CLIPBOARD_FILE_NAME = "SeaHawkClipboard";
     public final static String CLIPBOARD_COLLECTION_NAME = "Clipboard Collection";
@@ -41,7 +43,13 @@
     private File clipboardFile;
     private MobyDataJob query;  // lump all data into one query
     private MobyDataObjectSet collection;  // lump all data into one collection
-    private String previousImportDataType = null;
+    private MobyDataType previousImportDataType = null;
+    private MobyNamespace previousImportNS = null;
+
+    private Pattern commentRegex;
+    private Pattern scriptRegex;
+    private Pattern styleRegex;
+    private Pattern tagRegex;
 
     // Clipboard editing variables
     private JMenuItem deleteDataPopupItem;
@@ -88,6 +96,12 @@
 	setTransferHandler(new FileAndTextTransferHandler(cGUI, false)); // false = open data in current tab
 	editorPane.setTransferHandler(getTransferHandler());
 
+	// Setup regexes used for stripping HTML docs of their markup (for data pasting ops)
+	commentRegex = Pattern.compile("<!--.*?-->", Pattern.MULTILINE | Pattern.DOTALL);
+	scriptRegex = Pattern.compile("<script.*?</script>",  Pattern.MULTILINE | Pattern.DOTALL | Pattern.CASE_INSENSITIVE);
+	styleRegex = Pattern.compile("<style.*?</style>",  Pattern.MULTILINE | Pattern.DOTALL | Pattern.CASE_INSENSITIVE);
+	tagRegex = Pattern.compile("<.*?>", Pattern.MULTILINE | Pattern.DOTALL);
+
 	sGUI.setClipboard(this);	
     }
 
@@ -248,7 +262,11 @@
 	    logger.warn("Could not read contents of the URL to import to the clipboard ("+u+"):" +e);
 	    return;
 	}
-	
+	if(urlContents.indexOf("<html") != -1 || urlContents.indexOf("<HTML") != -1){
+	    urlContents = tagRegex.matcher(commentRegex.matcher(styleRegex.matcher(scriptRegex.matcher(urlContents).replaceAll("")).replaceAll("")).replaceAll("")).replaceAll("");
+	}
+	System.err.println(urlContents);
+
 	MobyDataType targetDataType = null;
 	if(collection != null){
 	    targetDataType = collection.getDataType();
@@ -277,47 +295,28 @@
 		return;
 	    }
 	}
-	// Otherwise we need to ask the user what data to import ("Paste as...")
-	// Implicitly...mobyDataFound.length > 1
-	String[] selectionValues = new String[mobyDataFound.length];
-	for(int i = 0; i < mobyDataFound.length; i++){
-	    selectionValues[i] = mobyDataFound[i].getDataType().getName();
-	    if(MobyTags.MOBYOBJECT.equals(selectionValues[i]) &&
-	       mobyDataFound[i].getPrimaryNamespace() != null){
-		selectionValues[i] += " (" + mobyDataFound[i].getPrimaryNamespace().getName() + ")";
-	    }
-	}
-	// Sort alphabetically
-	//Arrays.sort(selectionValues);
-	String initialSelectionValue = selectionValues[0];
-	if(previousImportDataType != null){
-	    for(String selectionValue: selectionValues){
-		if(previousImportDataType.equals(selectionValue)){
-		    initialSelectionValue = selectionValue;
-		    break;
-		}
-	    }
-	}
-	String selection = (String) JOptionPane.showInputDialog(this, 
-								"Paste data as...", 
-								"Data import choice", 
-								JOptionPane.PLAIN_MESSAGE, 
-								(Icon) null, 
-								selectionValues, 
-								initialSelectionValue);
-	if(selection == null){
-	    logger.warn("No data type for import selected, abandoning import");
+
+	// Otherwise we need the user to choose
+	new DataImportChoiceDialog(contentGUI, mobyDataFound, previousImportDataType, previousImportNS, this);
+    }
+
+    // Callback once user has selected the data to import from the DataImportChoiceDialog
+    public void importConfirmed(DataImportChoiceDialog dialog, MobyDataObject[] selectedData){	
+	if(selectedData == null){
+	    logger.warn("Got null for import selection, abandoning import");
 	    return;
 	}
-	for(int i = 0; i < selectionValues.length; i++){
-	    if(selection.equals(selectionValues[i])){
-		addCollectionData(mobyDataFound[i]);
-		previousImportDataType = selection;
-		return;
+	for(int i = 0; i < selectedData.length; i++){
+	    addCollectionData(selectedData[i], i == selectedData.length-1); // only update display on last import
+	    previousImportDataType = selectedData[i].getDataType();
+	    if(selectedData[i].getPrimaryNamespace() != null){
+		previousImportNS = selectedData[i].getPrimaryNamespace();
 	    }
 	}
     }
 
+    public void importCanceled(DataImportChoiceDialog dialog){}
+
     public boolean hasXMLSource(){
 	return true;
     }


From gordonp at dev.open-bio.org  Sun Apr 11 16:15:28 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Sun, 11 Apr 2010 16:15:28 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004112015.o3BKFS3Y017966@dev.open-bio.org>


gordonp
Sun Apr 11 16:15:28 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv17912/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	MobyContentPane.java 
Log Message:
Updates for proper support of data filtering when submitting to forward services
moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyContentPane.java,1.25,1.26
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java,v
retrieving revision 1.25
retrieving revision 1.26
diff -u -r1.25 -r1.26
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java	2010/04/10 00:40:17	1.25
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java	2010/04/11 20:15:28	1.26
@@ -532,7 +532,7 @@
 		isContentsXML = true;
 		// Is it the second stage of wrapping, where data results are being seen?
 		if(urlString.indexOf(WRAPPING_RESULTFILE_PREFIX) != -1){
-		    System.err.println("Wrapping service results");
+		    //System.err.println("Wrapping service results");
 		    isWrapping = true;
 		}
 		else{
@@ -1191,7 +1191,7 @@
 
 	// Complex case, load the doc fragment from the MOBY XML source file
 	if(docFragID != null && docFragID.length() > 0 && !targetURL.getHost().equals("moby")){
-	    return DataUtils.loadMobyDataFromXPointer(targetURL, filterHistory.get(getCurrentURL()));
+	    return DataUtils.loadMobyDataFromXPointer(targetURL, filteredData, filterHistory.get(getCurrentURL()));
 	}
 
 	// Simple case, build the object using the values encoded in the URL itself.
@@ -1256,8 +1256,13 @@
 
 	    // Get the input data for the *previous* service
 	    MobyDataJob inputData = DataUtils.getInputSample(srcDoc, SeahawkOptions.getRegistry());
+	    if(inputData == null){
+		// should only happen if Moby XML was loaded manually by a user, otherwise we've recorded this info...
+		logger.warn("No previous service info in Moby XML, 'previous input' option will not be displayed");
+		return;
+	    }
 	    for(MobyDataInstance previousMDI: inputData.getPrimaryData()){		
-		// add conditional of the current service as a criteria in user data for each previousMDI, 
+		    // add conditional of the current service as a criteria in user data for each previousMDI, 
 		// so PbE will properly reflect the logic of if(f1(x) matches filter){f2(x)}
 		DataUtils.addUserData(previousMDI, srcURL, getFilter());
 
@@ -1478,11 +1483,11 @@
                     }
 		else if(regex.matcher(((Element) node).getTextContent()).find()){
 		    matchingXPtrs.put(elementXPtr, Boolean.TRUE);
-		    System.err.println("Adding " + elementXPtr + " as " + matchingXPtrs.get(elementXPtr));
+		    //System.err.println("Adding " + elementXPtr + " as " + matchingXPtrs.get(elementXPtr));
 		}
 		else{
 		    matchingXPtrs.put(elementXPtr, Boolean.FALSE);
-		    System.err.println("Adding " + elementXPtr + " as " + matchingXPtrs.get(elementXPtr));
+		    //System.err.println("Adding " + elementXPtr + " as " + matchingXPtrs.get(elementXPtr));
 		}
 	    }
 	    else if(node instanceof Attr){
@@ -1494,12 +1499,12 @@
 		else if(regex.matcher(((Attr) node).getValue()).find()){
 		    // Mark the element to which the attribute belongs
 		    matchingXPtrs.put(attrParentXPtr, Boolean.TRUE);
-		    System.err.println("Adding " + attrParentXPtr + " attr parent as " + matchingXPtrs.get(attrParentXPtr));
+		    //System.err.println("Adding " + attrParentXPtr + " attr parent as " + matchingXPtrs.get(attrParentXPtr));
 		}
 		// so false doesn't override true for multi-attr elements
 		else if(!matchingXPtrs.containsKey(attrParentXPtr)){ 
 		    matchingXPtrs.put(attrParentXPtr, Boolean.FALSE);
-		    System.err.println("Adding " + attrParentXPtr + " attr parent as " + matchingXPtrs.get(attrParentXPtr));
+		    //System.err.println("Adding " + attrParentXPtr + " attr parent as " + matchingXPtrs.get(attrParentXPtr));
 		}
 		
 	    }
@@ -1518,7 +1523,7 @@
 		    if(!parentMatchingXPtrs.containsKey(currXPtr) || 
 		       !inversed && !parentMatchingXPtrs.get(currXPtr).booleanValue() ||
 		       inversed && parentMatchingXPtrs.get(currXPtr).booleanValue()){
-			System.err.println("Adding "+ matchingXPtr.getValue() + " for " + currXPtr);
+			//System.err.println("Adding "+ matchingXPtr.getValue() + " for " + currXPtr);
 			parentMatchingXPtrs.put(currXPtr, matchingXPtr.getValue());
 		    }
 		}
@@ -1732,7 +1737,7 @@
 	List<javax.swing.text.Element> links = new Vector<javax.swing.text.Element>();
 	for(int i = 0; i < el.getElementCount(); i++){
 	    javax.swing.text.Element childEl = el.getElement(i);
-	    System.err.println("Found child element " + childEl.getName());
+	    //System.err.println("Found child element " + childEl.getName());
 	    if(HTML.Tag.A.equals(childEl.getName())){
 		links.add(childEl);
 	    }
@@ -1979,10 +1984,10 @@
 	// normally it'd go to mouseDragged, but sometimes that's flakey so check manually for the 
 	// mouse button being down here.
 	if(overHyperlink && (e.getModifiersEx() & MouseEvent.BUTTON1_DOWN_MASK) == MouseEvent.BUTTON1_DOWN_MASK){
-	    System.err.println("Got wonky drag");
+	    //System.err.println("Got wonky drag");
 	    lastHyperlinkDragged = lastHyperlinkHovered;
 	    status.setText("Drop the hyperlink onto a Web form field to populate it");
-	    System.err.println("Dragging "+lastHyperlinkDragged);
+	    //System.err.println("Dragging "+lastHyperlinkDragged);
 	    getTransferHandler().exportAsDrag(this, e, TransferHandler.COPY);
 	}
 	else if(dragging){
@@ -1991,6 +1996,6 @@
     }
 
     public void lostOwnership(Clipboard clipboard, Transferable contents){
-	System.err.println("Lost clipboard ownership");
+	//System.err.println("Lost clipboard ownership");
     }
 }


From gordonp at dev.open-bio.org  Sun Apr 11 16:15:28 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Sun, 11 Apr 2010 16:15:28 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004112015.o3BKFSqr017948@dev.open-bio.org>


gordonp
Sun Apr 11 16:15:28 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util
In directory dev.open-bio.org:/tmp/cvs-serv17912/src/main/ca/ucalgary/seahawk/util

Modified Files:
	DataUtils.java 
Added Files:
	XPointerResolver.java 
Log Message:
Updates for proper support of data filtering when submitting to forward services
moby-live/Java/src/main/ca/ucalgary/seahawk/util XPointerResolver.java,NONE,1.1 DataUtils.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataUtils.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataUtils.java	2010/04/10 00:40:17	1.3
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataUtils.java	2010/04/11 20:15:28	1.4
@@ -450,7 +450,14 @@
 	}	
     }
 
-    public static MobyDataInstance loadMobyDataFromXPointer(URL targetURL, FilterSearch docFilter){
+    /**
+     * Get the data instance object associated with a given XPointer into a Moby XML doc
+     *
+     * @param targetURL of the form URLpath#/1/1/2/1 where /1/1/2/1 is an XPointer, or an standard xpath, to the part of the Moby XML doc to deserialize
+     * @param filteredXPtrs a map of the xpointers to data that should NOT be deserialized if children of the targetURL XPointer
+     * @param docFilter the current filter applied to the document in targetURL
+     */
+    public static MobyDataInstance loadMobyDataFromXPointer(URL targetURL, Map<String,String> filteredXPtrs, FilterSearch docFilter){
 	// Are we dealing with a simple object or a complex one?
 	MobyDataInstance mobyData = null;
 	
@@ -492,13 +499,35 @@
 	    return null;
 	}
 	
+	// Remove the filtered data from the doc before deserializing to a moby data instance
+	// That way the request actually reflects what is shown on the screen to the user.
+	if(filteredXPtrs != null){
+	    // Mark and sweep (if we just deleted as we found node, the XPointers could be 
+	    // wrong as they refer to ordinality)
+	    Vector<Node> nodesToDelete = new Vector<Node>();
+	    for(String xptr: filteredXPtrs.keySet()){
+		nodesToDelete.add(XPointerResolver.getNodeFromXPointer(domDoc, xptr));
+	    }
+
+	    // Delete
+	    for(Node nodeToDelete: nodesToDelete){
+		Node parent = nodeToDelete.getParentNode();
+		parent.removeChild(nodeToDelete);
+		// Get rid of Simple parents of deleted nodes, because empty Simple
+		// tags are not okay in Moby (causes parsing error)
+		if(MobyTags.SIMPLE.equals(parent.getLocalName())){
+		    parent.getParentNode().removeChild(parent);
+		}
+	    }
+	}
+
 	// Build and run the XPath statement
 	Element mobyObject = null;
 	NodeList idSearchResult = null;
 	Object xobject = null;
 	try{
 	    xobject = XPathFactory.newInstance().newXPath().evaluate(childXPath, 
-								     new InputSource(targetURL.openStream()), 
+								     domDoc, 
 								     XPathConstants.NODESET);
 						
 	    // Check the results


From gordonp at dev.open-bio.org  Wed Apr 14 18:02:05 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Wed, 14 Apr 2010 18:02:05 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004142202.o3EM252P007075@dev.open-bio.org>


gordonp
Wed Apr 14 18:02:04 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util
In directory dev.open-bio.org:/tmp/cvs-serv7013/src/main/ca/ucalgary/seahawk/util

Modified Files:
	DataUtils.java FilterSearch.java 
Added Files:
	MobyPayloadRequestListener.java MutableNodeList.java 
Log Message:
Changes to implement explicit 'for each' loops over Seahawk data lists (not quite functional yet, but compiles)
moby-live/Java/src/main/ca/ucalgary/seahawk/util MobyPayloadRequestListener.java,NONE,1.1 MutableNodeList.java,NONE,1.1 DataUtils.java,1.4,1.5 FilterSearch.java,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataUtils.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataUtils.java	2010/04/11 20:15:28	1.4
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataUtils.java	2010/04/14 22:02:04	1.5
@@ -4,6 +4,7 @@
 import java.net.URL;
 import java.util.*;
 import java.util.logging.*;
+import java.util.regex.*;
 import javax.xml.parsers.*;
 import javax.xml.transform.*;
 import javax.xml.transform.dom.DOMSource;
@@ -34,8 +35,12 @@
     public static final String TEMP_FILE_PREFIX = "seahawk";
     private static final String OUTPUT_SUFFIX = ".out.xml";
     private static final String INPUT_SUFFIX = ".in.xml";
-    private static DocumentBuilder docBuilder;
+    public static DocumentBuilder docBuilder;
     private static Transformer identityTransform;
+    public static XPathFactory xPathFactory;
+
+    public static final String ARTICLE_PEERS_MODE = "article_peers";
+    public static final String DATATYPE_PEERS_MODE = "datatype_peers";
 
     private static Logger logger = Logger.getLogger(DataUtils.class.getName());
 
@@ -54,6 +59,8 @@
 	} catch(Exception e){
 	    logger.log(Level.SEVERE, "Cannot get identity XSLT transform from configuration", e);
 	}
+
+	xPathFactory = XPathFactory.newInstance();
     }
 
     /**
@@ -176,7 +183,7 @@
 		// User data has the form srcURL#XpathSelectCriteria <tab> xptrActualDataSubmitted <tab> regexFilter 
 		// where the filter is optional 
 		String[] data = sampleData.getUserData().toString().split("\t");
-		System.err.println("Forward user data is " + sampleData.getUserData().toString());
+		//System.err.println("Forward user data is " + sampleData.getUserData().toString());
 		URL dataSrcURL = null;
 		try{
 		    dataSrcURL = new URL(data[0]);
@@ -437,7 +444,7 @@
 						"sync: the instance job '" + jobName + 
 						"' has no parameter '" + paramName + "'");
 			}
-			System.err.println("Setting user data val to " + attrValue + " for " + paramName);
+			//System.err.println("Setting user data val to " + attrValue + " for " + paramName);
       			contentInstance.get(jobName).get(paramName).setUserData(attrValue);		    
 		    }
 		    else{
@@ -451,24 +458,47 @@
     }
 
     /**
-     * Get the data instance object associated with a given XPointer into a Moby XML doc
+     * Loads targetURL, minus the nodes specified by the xpath keys in filteredXPtrs (map values are not currently used).
+     */
+    public static void filterDoc(Document domDoc, Map<String,String> filteredXPtrs){
+	 
+	if(domDoc == null){
+	    logger.log(Level.SEVERE, "Error: Could not get MOBY document as DOM (empty or malformed document?)");
+	    return;
+	}
+	
+	// Remove the filtered data from the doc before deserializing to a moby data instance
+	// That way the request actually reflects what is shown on the screen to the user.
+	if(filteredXPtrs != null){
+	    // Mark and sweep (if we just deleted as we found nodes, the XPointers could be 
+	    // wrong as they refer to ordinality)
+	    Vector<Node> nodesToDelete = new Vector<Node>();
+	    for(String xptr: filteredXPtrs.keySet()){
+		nodesToDelete.add(XPointerResolver.getNodeFromXPointer(domDoc, xptr));
+	    }
+
+	    // Delete
+	    for(Node nodeToDelete: nodesToDelete){
+		Node parent = nodeToDelete.getParentNode();
+		parent.removeChild(nodeToDelete);
+		// Get rid of Simple parents of deleted nodes, because empty Simple
+		// tags are not okay in Moby (causes parsing error)
+		if(MobyTags.SIMPLE.equals(parent.getLocalName())){
+		    parent.getParentNode().removeChild(parent);
+		}
+	    }
+	}
+    }
+
+    /**
+     * Get the data instance object associated with a given XPointer in a Moby XML doc.
      *
      * @param targetURL of the form URLpath#/1/1/2/1 where /1/1/2/1 is an XPointer, or an standard xpath, to the part of the Moby XML doc to deserialize
      * @param filteredXPtrs a map of the xpointers to data that should NOT be deserialized if children of the targetURL XPointer
      * @param docFilter the current filter applied to the document in targetURL
      */
     public static MobyDataInstance loadMobyDataFromXPointer(URL targetURL, Map<String,String> filteredXPtrs, FilterSearch docFilter){
-	// Are we dealing with a simple object or a complex one?
-	MobyDataInstance mobyData = null;
-	
-	// Find the DOM fragment corresponding to the MOBY ID anchor specified
-	// in the link URL by using an XPath statement on the source MOBY doc
-	//System.err.println("Retrieving complex object from XPointer " + targetURL);
-	
-	// A child Xpointer is of the form /1/2/1/1, specifying the DOM child 
-	// descent path from the root node to get to the target node.  The 
-	// equivalent XPath is /*[1]/*[2]/*[1]/*[1]
-	String childXPath = targetURL.getRef().replaceAll("/(\\d+)", "/*[$1]");
+
 	URL currentURL = null;
 	try{currentURL = new URL(targetURL.toString().replaceAll("#"+targetURL.getRef(), ""));}
 	catch(Exception e){
@@ -476,7 +506,6 @@
 	}
 
 	// Build the DOM
-	Element mobyDOMRoot = null;
 	Document domDoc = null;
 	try{
 	    domDoc = docBuilder.parse(targetURL.openStream());
@@ -489,46 +518,29 @@
 		       " could not be read (from " + targetURL + ")", ioe);
 	    return null;
 	}
+	// Does an in-place edit of domDoc
+	filterDoc(domDoc, filteredXPtrs);
+
+	// Are we dealing with a simple object or a complex one?
+	MobyDataInstance mobyData = null;
 	
-	if(domDoc != null){
-	    mobyDOMRoot = domDoc.getDocumentElement();
-	}
-	if(mobyDOMRoot == null){
-	    logger.log(Level.SEVERE, "Error: Could not get MOBY document as DOM from source URL " +
-		       targetURL + " (empty or malformed document?)");
-	    return null;
-	}
+	// Find the DOM fragment corresponding to the MOBY ID anchor specified
+	// in the link URL by using an XPath statement on the source MOBY doc
+	//System.err.println("Retrieving complex object from XPointer " + targetURL);
 	
-	// Remove the filtered data from the doc before deserializing to a moby data instance
-	// That way the request actually reflects what is shown on the screen to the user.
-	if(filteredXPtrs != null){
-	    // Mark and sweep (if we just deleted as we found node, the XPointers could be 
-	    // wrong as they refer to ordinality)
-	    Vector<Node> nodesToDelete = new Vector<Node>();
-	    for(String xptr: filteredXPtrs.keySet()){
-		nodesToDelete.add(XPointerResolver.getNodeFromXPointer(domDoc, xptr));
-	    }
-
-	    // Delete
-	    for(Node nodeToDelete: nodesToDelete){
-		Node parent = nodeToDelete.getParentNode();
-		parent.removeChild(nodeToDelete);
-		// Get rid of Simple parents of deleted nodes, because empty Simple
-		// tags are not okay in Moby (causes parsing error)
-		if(MobyTags.SIMPLE.equals(parent.getLocalName())){
-		    parent.getParentNode().removeChild(parent);
-		}
-	    }
-	}
+	// A child Xpointer is of the form /1/2/1/1, specifying the DOM child 
+	// descent path from the root node to get to the target node.  The 
+	// equivalent XPath is /*[1]/*[2]/*[1]/*[1]
+	String childXPath = targetURL.getRef().replaceAll("/(\\d+)", "/*[$1]");
 
 	// Build and run the XPath statement
 	Element mobyObject = null;
 	NodeList idSearchResult = null;
 	Object xobject = null;
 	try{
-	    xobject = XPathFactory.newInstance().newXPath().evaluate(childXPath, 
-								     domDoc, 
-								     XPathConstants.NODESET);
+	    xobject = xPathFactory.newXPath().evaluate(childXPath, 
+						       domDoc, 
+						       XPathConstants.NODESET);
 						
 	    // Check the results
 	    if(xobject != null){
@@ -603,7 +615,7 @@
      * Generalizes the element instance into an XPath retrieving it and all 
      * similarly nested elements (based on traversing the parent nodes and prepending their names)
      */
-    protected static String elementInContextToNameBasedXPath(Element targetElement){
+    public static String elementInContextToNameBasedXPath(Element targetElement){
 	String xpath = "";
 	
 	for(Element currentElement = targetElement; 
@@ -630,22 +642,20 @@
 		xpath = "/*[@"+MobyTags.OBJ_NAMESPACE + " = '" +
 		    currentElement.getAttribute(MobyTags.OBJ_NAMESPACE)+"']" + xpath;
 	    }
-	    else if(elName.equals(MobyTags.MOBYFLOAT) ||
-		    elName.equals(MobyTags.MOBYSTRING) ||
-		    elName.equals(MobyTags.MOBYBOOLEAN) ||
-		    elName.equals(MobyTags.MOBYINTEGER) ||
-		    elName.equals(MobyTags.MOBYDATETIME)){
+//	    else if(elName.equals(MobyTags.MOBYFLOAT) ||
+//		    elName.equals(MobyTags.MOBYSTRING) ||
+//		    elName.equals(MobyTags.MOBYBOOLEAN) ||
+//		    elName.equals(MobyTags.MOBYINTEGER) ||
+//		    elName.equals(MobyTags.MOBYDATETIME)){
 		// Assume that it isn't the primitive type, but rather the articleName
 		// that makes it appropriate to use.
-		xpath = "/*[@"+MobyTags.ARTICLENAME + " = '" +
-		    articleName+"']" + xpath;
-	    }
+//		xpath = "/*[@"+MobyTags.ARTICLENAME + " = '" +
+//		    articleName+"']" + xpath;
+//	    }
 	    else{
 		// It's a complex type.  Assume the type is why we are picking it.
 		// TODO: In future we may want to check if a parent type is allowed in 
-		// this slot, and generalize to that.  May also want to check that there isn't more
-		// than one member of this type at this level in a HAS relationship...
-		// in that case we probably want to go by articleName to catch the full semantics
+		// this slot, and generalize to that.  
 		xpath = "/"+elName + xpath;
 	    }
 	    if(!(currentElement.getParentNode() instanceof Element)){
@@ -696,6 +706,12 @@
     }
 
     /**
+     * Replace the selection xpath info in the data instance
+     */
+    public static void replaceUserData(MobyDataInstance mdi, String selectionXPath){
+    }
+
+    /**
      * Retrieves processing instructions embedded in Moby XML docs if they have the for <?seahawk attr="val"?>
      */
     public static String getSeahawkAttrFromDoc(URL docURL, String attrName) throws Exception{ 
@@ -777,4 +793,328 @@
 			    "any_namespace");
     }
       
+    // Recursively ascend the DOM tree and find out our place in its branching structure
+    public static String getXPtr(Node n){
+	if(n == null || n instanceof Document){
+	    return "";
+	}
+	Node parent = n.getParentNode();
+        if(parent == null && n instanceof Attr){
+	    parent = ((Attr) n).getOwnerElement();
+	}
+
+	NodeList children = parent.getChildNodes();
+	int nonElementCnt = 0;
+	for(int i = 0; i < children.getLength(); i++){
+	    if(!(children.item(i) instanceof Element)){
+		nonElementCnt++; 
+		continue;
+	    }
+	    if(n == children.item(i)){
+		return getXPtr(parent)+"/"+(i-nonElementCnt+1);
+	    }
+	}
+	return null;
+    }
+
+    /**
+     * If any moby object member is in a HAS relationship, add it to the list of filterable items
+     */
+    public static Boolean addHASXPtrs(List<String> filterList, Element object){
+	String tagName = object.getLocalName();
+	boolean isContainer = false;
+	MobyDataType mobyDataType = null;	
+	if(tagName.equals(MobyTags.MOBYDATA) || tagName.equals(MobyTags.COLLECTION) || tagName.equals(MobyTags.SIMPLE) ||
+	   tagName.equals(MobyTags.CROSSREFERENCE)){
+	    isContainer = true;
+	}
+	else{
+	    mobyDataType = MobyDataType.getDataType(tagName, SeahawkOptions.getRegistry());
+	    if(mobyDataType == null){
+		logger.log(Level.WARNING,
+                           "Found datatype unknown to the registry ("+object.getLocalName()+")");
+		return Boolean.FALSE;
+	    }
+	}
+
+	Boolean hasHAS = Boolean.FALSE; // does the object have a member with a HAS relationship?
+	NodeList members = object.getChildNodes();
+	for(int i = 0; i < members.getLength(); i++){
+	    if(!(members.item(i) instanceof Element)){
+		continue;
+	    }
+
+	    Element member = (Element) members.item(i);
+	    addHASXPtrs(filterList, member);
+
+	    if(!isContainer){
+		String memberName = member.getAttribute(MobyTags.ARTICLENAME);
+		MobyRelationship membership = mobyDataType.getChild(memberName);
+		//System.err.println("Relationship for " + tagName  + " member " + memberName + 
+		//		   " is " + (membership == null ? null : membership.getRelationshipType()));
+		if(membership != null && membership.getRelationshipType() == Central.iHAS){
+		    filterList.add(getXPtr(member));
+		    if(!hasHAS){
+			hasHAS = Boolean.TRUE;
+		    }
+		}
+	    }
+	}
+	return hasHAS;
+    }
+
+    /**
+     * For one-off filtering of a doc. Populates xPtrsToFilter, and returns the 
+     * whole doc which you can manipulate yourself (e.g. removing the nodes identified).
+     */
+    public static Document findFilteredNodes(URL targetURL, FilterSearch filter, 
+                                             Map<String,String> xPtrsToFilter){
+        Document unfilteredDoc = null;
+	try{
+	    unfilteredDoc = docBuilder.parse(targetURL.openStream());
+	} catch(Exception e){
+	    logger.log(Level.SEVERE,
+                       "Could not parse Moby document " + targetURL, e);
+	    return null;
+	}
+	findFilteredNodes(unfilteredDoc, filter, null, xPtrsToFilter, null, null, null, true);
+	return unfilteredDoc;
+    }
+
+    /**
+     * Returns a list of xptrs to filterable nodes in the targetDoc, an populates the list of 
+     * xptrs that should be filtered according to the provided filter.  In-place edited fields are
+     * xPtrsToFilter, jobXPtrs, currentSelectedData, and currentSelectionXPath 
+     * (for caching efficiency on multiple consecutive 
+     * calls to this method, such as a live typed search in the UI).  The latter three can be null if no caching is desired.
+     */
+    public static List<String> findFilteredNodes(Document targetDoc, FilterSearch filter, List<String> filterableXPtrs,
+		    		                 Map<String,String> xPtrsToFilter, Map<String,Boolean> jobXPtrs,
+                                                 MutableNodeList currentSelectedData, StringBuffer currentSelectionXPath, 
+						 boolean apply){
+	xPtrsToFilter.clear();
+
+	// Filter out any moby jobs, parameters, collection members or HAS members that aren't in the matchingNodes
+	if(filterableXPtrs == null){
+	    if(jobXPtrs == null){
+		jobXPtrs = new HashMap<String,Boolean>();
+            }
+            else{
+                jobXPtrs.clear();
+            }
+	    filterableXPtrs = new Vector<String>();
+	    NodeList nodes = targetDoc.getElementsByTagNameNS(MobyTags.MOBY_XML_NS, MobyTags.MOBYDATA);
+	    for(int i = 0; i < nodes.getLength(); i++){
+		String jobXPtr = getXPtr(nodes.item(i));		
+		filterableXPtrs.add(jobXPtr);
+		jobXPtrs.put(jobXPtr, addHASXPtrs(filterableXPtrs, (Element) nodes.item(i)));
+	    }
+		
+	    // Collections
+	    nodes = targetDoc.getElementsByTagNameNS(MobyTags.MOBY_XML_NS, MobyTags.COLLECTION);
+	    for(int i = 0; i < nodes.getLength(); i++){
+		String collectionXPtr = getXPtr(nodes.item(i));
+		NodeList collectionMembers = nodes.item(i).getChildNodes();
+		int nonElementCnt = 0;
+		for(int j = 0; j < collectionMembers.getLength(); j++){		    
+		    if(!(collectionMembers.item(j) instanceof Element)){
+			nonElementCnt++;
+			continue;
+		    }
+		    filterableXPtrs.add(collectionXPtr+"/"+(j-nonElementCnt+1)+"/1");
+		}
+	    }
+	}
+
+	if(!apply || filter == null || filter.getFilterRegex().toString().length() == 0){
+	    return filterableXPtrs;
+	}
+	// Otherwise make a list of xpointers to data that should be filtered
+	XPathOption xsel = filter.getSelectedXPath();
+	
+	// Find the applicable DOM nodes if not yet found, or if selection criteria have changed
+	if(currentSelectedData == null || currentSelectedData.isEmpty() || 
+           currentSelectionXPath == null || !currentSelectionXPath.toString().equals(xsel.getXPath())){
+            if(currentSelectionXPath == null){
+               currentSelectionXPath = new StringBuffer(xsel.getXPath());
+            }
+	    else{
+               currentSelectionXPath.replace(0, currentSelectionXPath.length(), xsel.getXPath());
+            }
+	    try{
+		if(currentSelectedData == null){
+                    currentSelectedData = new MutableNodeList();
+                }
+                else{
+                    currentSelectedData.clear();
+                }
+		currentSelectedData.addAll((NodeList) xPathFactory.newXPath().evaluate(currentSelectionXPath.toString(), 
+                                                                                       targetDoc, 
+                                                                                       XPathConstants.NODESET)); 
+	    } catch(Exception e){
+		logger.log(Level.SEVERE, 
+                           "Could not evaluate XPath (" + xsel.getXPath() + ")", e);
+		return filterableXPtrs;
+	    }
+	    //	    System.err.println("There are " + currentSelectedData.getLength() + 
+	    //		       " items selected in the document using XPath " + currentSelectionXPath);
+	}
+	
+	// Find just the data subset also matching the regex
+	Map<String,Boolean> matchingXPtrs = new LinkedHashMap<String,Boolean>();
+	// Build the FSA only once, for efficiency
+	Pattern regex = Pattern.compile(filter.getFilterRegex().toString(), 
+                                        Pattern.MULTILINE | Pattern.DOTALL | 
+                                         (filter.getCaseSensitivity() ? 0 : Pattern.CASE_INSENSITIVE));
+	for(int i = 0; i < currentSelectedData.getLength(); i++){
+	    Node node = currentSelectedData.item(i);	    
+	    if(node instanceof Element){
+		String elementXPtr = getXPtr(node);
+		if(matchingXPtrs.containsKey(elementXPtr) &&
+		   matchingXPtrs.get(elementXPtr).booleanValue()){
+		    	continue;  // already true, no 
+                    }
+		else if(regex.matcher(((Element) node).getTextContent()).find()){
+		    matchingXPtrs.put(elementXPtr, Boolean.TRUE);
+		    //System.err.println("Adding " + elementXPtr + " as " + matchingXPtrs.get(elementXPtr));
+		}
+		else{
+		    matchingXPtrs.put(elementXPtr, Boolean.FALSE);
+		    //System.err.println("Adding " + elementXPtr + " as " + matchingXPtrs.get(elementXPtr));
+		}
+	    }
+	    else if(node instanceof Attr){
+		String attrParentXPtr = getXPtr(((Attr) node).getOwnerElement());
+		if(matchingXPtrs.containsKey(attrParentXPtr) &&
+	 	   matchingXPtrs.get(attrParentXPtr).booleanValue()){
+		    continue;
+                }
+		else if(regex.matcher(((Attr) node).getValue()).find()){
+		    // Mark the element to which the attribute belongs
+		    matchingXPtrs.put(attrParentXPtr, Boolean.TRUE);
+		    //System.err.println("Adding " + attrParentXPtr + " attr parent as " + matchingXPtrs.get(attrParentXPtr));
+		}
+		// so false doesn't override true for multi-attr elements
+		else if(!matchingXPtrs.containsKey(attrParentXPtr)){ 
+		    matchingXPtrs.put(attrParentXPtr, Boolean.FALSE);
+		    //System.err.println("Adding " + attrParentXPtr + " attr parent as " + matchingXPtrs.get(attrParentXPtr));
+		}
+		
+	    }
+	    else{
+		logger.log(Level.WARNING, 
+			   "Found filter xpath result item that was not an Element or Attribute as expected ("+
+			    node.getClass().getName()+")");
+	    }
+	}
+	
+	boolean inversed = filter.getSelectionInversed();
+	Map<String,Boolean> parentMatchingXPtrs = new LinkedHashMap<String,Boolean>();
+	for(String currXPtr: filterableXPtrs){
+	    for(Map.Entry<String,Boolean> matchingXPtr: matchingXPtrs.entrySet()){
+		if(matchingXPtr.getKey().startsWith(currXPtr+"/")){ // a parent of the matching data
+		    // No positive example yet?
+		    if(!parentMatchingXPtrs.containsKey(currXPtr) || 
+		       !inversed && !parentMatchingXPtrs.get(currXPtr).booleanValue() ||
+		       inversed && parentMatchingXPtrs.get(currXPtr).booleanValue()){
+			//System.err.println("Adding "+ matchingXPtr.getValue() + " for " + currXPtr);
+			parentMatchingXPtrs.put(currXPtr, matchingXPtr.getValue());
+		    }
+		}
+	    }
+	}
+
+	matchingXPtrs.putAll(parentMatchingXPtrs);
+	for(String currXPtr: matchingXPtrs.keySet()){
+	    // Is part of the selection criteria, but doesn't match the regex
+	    boolean shouldFilter = false;
+	    if(!matchingXPtrs.get(currXPtr).booleanValue() &&
+	       // special condition: if "entire response" xpath is given, filter only at the job level
+	       (!currentSelectionXPath.toString().equals(FilterSearch.SELECT_ALL_XPATH) || jobXPtrs.containsKey(currXPtr))){
+		shouldFilter = true;
+	    }
+	    if(!inversed && shouldFilter ||
+	       inversed && !shouldFilter){ 
+		xPtrsToFilter.put(currXPtr, "todo");
+	    }	    
+	}
+
+	//todo: filter objects without the HAS field at all...
+	return filterableXPtrs;
+    }
+    // We need to enumerate the possible peer-sets for the selected data item.  Is the user interested in
+    // items in the same namespace, same data type, or same article name?
+    public static NodeList getPeerElements(Document doc, MobyDataInstance mobyData, String peerMode){
+        if(!(mobyData instanceof MobyPrimaryData)){
+            logger.log(Level.WARNING, "Tried to get peers of data that was not an instanceof MobyPrimaryData (was " + 
+                                      mobyData.getClass().getName()+ ")");
+	    return null;
+	}
+        MobyDataType dataTypeTemplate = ((MobyPrimaryData) mobyData).getDataType();
+
+	NodeList peerElements = null;
+        String peerGroupXPath = null;
+	if(mobyData.getUserData() != null){
+	    String[] userData = ((String) mobyData.getUserData()).split("\t");
+	    // first arg is url#nameBasedXPath 
+	    peerGroupXPath = userData[0].split("#", 2)[1];
+        }
+        else{
+	    // Fallback is to get all nodes with the same name...
+            // warning: need to set this in the userdata sent to the job, to jibe with taverna workflow export selection of nodes!
+	    logger.log(Level.WARNING, "No UserData for data instance, falling back to all peer elements of the same datatype");
+            peerGroupXPath = "//"+dataTypeTemplate.getName();
+	}
+
+        // just look at data type tag, regardless of nesting
+        if(DATATYPE_PEERS_MODE.equals(peerMode)){
+            peerGroupXPath = peerGroupXPath.replaceFirst("^.+/", "//"); 
+        }
+        else if(ARTICLE_PEERS_MODE.equals(peerMode)){ 
+            String xpathArticleCondition = "[@"+MobyTags.ARTICLENAME + "='" + mobyData.getName() +"']";
+            // Pass back modified selection xpath for userdata (enables PBE to capture the additonal semantics)
+            // This is done by replacing first tab delimited field url#selectionXPath with url#newXPath
+            String newUserData = mobyData.getUserData().toString().replaceFirst("^(.*?)#.*?(?=\\t)", 
+                                                                                "$1#"+peerGroupXPath+xpathArticleCondition);
+            mobyData.setUserData(newUserData);
+
+            // keep from job article name down
+            peerGroupXPath = peerGroupXPath.replaceFirst("^.*/(Collection|Simple)", "//*");
+	    // we want to go by articleName too to catch the full semantics of the peer group definition
+            peerGroupXPath += xpathArticleCondition;
+        }
+        else{
+            logger.log(Level.SEVERE, "Got unknown mode for peer selection, aborting (mode was "+peerMode+")");
+            return null;
+        }
+        // For xpaths given above, MOBY namespace is problem in XPath evaluation. 
+        // solution: eliminate Moby envelope path parts: full path doesn't resolve in xpath for unknown reasons
+        //.replaceAll("/(MOBY|mobyContent|mobyData|Collection|Simple)","/moby:$1"); //attempt 1
+        //.replaceAll("/([a-zA-Z_0-9\\-]+)(?=/|$)", "/*[local-name() = '$1']") //attempt 2
+        //.replaceAll("/([a-zA-Z_0-9\\-]+)\\[", "/*[local-name() = '$1' and "); //attempt 2 cont'd
+
+	try{
+            peerElements = (NodeList) xPathFactory.newXPath().evaluate(peerGroupXPath, 
+								       doc, 
+								       XPathConstants.NODESET);
+        } catch(Exception e){
+            logger.log(Level.SEVERE, "Could not evaluate UserData XPath "+peerGroupXPath, e);
+        }
+        System.err.println("Got " + peerElements.getLength() + " peers for " + peerGroupXPath);
+
+        return peerElements;
+    }
+
+    // given a node from a Moby XML dom, find the name of the mobyData job that's its parent
+    public static String findMobyJobName(Node n){
+        while(n != null && !n.getLocalName().equals(MobyTags.MOBYDATA)){
+            n = n.getParentNode();
+        }
+        if(n == null){
+            return null; // no mobyData parent
+        }
+        else{
+            return MobyPrefixResolver.getAttr((Element) n, MobyTags.QUERYID);
+        }
+    }
 }

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/FilterSearch.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/FilterSearch.java	2010/04/10 00:40:17	1.4
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/FilterSearch.java	2010/04/14 22:02:04	1.5
@@ -28,6 +28,20 @@
     public static final String SELECT_ALL_XPATH = "//* | //*/@*";
 
     /**
+     * A c-tor to manually populate the filter with a specific set of filter criteria.  
+     * No autopoulation of options is done.
+     */
+    public FilterSearch(String regex, XPathOption xpath, boolean case_sensitive, boolean inverse_selection){
+	filterRegex = new StringBuffer(regex);
+	xpathOptions = new Vector<XPathOption>();
+	xpathOptions.add(xpath);
+	setCaseSensitivity(case_sensitive);
+	setSelectionInversed(inverse_selection);
+    }
+
+    /**
+     * Autopopulates the possible search field values based on the incoming doc
+     *
      * @param docToFilter the document that will be used to determine what XPaths can be suggested
      * @param docBuilder the xml parser to use on the document
      *
@@ -106,4 +120,15 @@
     public Vector<XPathOption> getXPathOptions(){
 	return xpathOptions;
     }
+
+    public boolean equals(Object o){
+        if(o == null || !(o instanceof FilterSearch)){
+          return false;
+        }
+        FilterSearch other = (FilterSearch) o;
+        return filterRegex.toString().equals(other.filterRegex.toString()) &&
+               getSelectedXPath().getXPath().equals(other.getSelectedXPath().getXPath()) &&
+               caseSensitivity == other.caseSensitivity &&
+	       inverseSelection == other.inverseSelection;
+    }
 }


From gordonp at dev.open-bio.org  Wed Apr 14 18:02:04 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Wed, 14 Apr 2010 18:02:04 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004142202.o3EM24JD007053@dev.open-bio.org>


gordonp
Wed Apr 14 18:02:04 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv7013/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	MobyContentPane.java MobyServicesGUI.java 
Added Files:
	MobyPayloadCreator.java 
Log Message:
Changes to implement explicit 'for each' loops over Seahawk data lists (not quite functional yet, but compiles)
moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyPayloadCreator.java,NONE,1.1 MobyContentPane.java,1.26,1.27 MobyServicesGUI.java,1.17,1.18
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java,v
retrieving revision 1.26
retrieving revision 1.27
diff -u -r1.26 -r1.27
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java	2010/04/11 20:15:28	1.26
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java	2010/04/14 22:02:04	1.27
@@ -1,4 +1,3 @@
-
 package ca.ucalgary.seahawk.gui;
 
 // For external links
@@ -72,8 +71,8 @@
     public static final String SERVICE_CREATION_MSG = "Create a service returning this datatype";
     private static final int TAB_ICON_SPACER = 2;
 
-    private static String SEARCH_VISIBLE = "Search visible";
-    private static String SEARCH_HIDDEN = "Search hidden";
+    private static final String SEARCH_VISIBLE = "Search visible";
+    private static final String SEARCH_HIDDEN = "Search hidden";
 
     private static ImageIcon hourglassIcon; 
     private static ImageIcon failedIcon; 
@@ -105,10 +104,10 @@
     private Map<String,String> filteredData; //Map<xptrOfFilteredData,>
     private boolean filterChanged;
     private Document currentDoc; //the doc DOM being actively filtered
-    private NodeList currentSelectedData = null;
-    private String currentSelectionXPath = null;
-    private Map<String,Boolean> jobXPtrs = null;  // Map<xptr,has a HAS member>
+    private MutableNodeList currentSelectedData = null;
+    private StringBuffer currentSelectionXPath = null;
     private List<String> filterableNodes = null;  // List<xptr>
+    private Map<String,Boolean> jobXPtrs = null;  // Map<xptr,has a HAS member>
     private List<AttributeSet> origStyles = null;
     private boolean firstDocRendering = true;
 
@@ -141,20 +140,6 @@
     private final static String wsServletPath = "/SOAPServlet";
     private static Acme.Serve.Serve servletContainer;
     private static Map<String,MobyContentGUI> id2GuiMap;
-    private static DocumentBuilder docBuilder;
-    private static XPathFactory xPathFactory;
-
-    static{
-	xPathFactory = XPathFactory.newInstance();
-
-	DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
-	dbf.setNamespaceAware(true);
-	try{
-	    docBuilder = dbf.newDocumentBuilder();
-	} catch(Exception e){
-	    logger.warn("Cannot get XML parser from configuration", e);
-	}
-    }
 
     public MobyContentPane(MobyContentGUI cGUI, MobyServicesGUI sGUI, JTabbedPane parentComponent, DataFlowRecorder recorder, JLabel statusBar){
 	tabbedPane = parentComponent;
@@ -200,7 +185,9 @@
 	filterHistory = new HashMap<URL,FilterSearch>();
 	deletedFilters = new HashMap<URL,FilterSearch>();
 	xPtrsReferencedInNextService = new Vector<String>();
+        currentSelectedData = new MutableNodeList();
 	filteredData = new HashMap<String,String>();
+	jobXPtrs = new HashMap<String,Boolean>();
 
 	ClassLoader cl = getClass().getClassLoader();
 	if(cl == null){
@@ -738,9 +725,8 @@
 	// If this page has a filter associated with it before reload it
 	try{
 	    currentDoc = null;  // get rid of previous in-memory doc use for interactive filtering, if any
-	    currentSelectedData = null;
-	    currentSelectionXPath = null;
-	    jobXPtrs = null;
+	    currentSelectedData.clear();
+	    currentSelectionXPath = new StringBuffer();
 	    filterableNodes = null;
 	    origStyles = null;
 	    firstDocRendering = true;
@@ -1209,14 +1195,54 @@
 			       "not extract MOBY Data Object from " +targetURL);
 	    return;
 	}
+	if(!(mobyData instanceof MobyPrimaryData)){
+	    logger.warn("Cannot create MOBY service list for non-primary " +
+			"MOBY Data (was " +mobyData.getClass().getName()+")");
+	    return;
+	}
 
 	JPopupMenu popup = new DynamicJPopupMenu();
 	popup.setName(MOBY_SERVICE_POPUP_NAME);
 	addExtraMobyOptions(popup, mobyData, targetURL);
-	JMenuItem checkingLinksPopupItem = new JMenuItem("Check for services...");
+	JMenuItem checkingLinksPopupItem = new JMenuItem("Checking for services...");
 	popup.add(checkingLinksPopupItem);
 	popup.show(this, lastClickX+editorPane.getX(), lastClickY+editorPane.getY());
 	servicesGUI.addPopupOptions(mobyData, popup, true, getDefaultHandler()); // true = asynchronous
+
+	// It's possible that the current node clicked has peers that could also be submitted at the same time.
+	// In this case, create a "for each" option to submit all peers to the service.  We don't actually build
+	// the input data, but provde a callback listener to create the full submission envelope if the user 
+	// chooses the for each option.  The Moby data instance's userData gives us the current context, enabling us 
+        // to construct the correct payload in MobyPayloadCreator.createPayload() at any point in the future.
+        String origUserData = (String) mobyData.getUserData();
+        MobyPayloadRequestListener payloadCreator = new MobyPayloadCreator(this);
+        for(String peerMode: new String[]{DataUtils.ARTICLE_PEERS_MODE, DataUtils.DATATYPE_PEERS_MODE}){
+            // note that getPeerElements() will modify the userData to reflect the semantic of the requested peer mode
+            mobyData.setUserData(origUserData);
+            NodeList peerElements = DataUtils.getPeerElements(getCurrentDoc(), mobyData, peerMode);
+            if(peerElements.getLength() <= 1){
+                continue; // no 'for each' option if only one to process...
+            }
+            String each = "each <i>(" + peerElements.getLength() + " total)</i>";
+            if(peerMode.equals(DataUtils.ARTICLE_PEERS_MODE)){
+                each += " '"+mobyData.getName()+"'";
+            }
+            MobyDataType dataType = ((MobyPrimaryData) mobyData).getDataType();
+            if(mobyData instanceof MobyPrimaryDataSet){	 // Collection
+                servicesGUI.addPopupOptions((MobyPrimaryDataSet) mobyData, popup, true, getDefaultHandler(), payloadCreator, 
+					    (String) mobyData.getUserData(), each);
+            }
+            else if(MobyTags.MOBYOBJECT.equals(dataType.getName())){  
+                MobyNamespace namespace = null;
+                servicesGUI.addPopupOptions(namespace, popup, true, getDefaultHandler(), payloadCreator, 
+                                            (String) mobyData.getUserData(), each);
+            }
+            else{
+                servicesGUI.addPopupOptions(dataType, popup, true, getDefaultHandler(), payloadCreator, 
+                                            (String) mobyData.getUserData(), each);
+            }
+        }
+
 	status.setText("Shift+Click=Service in new tab, Ctrl+Click=Use default 2nd params");
 	if(popup.getSubElements().length > 0){
 	    popup.setSelected(null);
@@ -1228,6 +1254,15 @@
 	}
     }
 
+    Map<String,String> getFilteredData(){
+      return filteredData;
+    }
+
+    Map<String,Boolean> getJobXPtrs(){
+      return jobXPtrs;
+    }
+
+
     /**
      * Subclasses can use this method to expand the popup menu.  Be sure to call super.addExtraMobyOptions()
      */
@@ -1252,7 +1287,7 @@
 
 	//System.err.println("Should create a previous input menu item for " + mdi.getUserData());
 	try{
-	    Document srcDoc = docBuilder.parse(srcURL.openStream());
+	    Document srcDoc = DataUtils.docBuilder.parse(srcURL.openStream());
 
 	    // Get the input data for the *previous* service
 	    MobyDataJob inputData = DataUtils.getInputSample(srcDoc, SeahawkOptions.getRegistry());
@@ -1262,7 +1297,7 @@
 		return;
 	    }
 	    for(MobyDataInstance previousMDI: inputData.getPrimaryData()){		
-		    // add conditional of the current service as a criteria in user data for each previousMDI, 
+		// add conditional of the current service as a criteria in user data for each previousMDI, 
 		// so PbE will properly reflect the logic of if(f1(x) matches filter){f2(x)}
 		DataUtils.addUserData(previousMDI, srcURL, getFilter());
 
@@ -1271,6 +1306,7 @@
 	} catch(Exception e){
 	    logger.warn("Could not load previous service info, 'previous input' option will not be displayed", e);
 	}
+
     }
 
     /**
@@ -1392,231 +1428,41 @@
 	return null;
     }
 
-    /**
-     * Determine the parts of the XML document matching the FilterSearch criteria, and filter the view accordingly.
-     */
-    public void applyFilter(boolean apply){
-	if(!filterChanged){
-	    filterChanged = true;
-	}
-	filteredData.clear();
-
+    protected Document getCurrentDoc(){
 	if(currentDoc == null){  // parse the doc into memory if not already there
 	    try{
-		currentDoc = docBuilder.parse(getCurrentURL().openStream());
+		currentDoc = DataUtils.docBuilder.parse(getCurrentURL().openStream());
 	    } catch(Exception e){
 		logger.error("Could not parse Moby document " + getCurrentURL(), e);
-		return;
-	    }
-	}
-	// Filter out any moby jobs, parameters, collection members or HAS members that aren't in the matchingNodes
-	if(filterableNodes == null){
-	    jobXPtrs = new HashMap<String,Boolean>();
-	    filterableNodes = new Vector<String>();
-	    NodeList nodes = currentDoc.getElementsByTagNameNS(MobyTags.MOBY_XML_NS, MobyTags.MOBYDATA);
-	    for(int i = 0; i < nodes.getLength(); i++){
-		String jobXPtr = getXPtr(nodes.item(i));		
-		filterableNodes.add(jobXPtr);
-		jobXPtrs.put(jobXPtr, addHASXPtrs(filterableNodes, (Element) nodes.item(i)));
-	    }
-		
-	    // Collections
-	    nodes = currentDoc.getElementsByTagNameNS(MobyTags.MOBY_XML_NS, MobyTags.COLLECTION);
-	    for(int i = 0; i < nodes.getLength(); i++){
-		String collectionXPtr = getXPtr(nodes.item(i));
-		NodeList collectionMembers = nodes.item(i).getChildNodes();
-		int nonElementCnt = 0;
-		for(int j = 0; j < collectionMembers.getLength(); j++){		    
-		    if(!(collectionMembers.item(j) instanceof Element)){
-			nonElementCnt++;
-			continue;
-		    }
-		    filterableNodes.add(collectionXPtr+"/"+(j-nonElementCnt+1)+"/1");
-		}
+		return null;
 	    }
 	}
-
-	if(!apply || !filterHistory.containsKey(getCurrentURL()) ||
-	   (filterHistory.containsKey(getCurrentURL()) && 
-	    filterHistory.get(getCurrentURL()).getFilterRegex().toString().length() == 0)){
-	    // Show whole doc if no filter or if filter is blank, so nothing to do here
-	    if(firstDocRendering){
-		firstDocRendering = false;
-	    }
-	    else{
-		displayFilterEffect(); //need to cleanup previous state
-	    }
-	    return;
-	}
-	// Otherwise make a list of xpointers to data that should be grayed out
-	FilterSearch fs = filterHistory.get(getCurrentURL());
-	XPathOption xsel = fs.getSelectedXPath();
-	
-	// Find all the matching data
-	XPath xpath = xPathFactory.newXPath();
-	// Find the applicable DOM nodes if not yet found, or if selection criteria have changed
-	if(currentSelectedData == null || currentSelectionXPath == null || !currentSelectionXPath.equals(xsel.getXPath())){
-	    currentSelectionXPath = xsel.getXPath();
-	    try{
-		currentSelectedData = (NodeList) xpath.evaluate(currentSelectionXPath, currentDoc, XPathConstants.NODESET);
-	    } catch(Exception e){
-		logger.error("Could not evaluate XPath (" + xsel.getXPath() + ") over " + getCurrentURL(), e);
-		return;
-	    }
-	    //	    System.err.println("There are " + currentSelectedData.getLength() + 
-	    //		       " items selected in the document using XPath " + currentSelectionXPath);
-	}
-	
-	// Find just the data subset also matching the regex
-	Map<String,Boolean> matchingXPtrs = new LinkedHashMap<String,Boolean>();
-	// Build the FSA only once, for efficiency
-	Pattern regex = Pattern.compile(fs.getFilterRegex().toString(), 
-                                        Pattern.MULTILINE | Pattern.DOTALL | 
-                                         (fs.getCaseSensitivity() ? 0 : Pattern.CASE_INSENSITIVE));
-	for(int i = 0; i < currentSelectedData.getLength(); i++){
-	    Node node = currentSelectedData.item(i);	    
-	    if(node instanceof Element){
-		String elementXPtr = getXPtr(node);
-		if(matchingXPtrs.containsKey(elementXPtr) &&
-		   matchingXPtrs.get(elementXPtr).booleanValue()){
-		    	continue;  // already true, no 
-                    }
-		else if(regex.matcher(((Element) node).getTextContent()).find()){
-		    matchingXPtrs.put(elementXPtr, Boolean.TRUE);
-		    //System.err.println("Adding " + elementXPtr + " as " + matchingXPtrs.get(elementXPtr));
-		}
-		else{
-		    matchingXPtrs.put(elementXPtr, Boolean.FALSE);
-		    //System.err.println("Adding " + elementXPtr + " as " + matchingXPtrs.get(elementXPtr));
-		}
-	    }
-	    else if(node instanceof Attr){
-		String attrParentXPtr = getXPtr(((Attr) node).getOwnerElement());
-		if(matchingXPtrs.containsKey(attrParentXPtr) &&
-	 	   matchingXPtrs.get(attrParentXPtr).booleanValue()){
-		    continue;
-                }
-		else if(regex.matcher(((Attr) node).getValue()).find()){
-		    // Mark the element to which the attribute belongs
-		    matchingXPtrs.put(attrParentXPtr, Boolean.TRUE);
-		    //System.err.println("Adding " + attrParentXPtr + " attr parent as " + matchingXPtrs.get(attrParentXPtr));
-		}
-		// so false doesn't override true for multi-attr elements
-		else if(!matchingXPtrs.containsKey(attrParentXPtr)){ 
-		    matchingXPtrs.put(attrParentXPtr, Boolean.FALSE);
-		    //System.err.println("Adding " + attrParentXPtr + " attr parent as " + matchingXPtrs.get(attrParentXPtr));
-		}
-		
-	    }
-	    else{
-		logger.warn("Found filter xpath result item that was not an Element or Attribute as expected ("+
-			    node.getClass().getName()+")");
-	    }
-	}
-	
-	boolean inversed = fs.getSelectionInversed();
-	Map<String,Boolean> parentMatchingXPtrs = new LinkedHashMap<String,Boolean>();
-	for(String currXPtr: filterableNodes){
-	    for(Map.Entry<String,Boolean> matchingXPtr: matchingXPtrs.entrySet()){
-		if(matchingXPtr.getKey().startsWith(currXPtr+"/")){ // a parent of the matching data
-		    // No positive example yet?
-		    if(!parentMatchingXPtrs.containsKey(currXPtr) || 
-		       !inversed && !parentMatchingXPtrs.get(currXPtr).booleanValue() ||
-		       inversed && parentMatchingXPtrs.get(currXPtr).booleanValue()){
-			//System.err.println("Adding "+ matchingXPtr.getValue() + " for " + currXPtr);
-			parentMatchingXPtrs.put(currXPtr, matchingXPtr.getValue());
-		    }
-		}
-	    }
-	}
-
-	matchingXPtrs.putAll(parentMatchingXPtrs);
-	for(String currXPtr: matchingXPtrs.keySet()){
-	    // Is part of the selection criteria, but doesn't match the regex
-	    boolean shouldFilter = false;
-	    if(!matchingXPtrs.get(currXPtr).booleanValue() &&
-	       // special condition: if "entire response" xpath is given, filter only at the job level
-	       (!currentSelectionXPath.equals(FilterSearch.SELECT_ALL_XPATH) || jobXPtrs.containsKey(currXPtr))){
-		shouldFilter = true;
-	    }
-	    if(!inversed && shouldFilter ||
-	       inversed && !shouldFilter){ 
-		filteredData.put(currXPtr, "todo");
-	    }	    
-	}
-
-	//todo: filter objects without the HAS field at all...
-	
-	// apply gray out in the document display
-	displayFilterEffect();
+        return currentDoc;
     }
 
-    // If any moby object member is in a HAS relationship, add it to the list of filterable items
-    private Boolean addHASXPtrs(List<String> filterList, Element object){
-	String tagName = object.getLocalName();
-	boolean isContainer = false;
-	MobyDataType mobyDataType = null;	
-	if(tagName.equals(MobyTags.MOBYDATA) || tagName.equals(MobyTags.COLLECTION) || tagName.equals(MobyTags.SIMPLE) ||
-	   tagName.equals(MobyTags.CROSSREFERENCE)){
-	    isContainer = true;
-	}
-	else{
-	    mobyDataType = MobyDataType.getDataType(tagName, SeahawkOptions.getRegistry());
-	    if(mobyDataType == null){
-		logger.warn("Found datatype unknown to the registry ("+object.getLocalName()+")");
-		return Boolean.FALSE;
-	    }
+    /**
+     * Determine the parts of the XML document matching the FilterSearch criteria for the current doc, 
+     * and filter the view accordingly.  Used for interactive filtering in the display.
+     */
+    protected void applyFilter(boolean apply){
+	if(!filterChanged){
+	    filterChanged = true;
 	}
 
-	Boolean hasHAS = Boolean.FALSE; // does the object have a member with a HAS relationship?
-	NodeList members = object.getChildNodes();
-	for(int i = 0; i < members.getLength(); i++){
-	    if(!(members.item(i) instanceof Element)){
-		continue;
-	    }
-
-	    Element member = (Element) members.item(i);
-	    addHASXPtrs(filterList, member);
-
-	    if(!isContainer){
-		String memberName = member.getAttribute(MobyTags.ARTICLENAME);
-		MobyRelationship membership = mobyDataType.getChild(memberName);
-		//System.err.println("Relationship for " + tagName  + " member " + memberName + 
-		//		   " is " + (membership == null ? null : membership.getRelationshipType()));
-		if(membership != null && membership.getRelationshipType() == Central.iHAS){
-		    filterList.add(getXPtr(member));
-		    if(!hasHAS){
-			hasHAS = Boolean.TRUE;
-		    }
-		}
-	    }
+        FilterSearch filter = filterHistory.get(getCurrentURL());
+	filterableNodes = DataUtils.findFilteredNodes(getCurrentDoc(), filter, filterableNodes, filteredData, jobXPtrs,
+                                                      currentSelectedData, currentSelectionXPath, apply);
+ 
+	if((!apply || filter == null || filter.getFilterRegex().toString().length() == 0) && firstDocRendering){
+	    // Show whole doc if no filter or if filter is blank, so nothing to do here
+	    firstDocRendering = false;
 	}
-	return hasHAS;
+	// apply gray out in the document display, or need to cleanup previous state even if no filter now
+        else{
+	    displayFilterEffect();
+        }
     }
 
-    // Recursively ascend the DOM tree and find out our place in its branching structure
-    private String getXPtr(Node n){
-	if(n == null || n instanceof Document){
-	    return "";
-	}
-	Node parent = n.getParentNode();
-        if(parent == null && n instanceof Attr){
-	    parent = ((Attr) n).getOwnerElement();
-	}
-
-	NodeList children = parent.getChildNodes();
-	int nonElementCnt = 0;
-	for(int i = 0; i < children.getLength(); i++){
-	    if(!(children.item(i) instanceof Element)){
-		nonElementCnt++; 
-		continue;
-	    }
-	    if(n == children.item(i)){
-		return getXPtr(parent)+"/"+(i-nonElementCnt+1);
-	    }
-	}
-	return null;
-    }
 
     /**
      * Gray out parts of the HTML view if they are part of the filtered data.
@@ -1681,7 +1527,7 @@
 	// Gray out the mismatched textual data
 	for(Map.Entry<String,String> dataToFilter: filteredData.entrySet()){	    
 
-	    //System.err.println("Filtering "+dataToFilter.getKey());
+	    System.err.println("Filtering "+dataToFilter.getKey());
 	    javax.swing.text.AbstractDocument.AbstractElement htmlDiv = 
 		(javax.swing.text.AbstractDocument.AbstractElement) d.getElement(dataToFilter.getKey());
 	    if(htmlDiv == null){
@@ -1998,4 +1844,5 @@
     public void lostOwnership(Clipboard clipboard, Transferable contents){
 	//System.err.println("Lost clipboard ownership");
     }
+
 }

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java,v
retrieving revision 1.17
retrieving revision 1.18
diff -u -r1.17 -r1.18
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java	2010/04/09 15:55:48	1.17
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java	2010/04/14 22:02:04	1.18
@@ -1,11 +1,11 @@
 package ca.ucalgary.seahawk.gui;
 
 import ca.ucalgary.seahawk.services.MobyClient;
-import ca.ucalgary.seahawk.util.HTMLUtils;
-import ca.ucalgary.seahawk.util.SeahawkOptions;
+import ca.ucalgary.seahawk.util.*;
 
 import org.biomoby.shared.*;
 import org.biomoby.shared.data.*;
+import org.biomoby.shared.parser.MobyTags;
 import org.biomoby.client.CentralImpl;
 import org.biomoby.client.MobyRequest;
 import org.biomoby.client.MobyRequestEventHandler;
@@ -182,6 +182,7 @@
 	return handler;
     }
 
+    // synchronized so simultaneous requests don't get their input data mixed up
     public void setupServiceSecondaryData(MobyRequestEventHandler handler){
 	MobyDataInstance[] castInputs = new MobyDataInstance[primaryInput.length];
 	for(int i = 0; i < primaryInput.length; i++){
@@ -194,14 +195,17 @@
 	    castInputs[i] = (MobyDataInstance) primaryInput[i];
 	}
 
-	try{	    
-	    mobyRequest.setInput(castInputs);
-	    mobyRequest.setSecondaryInput(secondaryInputInstances);
-	} catch(MobyException me){
-	    me.printStackTrace();
-	    logger.warn("Error while trying to set service input: " + me);
-	}
-	executeService(handler);
+        // code from mobyRequest.setInput() to executeService() should always be synced to avoid input mixup between requests
+        synchronized(mobyRequest){
+	    try{	    
+	        mobyRequest.setInput(castInputs);
+	        mobyRequest.setSecondaryInput(secondaryInputInstances);
+	    } catch(MobyException me){
+	        me.printStackTrace();
+	        logger.warn("Error while trying to set service input: " + me);
+	    }
+	    executeService(handler);
+        }
     }
 
     protected void setupService(MobyService mobyService, MobyDataInstance mdi, int handlerHashCode, boolean useDefaultSecondaries){
@@ -217,18 +221,21 @@
 	System.arraycopy(primaryInputTemplate, 0, primaryInput, 0, primaryInput.length);
 
 	if(!hasSecondaryInput(mobyService)){
-	    try{
-		// Implement simple input (i.e. only one input argument)
-		mobyRequest.setInput(mdi, "");
-	    }
-	    catch(MobyException me){
-		logger.error("Failure in MOBY input, was not acceptable:" + me);
-		return;
-	    }
+            // code from mobyRequest.setInput() to executeService() should always be synced to avoid input mixup between requests
+            synchronized(mobyRequest){
+	        try{
+		    // Implement simple input (i.e. only one input argument)
+		    mobyRequest.setInput(mdi, "");
+	        }
+	        catch(MobyException me){
+		    logger.error("Failure in MOBY input, was not acceptable:" + me);
+		    return;
+	        }
 
-	    // No need for further info, just launch the request
-	    removePopupOptions();
-	    executeService(getHandlerByHashCode(handlerHashCode));
+	        // No need for further info, just launch the request
+	        removePopupOptions();
+	        executeService(getHandlerByHashCode(handlerHashCode));
+            }
 	}
 	else{
 	    // We need more info from the user to launch this service
@@ -502,7 +509,8 @@
     class OptionLoaderThread extends Thread{
 	Node targetNode = null;
 	MobyRequestEventHandler handler = null;
-	MobyDataInstance mobyData = null;
+	MobyPayloadRequestListener payloadCreator = null;
+	Object mobyData = null;
 	String extraMenuText = null;
 	JPopupMenu popupList;
 
@@ -513,11 +521,13 @@
 	    this.handler = handler;
 	}
 
-	public OptionLoaderThread(MobyDataInstance mobyData, JPopupMenu popupList, MobyRequestEventHandler handler, String extraMenuText){
+	public OptionLoaderThread(Object mobyData, JPopupMenu popupList, MobyRequestEventHandler handler, 
+                                  MobyPayloadRequestListener payloadCreator, String extraMenuText){
 	    super();
 	    this.mobyData = mobyData;
 	    this.popupList = popupList;
 	    this.handler = handler;
+            this.payloadCreator = payloadCreator;
 	    this.extraMenuText = extraMenuText;
 	}
 
@@ -526,7 +536,7 @@
 		addPopupOptions(targetNode, popupList, false, handler);
 	    }
 	    else if(mobyData != null){
-		addPopupOptions(mobyData, popupList, false, handler, extraMenuText);
+		addPopupOptions(mobyData, popupList, false, handler, payloadCreator, extraMenuText);
 	    }
 	    else{
 		logger.warn("Warning: OptionLoaderThread has no data to work with");
@@ -576,6 +586,30 @@
     }
 
     /**
+     * Creates a menu item based on the provided data type.  If a service is selected from here,
+     * a callback will be made to the MobyPayloadRequestListener for the actual submission data.
+     *
+     * @param payloadKey a key that will be used in the callback so the listener knows what payload the create
+     */
+    public void addPopupOptions(MobyDataType mobyDataType, JPopupMenu popupList, boolean asynchronous, 
+                                MobyRequestEventHandler handler, MobyPayloadRequestListener payloadCreator, 
+                                String payloadKey, String extraMenuText){
+        addPopupOptions(mobyDataType, popupList, asynchronous, handler, payloadCreator, extraMenuText);
+    }
+
+    public void addPopupOptions(MobyNamespace mobyNamespace, JPopupMenu popupList, boolean asynchronous, 
+                                MobyRequestEventHandler handler, MobyPayloadRequestListener payloadCreator, 
+                                String payloadKey, String extraMenuText){
+        addPopupOptions(mobyNamespace, popupList, asynchronous, handler, payloadCreator, extraMenuText);
+    }
+
+    public void addPopupOptions(MobyPrimaryDataSet collection, JPopupMenu popupList, boolean asynchronous, 
+                                MobyRequestEventHandler handler, MobyPayloadRequestListener payloadCreator, 
+                                String payloadKey, String extraMenuText){
+        addPopupOptions(collection, popupList, asynchronous, handler, payloadCreator, extraMenuText);
+    }
+
+    /**
      * Same as three arg addPopupOptions, but uses default response handler
      */
     public void addPopupOptions(MobyDataInstance mobyData, JPopupMenu popupList, boolean asynchronous){
@@ -586,13 +620,16 @@
      * Find the list of available services querying MobyCentral directly with a piece of data.
      */
     public void addPopupOptions(MobyDataInstance mobyData, JPopupMenu popupList, boolean asynchronous, MobyRequestEventHandler handler){
-	addPopupOptions(mobyData, popupList, asynchronous, handler, null);
+	addPopupOptions(mobyData, popupList, asynchronous, handler, null, null);
     }
 
     /**
      * Find the list of available services querying MobyCentral directly with a piece of data.
+     *
+     * @param mobyData a MobyDataInstance, or in the case of deferred data to be created by payloadCreator, a MobyDataType, MobyNamespace, or MobyPrimaryDataSet
      */
-    public void addPopupOptions(MobyDataInstance mobyData, JPopupMenu popupList, boolean asynchronous, MobyRequestEventHandler handler, String extraMenuText){
+    public void addPopupOptions(Object mobyData, JPopupMenu popupList, boolean asynchronous, 
+                                MobyRequestEventHandler handler, MobyPayloadRequestListener payloadCreator, String extraMenuText){
 
 	if(asynchronous){
 	    //Show the user that we're doing something...
@@ -605,7 +642,7 @@
 	    }
 
 	    // Call this method synchronously in a different thread
-	    OptionLoaderThread lt = new OptionLoaderThread(mobyData, popupList, handler, extraMenuText);
+	    OptionLoaderThread lt = new OptionLoaderThread(mobyData, popupList, handler, payloadCreator, extraMenuText);
 	    lt.start();
 	    return;
 	}
@@ -625,7 +662,9 @@
 	    popupList.setVisible(true);
 	}
 
-	addClipboardItem(submenu, mobyData);
+	if(mobyData instanceof MobyDataInstance){
+            addClipboardItem(submenu, (MobyDataInstance) mobyData);
+        }
 	submenu.add(getWaitItem(submenu));
 
  	MobyDataServiceAssocInstance serviceAssocObject = null;  
@@ -637,6 +676,15 @@
 	    else if(mobyData instanceof MobyDataObject){
 		serviceAssocObject = mobyClient.getServices((MobyDataObject) mobyData);
 	    }
+            // The data will be loaded later
+            else if(payloadCreator != null){
+                if(mobyData instanceof MobyPrimaryDataSet){
+                    //serviceAssocObject = mobyClient.getServices(new MobyDataObjectSetDeferred(mobyData, payloadCreator, requestKey));
+                }
+                else{
+                    //serviceAssocObject = mobyClient.getServices(new MobyDataObjectDeferred(mobyData, payloadCreator, requestKey));
+                }
+            }
 	    else{
 		logger.warn("Service options for objects other than MobyDataObject " +
 			    "and MobyDataObjectSet are not yet supported.");
@@ -1136,51 +1184,50 @@
 	return menu;
     }
 
-    public JMenu createObjectSubMenu(MobyDataInstance mdi, String extraMenuText){
-	if(!(mdi instanceof MobyPrimaryData)){
-	    logger.warn("Ignoring non-primary data object submitted to menu creation: " + mdi);
-	    return null;
-	}
-	
-	MobyPrimaryData targetData = (MobyPrimaryData) mdi;
-	String id = targetData.getId();
-	if(id == null){
-	    id = "";
-	}
-	else if(id.length() > MAX_ID_LEN+3){
-	    id = id.substring(0, MAX_ID_LEN)+"...";
-	}
-	
-	MobyDataType mobyDataType = targetData.getDataType();
-	String name = null;
-	if(mobyDataType == null){
-	    logger.warn("PG: Warning: no datatype associated with service " + 
-			targetData.getName());
-	}
-	else{
-	    name = mobyDataType.getName();
-	}
-	if("Object".equals(name)){
-	    MobyNamespace namespaces[] = targetData.getNamespaces();
-	    //System.err.println("Got base object with namespaces numbering " + namespaces.length);
-	    if(namespaces != null && namespaces.length > 0 && namespaces[0] != null){
-		//System.err.println("Checking namespace "+ namespaces[0].getName());
-		name = namespaces[0].getName();
+    /**
+     * Template object may be one of MobyPrimaryData, or in case of deferred content loading a 
+     * MobyNamespace, MobyDataType, or MobyPrimaryDataSet.
+     */
+    public JMenu createObjectSubMenu(Object templateObject, String extraMenuText){
+        String id = null;
+        MobyDataType mobyDataType = null;
+        String name = null;
+	MobyNamespace[] namespaces = null;
+	if(templateObject instanceof MobyPrimaryData){
+	    MobyPrimaryData targetData = (MobyPrimaryData) templateObject;
+	    mobyDataType = targetData.getDataType();
+	    namespaces = targetData.getNamespaces();
+	    id = targetData.getId();
+	    if(id == null){
+	        id = "";
 	    }
-	}
-	else{
-	    //System.err.println("Got complex object with datatype name " + name);
-	}
+	    else if(id.length() > MAX_ID_LEN+3){
+	        id = id.substring(0, MAX_ID_LEN)+"...";
+	    }
+	    if(MobyTags.MOBYOBJECT.equals(mobyDataType.getName()) &&
+               namespaces != null && namespaces.length > 0 && namespaces[0] != null){
+		name = namespaces[0].getName();
+            }
+            else{
+                name = mobyDataType.getName();
+            }
+        }
+        else if(templateObject instanceof MobyNamespace){
+            namespaces = new MobyNamespace[]{(MobyNamespace) templateObject};
+            mobyDataType = MobyDataType.getDataType(MobyTags.MOBYOBJECT, SeahawkOptions.getRegistry());
+            name = ((MobyNamespace) templateObject).getName();
+        }
+        else if(templateObject instanceof MobyDataType){
+            mobyDataType = (MobyDataType) templateObject;
+            name = ((MobyDataType) templateObject).getName();
+        }
+        else{
+            logger.error("Could not create submenu for object of unaccepted type "+templateObject.getClass().getName());
+        }
 	
-	// Make sure we have a fully documented data type object
-	mobyDataType = MobyDataType.getDataType(targetData.getDataType().getName(), SeahawkOptions.getRegistry());
 	String desc = null;
 	String datatype = null;
-	if(mobyDataType == null){
-	    logger.warn("PG: Warning (submenu): no datatype associated with service " + 
-			targetData.getName());
-	}
-	else{
+	if(mobyDataType != null){
 	    datatype = mobyDataType.getName();
 	    desc = mobyDataType.getDescription();
 	    if(desc == null || desc.length() == 0){
@@ -1189,19 +1236,12 @@
 	}
 	if(datatype != null && datatype.indexOf("objectclass:") != -1){ 
 	    //LSID type URN, truncate the prefix and keep the part a user would care about (last part, the class name)
-	    
 	    datatype = datatype.substring(datatype.indexOf("objectclass:")+12);
 	}
 
 	JMenu submenu = null;
-	MobyNamespace[] namespaces = targetData.getNamespaces();
 	// If not defined, derive a description from the Data Namespace
-	if(mobyDataType == null){
-	    desc = "Unknown datatype";
-	    submenu = new JMenu("Services for unknown datatype");
-	    assignMenuDataIndex(submenu);
-	}
-	else if("Object".equals(mobyDataType.getName())){
+	if(MobyTags.MOBYOBJECT.equals(mobyDataType.getName())){
 	    String mobydesc = "?";
 	    if(namespaces != null){
 		// Take the longest description
@@ -1214,20 +1254,30 @@
 		}
 	    }
 	    desc = "Record Identifier - " + mobydesc;
-	    submenu = new JMenu("Services for " + (extraMenuText == null ? "" : extraMenuText+" ")+datatype + ":" + id);
+	    if(templateObject instanceof MobyDataObjectSet){
+		datatype += " collection";
+	    }
+	    submenu = new JMenu("<html>Services for " + (extraMenuText == null ? "" : extraMenuText+" ") + 
+                                datatype + (id == null ? "" : ":" + id)+"</html>");
 	    assignMenuDataIndex(submenu);
 	}
-	else if("String".equals(mobyDataType.getName())){
-	    String sample = targetData.getName();
-	    if(sample == null){
-		sample = targetData.toString();
+	else if(MobyTags.MOBYSTRING.equals(mobyDataType.getName())){
+	    String sample = "";
+            if(templateObject instanceof MobyDataInstance){
+                sample = ((MobyDataInstance) templateObject).getName();
+                if(sample == null){
+		    sample = "\""+((MobyDataInstance) templateObject).toString()+"\"";
+	        }
+            }
+	    if(templateObject instanceof MobyDataObjectSet){
+		sample += " collection";
 	    }
 	    if(sample.length() > MAX_ID_LEN+3){
-		sample = sample.substring(0, MAX_ID_LEN)+"...";
+		sample = "\""+sample.substring(0, MAX_ID_LEN)+"...\"";
 	    }
 	    desc = "A piece of text";
-	    submenu = new JMenu("Services for "+(extraMenuText == null ? "" : extraMenuText+" ")+
-				"String \"" + sample + "\"");
+	    submenu = new JMenu("<html>Services for "+(extraMenuText == null ? "" : extraMenuText+" ")+
+				"String " + sample+"</html>");
 	    assignMenuDataIndex(submenu);
 	}
 	// Complex object
@@ -1240,17 +1290,18 @@
 		    desc += "["+namespaceDesc+"]";
 		}
 	    }
-	    if(targetData instanceof MobyDataObject && id != null && id.length() > 0){
+	    if(templateObject instanceof MobyDataObject && id != null && id.length() > 0){
 		objectLabel += ":" + id;
 	    }
-	    else if(targetData instanceof MobyDataObjectSet){
+	    else if(templateObject instanceof MobyDataObjectSet){
 		objectLabel += " collection";
 	    }
-	    submenu = new JMenu("Services for " + (extraMenuText == null ? "" : extraMenuText+" ")+objectLabel);
+	    submenu = new JMenu("<html>Services for " + (extraMenuText == null ? "" : extraMenuText+" ")+objectLabel+"</html>");
 	    assignMenuDataIndex(submenu);
 	}
 	desc = "Input data: " + desc;
 	desc = HTMLUtils.htmlifyToolTipText(desc, MAX_SERVICE_DESC_LEN);
+        System.err.println("New submenu has label " + submenu.getText());
 	submenu.setToolTipText(desc);
 	submenu.setName(SERVICE_SUBMENU_NAME);
 	return submenu;


From gordonp at dev.open-bio.org  Wed Apr 14 19:48:28 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Wed, 14 Apr 2010 19:48:28 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004142348.o3ENmSDf009599@dev.open-bio.org>


gordonp
Wed Apr 14 19:48:27 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util
In directory dev.open-bio.org:/tmp/cvs-serv9535/src/main/ca/ucalgary/seahawk/util

Modified Files:
	MobyPayloadRequestListener.java 
Added Files:
	MobyContentCreator.java MobyDataObjectDeferred.java 
	MobyDataObjectSetDeferred.java 
Log Message:
Additional commit related to initial implementation 'for each' in Seahawk service invocation
moby-live/Java/src/main/ca/ucalgary/seahawk/util MobyContentCreator.java,NONE,1.1 MobyDataObjectDeferred.java,NONE,1.1 MobyDataObjectSetDeferred.java,NONE,1.1 MobyPayloadRequestListener.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/MobyPayloadRequestListener.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/MobyPayloadRequestListener.java	2010/04/14 22:02:04	1.1
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/MobyPayloadRequestListener.java	2010/04/14 23:48:27	1.2
@@ -10,7 +10,10 @@
  */	
 public interface MobyPayloadRequestListener{
     /**
-     * @param requestKey the value given to the caller when the listener was registered (tells the listener what payload to create baesd on some internal naming convention for the listener)
+     * Assumes the listener knows what payload to create based on some internal context stored by the listener. 
+     * (i.e. you need to create a new listener specific to each deferred payload. 
+     *
+     * @param paramNameforJobs the name of the moby job  parameter to which each value should be assigned
      */
-    public org.biomoby.shared.data.MobyContentInstance createPayload(String requestKey, String paramNameforJobs); 
+    public org.biomoby.shared.data.MobyContentInstance createPayload(String paramNameforJobs); 
 }


From gordonp at dev.open-bio.org  Wed Apr 14 19:48:27 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Wed, 14 Apr 2010 19:48:27 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004142348.o3ENmRar009579@dev.open-bio.org>


gordonp
Wed Apr 14 19:48:27 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv9535/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	MobyContentPane.java MobyPayloadCreator.java 
	MobyServicesGUI.java 
Log Message:
Additional commit related to initial implementation 'for each' in Seahawk service invocation
moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyContentPane.java,1.27,1.28 MobyPayloadCreator.java,1.1,1.2 MobyServicesGUI.java,1.18,1.19
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java,v
retrieving revision 1.27
retrieving revision 1.28
diff -u -r1.27 -r1.28
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java	2010/04/14 22:02:04	1.27
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java	2010/04/14 23:48:27	1.28
@@ -1215,7 +1215,6 @@
 	// chooses the for each option.  The Moby data instance's userData gives us the current context, enabling us 
         // to construct the correct payload in MobyPayloadCreator.createPayload() at any point in the future.
         String origUserData = (String) mobyData.getUserData();
-        MobyPayloadRequestListener payloadCreator = new MobyPayloadCreator(this);
         for(String peerMode: new String[]{DataUtils.ARTICLE_PEERS_MODE, DataUtils.DATATYPE_PEERS_MODE}){
             // note that getPeerElements() will modify the userData to reflect the semantic of the requested peer mode
             mobyData.setUserData(origUserData);
@@ -1229,17 +1228,20 @@
             }
             MobyDataType dataType = ((MobyPrimaryData) mobyData).getDataType();
             if(mobyData instanceof MobyPrimaryDataSet){	 // Collection
-                servicesGUI.addPopupOptions((MobyPrimaryDataSet) mobyData, popup, true, getDefaultHandler(), payloadCreator, 
-					    (String) mobyData.getUserData(), each);
+                servicesGUI.addPopupOptions((MobyPrimaryDataSet) mobyData, popup, true, getDefaultHandler(), 
+					    new MobyPayloadCreator(this, (String) mobyData.getUserData()), 
+					    each);
             }
             else if(MobyTags.MOBYOBJECT.equals(dataType.getName())){  
                 MobyNamespace namespace = null;
-                servicesGUI.addPopupOptions(namespace, popup, true, getDefaultHandler(), payloadCreator, 
-                                            (String) mobyData.getUserData(), each);
+                servicesGUI.addPopupOptions(namespace, popup, true, getDefaultHandler(),
+					    new MobyPayloadCreator(this, (String) mobyData.getUserData()), 
+                                            each);
             }
             else{
-                servicesGUI.addPopupOptions(dataType, popup, true, getDefaultHandler(), payloadCreator, 
-                                            (String) mobyData.getUserData(), each);
+                servicesGUI.addPopupOptions(dataType, popup, true, getDefaultHandler(),
+					    new MobyPayloadCreator(this, (String) mobyData.getUserData()), 
+                                            each);
             }
         }
 
@@ -1301,7 +1303,7 @@
 		// so PbE will properly reflect the logic of if(f1(x) matches filter){f2(x)}
 		DataUtils.addUserData(previousMDI, srcURL, getFilter());
 
-		servicesGUI.addPopupOptions(previousMDI, popup, true, null, "previous input");
+		servicesGUI.addPopupOptions(previousMDI, popup, true, null, null, "previous input");
 	    }
 	} catch(Exception e){
 	    logger.warn("Could not load previous service info, 'previous input' option will not be displayed", e);

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyPayloadCreator.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyPayloadCreator.java	2010/04/14 22:02:04	1.1
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyPayloadCreator.java	2010/04/14 23:48:27	1.2
@@ -14,14 +14,16 @@
  */
 public class MobyPayloadCreator implements MobyPayloadRequestListener{
     private MobyContentPane srcPane;
+    private String requestKey;
 
     private static Logger logger = Logger.getLogger(MobyPayloadCreator.class.getName());
 
-    public MobyPayloadCreator(MobyContentPane pane){
+    public MobyPayloadCreator(MobyContentPane pane, String requestKey){
         srcPane = pane;
+	this.requestKey = requestKey;
     }
 
-    public MobyContentInstance createPayload(String requestKey, String targetJobArgName){
+    public MobyContentInstance createPayload(String targetJobArgName){
 	// The request key is the sample data's app context: 
         // url#xpath <tab> sample_xptr <tab> filter_regex <tab> filter_xpath <tab> xpath_desc <tab> case_sensitive_boolean <tab> inverse selection
         // from which we will build the peer dataset to submit.

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java,v
retrieving revision 1.18
retrieving revision 1.19
diff -u -r1.18 -r1.19
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java	2010/04/14 22:02:04	1.18
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java	2010/04/14 23:48:27	1.19
@@ -586,30 +586,6 @@
     }
 
     /**
-     * Creates a menu item based on the provided data type.  If a service is selected from here,
-     * a callback will be made to the MobyPayloadRequestListener for the actual submission data.
-     *
-     * @param payloadKey a key that will be used in the callback so the listener knows what payload the create
-     */
-    public void addPopupOptions(MobyDataType mobyDataType, JPopupMenu popupList, boolean asynchronous, 
-                                MobyRequestEventHandler handler, MobyPayloadRequestListener payloadCreator, 
-                                String payloadKey, String extraMenuText){
-        addPopupOptions(mobyDataType, popupList, asynchronous, handler, payloadCreator, extraMenuText);
-    }
-
-    public void addPopupOptions(MobyNamespace mobyNamespace, JPopupMenu popupList, boolean asynchronous, 
-                                MobyRequestEventHandler handler, MobyPayloadRequestListener payloadCreator, 
-                                String payloadKey, String extraMenuText){
-        addPopupOptions(mobyNamespace, popupList, asynchronous, handler, payloadCreator, extraMenuText);
-    }
-
-    public void addPopupOptions(MobyPrimaryDataSet collection, JPopupMenu popupList, boolean asynchronous, 
-                                MobyRequestEventHandler handler, MobyPayloadRequestListener payloadCreator, 
-                                String payloadKey, String extraMenuText){
-        addPopupOptions(collection, popupList, asynchronous, handler, payloadCreator, extraMenuText);
-    }
-
-    /**
      * Same as three arg addPopupOptions, but uses default response handler
      */
     public void addPopupOptions(MobyDataInstance mobyData, JPopupMenu popupList, boolean asynchronous){
@@ -678,16 +654,32 @@
 	    }
             // The data will be loaded later
             else if(payloadCreator != null){
-                if(mobyData instanceof MobyPrimaryDataSet){
-                    //serviceAssocObject = mobyClient.getServices(new MobyDataObjectSetDeferred(mobyData, payloadCreator, requestKey));
-                }
-                else{
-                    //serviceAssocObject = mobyClient.getServices(new MobyDataObjectDeferred(mobyData, payloadCreator, requestKey));
-                }
+                try{
+                    if(mobyData instanceof MobyPrimaryDataSet){
+			serviceAssocObject = mobyClient.getServices(new MobyDataObjectSetDeferred((MobyPrimaryDataSet) mobyData, 
+												  payloadCreator));
+		    }
+		    else if(mobyData instanceof MobyNamespace){
+			serviceAssocObject = mobyClient.getServices(new MobyDataObjectDeferred((MobyNamespace) mobyData, 
+											       payloadCreator));
+		    }
+		    else if(mobyData instanceof MobyDataType){
+			serviceAssocObject = mobyClient.getServices(new MobyDataObjectDeferred((MobyDataType) mobyData, 
+											       payloadCreator));
+		    }
+		    else{
+			logger.warn("Ignoring unrecognized template class (" + mobyData.getClass().getName()+
+				    ") for deferred data creation by a MobyPayloadRequestListener"); 
+			return;
+		    }
+		} catch(Exception e){
+		    logger.error("Could not create deferred Moby data object", e);
+		}
             }
 	    else{
 		logger.warn("Service options for objects other than MobyDataObject " +
-			    "and MobyDataObjectSet are not yet supported.");
+			    "and MobyDataObjectSet are not yet supported unless you " +
+			    "have defined a MobyPayloadRequestListener.");
 		return;
 	    }
 	} catch(Exception mobye){


From gordonp at dev.open-bio.org  Thu Apr 15 14:51:17 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Thu, 15 Apr 2010 14:51:17 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004151851.o3FIpHrB006441@dev.open-bio.org>


gordonp
Thu Apr 15 14:51:17 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data
In directory dev.open-bio.org:/tmp/cvs-serv6403/src/main/org/biomoby/shared/data

Modified Files:
	MobyContentInstance.java 
Log Message:
Made contents maintain insertion order by switching to LinkedHashMap for underlying Map storage
moby-live/Java/src/main/org/biomoby/shared/data MobyContentInstance.java,1.14,1.15
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyContentInstance.java,v
retrieving revision 1.14
retrieving revision 1.15
diff -u -r1.14 -r1.15
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyContentInstance.java	2008/01/14 22:54:19	1.14
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyContentInstance.java	2010/04/15 18:51:17	1.15
@@ -31,7 +31,7 @@
     private String serviceAuthURI = null;
     private String serviceNotes = null;
     private int xmlMode = MobyDataInstance.SERVICE_XML_MODE;
-    private HashMap<String, MobyDataJob> members;
+    private LinkedHashMap<String, MobyDataJob> members;
     private int autoID = 1;  // to name members without existing names
     private Vector<ServiceException> exceptions;
 
@@ -40,7 +40,7 @@
      * Useful if you are a client composing a query, or a server composing a response.
      */
     public MobyContentInstance(){
-	members = new HashMap<String, MobyDataJob>();
+	members = new LinkedHashMap<String, MobyDataJob>();
 	exceptions = new Vector<ServiceException>();
     }
 
@@ -106,7 +106,7 @@
 	    }
 	}
 	
-	members = new HashMap<String,MobyDataJob>();
+	members = new LinkedHashMap<String,MobyDataJob>();
 
 	// If we got this far, we're in the clear for the single envelope
 	// What we need to parse now is the one or more sets of data in the envelope


From gordonp at dev.open-bio.org  Fri Apr 16 13:29:21 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 16 Apr 2010 13:29:21 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004161729.o3GHTLfE014979@dev.open-bio.org>


gordonp
Fri Apr 16 13:29:21 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory dev.open-bio.org:/tmp/cvs-serv14943/src/main/org/biomoby/client

Modified Files:
	MobyRequest.java 
Log Message:
Fixed javadoc typo
moby-live/Java/src/main/org/biomoby/client MobyRequest.java,1.46,1.47
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java,v
retrieving revision 1.46
retrieving revision 1.47
diff -u -r1.46 -r1.47
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java	2010/03/29 20:42:48	1.46
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java	2010/04/16 17:29:21	1.47
@@ -238,7 +238,7 @@
 
     /**
      * This method will assign the provided secondary parameters to all primary input data currently
-     * in this object.  This is covenient if you are running 100 seqs through BLAST and only want to set
+     * in this object.  This is convenient if you are running 100 seqs through BLAST and only want to set
      * the parameters once.  If you instead want to set secondary input differently for all primary inputs, you'll
      * need to create a custom MobyContentInstance as input to setInput().
      *


From gordonp at dev.open-bio.org  Fri Apr 16 13:32:33 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 16 Apr 2010 13:32:33 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004161732.o3GHWXGF015279@dev.open-bio.org>


gordonp
Fri Apr 16 13:32:33 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services
In directory dev.open-bio.org:/tmp/cvs-serv15243/src/main/ca/ucalgary/seahawk/services

Modified Files:
	MobyClient.java 
Log Message:
Implemented proper logging, account for deferred data objects
moby-live/Java/src/main/ca/ucalgary/seahawk/services MobyClient.java,1.26,1.27
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/MobyClient.java,v
retrieving revision 1.26
retrieving revision 1.27
diff -u -r1.26 -r1.27
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/MobyClient.java	2010/04/11 01:58:05	1.26
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/MobyClient.java	2010/04/16 17:32:33	1.27
@@ -1,6 +1,6 @@
 package ca.ucalgary.seahawk.services;
 
-import ca.ucalgary.seahawk.util.SeahawkOptions;
+import ca.ucalgary.seahawk.util.*;
 
 import org.biomoby.client.*;
 import org.biomoby.registry.meta.*;
@@ -116,8 +116,8 @@
 	    docBuilder = dbf.newDocumentBuilder();
 	}
 	catch(ParserConfigurationException pce){
-	    System.err.println("Error: Could not find an XML parser, will not be able to use " +
-			       "MOBY xpath and regex mapper default behaviors: " + pce);
+	    logger.log(Level.SEVERE, "Error: Could not find an XML parser, will not be able to use " +
+		       "MOBY xpath and regex mapper default behaviors: ", pce);
 	}
 	ClassLoader cl = getClass().getClassLoader();
 	if(cl == null){
@@ -138,8 +138,8 @@
 	}
 	if(dataMappingXMLURL == null){
 	    if(rulesResource.length() != 0){ // if not left intentionally blank
-		System.err.println("Could not find MOBY data mapping resource '"+
-				   rulesResource+"'");
+		logger.log(Level.WARNING, "Could not find MOBY data mapping resource '"+
+				          rulesResource+"'");
 	    }
 	}
 	else{
@@ -147,7 +147,7 @@
 		addMappingsFromURL(dataMappingXMLURL);
 	    }
 	    catch(Exception e){
-		System.err.println("Error loading default data mapping rules ("+dataMappingXMLURL+"):" + e);
+		logger.log(Level.SEVERE, "Error loading default data mapping rules ("+dataMappingXMLURL+")", e);
                 e.printStackTrace();
 	    }
 	}
@@ -198,8 +198,8 @@
      */
     public void addMappingsFromURL(URL u) throws Exception{
 	if(docBuilder == null){
-	    System.err.println("Asked to add data mappings from file, " +
-			       "but no XML parser is available");
+	    logger.log(Level.SEVERE, "Asked to add data mappings from file, " +
+			             "but no XML parser is available");
 	    return;
 	}
 
@@ -229,13 +229,13 @@
 	}
 
 	if(nsContext.getNamespaceURI(prefix) != null){
-	    System.err.println("Prefix definition for " + prefix + " already exists, ignoring new definition");
+	    logger.log(Level.WARNING, "Prefix definition for " + prefix + " already exists, ignoring new definition");
 	    return;
 	}
 
 	String nsURI = e.getTextContent();
 	if(nsURI == null || nsURI.length() == 0){
-	    System.err.println("Prefix definition for " + prefix + " has a blank URI rule, ignoring");
+	    logger.log(Level.WARNING, "Prefix definition for " + prefix + " has a blank URI rule, ignoring");
 	    return;
 	}
 	nsContext.setPrefix(nsURI, prefix);	
@@ -264,7 +264,7 @@
 	    }
 
 	    if(!RULE_SET_TAG.equals(ruleSet.getLocalName())){
-		System.err.println("Skipping unexpected top level tag " + ruleSet.getLocalName());
+		logger.log(Level.WARNING, "Skipping unexpected top level tag " + ruleSet.getLocalName());
 		continue;
 	    }
 
@@ -304,18 +304,18 @@
 		}
 		else if(isArticleNameRule(ruleMember)){
 		    if(articleNameString != null && articleNameString.length() != 0){
-			System.err.println("Skipping unexpected article name definition node, " +
-					   "a valid article name rule has already been " +
-					   "created for this ruleset");
+			logger.log(Level.WARNING, "Skipping unexpected article name definition node, " +
+					          "a valid article name rule has already been " +
+					          "created for this ruleset");
 			continue;
 		    }
 		    articleNameString = ruleMember.getTextContent();
 		}
 		else if(isDataTypeRule(ruleMember)){
 		    if(dataTypeString != null && dataTypeString.length() != 0){
-			System.err.println("Skipping unexpected datatype definition node, " +
-					   "a valid datatype rule has already been " +
-					   "created for this ruleset");
+			logger.log(Level.WARNING, "Skipping unexpected datatype definition node, " +
+					          "a valid datatype rule has already been " +
+					          "created for this ruleset");
 			continue;
 		    }
 		    dataTypeString = getDataType(ruleMember);
@@ -328,15 +328,15 @@
 		}
 		// skip any Dublin Core metadata in validation
 		else if(!MobyPrefixResolver.DUBLIN_CORE_NAMESPACE.equals(ruleMember.getNamespaceURI())){
-		    System.err.println("Skipping unexpected "+RULE_SET_TAG+
-				       " child node " + ruleMember.getLocalName());
+		    logger.log(Level.WARNING, "Skipping unexpected "+RULE_SET_TAG+
+				              " child node " + ruleMember.getLocalName());
 		    continue;
 		} 
 	    }
 
 	    if(xpathStrings.size() == 0 && regexStrings.size() == 0 && urlRegexStrings.size() == 0){
-		System.err.println("Skipping namespace rule that has no xpath " +
-				   "url_regex or regex specs associated with it");
+		logger.log(Level.WARNING, "Skipping namespace rule that has no xpath " +
+				          "url_regex or regex specs associated with it");
 		// Next ruleset
 		continue;
 	    }
@@ -344,9 +344,9 @@
 	    // Simple object with just namespace & ID
 	    if(dataTypeString == null || dataTypeString.length() == 0){
 		if(memberMap.size() != 0){
-		    System.err.println("Warning: ignoring member rules, since " +
-				       "no datatype was defined for the ruleset " +
-				       "(base Object will be created)");
+		    logger.log(Level.WARNING, "Warning: ignoring member rules, since " +
+				              "no datatype was defined for the ruleset " +
+				              "(base Object will be created)");
 		}
 
 		for(int j = 0; j < xpathStrings.size(); j++){
@@ -362,8 +362,8 @@
 	    // Build complex object
 	    else{
 		if(memberMap.size() == 0){
-		    System.err.println("Complex datatype (" + dataTypeString + " was defined " +
-				       " in the ruleset, but no members were defined");
+		    logger.log(Level.WARNING, "Complex datatype (" + dataTypeString + " was defined " +
+				              " in the ruleset, but no members were defined");
 		}
 
 		for(int j = 0; j < xpathStrings.size(); j++){
@@ -465,7 +465,7 @@
 	    regexStrings.add(str);
 	}
 	else{
-	    System.err.println("Skipping blank regex rule"); 
+	    logger.log(Level.WARNING, "Skipping blank regex rule"); 
 	}
 
 	return str;
@@ -483,7 +483,7 @@
 	    urlRegexStrings.add(str);
 	}
 	else{
-	    System.err.println("Skipping blank url_regex rule"); 
+	    logger.log(Level.WARNING, "Skipping blank url_regex rule"); 
 	}
 
 	return str;
@@ -501,7 +501,7 @@
 	    xPathStrings.add(str);
 	}
 	else{
-	    System.err.println("Skipping blank XPath rule"); 
+	    logger.log(Level.WARNING, "Skipping blank XPath rule"); 
 	}
 
 	return str;
@@ -524,7 +524,7 @@
 	String memberNameKey = isPrimitiveDataType(dataTypeName) ? 
 	    MobyComplexBuilder.PRIMITIVE_VALUE_SENTINEL : memTag.getAttribute(DATATYPE_RULE_ATTR);
 	if(ruleValue == null || ruleValue.length() == 0){
-	    System.err.println("Object member " + memberNameKey + " has a blank value rule");
+	    logger.log(Level.WARNING, "Object member " + memberNameKey + " has a blank value rule");
 	}
 
 	String memberDataTypeSetting = memTag.getAttribute(DATATYPE_ATTR);
@@ -574,10 +574,10 @@
 		!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 (" + memberWhitespaceSetting + 
-			       "), overriding with default of " + WHITESPACE_ATTR_KEEP_VAL);
+	    logger.log(Level.WARNING, "Object member " + memberNameKey + 
+			              " has an unrecognized value for the " + WHITESPACE_ATTR +
+			              " attribute (" + memberWhitespaceSetting + 
+			              "), overriding with default of " + WHITESPACE_ATTR_KEEP_VAL);
 	    memberWhitespaceSetting = WHITESPACE_ATTR_KEEP_VAL;
 	}
 
@@ -587,14 +587,14 @@
 	}
 	else if(!memberEncodingSetting.equals(ENCODING_ATTR_NONE_VAL) &&
 		!memberEncodingSetting.equals(ENCODING_ATTR_BASE64_VAL)){
-	    System.err.println("Object member " + memberNameKey + 
-			       " has an unrecognized value for the " + ENCODING_ATTR +
-			       " attribute, overriding with default of " + ENCODING_ATTR_NONE_VAL);
+	    logger.log(Level.WARNING, "Object member " + memberNameKey + 
+			              " has an unrecognized value for the " + ENCODING_ATTR +
+			              " attribute, overriding with default of " + ENCODING_ATTR_NONE_VAL);
 	    memberWhitespaceSetting = ENCODING_ATTR_NONE_VAL;
 	}
 
 	if(membersMap.containsKey(memberNameKey)){
-	    System.err.println("Object member " + memberNameKey + " already exists, ignoring new definition");
+	    logger.log(Level.WARNING, "Object member " + memberNameKey + " already exists, ignoring new definition");
 	    return;
 	}
 
@@ -637,8 +637,8 @@
 					" cannot have empty children");
 		}
 		if(namespaceStrings.containsKey(keyName)){
-		    System.err.println("Ignoring duplicate namespace value rule for " +
-				       "namespace '" + keyName + "'");
+		    logger.log(Level.WARNING, "Ignoring duplicate namespace value rule for " +
+				              "namespace '" + keyName + "'");
 		    continue;
 		}
 		if(keyName != null && keyName.length() != 0){
@@ -649,7 +649,7 @@
 		}
 	    }
 	    else{
-		System.err.println("Skipping unexpected "+NAMESPACE_RULE_TAG+" child node " + specName);
+		logger.log(Level.WARNING, "Skipping unexpected "+NAMESPACE_RULE_TAG+" child node " + specName);
 		continue;
 	    }
 	}
@@ -716,13 +716,11 @@
 			    }
 			}
 			catch(MobyException me){
-			    System.err.println("Could not build Moby object from match:" + me);
-			    me.printStackTrace();
+			    logger.log(Level.SEVERE, "Could not build Moby object from match", me);
 			}
 		    }
 		} catch(Throwable t){  // Principally stack overflows
-		    System.err.println("Exception/Error ("+t+") while applying regex '"+pattern.pattern()+"' to text");
-		    t.printStackTrace(System.err);
+		    logger.log(Level.SEVERE, "Exception/Error ("+t+") while applying regex '"+pattern.pattern()+"' to text", t);
 		}
 	    }
 	}
@@ -765,11 +763,11 @@
 		// have the exact same contents as the same members who are their
 		// subtypes, as these are superfluous.
 
-		System.err.println("Multiple Moby objects were found in the text data, " +
-				   "but the request was to return a simple. " +
-				   "Only the first value in the collection has been returned.");
+		logger.log(Level.WARNING, "Multiple Moby objects were found in the text data, " +
+				          "but the request was to return a simple. " +
+				          "Only the first value in the collection has been returned.");
 		for(MobyDataObject result: results){
-		    System.err.println("Found object: " + result.getDataType().getName()); 
+		    logger.log(Level.WARNING, "Found object: " + result.getDataType().getName()); 
 		}
 		// TODO: should we instead return the one deepest in the hierarchy (or with the most members)?
 		return results.elementAt(0);
@@ -818,11 +816,11 @@
 		// have the exact same contents as the same members who are their
 		// subtypes, as these are superfluous.
 
-		System.err.println("Multiple Moby objects were found in the text data, " +
-				   "but the request was to return a simple. " +
-				   "Only the first value in the collection has been returned.");
+		logger.log(Level.WARNING, "Multiple Moby objects were found in the text data, " +
+				          "but the request was to return a simple. " +
+				          "Only the first value in the collection has been returned.");
 		for(MobyDataObject result: results){
-		    System.err.println("Found object: " + result.getDataType().getName()); 
+		    logger.log(Level.WARNING, "Found object: " + result.getDataType().getName()); 
 		}
 		// TODO: should we instead return the one deepest in the hierarchy (or with the most members)?
 		return results.elementAt(0);
@@ -916,11 +914,11 @@
 		// have the exact same contents as the same members who are their
 		// subtypes, as these are superfluous.
 
-		System.err.println("Multiple Moby objects were found in the text data, " +
-				   "but the request was to return a simple. " +
-				   "Only the first value in the collection has been returned.");
+		logger.log(Level.WARNING, "Multiple Moby objects were found in the text data, " +
+			                  "but the request was to return a simple. " +
+				          "Only the first value in the collection has been returned.");
 		for(MobyDataObject result: results){
-		    System.err.println("Found object: " + result.getDataType().getName()); 
+		    logger.log(Level.WARNING, "Found object: " + result.getDataType().getName()); 
 		}
 		// TODO: should we instead return the one deepest in the hierarchy (or with the most members)?
 		return results.elementAt(0);
@@ -994,12 +992,11 @@
 			    }
 			}
 			catch(MobyException me){
-			    System.err.println("Could not build Moby object from match:" + me);
-			    me.printStackTrace();
+			    logger.log(Level.SEVERE, "Could not build Moby object from match", me);
 			}
 		    }
 		} catch(Throwable t){ // Principally stack overflows
-		    System.err.println("Exception/Error ("+t+") while applying regex '"+pattern.pattern()+"' to binary data");
+		    logger.log(Level.SEVERE, "Exception/Error ("+t+") while applying regex '"+pattern.pattern()+"' to binary data", t);
 		}
 	    }
 	}
@@ -1050,7 +1047,7 @@
     public Map<String,MobyDataObject[]> getMobyObjectsURNMap(CharSequence textData, byte[] bytes){
 	Map results = new HashMap<String,MobyDataObject[]>();
 	if(regexMap.isEmpty()){
-	    System.out.println("The MOBY Client has not been provided any regex->moby data mappings!");
+	    logger.log(Level.WARNING, "The MOBY Client has not been provided any regex->moby data mappings!");
 	    return results;
 	}
 
@@ -1069,12 +1066,11 @@
 			}
 		    }
 		    catch(MobyException me){
-			System.err.println("Could not build Moby object from match (rule "+urn+"):" + me);
-			me.printStackTrace();
+			logger.log(Level.SEVERE, "Could not build Moby object from match (rule "+urn+")", me);
 		    }
 		}
 	    }catch(Throwable t){ // Principally stack overflows
-		System.err.println("Exception/Error ("+t+") while applying regex '"+pattern.pattern()+"' to text/binary");
+		logger.log(Level.SEVERE, "Exception/Error ("+t+") while applying regex '"+pattern.pattern()+"' to text/binary", t);
 	    }
 	    if(urn != null && !objectVector.isEmpty()){
 		results.put(urn, (MobyDataObject[]) objectVector.toArray(new MobyDataObject[objectVector.size()]));
@@ -1086,7 +1082,7 @@
 
     public MobyDataObject[] getMobyObjects(CharSequence textData, byte[] bytes){
 	if(regexMap.isEmpty()){
-	    System.out.println("The MOBY Client has not been provided any regex->moby data mappings!");
+	    logger.log(Level.WARNING, "The MOBY Client has not been provided any regex->moby data mappings!");
 	    return new MobyDataObject[0];
 	}
 
@@ -1109,12 +1105,11 @@
 			}
 		    }
 		    catch(MobyException me){
-			System.err.println("Could not build Moby object from match:" + me);
-			me.printStackTrace();
+			logger.log(Level.SEVERE, "Could not build Moby object from match", me);
 		    }
 		}
 	    }catch(Throwable t){ // Principally stack overflows
-		System.err.println("Exception/Error ("+t+") while applying regex '"+pattern.pattern()+"' to text/binary");
+		logger.log(Level.SEVERE, "Exception/Error ("+t+") while applying regex '"+pattern.pattern()+"' to text/binary", t);
 	    }
 	}
 
@@ -1142,7 +1137,7 @@
 
     public MobyDataObject[] getMobyObjects(URL url, String linkText, MobyDataType targetDataType){
 	if(urlRegexMap.isEmpty()){
-	    System.out.println("The MOBY Client has not been provided any url regex->moby data mappings!");
+	    logger.log(Level.WARNING, "The MOBY Client has not been provided any url regex->moby data mappings!");
 	    return new MobyDataObject[0];
 	}
 
@@ -1171,8 +1166,7 @@
 		    }
 		}
 		catch(MobyException me){
-		    System.err.println("Could not build Moby object from url regex match:" + me);
-		    me.printStackTrace();
+		    logger.log(Level.SEVERE, "Could not build Moby object from url regex match", me);
 		}
 	    }
 	}
@@ -1188,7 +1182,7 @@
 
 	// No xpaths to check
 	if(xpathMap.isEmpty()){
-	    System.out.println("The MOBY Client has not been provided any xpath->moby data mappings!");
+	    logger.log(Level.WARNING, "The MOBY Client has not been provided any xpath->moby data mappings!");
 	    return new MobyDataObject[0];
 	}
 	
@@ -1224,8 +1218,8 @@
 		    }
 		    
 		}catch(XPathExpressionException xpe2){
-		    System.err.println( "Warning: Cannot access resulting node list "+
-					"due to exception in its retrieval: " + xpe2);
+		    logger.log(Level.WARNING, "Warning: Cannot access resulting node list "+
+			       "due to exception in its retrieval: ", xpe2);
 		    return new Vector<MobyDataObject>();
 		}
 	    }
@@ -1241,9 +1235,9 @@
 		    }
 		}
 		else{ //not a node sequence
-		    System.out.println("Warning: the XPath expression ("+ xpath +
-				       ") did not return a node set, cannot select document elements."+
-				       " The returned object was of type "+ result.getClass().getName() );
+		    logger.log(Level.WARNING, "Warning: the XPath expression ("+ xpath +
+			                      ") did not return a node set, cannot select document elements."+
+				              " The returned object was of type "+ result.getClass().getName() );
 		    return new Vector<MobyDataObject>();
 		}
 	    }		
@@ -1253,8 +1247,8 @@
 	//xpe.printStackTrace();
 	    return new Vector<MobyDataObject>();
 	}catch(MobyException me){
-	    System.err.println("Warning: Cannot create objects from select nodes due " +
-			       " to exception in MOBY logic:" + me);
+	    logger.log(Level.WARNING, "Warning: Cannot create objects from select nodes due " +
+		       " to exception in MOBY logic:", me);
 	    return new Vector<MobyDataObject>();
 	}
 	
@@ -1270,7 +1264,7 @@
 
 	// No xpaths to check
 	if(xpathMap.isEmpty()){
-	    System.out.println("The MOBY Client has not been provided any xpath->moby data mappings!");
+	    logger.log(Level.WARNING, "The MOBY Client has not been provided any xpath->moby data mappings!");
 	    return results;
 	}
 	
@@ -1340,14 +1334,24 @@
 	    }
 
 	    if(mdos[i] instanceof MobyDataObject){
-		mobyDataServiceAssocInstances[i] = new MobyDataObjectSAI((MobyDataObject) mdos[i], mService);
+		if(mdos[i] instanceof MobyDataObjectDeferred){
+		    mobyDataServiceAssocInstances[i] = new MobyDataObjectDeferredSAI((MobyDataObjectDeferred) mdos[i], mService);
+		}
+		else{
+		    mobyDataServiceAssocInstances[i] = new MobyDataObjectSAI((MobyDataObject) mdos[i], mService);
+		}
 	    }
 	    else if(mdos[i] instanceof MobyDataObjectSet){
-		mobyDataServiceAssocInstances[i] = new MobyDataObjectSetSAI((MobyDataObjectSet) mdos[i], mService);
+		if(mdos[i] instanceof MobyDataObjectSetDeferred){
+		    mobyDataServiceAssocInstances[i] = new MobyDataObjectSetDeferredSAI((MobyDataObjectSetDeferred) mdos[i], mService);
+		}
+		else{
+		    mobyDataServiceAssocInstances[i] = new MobyDataObjectSetSAI((MobyDataObjectSet) mdos[i], mService);
+		}
 	    }
 	    else{
 		logger.log(Level.WARNING, "MobyClient could not handle service-associating an instance of " + mdos[i].getClass());
-		System.err.println("MobyClient could not handle service-associating an instance of " + mdos[i].getClass());
+		//System.err.println("MobyClient could not handle service-associating an instance of " + mdos[i].getClass());
 	    }
 	}
 	return mobyDataServiceAssocInstances; 
@@ -1363,7 +1367,7 @@
 
     public void addRegexMapping(String regexp, String[] mobyObj, String articleName, String urn){ //mobyObj<--mobyNamespaces
 	if(mobyObj == null){
-	    System.err.println("Ignoring empty namespace-only regex rule mappings");
+	    logger.log(Level.WARNING, "Ignoring empty namespace-only regex rule mappings");
 	    return;
 	}
 
@@ -1377,7 +1381,7 @@
 
     public void addURLRegexMapping(String url_regexp, String[] mobyObj, String articleName, String urn){ //mobyObj<--mobyNamespaces
 	if(mobyObj == null){
-	    System.err.println("Ignoring empty namespace-only url regex rule mappings");
+	    logger.log(Level.WARNING, "Ignoring empty namespace-only url regex rule mappings");
 	    return;
 	}
 
@@ -1466,7 +1470,7 @@
 
     protected void addRegexMapping(String regexp, Map<String,String> nsRules, String articleName, String ruleName, String urn){ //nsRules = Map<String ns, String regex_replacement>
 	if(nsRules == null || nsRules.size() == 0){
-	    System.err.println("Ignoring empty namespace-only regex rule mappings");
+	    logger.log(Level.WARNING, "Ignoring empty namespace-only regex rule mappings");
 	    return;
 	}
 
@@ -1475,7 +1479,7 @@
 
     protected void addURLRegexMapping(String url_regexp, Map<String,String> url_nsRules, String articleName, String urn){ //nsRules = Map<String ns, String regex_replacement>
 	if(url_nsRules == null || url_nsRules.size() == 0){
-	    System.err.println("Ignoring empty namespace-only url regex rule mappings");
+	    logger.log(Level.WARNING, "Ignoring empty namespace-only url regex rule mappings");
 	    return;
 	}
 
@@ -1517,8 +1521,8 @@
 	    if(memberRelationship.getRelationshipType() == Central.iHAS){
 		String[] rule = membersMap.get(memberRelationship.getName());
 		if(rule == null){
-		    System.err.println("Skipping HAS member "+memberRelationship.getName() + 
-				       " without an explicit rule (may be defined by inheritance?)");		    
+		    logger.log(Level.WARNING, "Skipping HAS member "+memberRelationship.getName() + 
+				              " without an explicit rule (may be defined by inheritance?)");		    
 		    continue;
 		}
 		Pattern pattern = Pattern.compile(newRegexp, Pattern.DOTALL | Pattern.COMMENTS);
@@ -1527,8 +1531,8 @@
 		    if(captured.containsKey(i)){ //autoboxed int
 			// Already encapsulated the capture group due to another
 			// HAS member, don't need to add anything
-			System.err.println("Skipping processing of capture group "+i+
-					   ", it's already been processed by another member in this rule");
+			logger.log(Level.WARNING, "Skipping processing of capture group "+i+
+					          ", it's already been processed by another member in this rule");
 			continue;
 		    }
 		    if(rule[0].matches("^.*\\$"+i+"(?=\\D.*|\\z)")){
@@ -1614,9 +1618,7 @@
 	    }
 
 	}catch(Exception e){
-	    System.err.println("Could not create regular expression statement from '" +
-			       regexp + "': " + e);
-	    e.printStackTrace();
+	    logger.log(Level.SEVERE, "Could not create regular expression statement from '" + regexp + "'", e);
 	}
     }
 
@@ -1651,15 +1653,15 @@
 		builderNameMap.put(urn, mcb);
 	    }
 	}catch(Exception e){
-	    System.err.println("Could not create URL regular expression statement from '" +
-			       url_regexp + "': " + e);
+	    logger.log(Level.SEVERE, "Could not create URL regular expression statement from '" +
+			             url_regexp + "': " + e);
 	    e.printStackTrace();
 	}
     }
 
     public void addXPathMapping(String xpath, String[] mobyObj){ //mobyObj<--mobyNamespaces
 	if(mobyObj == null){
-	    System.err.println("Ignoring empty namespace-only regex rule mappings");
+	    logger.log(Level.WARNING, "Ignoring empty namespace-only regex rule mappings");
 	    return;
 	}
 
@@ -1707,10 +1709,7 @@
 	}catch(Exception e){
 	    logger.log(Level.WARNING, 
 		       "Could not create XPath select statement from '" +
-			xpath_exp + "': " + e.getMessage());
-	    System.err.println("Could not create XPath select statement from '" +
-			       xpath_exp + "': " + e);
-
+		       xpath_exp + "': ", e);
 	}
     }
 
@@ -1773,8 +1772,8 @@
 		    else if(line.indexOf("\t") == 0){
 			String[] fields = line.trim().split(",");
 			if(fields.length != 2){ 
-			    System.err.println("Unrecognized line (not 2 comma delimited fields) " +
-					       "from ValidateService: " + line.trim());
+			    logger.log(Level.WARNING, "Unrecognized line (not 2 comma delimited fields) " +
+					              "from ValidateService: " + line.trim());
 			}
 			else if(fields[1].equals("true")){
 			    // service is okay, don't add to dead map
@@ -1783,8 +1782,8 @@
 			    isDeadMap.put(currentAuthority+":"+fields[0], "dead");
 			}
 			else{
-			    System.err.println("Unrecognized line (second field not 'true' or 'false') " +
-					       "from ValidateService: " + line.trim());			    
+			    logger.log(Level.WARNING, "Unrecognized line (second field not 'true' or 'false') " +
+					              "from ValidateService: " + line.trim());			    
 			}
 		    }
 		}


From gordonp at dev.open-bio.org  Fri Apr 16 13:33:26 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 16 Apr 2010 13:33:26 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004161733.o3GHXQBs015331@dev.open-bio.org>


gordonp
Fri Apr 16 13:33:25 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv15287/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	MobyContentPane.java MobyPayloadCreator.java 
	MobyServicesGUI.java 
Log Message:
First fully functional version of 'for each' service invocation in Seahawk
moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyContentPane.java,1.28,1.29 MobyPayloadCreator.java,1.2,1.3 MobyServicesGUI.java,1.19,1.20
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java,v
retrieving revision 1.28
retrieving revision 1.29
diff -u -r1.28 -r1.29
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java	2010/04/14 23:48:27	1.28
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java	2010/04/16 17:33:25	1.29
@@ -1175,9 +1175,23 @@
 
 	String docFragID = targetURL.getRef();  // We store the xpath in the anchor part of the URL
 
-	// Complex case, load the doc fragment from the MOBY XML source file
+	// Complex case, load the doc fragment from the MOBY XML source file 
+	// where the targetURL is url#xptr with xptr like /1/2/1/1
 	if(docFragID != null && docFragID.length() > 0 && !targetURL.getHost().equals("moby")){
-	    return DataUtils.loadMobyDataFromXPointer(targetURL, filteredData, filterHistory.get(getCurrentURL()));
+	    URL currentURL = null;
+	    try{currentURL = new URL(targetURL.toString().replaceAll("#"+targetURL.getRef(), ""));}
+	    catch(Exception e){
+		logger.error("Couldn't extract referenceless URL from " + targetURL, e);
+	    }
+	    // refers to currently loaded doc
+	    if(currentURL.equals(getCurrentURL())){
+		return DataUtils.loadMobyDataFromXPointer(currentURL, getCurrentDoc(), docFragID, 
+							  filteredData, filterHistory.get(getCurrentURL()));
+	    }
+	    // refers to another moby doc, let DataUtils resolve the doc for us
+	    else{
+		return DataUtils.loadMobyDataFromXPointer(targetURL, filteredData, filterHistory.get(getCurrentURL()));
+	    }
 	}
 
 	// Simple case, build the object using the values encoded in the URL itself.
@@ -1218,7 +1232,7 @@
         for(String peerMode: new String[]{DataUtils.ARTICLE_PEERS_MODE, DataUtils.DATATYPE_PEERS_MODE}){
             // note that getPeerElements() will modify the userData to reflect the semantic of the requested peer mode
             mobyData.setUserData(origUserData);
-            NodeList peerElements = DataUtils.getPeerElements(getCurrentDoc(), mobyData, peerMode);
+            NodeList peerElements = DataUtils.getPeerElements(getCurrentDoc(), mobyData, getFilteredData(), peerMode);
             if(peerElements.getLength() <= 1){
                 continue; // no 'for each' option if only one to process...
             }
@@ -1227,21 +1241,33 @@
                 each += " '"+mobyData.getName()+"'";
             }
             MobyDataType dataType = ((MobyPrimaryData) mobyData).getDataType();
+	    MobyNamespace[] namespaces = ((MobyPrimaryData) mobyData).getNamespaces();
             if(mobyData instanceof MobyPrimaryDataSet){	 // Collection
                 servicesGUI.addPopupOptions((MobyPrimaryDataSet) mobyData, popup, true, getDefaultHandler(), 
 					    new MobyPayloadCreator(this, (String) mobyData.getUserData()), 
 					    each);
             }
             else if(MobyTags.MOBYOBJECT.equals(dataType.getName())){  
-                MobyNamespace namespace = null;
-                servicesGUI.addPopupOptions(namespace, popup, true, getDefaultHandler(),
-					    new MobyPayloadCreator(this, (String) mobyData.getUserData()), 
-                                            each);
+		if(namespaces != null && namespaces.length > 0){
+		    servicesGUI.addPopupOptions(namespaces[0], popup, true, getDefaultHandler(),
+						new MobyPayloadCreator(this, (String) mobyData.getUserData()), 
+						each);
+		}
+		//else base object wth no namespace...useless!
             }
             else{
-                servicesGUI.addPopupOptions(dataType, popup, true, getDefaultHandler(),
-					    new MobyPayloadCreator(this, (String) mobyData.getUserData()), 
-                                            each);
+		// A non-base object, with a namespace too
+		if(namespaces != null && namespaces.length > 0){
+		    ((MobyPrimaryDataSimple) mobyData).setId(""); //anonymize
+		    servicesGUI.addPopupOptions((MobyPrimaryDataSimple) mobyData, popup, true, getDefaultHandler(),
+						new MobyPayloadCreator(this, (String) mobyData.getUserData()), 
+						each);
+		}
+		else{  //just the data type useful
+		    servicesGUI.addPopupOptions(dataType, popup, true, getDefaultHandler(),
+						new MobyPayloadCreator(this, (String) mobyData.getUserData()), 
+						each);
+		}
             }
         }
 
@@ -1286,13 +1312,21 @@
 	if(getFilter() == null){
 	    return;
 	}
+	String[] userData = mdi.getUserData() == null ? null : 
+	    mdi.getUserData().toString().split("\t");
+	// second user data arg is 
+	Node mdiNode = userData == null || userData.length < 2 ? null : 
+	    XPointerResolver.getNodeFromXPointer(getCurrentDoc(), userData[1]);
 
 	//System.err.println("Should create a previous input menu item for " + mdi.getUserData());
 	try{
 	    Document srcDoc = DataUtils.docBuilder.parse(srcURL.openStream());
 
+	    //System.err.println("Context node is "+mdiNode+ " from user data" + mdi.getUserData());
 	    // Get the input data for the *previous* service
-	    MobyDataJob inputData = DataUtils.getInputSample(srcDoc, SeahawkOptions.getRegistry());
+	    MobyDataJob inputData = DataUtils.getInputSample(srcDoc, 
+							     DataUtils.findMobyJobName(mdiNode), 
+							     SeahawkOptions.getRegistry());
 	    if(inputData == null){
 		// should only happen if Moby XML was loaded manually by a user, otherwise we've recorded this info...
 		logger.warn("No previous service info in Moby XML, 'previous input' option will not be displayed");
@@ -1529,7 +1563,7 @@
 	// Gray out the mismatched textual data
 	for(Map.Entry<String,String> dataToFilter: filteredData.entrySet()){	    
 
-	    System.err.println("Filtering "+dataToFilter.getKey());
+	    //System.err.println("Filtering "+dataToFilter.getKey());
 	    javax.swing.text.AbstractDocument.AbstractElement htmlDiv = 
 		(javax.swing.text.AbstractDocument.AbstractElement) d.getElement(dataToFilter.getKey());
 	    if(htmlDiv == null){

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyPayloadCreator.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyPayloadCreator.java	2010/04/14 23:48:27	1.2
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyPayloadCreator.java	2010/04/16 17:33:25	1.3
@@ -27,6 +27,7 @@
 	// The request key is the sample data's app context: 
         // url#xpath <tab> sample_xptr <tab> filter_regex <tab> filter_xpath <tab> xpath_desc <tab> case_sensitive_boolean <tab> inverse selection
         // from which we will build the peer dataset to submit.
+	System.err.println("Request key is " + requestKey);
 	String[] requestKeyFields = requestKey.split("\t");
 
 	String[] requestParts = requestKeyFields[0].split("#", 2);
@@ -50,20 +51,24 @@
 	Map<String,String> xptrsToFilter = new HashMap<String,String>();
 	FilterSearch filter = null;
 	// Was there a filter in the request?
-	if(requestKeyFields.length >= 6){
- 	    filter = new FilterSearch(requestKeyFields[1], 
-				      new XPathOption(requestKeyFields[2], requestKeyFields[3]), 
-                                      Boolean.parseBoolean(requestKeyFields[4]), 
-				      Boolean.parseBoolean(requestKeyFields[5]));
+	if(requestKeyFields.length >= 7){
+ 	    filter = new FilterSearch(requestKeyFields[2], 
+				      new XPathOption(requestKeyFields[3], requestKeyFields[4]), 
+                                      Boolean.parseBoolean(requestKeyFields[5]), 
+				      Boolean.parseBoolean(requestKeyFields[6]));
         }
 	Document doc = null;
         // Get the list of nodes to filter, using in-memory data if possible
 	if(targetURL.equals(srcPane.getCurrentURL())){
             doc = srcPane.getCurrentDoc();
 
-            if(filter.equals(srcPane.getFilter())){
+            if(filter == null){
+		xptrsToFilter = null;
+	    }
+	    else if(filter.equals(srcPane.getFilter())){
                 // no need to redo the filtering, it's the current display's filtering
-                xptrsToFilter = srcPane.getFilteredData(); 
+		System.err.println("Reusing current filter");
+                xptrsToFilter = srcPane.getFilteredData();
             }
             else{
                 // we have the doc loaded, but the filter has changed since
@@ -75,44 +80,33 @@
        	    doc = DataUtils.findFilteredNodes(targetURL, filter, xptrsToFilter);	    
         }
 
-	// Get the valid parts of the doc for forwarding.
-        if(!xptrsToFilter.isEmpty()){
-  	    if(doc == srcPane.getCurrentDoc()){
-                // clone, because it'll be edited below by the filter, and we don't want to mess up currentDoc...
-                doc = (Document) srcPane.getCurrentDoc().cloneNode(true);
-            }
-            DataUtils.filterDoc(doc, xptrsToFilter);
-        }
+	MobyDataInstance mobyDataContext = new MobyDataObject("whatever");
+	mobyDataContext.setUserData(requestKey);
+	NodeList peerElements = DataUtils.getPeerElements(doc, mobyDataContext, 
+							  xptrsToFilter, DataUtils.DATATYPE_PEERS_MODE);
 
-        // find the peers of templateElement and put them into a MobyContentInstance
+        // find the peers of defined by the userData selection constraints and put them into a MobyContentInstance
 	MobyContentInstance payload = new MobyContentInstance();
         Map<String,Integer> jobPrefixes = new LinkedHashMap<String,Integer>();
 
-        NodeList peerElements = null;
-        try{
-            peerElements = (NodeList) DataUtils.xPathFactory.newXPath().evaluate(selectionXPath, 
-                                                                                 doc, 
-                                                                                 XPathConstants.NODESET);
-        } catch(Exception e){
-            logger.log(Level.SEVERE, "Could not select nodes from "+targetURL+" with XPath " + selectionXPath, e);
-            return null;
-        }
+	System.err.println("Loading MobyContentInstance with "+peerElements.getLength()+" elements for xpath "+selectionXPath);
         for(int i = 0; i < peerElements.getLength(); i++){
             Element peerElement = (Element) peerElements.item(i);
 	    // Try to make the job names trackable to the inputs:
             // Name the jobs according to their original job + a iterated number suffix, e.g. originatingJob_1, originatingJob_2
             String jobKey = DataUtils.findMobyJobName(peerElement);
             if(!jobPrefixes.containsKey(jobKey)){
+                jobPrefixes.put(jobKey, new Integer(1));
                 if(peerElements.getLength() > 1){
                     jobKey += "_1"; // only add a suffix if multiple loop members for the job
                 }
-                jobPrefixes.put(jobKey, new Integer(1));
             }
             else{
                 int suffixCount = jobPrefixes.get(jobKey).intValue();
-                jobKey += "_"+suffixCount;
                 jobPrefixes.put(jobKey, new Integer(suffixCount+1));
+                jobKey += "_"+(suffixCount+1);
             }
+	    System.err.println("Adding job "+jobKey+" for "+peerElement.getLocalName());
             MobyDataInstance mdi  = null;
             try{
                 mdi = MobyDataObject.createInstanceFromDOM(peerElement, SeahawkOptions.getRegistry());

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java,v
retrieving revision 1.19
retrieving revision 1.20
diff -u -r1.19 -r1.20
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java	2010/04/14 23:48:27	1.19
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java	2010/04/16 17:33:25	1.20
@@ -182,9 +182,13 @@
 	return handler;
     }
 
-    // synchronized so simultaneous requests don't get their input data mixed up
+    /**
+     * Called when the 'Execute Service' button in the secondary input dialog in pushed.
+     * Section synchronized so simultaneous requests don't get their input data mixed up
+     */
     public void setupServiceSecondaryData(MobyRequestEventHandler handler){
 	MobyDataInstance[] castInputs = new MobyDataInstance[primaryInput.length];
+	MobyContentInstance mci = null;
 	for(int i = 0; i < primaryInput.length; i++){
 	    if(!(primaryInput[i] instanceof MobyDataInstance)){
 		logger.warn("Warning: setupServiceSecondaryData was called before the primary input" +
@@ -192,13 +196,34 @@
 			    " of class "+primaryInput[i].getClass().getName());
 		return;
 	    }
-	    castInputs[i] = (MobyDataInstance) primaryInput[i];
+	    // Is one of the params a 'for each'
+	    if(primaryInput[i] instanceof MobyContentCreator){
+		mci = ((MobyContentCreator) primaryInput[i]).getAllContents(primaryInput[i].getName());
+	    }
+	    else{
+		castInputs[i] = (MobyDataInstance) primaryInput[i];
+	    }
+	}
+	// Cross product of single value primary params with param that is a content creator array
+	if(mci != null){
+	    for(MobyDataJob job: mci.values()){
+		for(int i = 0; i < castInputs.length; i++){
+		    if(castInputs[i] != null){
+			job.put(castInputs[i].getName(), castInputs[i]);
+		    }
+		}
+	    }
 	}
 
         // code from mobyRequest.setInput() to executeService() should always be synced to avoid input mixup between requests
         synchronized(mobyRequest){
 	    try{	    
-	        mobyRequest.setInput(castInputs);
+	        if(mci != null){
+		    mobyRequest.setInput(mci);
+		}
+		else{
+		    mobyRequest.setInput(castInputs);
+		}
 	        mobyRequest.setSecondaryInput(secondaryInputInstances);
 	    } catch(MobyException me){
 	        me.printStackTrace();
@@ -224,8 +249,13 @@
             // code from mobyRequest.setInput() to executeService() should always be synced to avoid input mixup between requests
             synchronized(mobyRequest){
 	        try{
+		    if(mdi instanceof MobyContentCreator){
+			mobyRequest.setInput(((MobyContentCreator) mdi).getAllContents(primaryInput[0].getName()));
+		    }
 		    // Implement simple input (i.e. only one input argument)
-		    mobyRequest.setInput(mdi, "");
+		    else{
+			mobyRequest.setInput(mdi, "");
+		    }
 	        }
 	        catch(MobyException me){
 		    logger.error("Failure in MOBY input, was not acceptable:" + me);
@@ -539,7 +569,7 @@
 		addPopupOptions(mobyData, popupList, false, handler, payloadCreator, extraMenuText);
 	    }
 	    else{
-		logger.warn("Warning: OptionLoaderThread has no data to work with");
+		logger.warn("Warning: OptionLoaderThread has no data to work with", new Exception("Arrggh"));
 	    }
 	}
     }
@@ -646,27 +676,27 @@
  	MobyDataServiceAssocInstance serviceAssocObject = null;  
 // 	//Services for only the one piece of data
 	try{
-	    if(mobyData instanceof MobyDataObjectSet){
-		serviceAssocObject = mobyClient.getServices((MobyDataObjectSet) mobyData);
-	    }
-	    else if(mobyData instanceof MobyDataObject){
-		serviceAssocObject = mobyClient.getServices((MobyDataObject) mobyData);
-	    }
             // The data will be loaded later
-            else if(payloadCreator != null){
+            if(payloadCreator != null){
                 try{
                     if(mobyData instanceof MobyPrimaryDataSet){
 			serviceAssocObject = mobyClient.getServices(new MobyDataObjectSetDeferred((MobyPrimaryDataSet) mobyData, 
 												  payloadCreator));
 		    }
-		    else if(mobyData instanceof MobyNamespace){
-			serviceAssocObject = mobyClient.getServices(new MobyDataObjectDeferred((MobyNamespace) mobyData, 
+		    else if(mobyData instanceof MobyPrimaryDataSimple){  // pass in if datatype and namespace are useful
+			serviceAssocObject = mobyClient.getServices(new MobyDataObjectDeferred(((MobyPrimaryDataSimple) mobyData).getDataType(),
+											       ((MobyPrimaryDataSimple) mobyData).getNamespaces()[0],
 											       payloadCreator));
 		    }
 		    else if(mobyData instanceof MobyDataType){
 			serviceAssocObject = mobyClient.getServices(new MobyDataObjectDeferred((MobyDataType) mobyData, 
 											       payloadCreator));
 		    }
+		    else if(mobyData instanceof MobyNamespace){
+			System.err.println("Creating deferred dataset payload");
+			serviceAssocObject = mobyClient.getServices(new MobyDataObjectDeferred((MobyNamespace) mobyData, 
+											       payloadCreator));
+		    }
 		    else{
 			logger.warn("Ignoring unrecognized template class (" + mobyData.getClass().getName()+
 				    ") for deferred data creation by a MobyPayloadRequestListener"); 
@@ -675,6 +705,12 @@
 		} catch(Exception e){
 		    logger.error("Could not create deferred Moby data object", e);
 		}
+	    }
+	    else if(mobyData instanceof MobyDataObjectSet){
+		serviceAssocObject = mobyClient.getServices((MobyDataObjectSet) mobyData);
+	    }
+	    else if(mobyData instanceof MobyDataObject){
+		serviceAssocObject = mobyClient.getServices((MobyDataObject) mobyData);
             }
 	    else{
 		logger.warn("Service options for objects other than MobyDataObject " +
@@ -730,9 +766,6 @@
 		    logger.warn("Cannot add service options, cannot find " +
 				"parent moby object index for submenu " + 
 				submenu.getText());
-		    System.err.println("Cannot add service options, cannot find " +
-				"parent moby object index for submenu " + 
-				submenu.getText());
 		    return;
 		}
 		dataIndex = ((Integer) submenu2msIndex.get(parent)).intValue();
@@ -1250,7 +1283,7 @@
 		datatype += " collection";
 	    }
 	    submenu = new JMenu("<html>Services for " + (extraMenuText == null ? "" : extraMenuText+" ") + 
-                                datatype + (id == null ? "" : ":" + id)+"</html>");
+                                "<font color='red'>"+datatype + "</font>" + (id == null ? "" : ":" + id)+"</html>");
 	    assignMenuDataIndex(submenu);
 	}
 	else if(MobyTags.MOBYSTRING.equals(mobyDataType.getName())){
@@ -1269,7 +1302,7 @@
 	    }
 	    desc = "A piece of text";
 	    submenu = new JMenu("<html>Services for "+(extraMenuText == null ? "" : extraMenuText+" ")+
-				"String " + sample+"</html>");
+				"<font color='red'>String</font> " + sample+"</html>");
 	    assignMenuDataIndex(submenu);
 	}
 	// Complex object
@@ -1283,17 +1316,19 @@
 		}
 	    }
 	    if(templateObject instanceof MobyDataObject && id != null && id.length() > 0){
-		objectLabel += ":" + id;
+		objectLabel += "<font color='red'>"+objectLabel+"</font>:" + id;
 	    }
 	    else if(templateObject instanceof MobyDataObjectSet){
-		objectLabel += " collection";
+		objectLabel = "<font color='red'>"+objectLabel+" collection</font>";
+	    }
+	    else{
+		objectLabel = "<font color='red'>"+objectLabel+"</font>";
 	    }
 	    submenu = new JMenu("<html>Services for " + (extraMenuText == null ? "" : extraMenuText+" ")+objectLabel+"</html>");
 	    assignMenuDataIndex(submenu);
 	}
 	desc = "Input data: " + desc;
 	desc = HTMLUtils.htmlifyToolTipText(desc, MAX_SERVICE_DESC_LEN);
-        System.err.println("New submenu has label " + submenu.getText());
 	submenu.setToolTipText(desc);
 	submenu.setName(SERVICE_SUBMENU_NAME);
 	return submenu;


From gordonp at dev.open-bio.org  Fri Apr 16 13:33:26 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 16 Apr 2010 13:33:26 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004161733.o3GHXQvK015367@dev.open-bio.org>


gordonp
Fri Apr 16 13:33:26 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util
In directory dev.open-bio.org:/tmp/cvs-serv15287/src/main/ca/ucalgary/seahawk/util

Modified Files:
	DataFlowRecorder.java DataUtils.java FilterSearch.java 
	MobyDataObjectDeferred.java XPointerResolver.java 
Added Files:
	MobyDataObjectDeferredSAI.java 
	MobyDataObjectSetDeferredSAI.java 
Log Message:
First fully functional version of 'for each' service invocation in Seahawk
moby-live/Java/src/main/ca/ucalgary/seahawk/util MobyDataObjectDeferredSAI.java,NONE,1.1 MobyDataObjectSetDeferredSAI.java,NONE,1.1 DataFlowRecorder.java,1.4,1.5 DataUtils.java,1.5,1.6 FilterSearch.java,1.5,1.6 MobyDataObjectDeferred.java,1.1,1.2 XPointerResolver.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataFlowRecorder.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataFlowRecorder.java	2010/04/10 00:40:17	1.4
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataFlowRecorder.java	2010/04/16 17:33:26	1.5
@@ -321,7 +321,7 @@
 		data = sampleData.getUserData().toString().split("\t");
 		//options: selection + filter + cond, selection + cond, or cond only
 		if(data.length == 14 || data.length == 8 || data.length == 6){
-		    System.err.println("Adding conditional for " + resultURLString);
+		    //		    System.err.println("Adding conditional for " + resultURLString);
 		    String conditionURL = data[data.length-6];
 		    String conditionRegex = data[data.length-5];
 		    XPathOption conditionXPath = new XPathOption(data[data.length-4], data[data.length-3]);
@@ -334,10 +334,10 @@
 		    System.arraycopy(data, 0, conditionlessData, 0, data.length-6);
 		    data = conditionlessData;
 		}
-		else{
-		    System.err.println("Skipping conditional, only " + data.length + 
-				       "members in provenance data for " + resultURLString);
-		}
+// 		else{
+// 		    System.err.println("Skipping conditional, only " + data.length + 
+// 				       "members in provenance data for " + resultURLString);
+// 		}
 	    }
 
 	    // true means treat as a collection if that's what the sample data is
@@ -447,7 +447,7 @@
 		// Remember that sd is the loop's original MobyDataInstance before it's been coerced into a MobyPrimaryData, 
 		// which doesn't have XML modes, etc.
 		String inputKey = getInputKey(sd);
-		System.err.println("Input key for " + processorName + " is " + inputKey);
+		//		System.err.println("Input key for " + processorName + " is " + inputKey);
 
 		String[] mobifyingProcessorNameAndPorts = null;
 		if(input2Processor.containsKey(inputKey)){
@@ -930,7 +930,7 @@
 		// supertype of the output from the other service!		
 		if(namespace != null){
 		    MobyNamespace nsObj = MobyNamespace.getNamespace(namespace, getRegistryFromService(srcService));
-		    System.err.println("About to create namespace filter for "+ srcProcessor + " port " + portName + " when srcPort was " + srcPort);
+		    //		    System.err.println("About to create namespace filter for "+ srcProcessor + " port " + portName + " when srcPort was " + srcPort);
 		    return createNamespaceFilter(nsObj, srcProcessor, portName, processors, datalinks, doc);
 		}
 		else if(xrefNs != null){
@@ -1103,7 +1103,7 @@
 	throws Exception{
 
 	String decompKey = srcProcessor+"\n"+srcPort+"\n"+xpath;
-	System.err.println("Decomp key is " + decompKey);
+	//	System.err.println("Decomp key is " + decompKey);
 	// Has this decomp already been created in another branch?
 	if(decomp2Processor.containsKey(decompKey)){
 	    return decomp2Processor.get(decompKey);

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataUtils.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataUtils.java	2010/04/14 22:02:04	1.5
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataUtils.java	2010/04/16 17:33:26	1.6
@@ -166,6 +166,7 @@
 	Document resultDom = docBuilder.parse(serviceResultURL.openStream());
 	
 	Registry registry = getRegistry(resultDom);
+	//todo: check all jobs, not just a sample
 	MobyDataJob sampleJob = getInputSample(resultDom, registry);
 	    
 	// Trace the inputs that came from the current document 
@@ -343,6 +344,13 @@
      * @param responseDom the XML DOM for the answer from a Moby Web service called in Seahawk
      */
     public static MobyDataJob getInputSample(Document responseDom, Registry registry) throws Exception{
+	return getInputSample(responseDom, null, registry);
+    }
+
+    /**
+     * Same as two-arg, but retrieves a specific job's input (or null if not a job name found in the doc).
+     */
+    public static MobyDataJob getInputSample(Document responseDom, String jobName, Registry registry) throws Exception{
 	Document inputDoc = getInputDoc(responseDom);
 	if(inputDoc == null){
 	    return null;
@@ -360,11 +368,14 @@
 	    throw new Exception("Could not parse Moby output message from the given DOM");
 	}
 
+	if(jobName != null){
+	    return inputPayload.get(jobName);
+	}
 	// Pick a job that produced output, if given the choice of more that one
-	for(String jobName: inputPayload.keySet()){
-	    if(outputPayload.containsKey(jobName) &&
-	       outputPayload.get(jobName).size() > 0){
-		return inputPayload.get(jobName);
+	for(String jobID: inputPayload.keySet()){
+	    if(outputPayload.containsKey(jobID) &&
+	       outputPayload.get(jobID).size() > 0){
+		return inputPayload.get(jobID);
 	    }
 	}
 	return (MobyDataJob) inputPayload.values().iterator().next();
@@ -460,9 +471,9 @@
     /**
      * Loads targetURL, minus the nodes specified by the xpath keys in filteredXPtrs (map values are not currently used).
      */
-    public static void filterDoc(Document domDoc, Map<String,String> filteredXPtrs){
+    public static void filterNodes(Node rootNode, Map<String,String> filteredXPtrs){
 	 
-	if(domDoc == null){
+	if(rootNode == null){
 	    logger.log(Level.SEVERE, "Error: Could not get MOBY document as DOM (empty or malformed document?)");
 	    return;
 	}
@@ -474,7 +485,7 @@
 	    // wrong as they refer to ordinality)
 	    Vector<Node> nodesToDelete = new Vector<Node>();
 	    for(String xptr: filteredXPtrs.keySet()){
-		nodesToDelete.add(XPointerResolver.getNodeFromXPointer(domDoc, xptr));
+		nodesToDelete.add(XPointerResolver.getNodeFromXPointer(rootNode, xptr));
 	    }
 
 	    // Delete
@@ -497,86 +508,54 @@
      * @param filteredXPtrs a map of the xpointers to data that should NOT be deserialized if children of the targetURL XPointer
      * @param docFilter the current filter applied to the document in targetURL
      */
-    public static MobyDataInstance loadMobyDataFromXPointer(URL targetURL, Map<String,String> filteredXPtrs, FilterSearch docFilter){
-
-	URL currentURL = null;
-	try{currentURL = new URL(targetURL.toString().replaceAll("#"+targetURL.getRef(), ""));}
-	catch(Exception e){
-	    logger.log(Level.SEVERE, "Couldn't extract referenceless URL from " + targetURL, e);
-	}
-
-	// Build the DOM
-	Document domDoc = null;
-	try{
-	    domDoc = docBuilder.parse(targetURL.openStream());
-	} catch(org.xml.sax.SAXException saxe){
-	    logger.log(Level.SEVERE, "The document defining the MOBY data " +
-		       "could not be parsed", saxe);
-	    return null;
-	} catch(java.io.IOException ioe){
-	    logger.log(Level.SEVERE, "The document defining the MOBY data " +
-		       " could not be read (from " + targetURL + ")", ioe);
-	    return null;
-	}
-	// Does an in-place edit of domDoc
-	filterDoc(domDoc, filteredXPtrs);
-
+     public static MobyDataInstance loadMobyDataFromXPointer(URL targetURL, Map<String,String> filteredXPtrs, 
+							     FilterSearch docFilter){
+	 
+	 URL currentURL = null;
+	 try{currentURL = new URL(targetURL.toString().replaceAll("#"+targetURL.getRef(), ""));}
+	 catch(Exception e){
+	     logger.log(Level.SEVERE, "Couldn't extract referenceless URL from " + targetURL, e);
+	 }
+	 
+	 // Build the DOM
+	 Document domDoc = null;
+	 try{
+	     domDoc = docBuilder.parse(targetURL.openStream());
+	 } catch(org.xml.sax.SAXException saxe){
+	     logger.log(Level.SEVERE, "The document defining the MOBY data " +
+			"could not be parsed", saxe);
+	     return null;
+	 } catch(java.io.IOException ioe){
+	     logger.log(Level.SEVERE, "The document defining the MOBY data " +
+			" could not be read (from " + targetURL + ")", ioe);
+	     return null;
+	 }
+	 
+	 return loadMobyDataFromXPointer(currentURL, domDoc, targetURL.getRef(), filteredXPtrs, docFilter);
+    }
+    
+    public static MobyDataInstance loadMobyDataFromXPointer(URL docURL, Document domDoc, String targetXptr, 
+							    Map<String,String> filteredXPtrs, FilterSearch docFilter){
 	// Are we dealing with a simple object or a complex one?
 	MobyDataInstance mobyData = null;
 	
 	// Find the DOM fragment corresponding to the MOBY ID anchor specified
 	// in the link URL by using an XPath statement on the source MOBY doc
-	//System.err.println("Retrieving complex object from XPointer " + targetURL);
 	
 	// A child Xpointer is of the form /1/2/1/1, specifying the DOM child 
-	// descent path from the root node to get to the target node.  The 
-	// equivalent XPath is /*[1]/*[2]/*[1]/*[1]
-	String childXPath = targetURL.getRef().replaceAll("/(\\d+)", "/*[$1]");
-
-	// Build and run the XPath statement
-	Element mobyObject = null;
-	NodeList idSearchResult = null;
-	Object xobject = null;
-	try{
-	    xobject = xPathFactory.newXPath().evaluate(childXPath, 
-						       domDoc, 
-						       XPathConstants.NODESET);
-						
-	    // Check the results
-	    if(xobject != null){
-		idSearchResult = (NodeList) xobject;
-	    }
-	    else{
-		logger.log(Level.WARNING,"Could not find Moby object in document " + currentURL + 
-			   ", referred to by the reference ID in Moby link " + targetURL +
-			   " (document changed?)");
-		return null;
-	    }
-	}
-	catch(Exception e){// Syntax error
-	    logger.log(Level.SEVERE, "Error: Could not search Moby data instance for XPath " + 
-		       childXPath + ")",  e);
-	    return null;
-	}
+	// descent path from the root node to get to the target node. 
+	Element mobyObject = (Element) XPointerResolver.getNodeFromXPointer(domDoc, targetXptr);
 	
-	if(idSearchResult.getLength() == 0){
-	    logger.log(Level.WARNING, "Error: Could not find Moby data instance with XPath (" + childXPath + 
-		       " in " + targetURL);
-	    return null;
-	}
-	if(idSearchResult.getLength() > 1){
-	    logger.log(Level.WARNING, "Error: Moby data instance could not beresolved because " +
-		       "there are multiple elements with XPath " + childXPath + " in " +
-		       currentURL);
-	    return null;
-	}
-	if(!(idSearchResult.item(0) instanceof Element)){
-	    logger.log(Level.WARNING, "Error: Moby data instance with XPath " + childXPath + " in " +
-		       currentURL + " was not an element as required!");
-	    return null;
+	// Does an in-place edit of domDoc
+	// Check if the returned data was supposed to be filtered.  If so, don't filter.
+	if(filteredXPtrs != null && !filteredXPtrs.isEmpty() && !filteredXPtrs.containsKey(targetXptr)){
+	    // Otherwise filter, so child elements of the data to return reflect the current filter conditions 
+	    // (e.g. a collection may be filtered to just a subset based on namespace, so retrieving the collection should only 
+	    // return that subset of children).
+	    domDoc = (Document) domDoc.cloneNode(true); // true == deep
+	    filterNodes(domDoc, filteredXPtrs);
 	}
-	mobyObject = (Element) idSearchResult.item(0);
-	
+
 	// Create the Java MOBY API object based on the linked document DOM fragment
 	try{
 	    MobyDataInstance mdi = MobyDataObject.createInstanceFromDOM(mobyObject, SeahawkOptions.getRegistry());
@@ -587,8 +566,8 @@
 		mobyData = mdi;
 	    }
 	    else{
-		logger.log(Level.WARNING, "Error: Moby data instance retrieved with XPath " + childXPath + " in " +
-			   currentURL + " was not a primary MOBY input object as expected");
+		logger.log(Level.WARNING, "Error: Moby data instance retrieved with XPath " + targetXptr +
+			   " was not a primary MOBY input object as expected");
 		return null;
 	    }
 
@@ -600,8 +579,8 @@
 
 	    // For workflow creation, etc. associate the potential input data with its source generalized XPath
 	    // Also, if there is currently a filter on the doc, store it too as useful info for workflow creation.
-	    setUserData(mobyData, currentURL, elementInContextToNameBasedXPath(mobyObject), 
-			targetURL.getRef(), docFilter);
+	    setUserData(mobyData, docURL, elementInContextToNameBasedXPath(mobyObject), 
+			targetXptr, docFilter);
 	}
 	catch(MobyException mobye){  // Logic error
 	    logger.log(Level.SEVERE, "Error: Could not construct Moby data instance from document fragment: ", 
@@ -656,6 +635,7 @@
 		// It's a complex type.  Assume the type is why we are picking it.
 		// TODO: In future we may want to check if a parent type is allowed in 
 		// this slot, and generalize to that.  
+		// Also, account for namespace if present?
 		xpath = "/"+elName + xpath;
 	    }
 	    if(!(currentElement.getParentNode() instanceof Element)){
@@ -784,7 +764,7 @@
     /**
      * Find out which registry the service that created the reponse is registered in.
      * 
-     * @param responseURL the service response whose origin we should trace
+     * @param responseDoc the service response whose origin we should trace
      */
     public static Registry getRegistry(Document responseDoc) throws Exception{
         String endpointURL = getSeahawkAttrFromDoc(responseDoc, REGISTRY_ATTR);
@@ -1035,16 +1015,20 @@
 	    }
 	    if(!inversed && shouldFilter ||
 	       inversed && !shouldFilter){ 
-		xPtrsToFilter.put(currXPtr, "todo");
+		xPtrsToFilter.put(currXPtr, "whatever");
 	    }	    
 	}
 
 	//todo: filter objects without the HAS field at all...
 	return filterableXPtrs;
     }
-    // We need to enumerate the possible peer-sets for the selected data item.  Is the user interested in
-    // items in the same namespace, same data type, or same article name?
-    public static NodeList getPeerElements(Document doc, MobyDataInstance mobyData, String peerMode){
+
+    /**
+     * We need to enumerate the possible peer-sets for the selected data item.  Is the user interested in
+     * items in the same namespace/data type, or same article name?
+     */
+    public static NodeList getPeerElements(Document doc, MobyDataInstance mobyData, 
+					   Map<String,String> xPtrsToFilter, String peerMode){
         if(!(mobyData instanceof MobyPrimaryData)){
             logger.log(Level.WARNING, "Tried to get peers of data that was not an instanceof MobyPrimaryData (was " + 
                                       mobyData.getClass().getName()+ ")");
@@ -1054,10 +1038,13 @@
 
 	NodeList peerElements = null;
         String peerGroupXPath = null;
+	Node contextNode = null;
 	if(mobyData.getUserData() != null){
 	    String[] userData = ((String) mobyData.getUserData()).split("\t");
 	    // first arg is url#nameBasedXPath 
 	    peerGroupXPath = userData[0].split("#", 2)[1];
+	    contextNode = XPointerResolver.getNodeFromXPointer(doc, userData[1]);
+	    //System.err.println("Loaded context node " + userData[1] + " as " + contextNode);
         }
         else{
 	    // Fallback is to get all nodes with the same name...
@@ -1079,7 +1066,7 @@
             mobyData.setUserData(newUserData);
 
             // keep from job article name down
-            peerGroupXPath = peerGroupXPath.replaceFirst("^.*/(Collection|Simple)", "//*");
+            //peerGroupXPath = peerGroupXPath.replaceFirst("^.*?/(Collection|Simple)", "//*");
 	    // we want to go by articleName too to catch the full semantics of the peer group definition
             peerGroupXPath += xpathArticleCondition;
         }
@@ -1090,17 +1077,58 @@
         // For xpaths given above, MOBY namespace is problem in XPath evaluation. 
         // solution: eliminate Moby envelope path parts: full path doesn't resolve in xpath for unknown reasons
         //.replaceAll("/(MOBY|mobyContent|mobyData|Collection|Simple)","/moby:$1"); //attempt 1
-        //.replaceAll("/([a-zA-Z_0-9\\-]+)(?=/|$)", "/*[local-name() = '$1']") //attempt 2
-        //.replaceAll("/([a-zA-Z_0-9\\-]+)\\[", "/*[local-name() = '$1' and "); //attempt 2 cont'd
+        peerGroupXPath = peerGroupXPath.replaceAll("/([a-zA-Z_0-9\\-]+)", "/d:$1");
 
 	try{
-            peerElements = (NodeList) xPathFactory.newXPath().evaluate(peerGroupXPath, 
-								       doc, 
-								       XPathConstants.NODESET);
+	    XPath xpath = xPathFactory.newXPath();
+	    if(contextNode != null){
+		xpath.setNamespaceContext(new NamespaceContextImpl(contextNode, "d"));
+	    }
+            peerElements = (NodeList) xpath.evaluate(peerGroupXPath, 
+						     doc, 
+						     XPathConstants.NODESET);
         } catch(Exception e){
             logger.log(Level.SEVERE, "Could not evaluate UserData XPath "+peerGroupXPath, e);
         }
-        System.err.println("Got " + peerElements.getLength() + " peers for " + peerGroupXPath);
+        //System.err.println("Got " + peerElements.getLength() + " peers for " + peerGroupXPath);
+
+	// Remove peers that are currently filtered.  Seems to be quicker than cloning the doc, 
+	// filtering the node, then running the xpath.  Assumes you don't do much with peerElements
+	// afterwards, or you should apply the filter to remove errant children, etc.)
+	if(xPtrsToFilter != null && !xPtrsToFilter.isEmpty()){
+	    MutableNodeList filterPassedPeers = new MutableNodeList();
+	    for(int i = 0; i < peerElements.getLength(); i++){
+		boolean filtered = false;
+		String peerXPtr = getXPtr(peerElements.item(i));
+		// Check all ancestors to see if they are filtered
+		for(String ancestorXPtr = peerXPtr; 
+		    ancestorXPtr.length() > 0;
+		    ancestorXPtr = ancestorXPtr.replaceFirst("/\\d+$", "")){		
+		    if(xPtrsToFilter.containsKey(ancestorXPtr)){
+			filtered = true;
+			break;
+		    }
+		}
+		if(!filtered){
+		    Element peerElement = (Element) peerElements.item(i);
+		    // Now check if any child nodes need to be filtered
+		    Map<String,String> childrenToDelete = new HashMap<String,String>();
+		    for(String xptr: xPtrsToFilter.keySet()){
+			// is it a child of the peer about to be put in the "passed filter" list? 
+			if(xptr.indexOf(peerXPtr+"/") == 0){
+			    childrenToDelete.put(xptr.substring(peerXPtr.length()), "whatever");
+			}
+		    }
+		    if(!childrenToDelete.isEmpty()){
+			peerElement = (Element) peerElements.item(i).cloneNode(true); //true = deep copy
+			filterNodes(peerElement, childrenToDelete);
+		    }
+		    filterPassedPeers.add(peerElement);
+		}
+	    }
+	    peerElements = filterPassedPeers;
+	    //System.err.println("Got " + peerElements.getLength() + " peers that passed the filter");
+	}
 
         return peerElements;
     }

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/FilterSearch.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/FilterSearch.java	2010/04/14 22:02:04	1.5
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/FilterSearch.java	2010/04/16 17:33:26	1.6
@@ -121,11 +121,17 @@
 	return xpathOptions;
     }
 
+    public String toString(){
+	return filterRegex.toString()+"\t"+getSelectedXPath().getXPath()+"\t"+
+	    getSelectedXPath().getDesc()+"\t"+caseSensitivity+"\t"+inverseSelection;
+    }
+
     public boolean equals(Object o){
         if(o == null || !(o instanceof FilterSearch)){
           return false;
         }
         FilterSearch other = (FilterSearch) o;
+	//System.err.println("Comparing "+this+"\n\nand\n\n"+o);
         return filterRegex.toString().equals(other.filterRegex.toString()) &&
                getSelectedXPath().getXPath().equals(other.getSelectedXPath().getXPath()) &&
                caseSensitivity == other.caseSensitivity &&

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/MobyDataObjectDeferred.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/MobyDataObjectDeferred.java	2010/04/14 23:48:27	1.1
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/MobyDataObjectDeferred.java	2010/04/16 17:33:26	1.2
@@ -15,8 +15,8 @@
 	super(MobyDataType.getDataType(MobyTags.MOBYOBJECT, SeahawkOptions.getRegistry()), ns, "any_id");
 	dataCreator = listener;
     }
-    public MobyDataObjectDeferred(MobyDataType dt, MobyPayloadRequestListener listener){
-	super(dt);
+    public MobyDataObjectDeferred(MobyDataType dt, MobyPayloadRequestListener listener) throws Exception{
+	super(dt, new MobyNamespace("unknown"), "any_id");
 	dataCreator = listener;
     }
     public MobyDataObjectDeferred(MobyDataType dt, MobyNamespace ns, MobyPayloadRequestListener listener) throws Exception{

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/XPointerResolver.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/XPointerResolver.java	2010/04/11 20:15:28	1.1
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/XPointerResolver.java	2010/04/16 17:33:26	1.2
@@ -15,20 +15,24 @@
      * Note, this currently only works for stuff like /1/1/2/3/1/67, 
      * not all XPointers, which includes functions, etc.
      */
-    public static Node getNodeFromXPointer(Document d, String xptr){
-        if(d == null || xptr == null || xptr.length() < 2 || !xptr.startsWith("/1")){
+    public static Node getNodeFromXPointer(Node rootNode, String xptr){
+        if(rootNode == null || xptr == null || xptr.length() < 2){
 	    return null;
         }
-	Node currentNode = d.getDocumentElement();
+	Node currentNode = rootNode;
 	if(currentNode == null){
 	    return null;
 	}
-	if(xptr.equals("/1")){
-	    return currentNode;
-	}
+	if(rootNode instanceof Document){
+	    currentNode = ((Document) rootNode).getDocumentElement();
+	    if(xptr.equals("/1")){
+		return currentNode;
+	    }
         
-	// Get rid of leading "/1/"
-	String[] ordinal_steps = xptr.substring(3).split("/");
+	    // Get rid of leading "/1/"
+	    xptr = xptr.substring(3);
+	}
+	String[] ordinal_steps = xptr.split("/");
 	if(ordinal_steps.length == 0){
 	    return currentNode;
 	}    


From gordonp at dev.open-bio.org  Fri Apr 16 15:58:26 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 16 Apr 2010 15:58:26 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004161958.o3GJwQk7018588@dev.open-bio.org>


gordonp
Fri Apr 16 15:58:26 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services
In directory dev.open-bio.org:/tmp/cvs-serv18552/src/main/ca/ucalgary/seahawk/services

Modified Files:
	MobyClient.java 
Log Message:
Fixed logging messaages
moby-live/Java/src/main/ca/ucalgary/seahawk/services MobyClient.java,1.27,1.28
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/MobyClient.java,v
retrieving revision 1.27
retrieving revision 1.28
diff -u -r1.27 -r1.28
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/MobyClient.java	2010/04/16 17:32:33	1.27
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/MobyClient.java	2010/04/16 19:58:26	1.28
@@ -84,9 +84,7 @@
      * new registry will NOT be reflected here.
      */
     public MobyClient() throws MobyException{
-	this(SeahawkOptions.getRegistry() == null ? 
-	     RegistryCache.getDefaultRegistry() :
-	     SeahawkOptions.getRegistry());
+	this(SeahawkOptions.getRegistry());
     }
 
     /**


From gordonp at dev.open-bio.org  Fri Apr 16 15:59:01 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 16 Apr 2010 15:59:01 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004161959.o3GJx1sF018632@dev.open-bio.org>


gordonp
Fri Apr 16 15:59:01 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory dev.open-bio.org:/tmp/cvs-serv18596/src/main/org/biomoby/client

Modified Files:
	CentralImpl.java 
Log Message:
Fixed logging messages
moby-live/Java/src/main/org/biomoby/client CentralImpl.java,1.64,1.65
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java,v
retrieving revision 1.64
retrieving revision 1.65
diff -u -r1.64 -r1.65
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java	2010/03/29 19:48:28	1.64
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java	2010/04/16 19:59:01	1.65
@@ -131,7 +131,7 @@
     public static final String CENTRAL_IMPL_RESOURCE_NAME = "org.biomoby.client.CentralImpl";
     /** The class to use for getDefaultCentral if all else fails */
     public static final String DEFAULT_CENTRAL_IMPL_CLASSNAME = "org.biomoby.client.CentralDigestCachedImpl";
-    private static Logger logger = Logger.getLogger("org.biomoby.client.CentralImpl");
+    private static Logger logger = Logger.getLogger(CentralImpl.class.getName());
 
    /**
     * Thread local that gives each thread its own
@@ -1888,7 +1888,7 @@
 	ClassLoader classLoader = Thread.currentThread().getContextClassLoader();
 	URL resURL = classLoader.getResource("META-INF/services/"+CENTRAL_IMPL_RESOURCE_NAME);
 	if(resURL != null){
-	    System.err.println("Loading "+resURL);
+	    logger.log(Level.CONFIG, "Loading "+resURL);
 	    try{
 		LineNumberReader reader = new LineNumberReader(new InputStreamReader(resURL.openStream()));
 		for(String line = reader.readLine(); line != null; line = reader.readLine()){
@@ -1904,9 +1904,7 @@
 	    }
 	}
 	try{
-	    if(Boolean.getBoolean("moby.debug")){
-		System.err.println("Central class is  "+className+ " for " + reg);
-	    }
+	    logger.log(Level.CONFIG, "Central class is  "+className+ " for " + reg);
 	    Class clazz = Class.forName(className);
 	    if(reg == null){  // should use default nullary c-tor
 		defaultCentrals.put("", (CentralImpl) clazz.newInstance());


From gordonp at dev.open-bio.org  Fri Apr 16 16:36:17 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 16 Apr 2010 16:36:17 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004162036.o3GKaHua019856@dev.open-bio.org>


gordonp
Fri Apr 16 16:36:17 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv19820/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	MobyContentClipboard.java 
Log Message:
Switched to java.util.logging.*
moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyContentClipboard.java,1.10,1.11
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentClipboard.java,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentClipboard.java	2010/04/11 02:25:03	1.10
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentClipboard.java	2010/04/16 20:36:17	1.11
@@ -21,6 +21,7 @@
 import java.io.FileOutputStream;
 import java.net.URL;
 import java.util.*;
+import java.util.logging.*;
 import java.util.regex.Pattern;
 
 /**
@@ -54,7 +55,8 @@
     // Clipboard editing variables
     private JMenuItem deleteDataPopupItem;
     private MobyDataInstance itemToDelete;
-    private static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(MobyContentClipboard.class);
+    private static Logger logger = Logger.getLogger(MobyContentClipboard.class.getName());
+
     public MobyContentClipboard(MobyContentGUI cGUI, MobyServicesGUI sGUI, JTabbedPane parentComponent, 
 				DataFlowRecorder recorder, JLabel statusBar){
 	super(cGUI, sGUI, parentComponent, recorder, statusBar);
@@ -66,7 +68,7 @@
     	if(clipboardIcon == null){
 	    URL u = cl.getResource(CLIPBOARD_TAB_ICON_RESOURCE);
 	    if(u == null){
-		logger.warn("Could not find icon resource " + CLIPBOARD_TAB_ICON_RESOURCE);
+		logger.log(Level.WARNING, "Could not find icon resource " + CLIPBOARD_TAB_ICON_RESOURCE);
 	    }
 	    else{
 		clipboardIcon = new ImageIcon(u);
@@ -86,7 +88,7 @@
 	    clipboardFile = File.createTempFile(CLIPBOARD_FILE_NAME, ".xml");
 	}
 	catch(Exception e){
-	    logger.error("Clipboard failed to initialize, cannot create temp file:" + e);
+	    logger.log(Level.SEVERE, "Clipboard failed to initialize, cannot create temp file", e);
 	    return;
 	}
 	clipboardFile.deleteOnExit();
@@ -134,7 +136,7 @@
 	// (i.e. don't delete subparts of object)
 	if(!(mdi instanceof MobyDataObject) || !collection.contains(mdi)){
 	    mdi.setXmlMode(MobyDataInstance.SERVICE_XML_MODE);
-	    System.err.println("Skipping " + mdi.toXML());
+	    logger.log(Level.WARNING, "Skipping " + mdi.toXML());
 	    mdi.setXmlMode(MobyDataInstance.CENTRAL_XML_MODE);
 	    return;
 	}
@@ -160,7 +162,7 @@
 	    }
 	}
 	else{
-	    logger.warn("Clipboard: ignoring unrecognized source of event " + e);
+	    logger.log(Level.WARNING, "Clipboard: ignoring unrecognized source of event ", e);
 	}
     }
 
@@ -186,7 +188,7 @@
 
     public void addCollectionData(MobyDataInstance mdi, boolean updateDisplay){	
 	if(mdi == null){
-	    logger.warn("Cannot add null object to the clipboard.");
+	    logger.log(Level.WARNING, "Cannot add null object to the clipboard.");
 	    return;
 	}
 	if(!query.containsKey(CLIPBOARD_COLLECTION_NAME)){
@@ -200,9 +202,9 @@
 	    collection.add((MobyDataObject) mdi);
 	}
 	else{
-	    logger.warn("Cannot add object of class " + mdi.getClass() +
-			" to the clipboard, only MobyDataObject and MobyDataObjectSet" +
-			" are supported");
+	    logger.log(Level.WARNING, "Cannot add object of class " + mdi.getClass() +
+			              " to the clipboard, only MobyDataObject and MobyDataObjectSet" +
+			              " are supported");
 	    return;
 	}
 
@@ -246,26 +248,26 @@
 		return;
 	    }
 	} catch(Exception e){
-	    logger.warn("Could not transform binary file ("+u+"): " + e);
+	    logger.log(Level.WARNING, "Could not transform binary file ("+u+")", e);
 	}
 
 	// Not binary, see if it's text that's convertible to MOBY data
 	MobyClient client = servicesGUI.getMobyClient();
 	if(client == null){
-	    logger.warn("Could not get MOBY client from MOBY services GUI, " +
-			"cannot transform incoming clipboard data to MOBY objects");
+	    logger.log(Level.WARNING, "Could not get MOBY client from MOBY services GUI, " +
+			              "cannot transform incoming clipboard data to MOBY objects");
 	}
 	String urlContents = null;
 	try{
 	    urlContents = HTMLUtils.getURLContents(u);
 	} catch(Exception e){
-	    logger.warn("Could not read contents of the URL to import to the clipboard ("+u+"):" +e);
+	    logger.log(Level.WARNING, "Could not read contents of the URL to import to the clipboard ("+u+")", e);
 	    return;
 	}
 	if(urlContents.indexOf("<html") != -1 || urlContents.indexOf("<HTML") != -1){
 	    urlContents = tagRegex.matcher(commentRegex.matcher(styleRegex.matcher(scriptRegex.matcher(urlContents).replaceAll("")).replaceAll("")).replaceAll("")).replaceAll("");
 	}
-	System.err.println(urlContents);
+	logger.log(Level.FINE, urlContents);
 
 	MobyDataType targetDataType = null;
 	if(collection != null){
@@ -303,7 +305,7 @@
     // Callback once user has selected the data to import from the DataImportChoiceDialog
     public void importConfirmed(DataImportChoiceDialog dialog, MobyDataObject[] selectedData){	
 	if(selectedData == null){
-	    logger.warn("Got null for import selection, abandoning import");
+	    logger.log(Level.WARNING, "Got null for import selection, abandoning import");
 	    return;
 	}
 	for(int i = 0; i < selectedData.length; i++){
@@ -334,7 +336,7 @@
 	    return clipboardFile.toURI().toURL();
 	}
 	catch(java.net.MalformedURLException murle){
-	    logger.warn("Could not get clipboard file URL: " + murle);
+	    logger.log(Level.WARNING, "Could not get clipboard file URL from "+clipboardFile, murle);
 	    return null;
 	}
     }
@@ -348,8 +350,7 @@
 	    gotoURL(clipboardFile.toURI().toURL(), false);
 	}
 	catch(Exception e){
-	    logger.error("Clipboard failed to update the display, cannot write or load temp file:" + e);
-	    e.printStackTrace();
+	    logger.log(Level.SEVERE, "Clipboard failed to update the display, cannot write or load temp file", e);
 	    return;
 	}
 	tabbedPane.setTitleAt(tabbedPane.indexOfComponent(this), CLIPBOARD_TAB_NAME + 


From gordonp at dev.open-bio.org  Sat Apr 17 20:23:42 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Sat, 17 Apr 2010 20:23:42 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004180023.o3I0NgZd027546@dev.open-bio.org>


gordonp
Sat Apr 17 20:23:42 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util
In directory dev.open-bio.org:/tmp/cvs-serv27510/src/main/ca/ucalgary/seahawk/util

Modified Files:
	DataFlowRecorder.java 
Log Message:
Fixed so no problem when original data comes from the clipboard, or a saved moby xml file
moby-live/Java/src/main/ca/ucalgary/seahawk/util DataFlowRecorder.java,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataFlowRecorder.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataFlowRecorder.java	2010/04/16 17:33:26	1.5
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataFlowRecorder.java	2010/04/18 00:23:42	1.6
@@ -342,6 +342,7 @@
 
 	    // true means treat as a collection if that's what the sample data is
 	    String sinkPortName = getPortName(sampleData, true);
+	    // No user data means non-moby origin...backtracking stops.
 	    if(data != null && data.length != 0){
 		URL dataSrcURL = null;
 		try{
@@ -351,6 +352,16 @@
 			       "a provenance URL as expected URL (" + sampleData.getUserData().toString() + ")");
 		    continue;
 		}
+
+		// If srcService == null, the input source for this param was a Moby doc that wasn't a 
+		// service output, e.g. the clipboard or an old doc loaded from file.
+		MobyService srcService = DataUtils.getService(dataSrcURL);
+		if(srcService == null){
+		    addWorkflowInput(processorName, condPassProcessorAndPorts, sinkPortName, sampleData, 
+				     datalinks, processors, inputPorts, doc);
+		    continue;
+		}
+
 		// recursion for workflow creation by backtracking service input provenance
 		String feedingProcessorName = null;
 		String feedingProcessorPort = null;
@@ -429,52 +440,57 @@
 	    }
 	    // Otherwise it's a workflow input the user will need to specify
 	    else{
-		// pName is editable name for input processor target...
-		// allows injection of condition without affecting method's return value
-		String pName = processorName; 
-		if(condPassProcessorAndPorts != null){
-		    // inject condition filter between data creator and current service 
-		    datalinks.appendChild(createDataLinkElement(condPassProcessorAndPorts[0],
-								condPassProcessorAndPorts[2],
-								pName,
-								sinkPortName,
-								doc));
-		    pName = condPassProcessorAndPorts[0];
-		    sinkPortName = condPassProcessorAndPorts[1];
-		}
-		// The sample data may be used in more than one branch of the flow...avoid duplication
-		// Get the real data XML, to see if we've encountered it before as input (it'd be in the hash)
-		// Remember that sd is the loop's original MobyDataInstance before it's been coerced into a MobyPrimaryData, 
-		// which doesn't have XML modes, etc.
-		String inputKey = getInputKey(sd);
-		//		System.err.println("Input key for " + processorName + " is " + inputKey);
-
-		String[] mobifyingProcessorNameAndPorts = null;
-		if(input2Processor.containsKey(inputKey)){
-		    mobifyingProcessorNameAndPorts = input2Processor.get(inputKey);		    
-		}
-		else{
-		    if(sampleData.getDataType().getName().equals(MobyTags.MOBYOBJECT)){
-			mobifyingProcessorNameAndPorts = addIdMobifyingProcessor(processors, datalinks, inputPorts,
-										 sampleData, doc);
-			input2Processor.put(inputKey, mobifyingProcessorNameAndPorts);
-		    }
-		    else{
-			// TODO: Need to build complex input from MOB rule or spreadsheet fields?
-		    }
-		}
-		// link the created data to the workflow service
-		datalinks.appendChild(createDataLinkElement(mobifyingProcessorNameAndPorts[0], 
-							    mobifyingProcessorNameAndPorts[1], 
-							    pName, sinkPortName, 
-							    doc));
+		addWorkflowInput(processorName, condPassProcessorAndPorts, sinkPortName, sampleData, 
+				 datalinks, processors, inputPorts, doc);
 	    }
-
 	}
 
 	return processorName;
     }
 
+    private void addWorkflowInput(String pName, String[] condPassProcessorAndPorts, String sinkPortName, 
+				  MobyPrimaryData sampleData, Element datalinks, Element processors, 
+				  Element inputPorts, Document doc) throws Exception{
+	// pName is editable name for input processor target...
+	// allows injection of condition without affecting method's return value
+	if(condPassProcessorAndPorts != null){
+	    // inject condition filter between data creator and current service 
+	    datalinks.appendChild(createDataLinkElement(condPassProcessorAndPorts[0],
+							condPassProcessorAndPorts[2],
+							pName,
+							sinkPortName,
+							doc));
+	    pName = condPassProcessorAndPorts[0];
+	    sinkPortName = condPassProcessorAndPorts[1];
+	}
+	// The sample data may be used in more than one branch of the flow...avoid duplication
+	// Get the real data XML, to see if we've encountered it before as input (it'd be in the hash)
+	// Remember that sd is the loop's original MobyDataInstance before it's been coerced into a MobyPrimaryData, 
+	// which doesn't have XML modes, etc.
+	String inputKey = getInputKey((MobyDataInstance) sampleData);
+	//		System.err.println("Input key for " + processorName + " is " + inputKey);
+	
+	String[] mobifyingProcessorNameAndPorts = null;
+	if(input2Processor.containsKey(inputKey)){
+	    mobifyingProcessorNameAndPorts = input2Processor.get(inputKey);		    
+	}
+	else{
+	    if(sampleData.getDataType().getName().equals(MobyTags.MOBYOBJECT)){
+		mobifyingProcessorNameAndPorts = addIdMobifyingProcessor(processors, datalinks, inputPorts,
+									 sampleData, doc);
+		input2Processor.put(inputKey, mobifyingProcessorNameAndPorts);
+	    }
+	    else{
+		// TODO: Need to build complex input from MOB rule or spreadsheet fields?
+	    }
+	}
+	// link the created data to the workflow service
+	datalinks.appendChild(createDataLinkElement(mobifyingProcessorNameAndPorts[0], 
+						    mobifyingProcessorNameAndPorts[1], 
+						    pName, sinkPortName, 
+						    doc));	
+    }
+
     // returns the same value for moby sample data instances containing the same data in XML form
     private String getInputKey(MobyDataInstance sd){
 	int oldXmlMode = sd.getXmlMode();


From gordonp at dev.open-bio.org  Sat Apr 17 20:31:49 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Sat, 17 Apr 2010 20:31:49 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004180031.o3I0VnZ0028062@dev.open-bio.org>


gordonp
Sat Apr 17 20:31:49 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv28026/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	MobyServicesGUI.java 
Log Message:
Switched from Object to ID for basic object label, more intuitive for users
moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyServicesGUI.java,1.20,1.21
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java,v
retrieving revision 1.20
retrieving revision 1.21
diff -u -r1.20 -r1.21
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java	2010/04/16 17:33:25	1.20
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java	2010/04/18 00:31:49	1.21
@@ -693,7 +693,6 @@
 											       payloadCreator));
 		    }
 		    else if(mobyData instanceof MobyNamespace){
-			System.err.println("Creating deferred dataset payload");
 			serviceAssocObject = mobyClient.getServices(new MobyDataObjectDeferred((MobyNamespace) mobyData, 
 											       payloadCreator));
 		    }
@@ -1175,7 +1174,7 @@
     }
 
     public JMenu addOutputTypeSubMenu(JMenu parentMenu, MobyDataType type){
-	JMenu menu = new JMenu("Result type: " + type.getName());
+	JMenu menu = new JMenu("Result type: " + (type.getName().equals(MobyTags.MOBYOBJECT) ? "ID" : type.getName()));
 
 	MobyDataType[] typeLineage = type.getLineage();
 	String commonAncestorDesc = "";


From gordonp at dev.open-bio.org  Sat Apr 17 20:33:05 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Sat, 17 Apr 2010 20:33:05 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004180033.o3I0X5V4028106@dev.open-bio.org>


gordonp
Sat Apr 17 20:33:05 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv28070/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	MobySaveDialog.java 
Log Message:
Stripped seahawk preocessing instructions from saved XML as they can confuse on reload.  Workflow export is default save option now.
moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobySaveDialog.java,1.8,1.9
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobySaveDialog.java,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobySaveDialog.java	2010/03/29 19:53:16	1.8
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobySaveDialog.java	2010/04/18 00:33:05	1.9
@@ -92,11 +92,11 @@
 		    fileChooser.setName(FILE_CHOOSER_SAVE_TITLE);
 		    fileChooser.setFileHidingEnabled(false);
 		    fileChooser.setFileSelectionMode(JFileChooser.FILES_ONLY);
-		    fileChooser.addChoosableFileFilter(new DescriptiveFileFilter(HTML_EXT, HTML_DESC));
 		    if(document.hasXMLSource()){
 			fileChooser.addChoosableFileFilter(new DescriptiveFileFilter(T2FLOW_EXT, T2FLOW_DESC));
 			fileChooser.addChoosableFileFilter(new DescriptiveFileFilter(XML_EXT, XML_DESC));
 		    }
+		    fileChooser.addChoosableFileFilter(new DescriptiveFileFilter(HTML_EXT, HTML_DESC));
 		    fileChooser.setAcceptAllFileFilterUsed(false);
 		    if(lastDirOpened != null){
 			fileChooser.setCurrentDirectory(lastDirOpened);
@@ -318,7 +318,9 @@
 		    try {
 			OutputStream ostream = new FileOutputStream(f);
 			String xml = document.getXMLSource();
-			ostream.write(xml.getBytes());
+			// Before saving, strip out the Seahawk processing instructions, which will 
+			// confuse Seahawk if we reload the XML doc later.
+			ostream.write(xml.replaceAll("<\\?"+DataUtils.PI_TARGET+".*?\\?>","").getBytes());
 			ostream.flush();
 			ostream.close();
 		    } catch (Exception ex) {


From gordonp at dev.open-bio.org  Sat Apr 17 20:33:56 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Sat, 17 Apr 2010 20:33:56 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004180033.o3I0Xu7J028150@dev.open-bio.org>


gordonp
Sat Apr 17 20:33:56 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv28114/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	MobyPayloadCreator.java 
Log Message:
Cleaner logging
moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyPayloadCreator.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyPayloadCreator.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyPayloadCreator.java	2010/04/16 17:33:25	1.3
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyPayloadCreator.java	2010/04/18 00:33:56	1.4
@@ -27,7 +27,7 @@
 	// The request key is the sample data's app context: 
         // url#xpath <tab> sample_xptr <tab> filter_regex <tab> filter_xpath <tab> xpath_desc <tab> case_sensitive_boolean <tab> inverse selection
         // from which we will build the peer dataset to submit.
-	System.err.println("Request key is " + requestKey);
+	logger.log(Level.FINER, "Request key is " + requestKey);
 	String[] requestKeyFields = requestKey.split("\t");
 
 	String[] requestParts = requestKeyFields[0].split("#", 2);
@@ -67,7 +67,7 @@
 	    }
 	    else if(filter.equals(srcPane.getFilter())){
                 // no need to redo the filtering, it's the current display's filtering
-		System.err.println("Reusing current filter");
+		logger.log(Level.FINE, "Reusing current filter");
                 xptrsToFilter = srcPane.getFilteredData();
             }
             else{
@@ -89,7 +89,7 @@
 	MobyContentInstance payload = new MobyContentInstance();
         Map<String,Integer> jobPrefixes = new LinkedHashMap<String,Integer>();
 
-	System.err.println("Loading MobyContentInstance with "+peerElements.getLength()+" elements for xpath "+selectionXPath);
+	logger.log(Level.FINE, "Loading MobyContentInstance with "+peerElements.getLength()+" elements for xpath "+selectionXPath);
         for(int i = 0; i < peerElements.getLength(); i++){
             Element peerElement = (Element) peerElements.item(i);
 	    // Try to make the job names trackable to the inputs:
@@ -106,7 +106,7 @@
                 jobPrefixes.put(jobKey, new Integer(suffixCount+1));
                 jobKey += "_"+(suffixCount+1);
             }
-	    System.err.println("Adding job "+jobKey+" for "+peerElement.getLocalName());
+	    logger.log(Level.FINE, "Adding job "+jobKey+" for "+peerElement.getLocalName());
             MobyDataInstance mdi  = null;
             try{
                 mdi = MobyDataObject.createInstanceFromDOM(peerElement, SeahawkOptions.getRegistry());


From gordonp at dev.open-bio.org  Fri Apr 23 01:15:42 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 23 Apr 2010 01:15:42 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004230515.o3N5FglD024507@dev.open-bio.org>


gordonp
Fri Apr 23 01:15:42 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util
In directory dev.open-bio.org:/tmp/cvs-serv24471/src/main/ca/ucalgary/services/util

Modified Files:
	PBERecorder.java 
Log Message:
Truncate long example data abruptly if it has no whitespace
moby-live/Java/src/main/ca/ucalgary/services/util PBERecorder.java,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/PBERecorder.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/PBERecorder.java	2010/03/29 20:59:54	1.4
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/PBERecorder.java	2010/04/23 05:15:41	1.5
@@ -795,7 +795,10 @@
 	}
 
 	int end = text.length();
-	if(start + targetWord.length() + numChars < text.length()){
+	if(text.indexOf(" ") == -1){
+	    end = numChars;
+	}
+	else if(start + targetWord.length() + numChars < text.length()){
 	    end = start + targetWord.length() + numChars;
 	    // break at a word boundary
 	    while(end < text.length() && !Character.isWhitespace(text.charAt(end))){


From gordonp at dev.open-bio.org  Fri Apr 23 01:16:45 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 23 Apr 2010 01:16:45 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004230516.o3N5GjOm024551@dev.open-bio.org>


gordonp
Fri Apr 23 01:16:45 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services
In directory dev.open-bio.org:/tmp/cvs-serv24515/src/main/ca/ucalgary/seahawk/services

Modified Files:
	TextClient.java 
Log Message:
Better Dublin Core support, added getPossibleTextTypes() for drag and drop export
moby-live/Java/src/main/ca/ucalgary/seahawk/services TextClient.java,1.7,1.8
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/TextClient.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/TextClient.java	2009/06/09 19:22:21	1.7
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/TextClient.java	2010/04/23 05:16:45	1.8
@@ -8,13 +8,15 @@
 
 import org.w3c.dom.*;
 
-import javax.xml.transform.stream.*;
-import javax.xml.transform.*;
 import javax.xml.parsers.*;
+import javax.xml.transform.*;
+import javax.xml.transform.dom.DOMSource;
+import javax.xml.transform.stream.*;
 
 import java.io.*;
 import java.net.URL;
 import java.util.*;
+import java.util.logging.*;
 
 /**
  * This class uses XSLT rules to transform MOBY XML data representation
@@ -24,20 +26,26 @@
  */
 public class TextClient{
 
+    public static final String DATA_MAPPING_XSLT_RESOURCE = "ca/ucalgary/seahawk/resources/mobyRules.xsl";
+    public static final String RESOURCE_SYSTEM_PROPERTY = "seahawk.textrules";
+
     public final static String XSLT_NS = "http://www.w3.org/1999/XSL/Transform";
     public final static String XSLT_MODE_VAR = "selectedACDTypeTarget";
 
     private Vector<Transformer> moby2textConverters;  // XSLT engine
     private TransformerFactory transFactory;
     private DocumentBuilder docBuilder;
+    private URL dataMappingXSLTURL;
     //private Map<String,Transformer> id; //todo: unique xslt doc id (e.g. LSID or URL) -> transformer
 
     private Map<String, Vector<String>> typeTemplates;  //mobytype -> Vector(xsltrule1, xsltrule2,...)
     private Map<String, Vector<MobyNamespace>> typeNsRestrictions;  //mobytype -> Vector(mobynamespace1, ...)
     private Map<String, String> templateMode;
-    private String id;
+    private Map<String,String> templateIds; // template name -> URN
     private Registry registry;
 
+    private static Logger logger = Logger.getLogger(TextClient.class.getName());
+
     public TextClient() throws Exception{
 	this(SeahawkOptions.getRegistry() == null ? 
 	     RegistryCache.getDefaultRegistry() :
@@ -60,16 +68,95 @@
 	typeTemplates = new HashMap<String, Vector<String>>();
 	typeNsRestrictions = new HashMap<String, Vector<MobyNamespace>>();
 	templateMode = new HashMap<String, String>();
+	templateIds = new HashMap<String, String>();
+
+	ClassLoader cl = getClass().getClassLoader();
+	if(cl == null){
+	    cl = ClassLoader.getSystemClassLoader();
+	}
+        String rulesResource = System.getProperty(RESOURCE_SYSTEM_PROPERTY);
+        if(rulesResource == null){
+	  dataMappingXSLTURL = cl.getResource(DATA_MAPPING_XSLT_RESOURCE);
+        }
+	else if(rulesResource.length() != 0){
+	    // See if it's a URL
+	    try{
+		dataMappingXSLTURL = new URL(rulesResource);
+	    }
+	    catch(Exception e){
+		dataMappingXSLTURL = cl.getResource(rulesResource);
+	    }
+	}
+	if(dataMappingXSLTURL == null){
+	    if(rulesResource.length() != 0){ // if not left intentionally blank
+		logger.log(Level.WARNING, "Could not find MOBY to text mapping resource '"+
+				          rulesResource+"'");
+	    }
+	}
+	else{
+	    try{
+		addMappingsFromURL(dataMappingXSLTURL);
+	    }
+	    catch(Exception e){
+		logger.log(Level.SEVERE, "Error loading default data mapping rules ("+dataMappingXSLTURL+")", e);
+                e.printStackTrace();
+	    }
+	}
+    }
+
+    public String[] getPossibleTextTypes(MobyPrimaryData dataTemplate, boolean mustHaveURN){
+	Vector<String> possibleTypes = new Vector<String>();
+	// Search for templates matching the given type or one of its parent types,
+	// and see if they create the given text type (indicated by the template's mode attribute)
+	for(MobyDataType type = dataTemplate.getDataType();
+	    type != null;
+	    type = type.getParent()){
+	    if(typeTemplates.containsKey(type.getName())){
+		// These two vectors should be of the same length!
+		Vector<String> templateNames = typeTemplates.get(type.getName());
+		Vector<MobyNamespace> nsRestrictions = typeNsRestrictions.get(type.getName());
+		for(int i = 0; i < templateNames.size(); i++){
+		    String templateName = templateNames.elementAt(i);
+		    if(mustHaveURN && getTemplateURN(templateName) == null){
+			continue;
+		    }
+
+		    // the template input moby datatype is the same type as we have an instance of
+		    String textType = templateMode.get(templateName); // mode and text type name are one and the same
+		    // does set-ness match?
+		    if(dataTemplate instanceof MobyPrimaryDataSet){
+			if(templateName.startsWith("Collection-")){
+			    possibleTypes.add(textType);	
+			}
+		    }
+		    else{
+			if(!templateName.startsWith("Collection-")){
+			    possibleTypes.add(textType);
+			}
+		    }
+		    // Is there a namespace restriction on the transformation rule?
+		    MobyNamespace ns = nsRestrictions.elementAt(i);
+		    if(ns != null){
+			for(MobyNamespace n: dataTemplate.getNamespaces()){
+			    if(ns.equals(n)){
+				possibleTypes.add(textType);
+			    }
+			}
+		    }
+		}
+	    }
+	}
+	return possibleTypes.toArray(new String[possibleTypes.size()]);
+    }
+
+    public String getTemplateURN(String templateName){
+	return templateIds.get(templateName);
     }
 
     /**
      * @return the data format the xslt creates (the last template mode attribute in the file) 
      */
     public synchronized String addMappingsFromURL(URL xsltURL) throws Exception{
-        StreamSource stylesheet = new StreamSource(xsltURL.toString());
-	// Prepend to list, so later rules can override ones specified earlier
-	moby2textConverters.insertElementAt(transFactory.newTransformer(stylesheet), 0);
-
 	// We actually need to read in the XSLT file and keep track of the template
 	// names, modes, etc..  Currently, this will not follow links that
 	// import other stylesheets into the one being examined.
@@ -80,7 +167,6 @@
             throw new Exception("Error: Could not get XSLT document as DOM from source URL " 
 				+ xsltURL + " (empty or malformed document?)");
         }
-	getId(xsltDOMRoot);  // retrieve the dublin core metadata
 
 	String mode = null; // returned in the end
 
@@ -93,6 +179,9 @@
 		continue;
 	    }
 	    String templateName = template.getAttribute("name");
+
+	    templateIds.put(templateName, getId(template));
+
 	    String m = template.getAttribute("mode");
 	    if(m != null && m.trim().length() > 0){
 		mode = template.getAttribute("mode");
@@ -150,12 +239,16 @@
 	    typeNsRestrictions.get(templateNameParts[0]).insertElementAt(ns, 0);	    
 	}
 
+        DOMSource stylesheet = new DOMSource(domDoc);
+	// Prepend to list, so later rules can override ones specified earlier
+	moby2textConverters.insertElementAt(transFactory.newTransformer(stylesheet), 0);
+
 	//System.err.println("Mode returned by " + xsltURL + " is " + mode);
 	return mode; // return the last mode value in the file (useful when mapping XSLT -> data format)
     }
 
     // Looks for Dublin Core metadata
-    private void getId(Element xsltDOMRoot){
+    private String getId(Element xsltDOMRoot){
 	NodeList idElements = xsltDOMRoot.getElementsByTagNameNS(MobyPrefixResolver.DUBLIN_CORE_NAMESPACE,
 								 "identifier");
 	if(idElements.getLength() == 0){
@@ -163,13 +256,17 @@
 							     "source");
 	}
 	if(idElements.getLength() == 0){
-	    return;
+	    return null;
 	}
 	if(idElements.getLength() != 1){
 	    System.err.println("More than one Dublin Core identifier was found, cannot disambiguate.");
-	    return;
+	    return null;
 	}
-	id = idElements.item(0).getTextContent();
+	String id = idElements.item(0).getTextContent();
+	// remove child so id doesn't show up in the xslt output!
+	idElements.item(0).getParentNode().removeChild(idElements.item(0));
+	System.err.println("Found and removed "+id);
+	return id;
     }
 
    /**
@@ -374,17 +471,17 @@
 				e);
 	}	 
 	
-	if(client.id == null){
+	if(client.templateIds.isEmpty()){
 	    throw new Exception("Internal error: loaded the transformation rule (URI " + ruleURI + 
 				") from " + ruleSource + " but could not retrieve it from TextClient " +
 				"using the URI.  Make sure the transformation rule contains a Dublin Core " +
 				"identifier element specifying this URI.");
 	}
-	else if(!client.id.equals(ruleURI)){
+	else if(!client.templateIds.containsValue(ruleURI)){
 	    throw new Exception("Internal error: loaded the transformation rule (URI " + ruleURI + 
 				") from " + ruleSource + " but could not retrieve it from TextClient " +
 				"using the URI.  The given Dublin Core info for the rule actually loaded " +
-				"was " + client.id);
+				"was " + client.templateIds.values().iterator().next());
 	}
 	else{
 	    template = new MobyPrimaryDataSimple("templateRuleReturnedObject");
@@ -398,7 +495,7 @@
 	    if(dataTypeNames.size() > 1){
 		throw new Exception("Multiple TextClient rules were loaded from " + ruleSource +
 				    ", please separate them out into separate XSLT files to ensure " +
-				    "they can be referenced inidivudually and unambiguously.");
+				    "they can be referenced indivudually and unambiguously.");
 	    }
 	    MobyDataType type = MobyDataType.getDataType(dataTypeNames.toArray()[0].toString(), client.getRegistry());
 	    template.setDataType(type);


From gordonp at dev.open-bio.org  Fri Apr 23 01:17:28 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 23 Apr 2010 01:17:28 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004230517.o3N5HSKc024595@dev.open-bio.org>


gordonp
Fri Apr 23 01:17:28 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv24559/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	SeahawkTransferable.java 
Log Message:
Better complex object drag and drop export support
moby-live/Java/src/main/ca/ucalgary/seahawk/gui SeahawkTransferable.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java	2009/06/09 19:46:48	1.1
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java	2010/04/23 05:17:28	1.2
@@ -1,9 +1,15 @@
 package ca.ucalgary.seahawk.gui;
 
+import ca.ucalgary.seahawk.util.SeahawkOptions;
+import ca.ucalgary.seahawk.services.TextClient;
+
+import org.biomoby.shared.MobyPrimaryData;
 import org.biomoby.shared.data.*;
 
 import java.awt.datatransfer.*;
+import javax.swing.JOptionPane;
 import java.util.*;
+import java.util.logging.*;
 
 /**
  * This class handles the export of data from the Seahawk interface into other applications,
@@ -16,9 +22,20 @@
     private String lastPastedValue;
     private String lastTransformRuleURI;
 
+    private static TextClient textClient;
+    private static Logger logger = Logger.getLogger(SeahawkTransferable.class.getName());
+
     public SeahawkTransferable(MobyContentPane p){
 	pane = p;
     }
+    
+    private synchronized TextClient getTextClient() throws Exception{
+	if(textClient == null){
+	    textClient = new TextClient(SeahawkOptions.getRegistry());
+	    //auto populate the rules
+	}
+	return textClient;
+    }
 
     public Object getTransferData(DataFlavor flavor) 
 	throws UnsupportedFlavorException, java.io.IOException{
@@ -28,7 +45,7 @@
 	Class clazz = flavor.getRepresentationClass();
 	
 	// Essentially, we let the user drag Moby objects or submembers rather than substrings of members' text
-	// so that we can make simple rules for decomposition in programming-by-example.  OR an XSLT "DEM" rulew
+	// so that we can make simple rules for decomposition in programming-by-example.  OR an XSLT "DEM" rules
 	// could be applied to provide a particular format e.g. DNASequence -> FastA
 	String fieldString = null;
 	String transformRuleURI = null;
@@ -54,12 +71,38 @@
 	    fieldString = ((MobyDataObject) field).getValue().toString();
 	    transformRuleURI = "urn:lsid:bioxml.info:mobyLoweringSchemaMapping:DateTime2String";
 	}
-	else if(field instanceof MobyDataObjectVector){	    
-	}
-	else if(field instanceof MobyDataObjectSet){
+	else if(field instanceof MobyDataObjectVector){	
+	    //todo?
 	}
 	else if(field instanceof MobyDataComposite){
-	    // todo: Is there a DEM rule we can use?
+	    try{
+		// Is there a DEM rule we can use?
+		boolean ONLY_IF_HAS_URN = true;
+		String[] formatChoices = getTextClient().getPossibleTextTypes((MobyPrimaryData) field, ONLY_IF_HAS_URN);
+		String targetTextType = null;
+		if(formatChoices != null && formatChoices.length != 0){
+		    if(formatChoices.length == 1){
+			targetTextType = formatChoices[0];
+		    }
+		    else{
+			// Give the user a choice
+			targetTextType = formatChoices[0];
+			logger.log(Level.INFO, "Chose "+formatChoices[0]+" instead of "+formatChoices[1]);
+// 			targetTextType = (String) JOptionPane.showInputDialog(pane
+// 									      "Please select a text format to convert to",
+// 									      "Format choices available",
+// 									      JOptionPane.QUESTION_MESSAGE,
+// 									      null,
+// 									      formatChoices,
+// 									      formatChoices[0]);
+		    }
+		}
+		fieldString = getTextClient().getText(field, targetTextType);
+		transformRuleURI = getTextClient().getTemplateURN(targetTextType);
+	    } catch(Exception e){
+		pane.setStatus("Could not transform Moby object to text: " + e.getMessage());
+		logger.log(Level.SEVERE, "Could not transform Moby object to text: ", e);
+	    }
 	}
 	else{
 	    // Must be just a base MobyDataObject


From gordonp at dev.open-bio.org  Fri Apr 23 01:18:13 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 23 Apr 2010 01:18:13 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004230518.o3N5IDig024639@dev.open-bio.org>


gordonp
Fri Apr 23 01:18:13 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv24603/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	MobyServicesGUI.java 
Log Message:
Fixed duplication in complex object labels when they have namespaces too
moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyServicesGUI.java,1.21,1.22
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java,v
retrieving revision 1.21
retrieving revision 1.22
diff -u -r1.21 -r1.22
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java	2010/04/18 00:31:49	1.21
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java	2010/04/23 05:18:13	1.22
@@ -1315,7 +1315,7 @@
 		}
 	    }
 	    if(templateObject instanceof MobyDataObject && id != null && id.length() > 0){
-		objectLabel += "<font color='red'>"+objectLabel+"</font>:" + id;
+		objectLabel = "<font color='red'>"+objectLabel+"</font>:" + id;
 	    }
 	    else if(templateObject instanceof MobyDataObjectSet){
 		objectLabel = "<font color='red'>"+objectLabel+" collection</font>";


From gordonp at dev.open-bio.org  Fri Apr 23 01:19:10 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 23 Apr 2010 01:19:10 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004230519.o3N5JAnp024685@dev.open-bio.org>


gordonp
Fri Apr 23 01:19:10 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv24649/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	MobySaveDialog.java 
Log Message:
Removed redundant popup of single tab export if canceled
moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobySaveDialog.java,1.9,1.10
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobySaveDialog.java,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobySaveDialog.java	2010/04/18 00:33:05	1.9
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobySaveDialog.java	2010/04/23 05:19:10	1.10
@@ -92,11 +92,11 @@
 		    fileChooser.setName(FILE_CHOOSER_SAVE_TITLE);
 		    fileChooser.setFileHidingEnabled(false);
 		    fileChooser.setFileSelectionMode(JFileChooser.FILES_ONLY);
+		    fileChooser.addChoosableFileFilter(new DescriptiveFileFilter(HTML_EXT, HTML_DESC));
 		    if(document.hasXMLSource()){
-			fileChooser.addChoosableFileFilter(new DescriptiveFileFilter(T2FLOW_EXT, T2FLOW_DESC));
 			fileChooser.addChoosableFileFilter(new DescriptiveFileFilter(XML_EXT, XML_DESC));
+			fileChooser.addChoosableFileFilter(new DescriptiveFileFilter(T2FLOW_EXT, T2FLOW_DESC));
 		    }
-		    fileChooser.addChoosableFileFilter(new DescriptiveFileFilter(HTML_EXT, HTML_DESC));
 		    fileChooser.setAcceptAllFileFilterUsed(false);
 		    if(lastDirOpened != null){
 			fileChooser.setCurrentDirectory(lastDirOpened);
@@ -277,7 +277,8 @@
 
 	    // Waits until workflowConfirmed or workflowCanceled is called by the preview dialog
 	    dialog.available.acquire();
-	    return dialog.exportConfirmed;
+	    // Check choice, because if the user cancelled the dialog, don't show it again regardless
+	    return choice == 1 ? true : dialog.exportConfirmed;
 	} catch (Exception ex) {
 	    ex.printStackTrace();
 	    JOptionPane.showMessageDialog(null, "Cannot save the Seahawk tab history as a Taverna workflow: "+ex, 


From gordonp at dev.open-bio.org  Fri Apr 23 01:20:00 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 23 Apr 2010 01:20:00 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004230520.o3N5K0NK024729@dev.open-bio.org>


gordonp
Fri Apr 23 01:20:00 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv24693/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	MobyContentPane.java 
Log Message:
Fixed bug with support of plus sign in URLs to wrap as services
moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyContentPane.java,1.29,1.30
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java,v
retrieving revision 1.29
retrieving revision 1.30
diff -u -r1.29 -r1.30
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java	2010/04/16 17:33:25	1.29
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java	2010/04/23 05:20:00	1.30
@@ -273,6 +273,10 @@
 	}
     }
 
+    public void setStatus(String msg){
+	status.setText(msg);
+    }
+
     // servletPath is either the CGI or SOAP servlet
     private void createService(String servletPath){
 	// item name, set by MobyContentGUI's processResults(), is namedXPath#numericXPtr
@@ -459,7 +463,7 @@
 				   "Please manually launch a browser and go to the URL " +
 				   u);
 	    }
-	    desktop.browse(u.toURI());
+	    desktop.browse(new java.net.URI(u.toURI().toString().replace("+", "%2B")));
 	} catch (java.net.URISyntaxException urise){
 	    logger.error("Could not create URI from URL ("+u+"): " + urise);
 	} catch (java.io.IOException ioe){


From gordonp at dev.open-bio.org  Fri Apr 23 01:21:42 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 23 Apr 2010 01:21:42 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004230521.o3N5LgTu024871@dev.open-bio.org>


gordonp
Fri Apr 23 01:21:42 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources
In directory dev.open-bio.org:/tmp/cvs-serv24839/src/main/ca/ucalgary/seahawk/resources

Added Files:
	mobyRules.xsl 
Log Message:
Sibling of mobyRules.xsl in src/main/ca/ucalgary/services/resources, but with nicer format names and Dublin Core IDs for Daggoo wrapping
moby-live/Java/src/main/ca/ucalgary/seahawk/resources mobyRules.xsl,NONE,1.1

From gordonp at dev.open-bio.org  Sat Apr 24 13:23:27 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Sat, 24 Apr 2010 13:23:27 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004241723.o3OHNRQZ007370@dev.open-bio.org>


gordonp
Sat Apr 24 13:23:27 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv7331/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	MobySecondaryInputGUI.java MobyServicesGUI.java 
Added Files:
	ServiceChoiceListener.java ServiceSearchDialog.java 
Log Message:
Initial commit of service search dialog
moby-live/Java/src/main/ca/ucalgary/seahawk/gui ServiceChoiceListener.java,NONE,1.1 ServiceSearchDialog.java,NONE,1.1 MobySecondaryInputGUI.java,1.7,1.8 MobyServicesGUI.java,1.22,1.23
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobySecondaryInputGUI.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/gui/MobySecondaryInputGUI.java	2007/12/06 17:32:32	1.7
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobySecondaryInputGUI.java	2010/04/24 17:23:26	1.8
@@ -1,4 +1,3 @@
-
 package ca.ucalgary.seahawk.gui;
 
 import ca.ucalgary.seahawk.services.MobyClient;

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java,v
retrieving revision 1.22
retrieving revision 1.23
diff -u -r1.22 -r1.23
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java	2010/04/23 05:18:13	1.22
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java	2010/04/24 17:23:26	1.23
@@ -27,7 +27,7 @@
  * Implementation of the actually popup menu that lists services available, and invokes them.
  */
 
-public class MobyServicesGUI implements ActionListener, Comparator<MobyService>, PopupMenuListener{
+public class MobyServicesGUI implements ActionListener, Comparator<MobyService>, PopupMenuListener, ServiceChoiceListener{
     public final static int MAX_ID_LEN = 30;
     public final static String SERVICE_SUBMENU_NAME = "seahawkPopupSubMenuName";
 
@@ -35,6 +35,10 @@
     public final static int MAX_SERVICES_PER_SUBMENU = 12;  
     public final static int MAX_SERVICE_DESC_LEN = 50;
     public final static String CLIPBOARD_CMD = "clipboard";
+    public final static String SERVICESEARCH_CMD = "service_search";
+    public final static String SEARCH_LABEL = "Find service by keyword...";
+    public final static String CLIPBOARD_LABEL = "Add to clipboard";
+
     /** Always spring MOBY response in a new window if this modifier is present for a click */
     public final static int USE_DEFAULT_HANDLER_MASK  = ActionEvent.SHIFT_MASK;
     public final static int USE_DEFAULT_SECONDARIES_MASK  = ActionEvent.CTRL_MASK;
@@ -57,6 +61,7 @@
     int maxDataDesc = 22;
     // tracks nested submenus to root submenus of choices popup
     private Map<JMenu, JMenu> service2submenu; 
+    private Map<JMenuItem, JMenu> search2submenu; 
     private Map<JComponent,Integer> submenu2msIndex;
     private Map<JMenu,JMenuItem> submenu2waitItem;
     // for storing callbacks to other than the default response handler
@@ -75,6 +80,7 @@
 	submenu2msIndex = new HashMap<JComponent,Integer>();
 	submenu2waitItem = new HashMap<JMenu,JMenuItem>();
 	service2submenu = new HashMap<JMenu,JMenu>();
+	search2submenu = new HashMap<JMenuItem,JMenu>();
 	specificHandlers = new HashMap<Integer,WeakReference<MobyRequestEventHandler>>();
     }
 
@@ -124,6 +130,20 @@
 		}
 		return;
 	    }
+	    if(service.equals(SERVICESEARCH_CMD)){
+		synchronized(ms){
+		    if(ms[which_data] == null){
+			logger.warn("Ignoring searvice search in " + getClass().getName() +
+				    ", the data to add is currently null (index "+which_data+")"+
+				    ", from source " + e.getSource());
+			removePopupOptions(e.getSource());
+			return;
+		    }
+		    setupSearchData(search2submenu.get((JMenuItem) e.getSource()), ms[which_data]);
+		    removePopupOptions(e.getSource());
+		}
+		return;   
+	    }
 	    // Otherwise call a remote service
 	    int which_service = Integer.parseInt(service);
 
@@ -322,7 +342,7 @@
     }
 
     /**
-     * If the popup is cancelled, we want to remove any data we've stored, and kill any 
+     * If the popup is canceled, we want to remove any data we've stored, and kill any 
      * requests to MOBYCentral.
      */
     public void popupMenuCanceled(PopupMenuEvent e){
@@ -533,6 +553,7 @@
 	
 	for(int i = 0; i < submenus.length; i++){
 	    addServicesToSubMenu(submenus[i], serviceAssocObjects[i], handler);
+	    addSearchItem(submenus[i], 1);
 	}
     }
 
@@ -595,6 +616,7 @@
 		    //}}.start();
 	    }
 	    service2submenu.clear();
+	    search2submenu.clear();
 	    submenu2msIndex.clear();
 	    submenu2waitItem.clear();
 	    ms = new MobyDataServiceAssocInstance[0];
@@ -732,6 +754,7 @@
 	}
 
 	addServicesToSubMenu(submenu, serviceAssocObject, handler);
+        addSearchItem(submenu, 0);
     }
 
     protected synchronized void addServicesToSubMenu(JMenu submenu, MobyDataServiceAssocInstance msadi){
@@ -1333,6 +1356,15 @@
 	return submenu;
     }
 
+    public void serviceSelected(ServiceSearchDialog dialog, javax.swing.JMenuItem selectedServiceItem){
+	actionPerformed(new ActionEvent(selectedServiceItem, 1, selectedServiceItem.getActionCommand()));
+	removePopupOptions();
+    }
+
+    public void selectionCanceled(ServiceSearchDialog dialog){
+	removePopupOptions();  //cleanup stored data
+    }
+
     private synchronized int assignMenuDataIndex(JMenu submenu){
 	// Make the services array bigger, then copy over existing data, 
 	// leaving a blank at the end to be filled in by addServicesToSubMenu
@@ -1370,6 +1402,64 @@
 	}
     }
 
+    /**
+     * Removes the popup menu and replaces it with a window that has a filter widget
+     * over the list of services from the original popup.
+     */
+    protected void setupSearchData(JMenu objectMenu, MobyDataInstance mobyData){
+	// Setup the chooser dialog
+	ServiceSearchDialog searchDialog = new ServiceSearchDialog(null, 
+								   objectMenu.getText().replaceFirst("Services for", "Run "), 
+								   this);
+	addMenuOptionsToSearch(searchDialog, objectMenu);
+
+	searchDialog.initializeList();
+	searchDialog.pack();
+	searchDialog.setVisible(true);
+    }
+
+    private void addMenuOptionsToSearch(ServiceSearchDialog searchDialog, MenuElement menuElement){
+	if(menuElement instanceof JPopupMenu || menuElement instanceof JMenu){
+	    for(MenuElement subMenuElement: menuElement.getSubElements()){
+		addMenuOptionsToSearch(searchDialog, subMenuElement);
+	    }
+	}
+	else if(menuElement instanceof JMenuItem){ // leaf defining a service
+	    JMenuItem serviceItem = (JMenuItem) menuElement;
+	    String label = serviceItem.getText();
+	    if(label.equals(SEARCH_LABEL) || label.equals(CLIPBOARD_LABEL)){
+		return; // not real services
+	    }
+	    serviceItem.setText(label.replaceFirst("Run ", ""));
+	    searchDialog.addOption(serviceItem, false);
+	}
+	else{
+	    System.err.println("Got dead end with "+menuElement.getClass().getName());
+	}
+    }
+
+    public void addSearchItem(JMenu menu, int location){
+	if(menu == null){
+	    logger.warn("Cannot add service search option, menu reference passed in was null");
+	    return;
+	}
+
+	if(!submenu2msIndex.containsKey(menu)){
+	    logger.warn("Cannot add service search option, cannot find " +
+			"moby object list index for menu " + 
+			menu.getText());
+	    return;
+	}
+
+
+	int dataIndex = ((Integer) submenu2msIndex.get(menu)).intValue();
+	JMenuItem searchItem = new JMenuItem(SEARCH_LABEL);
+	searchItem.setActionCommand("MOBY:"+dataIndex+":"+SERVICESEARCH_CMD);
+	searchItem.addActionListener(this);
+	menu.add(searchItem, location);	
+	search2submenu.put(searchItem, menu);
+    }
+
     public void addClipboardItem(JMenu menu, MobyDataInstance mobyData){
 	if(menu == null){
 	    logger.warn("Cannot add clipboard option, menu reference passed in was null");
@@ -1408,11 +1498,11 @@
 	}
 	else{
 	    logger.warn("Clipboard option for objects other than MobyDataObject " +
-			       "and MobyDataObjectSet are not yet supported:"+mobyData);
+			"and MobyDataObjectSet are not yet supported:"+mobyData);
 	    return;
 	}
 
-	JMenuItem clipItem = new JMenuItem("Add to clipboard");
+	JMenuItem clipItem = new JMenuItem(CLIPBOARD_LABEL);
 	clipItem.setActionCommand("MOBY:"+dataIndex+":"+CLIPBOARD_CMD);
 	clipItem.addActionListener(this);
 	menu.add(clipItem);


From gordonp at dev.open-bio.org  Mon Apr 26 12:25:36 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Mon, 26 Apr 2010 12:25:36 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004261625.o3QGPasj025559@dev.open-bio.org>


gordonp
Mon Apr 26 12:25:36 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util
In directory dev.open-bio.org:/tmp/cvs-serv25523/src/main/ca/ucalgary/seahawk/util

Modified Files:
	DataUtils.java 
Log Message:
Ensured that moby namepsace is defined for xpath
moby-live/Java/src/main/ca/ucalgary/seahawk/util DataUtils.java,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataUtils.java,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataUtils.java	2010/04/16 17:33:26	1.6
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataUtils.java	2010/04/26 16:25:36	1.7
@@ -1044,7 +1044,7 @@
 	    // first arg is url#nameBasedXPath 
 	    peerGroupXPath = userData[0].split("#", 2)[1];
 	    contextNode = XPointerResolver.getNodeFromXPointer(doc, userData[1]);
-	    //System.err.println("Loaded context node " + userData[1] + " as " + contextNode);
+	    System.err.println("Loaded context node " + userData[1] + " as " + contextNode);
         }
         else{
 	    // Fallback is to get all nodes with the same name...
@@ -1082,13 +1082,16 @@
 	try{
 	    XPath xpath = xPathFactory.newXPath();
 	    if(contextNode != null){
-		xpath.setNamespaceContext(new NamespaceContextImpl(contextNode, "d"));
+		NamespaceContextImpl nsContext = new NamespaceContextImpl(contextNode, "d");
+		nsContext.setPrefix(MobyPrefixResolver.MOBY_XML_NAMESPACE, "d");
+		xpath.setNamespaceContext(nsContext);
 	    }
             peerElements = (NodeList) xpath.evaluate(peerGroupXPath, 
 						     doc, 
 						     XPathConstants.NODESET);
         } catch(Exception e){
             logger.log(Level.SEVERE, "Could not evaluate UserData XPath "+peerGroupXPath, e);
+	    return null;
         }
         //System.err.println("Got " + peerElements.getLength() + " peers for " + peerGroupXPath);
 


From gordonp at dev.open-bio.org  Mon Apr 26 12:26:18 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Mon, 26 Apr 2010 12:26:18 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004261626.o3QGQIZl025603@dev.open-bio.org>


gordonp
Mon Apr 26 12:26:18 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv25567/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	ServiceSearchDialog.java 
Log Message:
Case insensitive service name highlighting during search
moby-live/Java/src/main/ca/ucalgary/seahawk/gui ServiceSearchDialog.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/ServiceSearchDialog.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/ServiceSearchDialog.java	2010/04/24 17:23:27	1.1
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/ServiceSearchDialog.java	2010/04/26 16:26:18	1.2
@@ -127,6 +127,10 @@
 						Pattern.DOTALL | Pattern.CASE_INSENSITIVE | Pattern.MULTILINE);
 	activeChoices.clear();
 	for(JMenuItem serviceChoice: serviceChoices){
+	    if(serviceChoice.getText() == null){
+		continue;
+	    }
+	    
 	    String label = serviceChoice.getText().replaceAll("<.*?>", "").replaceAll("see description", "");
 	    // get rid of any coloring
 
@@ -134,12 +138,15 @@
 	    if(searchTerm == null || searchTerm.trim().length() == 0){
 		serviceChoice.setText(label);
 		activeChoices.addElement(serviceChoice);
+		continue;
 	    }
+	    Matcher matcher = searchPattern.matcher(label);
 	    // In the label?
-	    else if(serviceChoice.getText() != null &&
-		    searchPattern.matcher(label).find()){
-		label = label.replaceAll("("+searchTerm+")", "<font color='red'>$1</font>");
-		serviceChoice.setText("<html>"+label+"</html>");
+	    if(matcher.find()){
+		label = label.substring(0, matcher.start())+"<font color='red'>" +
+		    matcher.group(0) + "</font>" +
+		    (matcher.end() >= label.length() ? "" : label.substring(matcher.end()));
+		serviceChoice.setText("<html>" + label + "</html>");
 		activeChoices.addElement(serviceChoice);
 	    }
 	    // In the tooltip?


From gordonp at dev.open-bio.org  Mon Apr 26 12:27:31 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Mon, 26 Apr 2010 12:27:31 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004261627.o3QGRVV6025647@dev.open-bio.org>


gordonp
Mon Apr 26 12:27:31 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv25611/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	MobyServicesGUI.java 
Log Message:
Better UI refresh
moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyServicesGUI.java,1.23,1.24
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java,v
retrieving revision 1.23
retrieving revision 1.24
diff -u -r1.23 -r1.24
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java	2010/04/24 17:23:26	1.23
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java	2010/04/26 16:27:31	1.24
@@ -554,6 +554,7 @@
 	for(int i = 0; i < submenus.length; i++){
 	    addServicesToSubMenu(submenus[i], serviceAssocObjects[i], handler);
 	    addSearchItem(submenus[i], 1);
+	    refreshMenu(submenus[i]);
 	}
     }
 
@@ -755,6 +756,7 @@
 
 	addServicesToSubMenu(submenu, serviceAssocObject, handler);
         addSearchItem(submenu, 0);
+	refreshMenu(submenu);
     }
 
     protected synchronized void addServicesToSubMenu(JMenu submenu, MobyDataServiceAssocInstance msadi){
@@ -1121,7 +1123,9 @@
 	    }
 	    submenu.add(mobyItem);
 	}
+    }
 
+    protected void refreshMenu(JMenu submenu){
 	// Causes resizing based on new items
 	if(submenu.isPopupMenuVisible()){
 	    submenu.setPopupMenuVisible(false);


From gordonp at dev.open-bio.org  Mon Apr 26 12:28:11 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Mon, 26 Apr 2010 12:28:11 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004261628.o3QGSB9E025691@dev.open-bio.org>


gordonp
Mon Apr 26 12:28:11 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv25655/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	FilterSearchWidget.java 
Log Message:
Proper update of selected XPath when search restored
moby-live/Java/src/main/ca/ucalgary/seahawk/gui FilterSearchWidget.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/FilterSearchWidget.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/FilterSearchWidget.java	2010/04/10 00:40:17	1.3
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/FilterSearchWidget.java	2010/04/26 16:28:11	1.4
@@ -112,6 +112,7 @@
 
 	docPartOptions.setEnabled(true);
 	docPartOptions.setModel(new DefaultComboBoxModel(fs.getXPathOptions()));
+	docPartOptions.setSelectedItem(fs.getSelectedXPath());
 	currentFilterSearch = fs;  // done in this order so no feedback as DocumentEvents while setting fields programmatically
     }
 


From gordonp at dev.open-bio.org  Mon Apr 26 12:29:13 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Mon, 26 Apr 2010 12:29:13 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004261629.o3QGTD4M025779@dev.open-bio.org>


gordonp
Mon Apr 26 12:29:13 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv25739/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	MobyContentPane.java MobyPayloadCreator.java 
Log Message:
Account for possibility of null peer elements list
moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyContentPane.java,1.30,1.31 MobyPayloadCreator.java,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java,v
retrieving revision 1.30
retrieving revision 1.31
diff -u -r1.30 -r1.31
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java	2010/04/23 05:20:00	1.30
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java	2010/04/26 16:29:13	1.31
@@ -1237,7 +1237,7 @@
             // note that getPeerElements() will modify the userData to reflect the semantic of the requested peer mode
             mobyData.setUserData(origUserData);
             NodeList peerElements = DataUtils.getPeerElements(getCurrentDoc(), mobyData, getFilteredData(), peerMode);
-            if(peerElements.getLength() <= 1){
+            if(peerElements == null || peerElements.getLength() <= 1){
                 continue; // no 'for each' option if only one to process...
             }
             String each = "each <i>(" + peerElements.getLength() + " total)</i>";

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyPayloadCreator.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyPayloadCreator.java	2010/04/18 00:33:56	1.4
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyPayloadCreator.java	2010/04/26 16:29:13	1.5
@@ -85,8 +85,12 @@
 	NodeList peerElements = DataUtils.getPeerElements(doc, mobyDataContext, 
 							  xptrsToFilter, DataUtils.DATATYPE_PEERS_MODE);
 
-        // find the peers of defined by the userData selection constraints and put them into a MobyContentInstance
 	MobyContentInstance payload = new MobyContentInstance();
+	if(peerElements == null){
+	    return payload;
+	}
+
+        // find the peers of defined by the userData selection constraints and put them into a MobyContentInstance
         Map<String,Integer> jobPrefixes = new LinkedHashMap<String,Integer>();
 
 	logger.log(Level.FINE, "Loading MobyContentInstance with "+peerElements.getLength()+" elements for xpath "+selectionXPath);


From gordonp at dev.open-bio.org  Mon Apr 26 13:50:34 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Mon, 26 Apr 2010 13:50:34 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004261750.o3QHoXg0029187@dev.open-bio.org>


gordonp
Mon Apr 26 13:50:33 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv29151/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	FilterSearchWidget.java 
Log Message:
Kung foo with semaphores to let search filter only apply every 600ms or so when typing a longer string
moby-live/Java/src/main/ca/ucalgary/seahawk/gui FilterSearchWidget.java,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/FilterSearchWidget.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/FilterSearchWidget.java	2010/04/26 16:28:11	1.4
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/FilterSearchWidget.java	2010/04/26 17:50:33	1.5
@@ -5,6 +5,7 @@
 import java.awt.Dimension;
 import java.awt.event.*;
 import java.net.URL;
+import java.util.concurrent.*;
 import java.util.logging.*;
 import javax.swing.*;
 import javax.swing.event.*; 
@@ -22,6 +23,8 @@
     private JTextField searchField;
     private JComboBox docPartOptions;
     private MobyContentPane contentPane;
+    private Semaphore semaphore; // for search update delays in multikeystroke
+
     public static final String CASE_SENSITIVE_ICON_RESOURCE = "ca/ucalgary/seahawk/resources/images/case_sensitive.png";
     public static final String CASE_INSENSITIVE_ICON_RESOURCE = "ca/ucalgary/seahawk/resources/images/case_insensitive.png";
     private static final String IF_TEXT = "<html><u>if</u></html>";
@@ -48,6 +51,8 @@
 	closeIcon.addMouseListener(new Closer(this));
 	closeIcon.setToolTipText("Remove filter criteria");
 
+	semaphore = new Semaphore(1);  //1 search update for a given timeframe
+
 	Dimension buttonSize = new Dimension(24,24);
 	caseButton = new JToggleButton(new ImageIcon(cl.getResource(CASE_SENSITIVE_ICON_RESOURCE)));
 	caseButton.setDisabledIcon(new ImageIcon(cl.getResource(CASE_INSENSITIVE_ICON_RESOURCE)));
@@ -162,8 +167,10 @@
 	    return;
 	}
 	StringBuffer sb = currentFilterSearch.getFilterRegex();
-	sb.replace(0, sb.length(), searchField.getText());
-	contentPane.applyFilter(true);
+	synchronized(searchField){
+	    sb.replace(0, sb.length(), searchField.getText());
+	}
+	applyFilterWhenSuitable();
     }
 
     public void insertUpdate(DocumentEvent e){
@@ -171,8 +178,10 @@
 	    return;
 	}
 	StringBuffer sb = currentFilterSearch.getFilterRegex();
-	sb.replace(0, sb.length(), searchField.getText());
-	contentPane.applyFilter(true);
+	synchronized(searchField){
+	    sb.replace(0, sb.length(), searchField.getText());
+	}
+	applyFilterWhenSuitable();
     }
 
     public void removeUpdate(DocumentEvent e){
@@ -180,10 +189,53 @@
 	    return;
 	}
 	StringBuffer sb = currentFilterSearch.getFilterRegex();
-	sb.replace(0, sb.length(), searchField.getText());
-	contentPane.applyFilter(true);
+	synchronized(searchField){
+	    sb.replace(0, sb.length(), searchField.getText());
+	}
+	applyFilterWhenSuitable();
     }
 
+    // Waits 600 milliseconds to see if the user is typing a phrase, rather than 
+    // filtering for each letter added, which can be slow
+    private void applyFilterWhenSuitable(){
+	try{
+	    final Semaphore sem = semaphore;
+	    final MobyContentPane pane = contentPane;
+	    final JTextField sf = searchField;
+	    if(sem.tryAcquire()){
+		new Thread(){
+		    public void run(){
+			try{
+			    Thread.sleep(500);
+			}
+			catch(Exception e){
+			    logger.log(Level.WARNING, 
+				       "Delay less than 400ms on search input due to interrupt", 
+				       e);
+			}
+			synchronized(sf){
+			    try{
+				// Give 100ms for other threads past sb.replace() in DocumentListener callbacks to 
+				// try to acquire a permit, avoiding redundant applyFiolter call
+				Thread.sleep(100);
+			    }
+			    catch(Exception e){
+				logger.log(Level.WARNING, 
+					   "Delay less than 100ms on search input due to interrupt", 
+					   e);
+			    }
+			    pane.applyFilter(true);	
+			    sem.release();
+			}
+		    }
+		}.start();
+	    }
+	}catch(Exception e){
+	    logger.log(Level.SEVERE, "Search result updater was interrupted while waiting for a semaphore," +
+		                     "GUI may not reflect search field", e);
+	}
+	// else, it's going to be updated soon anyway with the latest string buffer...just return
+    }
 
     class Closer extends MouseAdapter{
 	boolean active = false;


From gordonp at dev.open-bio.org  Fri Apr  9 02:23:15 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Thu, 8 Apr 2010 22:23:15 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004090223.o392NFDP006711@dev.open-bio.org>


gordonp
Thu Apr  8 22:23:15 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources/images
In directory dev.open-bio.org:/tmp/cvs-serv6679/src/main/ca/ucalgary/seahawk/resources/images

Added Files:
	case_insensitive.png case_sensitive.png 
Log Message:
Icon for search filter's case sensitivity
moby-live/Java/src/main/ca/ucalgary/seahawk/resources/images case_insensitive.png,NONE,1.1 case_sensitive.png,NONE,1.1


From gordonp at dev.open-bio.org  Fri Apr  9 15:47:04 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 9 Apr 2010 11:47:04 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004091547.o39Fl4m3001186@dev.open-bio.org>


gordonp
Fri Apr  9 11:47:03 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources
In directory dev.open-bio.org:/tmp/cvs-serv1154/src/main/ca/ucalgary/seahawk/resources

Added Files:
	PassFilterBeanShell FlattenListBeanShell 
Log Message:
Taverna beanshells used in Seahawk's programming-by-example system
moby-live/Java/src/main/ca/ucalgary/seahawk/resources PassFilterBeanShell,NONE,1.1 FlattenListBeanShell,NONE,1.1


From gordonp at dev.open-bio.org  Fri Apr  9 15:48:19 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 9 Apr 2010 11:48:19 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004091548.o39FmJJf001286@dev.open-bio.org>


gordonp
Fri Apr  9 11:48:19 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util
In directory dev.open-bio.org:/tmp/cvs-serv1250/src/main/ca/ucalgary/seahawk/util

Modified Files:
	FilterSearch.java 
Log Message:
Added case sensitivity, constant for select-all xpath
moby-live/Java/src/main/ca/ucalgary/seahawk/util FilterSearch.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/FilterSearch.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/FilterSearch.java	2010/03/29 19:49:52	1.2
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/FilterSearch.java	2010/04/09 15:48:19	1.3
@@ -20,9 +20,11 @@
 public class FilterSearch{
 
     private URL docURL;
+    private boolean caseSensitivity = false;
     private StringBuffer filterRegex;
     private Vector<XPathOption> xpathOptions;
     private int xpathSelected = 0;
+    public static final String SELECT_ALL_XPATH = "//* | //*/@*";
 
     /**
      * @param docToFilter the document that will be used to determine what XPaths can be suggested
@@ -34,7 +36,7 @@
 	docURL = docToFilter;
 	filterRegex = new StringBuffer();
 	xpathOptions = new Vector<XPathOption>();
-	xpathOptions.add(new XPathOption("//*", "entire document"));
+	xpathOptions.add(new XPathOption(SELECT_ALL_XPATH, "entire response"));
 	Document domDoc = docBuilder.parse(docURL.openStream());
 	// Get the moby jobs
 	NodeList jobs = domDoc.getDocumentElement().getElementsByTagNameNS(MobyPrefixResolver.MOBY_XML_NAMESPACE, MobyTags.MOBYDATA);
@@ -72,6 +74,14 @@
 	}
     }
 
+    public boolean getCaseSensitivity(){
+	return caseSensitivity;
+    }
+
+    public void setCaseSensitivity(boolean sensitivity){
+	caseSensitivity = sensitivity;
+    }
+
     public void setSelectedXPath(int cursor){
 	xpathSelected = cursor;
     }



From gordonp at dev.open-bio.org  Fri Apr  9 15:49:18 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 9 Apr 2010 11:49:18 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004091549.o39FnI8b001330@dev.open-bio.org>


gordonp
Fri Apr  9 11:49:18 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources
In directory dev.open-bio.org:/tmp/cvs-serv1294/src/main/ca/ucalgary/seahawk/resources

Modified Files:
	RegexFilterBeanShell 
Log Message:
Added case sensitivity, eliminated auto-attr matching since select-all xpath has been fixed
moby-live/Java/src/main/ca/ucalgary/seahawk/resources RegexFilterBeanShell,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources/RegexFilterBeanShell,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources/RegexFilterBeanShell	2010/03/17 20:03:06	1.1
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources/RegexFilterBeanShell	2010/04/09 15:49:18	1.2
@@ -1,4 +1,5 @@
 import java.util.*;
+import java.util.regex.Pattern;
 import org.dom4j.*;
 import org.dom4j.io.SAXReader;
 
@@ -13,24 +14,18 @@
 int i = 1;
 Map collections = new LinkedHashMap();
 Map collectionsEnd = new HashMap();
-select: for (Iterator iter = nodelist.iterator(); iter.hasNext();) {
+Pattern pattern = Pattern.compile(regex, Pattern.MULTILINE | Pattern.DOTALL | (Boolean.parseBoolean(case_sensitive) ? 0 : Pattern.CASE_INSENSITIVE));
+for (Iterator iter = nodelist.iterator(); iter.hasNext();) {
         Node node = (Node) iter.next();
         boolean match = false;
         switch(node.getNodeType()){
                 case Node.ELEMENT_NODE:
-                        if(node.getText().matches(".*?"+regex+".*")){
+                        if(pattern.matcher(node.getText()).find()){
                                 match = true;
                         }
-                        else{
-                                for(Object attr: ((Element) node).attributeIterator()){
-                                        if(((Attribute) attr).getValue().matches(".*?"+regex+".*")){
-                                                match = true; break;
-                                        }
-                                }
-                        }
                         break;
                 case Node.ATTRIBUTE_NODE:
-                        if(node.getValue().matches(".*?"+regex+".*")){
+                        if(pattern.matcher(node.getValue()).find()){
                                 match = true;
                         }
                         break;



From gordonp at dev.open-bio.org  Fri Apr  9 15:50:09 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 9 Apr 2010 11:50:09 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004091550.o39Fo903001396@dev.open-bio.org>


gordonp
Fri Apr  9 11:50:09 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv1360/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	FilterSearchWidget.java 
Log Message:
Added case sensitivity
moby-live/Java/src/main/ca/ucalgary/seahawk/gui FilterSearchWidget.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/FilterSearchWidget.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/FilterSearchWidget.java	2010/03/17 20:20:47	1.1
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/FilterSearchWidget.java	2010/04/09 15:50:09	1.2
@@ -17,9 +17,13 @@
 
     private FilterSearch currentFilterSearch;
     private JLabel closeIcon;
+    private JToggleButton caseButton;
     private JTextField searchField;
     private JComboBox docPartOptions;
     private MobyContentPane contentPane;
+    public static final String CASE_SENSITIVE_ICON_RESOURCE = "ca/ucalgary/seahawk/resources/images/case_sensitive.png";
+    public static final String CASE_INSENSITIVE_ICON_RESOURCE = "ca/ucalgary/seahawk/resources/images/case_insensitive.png";
+    private static final String CASE_BUTTON_NAME = "case_sensitivity_button"; 
 
     private static Logger logger = Logger.getLogger(FilterSearchWidget.class.getName());
 
@@ -27,7 +31,8 @@
 	super();
 
 	contentPane = mcp;
-	URL u = Thread.currentThread().getContextClassLoader().getResource(CloseTabIcon.CLOSE_TAB_ICON_RESOURCE);
+	ClassLoader cl = Thread.currentThread().getContextClassLoader();
+	URL u = cl.getResource(CloseTabIcon.CLOSE_TAB_ICON_RESOURCE);
 	if(u == null){
 	    throw new Exception("Could not find icon resource " + CloseTabIcon.CLOSE_TAB_ICON_RESOURCE);
 	}
@@ -37,9 +42,22 @@
 	closeIcon.addMouseListener(new Closer(this));
 	closeIcon.setToolTipText("Remove filter criteria");
 
+	Dimension buttonSize = new Dimension(24,24);
+	caseButton = new JToggleButton(new ImageIcon(cl.getResource(CASE_SENSITIVE_ICON_RESOURCE)));
+	caseButton.setDisabledIcon(new ImageIcon(cl.getResource(CASE_INSENSITIVE_ICON_RESOURCE)));
+	caseButton.setToolTipText("Toggles the case sensitivity of the filter");
+	caseButton.setPreferredSize(buttonSize);
+	caseButton.setEnabled(true);
+	caseButton.setSelected(false);
+	caseButton.addActionListener(this);
+	caseButton.setMargin(new java.awt.Insets(2,2,2,2));
+        caseButton.setName(CASE_BUTTON_NAME); // so test cases can find the component
+
 	setLayout(new BoxLayout(this, BoxLayout.LINE_AXIS));
 	add(closeIcon);
 	add(Box.createRigidArea(new Dimension(5,0)));
+	add(caseButton);
+	add(Box.createRigidArea(new Dimension(5,0)));
 	add(new JLabel("Show data if "));
 	add(Box.createRigidArea(new Dimension(5,0)));
 	searchField = new JTextField(25);
@@ -62,11 +80,15 @@
     public void setFilter(FilterSearch fs){
 	currentFilterSearch = null;
 	if(fs == null){
+	    caseButton.setEnabled(false);
 	    searchField.setEnabled(false);
 	    docPartOptions.setEnabled(false);
 	    return;
 	}
 
+	caseButton.setEnabled(true);
+	caseButton.setSelected(fs.getCaseSensitivity());
+
 	searchField.setEnabled(true);
 	searchField.setText(fs.getFilterRegex().toString());
 
@@ -79,7 +101,15 @@
      * Called when the user has changed the xpath
      */
     public void actionPerformed(ActionEvent e){
-	if(currentFilterSearch == null || e.getSource() != docPartOptions){
+	if(e.getSource() == caseButton){
+	    if(currentFilterSearch == null){
+	        return;
+            }
+            currentFilterSearch.setCaseSensitivity(caseButton.isSelected());
+	    contentPane.applyFilter(true);
+	    return;
+        }
+	else if(currentFilterSearch == null || e.getSource() != docPartOptions){
 	    return;
 	}
 	currentFilterSearch.setSelectedXPath(docPartOptions.getSelectedIndex());



From gordonp at dev.open-bio.org  Fri Apr  9 15:51:53 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 9 Apr 2010 11:51:53 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004091551.o39FprFb001496@dev.open-bio.org>


gordonp
Fri Apr  9 11:51:53 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv1460/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	MobyContentClipboard.java 
Log Message:
data xml src passthrough to enable 'previous input' services
moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyContentClipboard.java,1.8,1.9
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentClipboard.java,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentClipboard.java	2010/03/29 19:47:02	1.8
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentClipboard.java	2010/04/09 15:51:53	1.9
@@ -113,8 +113,8 @@
 	return false;
     }
 
-    protected void addExtraMobyOptions(JPopupMenu popup, MobyDataInstance mdi){
-	super.addExtraMobyOptions(popup, mdi);
+    protected void addExtraMobyOptions(JPopupMenu popup, MobyDataInstance mdi, URL srcURL){
+	super.addExtraMobyOptions(popup, mdi, srcURL);
 
 	// Only process if the passed in data is one of the top level collection elements
 	// (i.e. don't delete subparts of object)



From gordonp at dev.open-bio.org  Fri Apr  9 15:54:17 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 9 Apr 2010 11:54:17 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004091554.o39FsHP8001666@dev.open-bio.org>


gordonp
Fri Apr  9 11:54:16 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv1630/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	MobyContentPane.java 
Log Message:
Fixes to highlighting, added case sensitive search, added 'previous input' service options (equivalent to an if condition in PbE)
moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyContentPane.java,1.23,1.24
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java,v
retrieving revision 1.23
retrieving revision 1.24
diff -u -r1.23 -r1.24
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java	2010/03/29 19:54:36	1.23
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java	2010/04/09 15:54:16	1.24
@@ -107,6 +107,7 @@
     private Document currentDoc; //the doc DOM being actively filtered
     private NodeList currentSelectedData = null;
     private String currentSelectionXPath = null;
+    private Map<String,Boolean> jobXPtrs = null;  // Map<xptr,has a HAS member>
     private List<String> filterableNodes = null;  // List<xptr>
     private List<AttributeSet> origStyles = null;
     private boolean firstDocRendering = true;
@@ -442,9 +443,6 @@
 	    srv.addServlet(servletPath, servlet); // our deployment
 	}
 	else if(contentGUI.getServletContainer().getServlet(servletPath) == null){
-	    PBERecorder recorder = new PBERecorder();
-	    recorder.setGUIMap(id2GuiMap);
-	    servlet.setRecorder(recorder);
 	    contentGUI.getServletContainer().addServlet(servletPath, servlet); 
 	}
 
@@ -742,6 +740,7 @@
 	    currentDoc = null;  // get rid of previous in-memory doc use for interactive filtering, if any
 	    currentSelectedData = null;
 	    currentSelectionXPath = null;
+	    jobXPtrs = null;
 	    filterableNodes = null;
 	    origStyles = null;
 	    firstDocRendering = true;
@@ -774,6 +773,13 @@
 	return history.elementAt(historyIndex);
     }
 
+    protected URL getPreviousURL(){
+	if(historyIndex < 1 || historyIndex > history.size()){
+	    return null;
+	}
+	return history.elementAt(historyIndex-1);
+    }
+
     public boolean canFilter(){
 	return hasXMLSource();
     }
@@ -809,6 +815,7 @@
 		xPtrsReferencedInNextService = DataUtils.getInputXPtrs(history.elementAt(historyIndex+1), history.elementAt(historyIndex));
 	    } catch(Exception e){
 		logger.error("Cannot get the provenance data from "+history.elementAt(historyIndex+1), e);
+                return false;
 	    }
 	    
 	}
@@ -1187,7 +1194,8 @@
 	    return DataUtils.loadMobyDataFromXPointer(targetURL, filterHistory.get(getCurrentURL()));
 	}
 
-	// Simple case, build the object using the values encoded in the URL itself
+	// Simple case, build the object using the values encoded in the URL itself.
+	// Currently this is not used because it messes up provenance tracking for PbE
 	else{
 	    return loadMobyDataFromURLQuery(targetURL);
 	}
@@ -1204,7 +1212,7 @@
 
 	JPopupMenu popup = new DynamicJPopupMenu();
 	popup.setName(MOBY_SERVICE_POPUP_NAME);
-	addExtraMobyOptions(popup, mobyData);
+	addExtraMobyOptions(popup, mobyData, targetURL);
 	JMenuItem checkingLinksPopupItem = new JMenuItem("Check for services...");
 	popup.add(checkingLinksPopupItem);
 	popup.show(this, lastClickX+editorPane.getX(), lastClickY+editorPane.getY());
@@ -1223,7 +1231,7 @@
     /**
      * Subclasses can use this method to expand the popup menu.  Be sure to call super.addExtraMobyOptions()
      */
-    protected void addExtraMobyOptions(JPopupMenu popup, MobyDataInstance mdi){
+    protected void addExtraMobyOptions(JPopupMenu popup, MobyDataInstance mdi, URL srcURL){
 	// If we are wrapping a service, and you're getting the context menu, you must be 
 	// looking at service results, in which case let's give the option to create a service.
 	if(isWrapping){
@@ -1231,7 +1239,34 @@
 	    popup.add(createServicePopupItem);
 	    popup.setVisible(true);	    
 	}
+	// todo: 
+	// The item below is mainly to allow X to be used in service Y if running service Z on X meets some filter criteria.
+	// This is a common task in bioinformatics workflows.
+	// Backtrack from data to input used for service that generated the data.
+
+	// Here's an important point: if there is no filter on the current doc, we shouldn't be offering
+	// a "previous input" option, because the current doc's service contributed nothing to deciding 
+	// on how to proceed (no "if" conditon).
+	if(getFilter() == null){
+	    return;
+	}
+
+	//System.err.println("Should create a previous input menu item for " + mdi.getUserData());
+	try{
+	    Document srcDoc = docBuilder.parse(srcURL.openStream());
 
+	    // Get the input data for the *previous* service
+	    MobyDataJob inputData = DataUtils.getInputSample(srcDoc, SeahawkOptions.getRegistry());
+	    for(MobyDataInstance previousMDI: inputData.getPrimaryData()){		
+		// add conditional of the current service as a criteria in user data for each previousMDI, 
+		// so PbE will properly reflect the logic of if(f1(x) matches filter){f2(x)}
+		DataUtils.addUserData(previousMDI, srcURL, getFilter());
+
+		servicesGUI.addPopupOptions(previousMDI, popup, true, null, "previous input");
+	    }
+	} catch(Exception e){
+	    logger.warn("Could not load previous service info, 'previous input' option will not be displayed", e);
+	}
     }
 
     /**
@@ -1372,11 +1407,13 @@
 	}
 	// Filter out any moby jobs, parameters, collection members or HAS members that aren't in the matchingNodes
 	if(filterableNodes == null){
+	    jobXPtrs = new HashMap<String,Boolean>();
 	    filterableNodes = new Vector<String>();
 	    NodeList nodes = currentDoc.getElementsByTagNameNS(MobyTags.MOBY_XML_NS, MobyTags.MOBYDATA);
 	    for(int i = 0; i < nodes.getLength(); i++){
-		filterableNodes.add(getXPtr(nodes.item(i)));
-		addHASXPtrs(filterableNodes, (Element) nodes.item(i));
+		String jobXPtr = getXPtr(nodes.item(i));		
+		filterableNodes.add(jobXPtr);
+		jobXPtrs.put(jobXPtr, addHASXPtrs(filterableNodes, (Element) nodes.item(i)));
 	    }
 		
 	    // Collections
@@ -1429,26 +1466,43 @@
 	// Find just the data subset also matching the regex
 	Map<String,Boolean> matchingXPtrs = new LinkedHashMap<String,Boolean>();
 	// Build the FSA only once, for efficiency
-	Pattern regex = Pattern.compile(fs.getFilterRegex().toString(), Pattern.MULTILINE);
+	Pattern regex = Pattern.compile(fs.getFilterRegex().toString(), 
+                                        Pattern.MULTILINE | Pattern.DOTALL | 
+                                         (fs.getCaseSensitivity() ? 0 : Pattern.CASE_INSENSITIVE));
 	for(int i = 0; i < currentSelectedData.getLength(); i++){
 	    Node node = currentSelectedData.item(i);	    
 	    if(node instanceof Element){
-		if(regex.matcher(((Element) node).getTextContent()).find()){
-		    matchingXPtrs.put(getXPtr(node), Boolean.TRUE);
+		String elementXPtr = getXPtr(node);
+		if(matchingXPtrs.containsKey(elementXPtr) &&
+		   matchingXPtrs.get(elementXPtr).booleanValue()){
+		    	continue;  // already true, no 
+                    }
+		else if(regex.matcher(((Element) node).getTextContent()).find()){
+		    matchingXPtrs.put(elementXPtr, Boolean.TRUE);
+		    System.err.println("Adding " + elementXPtr + " as " + matchingXPtrs.get(elementXPtr));
 		}
 		else{
-		    matchingXPtrs.put(getXPtr(node), Boolean.FALSE);
+		    matchingXPtrs.put(elementXPtr, Boolean.FALSE);
+		    System.err.println("Adding " + elementXPtr + " as " + matchingXPtrs.get(elementXPtr));
 		}
-		//System.err.println("Adding " + getXPtr(node) + " as " + matchingXPtrs.get(getXPtr(node)));
 	    }
 	    else if(node instanceof Attr){
-		if(regex.matcher(((Attr) node).getValue()).find()){
+		String attrParentXPtr = getXPtr(((Attr) node).getOwnerElement());
+		if(matchingXPtrs.containsKey(attrParentXPtr) &&
+	 	   matchingXPtrs.get(attrParentXPtr).booleanValue()){
+		    continue;
+                }
+		else if(regex.matcher(((Attr) node).getValue()).find()){
 		    // Mark the element to which the attribute belongs
-		    matchingXPtrs.put(getXPtr(((Attr) node).getOwnerElement()), Boolean.TRUE);
+		    matchingXPtrs.put(attrParentXPtr, Boolean.TRUE);
+		    System.err.println("Adding " + attrParentXPtr + " attr parent as " + matchingXPtrs.get(attrParentXPtr));
 		}
-		else{
-		    matchingXPtrs.put(getXPtr(((Attr) node).getOwnerElement()), Boolean.FALSE);
+		// so false doesn't override true for multi-attr elements
+		else if(!matchingXPtrs.containsKey(attrParentXPtr)){ 
+		    matchingXPtrs.put(attrParentXPtr, Boolean.FALSE);
+		    System.err.println("Adding " + attrParentXPtr + " attr parent as " + matchingXPtrs.get(attrParentXPtr));
 		}
+		
 	    }
 	    else{
 		logger.warn("Found filter xpath result item that was not an Element or Attribute as expected ("+
@@ -1462,7 +1516,7 @@
 		if(matchingXPtr.getKey().startsWith(currXPtr+"/")){ // a parent of the matching data
 		    // No positive example yet?
 		    if(!parentMatchingXPtrs.containsKey(currXPtr) || !parentMatchingXPtrs.get(currXPtr).booleanValue()){
-			//System.err.println("Adding "+ matchingXPtr.getValue() + " for " + currXPtr);
+			System.err.println("Adding "+ matchingXPtr.getValue() + " for " + currXPtr);
 			parentMatchingXPtrs.put(currXPtr, matchingXPtr.getValue());
 		    }
 		}
@@ -1472,7 +1526,9 @@
 	matchingXPtrs.putAll(parentMatchingXPtrs);
 	for(String currXPtr: matchingXPtrs.keySet()){
 	    // Is part of the selection criteria, but doesn't match the regex
-	    if(!matchingXPtrs.get(currXPtr).booleanValue()){
+	    if(!matchingXPtrs.get(currXPtr).booleanValue() &&
+	       // special condition: if "entire document" xpath is given, filter only at the job level
+	       (!currentSelectionXPath.equals(FilterSearch.SELECT_ALL_XPATH) || jobXPtrs.containsKey(currXPtr))){
 		filteredData.put(currXPtr, "todo");
 	    }
 	}
@@ -1484,7 +1540,7 @@
     }
 
     // If any moby object member is in a HAS relationship, add it to the list of filterable items
-    private void addHASXPtrs(List<String> filterList, Element object){
+    private Boolean addHASXPtrs(List<String> filterList, Element object){
 	String tagName = object.getLocalName();
 	boolean isContainer = false;
 	MobyDataType mobyDataType = null;	
@@ -1496,10 +1552,11 @@
 	    mobyDataType = MobyDataType.getDataType(tagName, SeahawkOptions.getRegistry());
 	    if(mobyDataType == null){
 		logger.warn("Found datatype unknown to the registry ("+object.getLocalName()+")");
-		return;
+		return Boolean.FALSE;
 	    }
 	}
 
+	Boolean hasHAS = Boolean.FALSE; // does the object have a member with a HAS relationship?
 	NodeList members = object.getChildNodes();
 	for(int i = 0; i < members.getLength(); i++){
 	    if(!(members.item(i) instanceof Element)){
@@ -1516,9 +1573,13 @@
 		//		   " is " + (membership == null ? null : membership.getRelationshipType()));
 		if(membership != null && membership.getRelationshipType() == Central.iHAS){
 		    filterList.add(getXPtr(member));
+		    if(!hasHAS){
+			hasHAS = Boolean.TRUE;
+		    }
 		}
 	    }
 	}
+	return hasHAS;
     }
 
     // Recursively ascend the DOM tree and find out our place in its branching structure
@@ -1527,6 +1588,9 @@
 	    return "";
 	}
 	Node parent = n.getParentNode();
+        if(parent == null && n instanceof Attr){
+	    parent = ((Attr) n).getOwnerElement();
+	}
 
 	NodeList children = parent.getChildNodes();
 	int nonElementCnt = 0;
@@ -1624,19 +1688,27 @@
 	int matchCount = 0;
 	if(fs != null && fs.getFilterRegex().length() > 0){
 	    try{
+                Map<String,Boolean> highlights = new HashMap<String,Boolean>();
 		javax.swing.text.LayeredHighlighter.LayerPainter painter = 
 		    new DefaultHighlighter.DefaultHighlightPainter(Color.yellow);
-		Pattern p = Pattern.compile(fs.getFilterRegex().toString(), Pattern.MULTILINE);
+		Pattern p = Pattern.compile(fs.getFilterRegex().toString(), 
+				            Pattern.MULTILINE | Pattern.DOTALL | 
+                                             (fs.getCaseSensitivity() ? 0 : Pattern.CASE_INSENSITIVE));
 		for(String filterable: filterableNodes){
 		    javax.swing.text.Element el = d.getElement(filterable);
 		    String fragment = d.getText(el.getStartOffset(),
 						el.getEndOffset() - el.getStartOffset());
 		    Matcher matcher = p.matcher(fragment);
 		    while (matcher.find()) {
-			h.addHighlight(el.getStartOffset() + matcher.start(),
-				       el.getStartOffset() + matcher.end(),
-				       painter);
-			matchCount++;
+			// Only count match if not already highlighted in a containing filterable node
+			// todo: in future, avoid looking in text bits already checked, for efficiency
+			int hstart = el.getStartOffset() + matcher.start();
+                        int hend = el.getStartOffset() + matcher.end();
+			if(!highlights.containsKey(""+hstart+","+hend)){
+			    h.addHighlight(hstart, hend, painter);
+			    matchCount++;
+			    highlights.put(""+hstart+","+hend, Boolean.TRUE);
+                        }	
 		    }
 		}
 	    } catch(Exception e){
@@ -1687,6 +1759,7 @@
 	    searchPanel.add(filterSearchWidget);
 	    searchPanel.revalidate();
 	    revalidate(); // redo the panel layout
+	    applyFilter(true);
 	}
 	else{
 	    // have a backup, so if re-enabled the old search is restored
@@ -1768,6 +1841,11 @@
 		    }
 		}
 	    }
+	    // todo: If the selection was over the Moby XML display, harvest the set of data and show options for those
+	    // from experience, users try to highlight the whole data and send forward to the next service rather than
+	    // just picking an example value.
+
+	    // If display was not moby data links, but rather just text of some sort, do data recognition over it.
 	    MobyDataInstance[] mobyData = loadMobyDataFromString(selectedTextData);
 	    if(mobyData == null || mobyData.length == 0){
 		logger.warn("No MobyData could be made from the selected text");



From gordonp at dev.open-bio.org  Fri Apr  9 15:55:49 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 9 Apr 2010 11:55:49 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004091555.o39FtnLh001766@dev.open-bio.org>


gordonp
Fri Apr  9 11:55:48 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv1730/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	MobyServicesGUI.java 
Log Message:
Added ability to customize top level menu items with extra text (used initially by 'previous input' feature)
moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyServicesGUI.java,1.16,1.17
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java,v
retrieving revision 1.16
retrieving revision 1.17
diff -u -r1.16 -r1.17
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java	2009/06/09 19:27:56	1.16
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java	2010/04/09 15:55:48	1.17
@@ -442,7 +442,7 @@
 	    // Create the top level menu items for these moby objects right away
 	    submenus = new JMenu[mobyObjects.length];
 	    for(int i = 0; i < mobyObjects.length; i++){
-		JMenu submenu = createObjectSubMenu(mobyObjects[i]);
+		JMenu submenu = createObjectSubMenu(mobyObjects[i], null);
 		if(submenu == null){
 		    continue;
 		}
@@ -503,6 +503,7 @@
 	Node targetNode = null;
 	MobyRequestEventHandler handler = null;
 	MobyDataInstance mobyData = null;
+	String extraMenuText = null;
 	JPopupMenu popupList;
 
 	public OptionLoaderThread(Node targetNode, JPopupMenu popupList, MobyRequestEventHandler handler){
@@ -512,11 +513,12 @@
 	    this.handler = handler;
 	}
 
-	public OptionLoaderThread(MobyDataInstance mobyData, JPopupMenu popupList, MobyRequestEventHandler handler){
+	public OptionLoaderThread(MobyDataInstance mobyData, JPopupMenu popupList, MobyRequestEventHandler handler, String extraMenuText){
 	    super();
 	    this.mobyData = mobyData;
 	    this.popupList = popupList;
 	    this.handler = handler;
+	    this.extraMenuText = extraMenuText;
 	}
 
 	public void run(){
@@ -524,7 +526,7 @@
 		addPopupOptions(targetNode, popupList, false, handler);
 	    }
 	    else if(mobyData != null){
-		addPopupOptions(mobyData, popupList, false, handler);
+		addPopupOptions(mobyData, popupList, false, handler, extraMenuText);
 	    }
 	    else{
 		logger.warn("Warning: OptionLoaderThread has no data to work with");
@@ -584,6 +586,13 @@
      * Find the list of available services querying MobyCentral directly with a piece of data.
      */
     public void addPopupOptions(MobyDataInstance mobyData, JPopupMenu popupList, boolean asynchronous, MobyRequestEventHandler handler){
+	addPopupOptions(mobyData, popupList, asynchronous, handler, null);
+    }
+
+    /**
+     * Find the list of available services querying MobyCentral directly with a piece of data.
+     */
+    public void addPopupOptions(MobyDataInstance mobyData, JPopupMenu popupList, boolean asynchronous, MobyRequestEventHandler handler, String extraMenuText){
 
 	if(asynchronous){
 	    //Show the user that we're doing something...
@@ -596,13 +605,13 @@
 	    }
 
 	    // Call this method synchronously in a different thread
-	    OptionLoaderThread lt = new OptionLoaderThread(mobyData, popupList, handler);
+	    OptionLoaderThread lt = new OptionLoaderThread(mobyData, popupList, handler, extraMenuText);
 	    lt.start();
 	    return;
 	}
 
 	// Create submenu for this object
-	JMenu submenu = createObjectSubMenu(mobyData);
+	JMenu submenu = createObjectSubMenu(mobyData, extraMenuText);
 	// Add option to copy object to clipboard.  We don't need to wait until services are found.
 	if(submenu == null){
 	    return;
@@ -1127,7 +1136,7 @@
 	return menu;
     }
 
-    public JMenu createObjectSubMenu(MobyDataInstance mdi){
+    public JMenu createObjectSubMenu(MobyDataInstance mdi, String extraMenuText){
 	if(!(mdi instanceof MobyPrimaryData)){
 	    logger.warn("Ignoring non-primary data object submitted to menu creation: " + mdi);
 	    return null;
@@ -1205,7 +1214,7 @@
 		}
 	    }
 	    desc = "Record Identifier - " + mobydesc;
-	    submenu = new JMenu("Services for " + datatype + ":" + id);
+	    submenu = new JMenu("Services for " + (extraMenuText == null ? "" : extraMenuText+" ")+datatype + ":" + id);
 	    assignMenuDataIndex(submenu);
 	}
 	else if("String".equals(mobyDataType.getName())){
@@ -1217,7 +1226,8 @@
 		sample = sample.substring(0, MAX_ID_LEN)+"...";
 	    }
 	    desc = "A piece of text";
-	    submenu = new JMenu("Services for String \"" + sample + "\"");
+	    submenu = new JMenu("Services for "+(extraMenuText == null ? "" : extraMenuText+" ")+
+				"String \"" + sample + "\"");
 	    assignMenuDataIndex(submenu);
 	}
 	// Complex object
@@ -1236,7 +1246,7 @@
 	    else if(targetData instanceof MobyDataObjectSet){
 		objectLabel += " collection";
 	    }
-	    submenu = new JMenu("Services for " + objectLabel);
+	    submenu = new JMenu("Services for " + (extraMenuText == null ? "" : extraMenuText+" ")+objectLabel);
 	    assignMenuDataIndex(submenu);
 	}
 	desc = "Input data: " + desc;



From gordonp at dev.open-bio.org  Fri Apr  9 15:57:46 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 9 Apr 2010 11:57:46 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004091557.o39FvkSp001872@dev.open-bio.org>


gordonp
Fri Apr  9 11:57:46 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util
In directory dev.open-bio.org:/tmp/cvs-serv1836/src/main/ca/ucalgary/seahawk/util

Modified Files:
	DataUtils.java 
Log Message:
Added support for case sensitive searches, and 'previous input' conditional service execution
moby-live/Java/src/main/ca/ucalgary/seahawk/util DataUtils.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataUtils.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataUtils.java	2010/03/29 19:58:17	1.1
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataUtils.java	2010/04/09 15:57:46	1.2
@@ -117,7 +117,7 @@
 		    if(newFilter != null){
 			XPathOption xsel = newFilter.getSelectedXPath();
 			newProvenanceData += "\t"+newFilter.getFilterRegex()+
-			    "\t"+xsel.getXPath()+"\t"+xsel.getDesc();
+			    "\t"+xsel.getXPath()+"\t"+xsel.getDesc()+"\t"+newFilter.getCaseSensitivity();
 		    }
 		    pi.setData(attr_val[0]+"=\""+newProvenanceData+"\"");
 		}
@@ -300,7 +300,7 @@
 	return temp.toURI().toURL();
     }
 
-    private static URL getInputURL(Document responseDom) throws Exception{
+    public static URL getInputURL(Document responseDom) throws Exception{
 	String inputAddr = getSeahawkAttrFromDoc(responseDom, SERVICEINPUT_ATTR);
 	if(inputAddr == null){
 	    return null;
@@ -315,7 +315,11 @@
 	}
     }
 
-    private static Document getInputDoc(Document responseDom) throws Exception{
+    public static Document getInputDoc(Document responseDom) throws Exception{
+	URL inputURL = getInputURL(responseDom);
+	if(inputURL == null){
+	    return null;
+	}
 	try{
 	    return docBuilder.parse(getInputURL(responseDom).openStream());
 	} catch(org.xml.sax.SAXException saxe){
@@ -332,6 +336,9 @@
      */
     public static MobyDataJob getInputSample(Document responseDom, Registry registry) throws Exception{
 	Document inputDoc = getInputDoc(responseDom);
+	if(inputDoc == null){
+	    return null;
+	}
 	MobyContentInstance inputPayload = MobyDataUtils.fromXMLDocument(inputDoc.getDocumentElement(),
 									 registry);
 	if(inputPayload == null || inputPayload.size() == 0){
@@ -633,12 +640,30 @@
 	
 	if(fs != null && fs.getFilterRegex().length() > 0){
 	    XPathOption xsel = fs.getSelectedXPath();
-	    userData.append("\t"+fs.getFilterRegex()+"\t"+xsel.getXPath()+"\t"+xsel.getDesc());
+	    userData.append("\t"+fs.getFilterRegex()+"\t"+xsel.getXPath()+"\t"+xsel.getDesc()+"\t"+fs.getCaseSensitivity());
 	}
 	mobyData.setUserData(userData.toString());
     }
 
     /**
+     * Record a condition for data acceptability, 
+     * another service call with an output filter criteria. i.e. records if(f1(x) matches f1's output filter){...}
+     */
+    public static void addUserData(MobyDataInstance mdi, URL conditionalOutputURL, FilterSearch filter){
+	String filterSpec = "";
+	if(filter != null && filter.getFilterRegex().length() > 0){
+	    XPathOption xsel = filter.getSelectedXPath();
+	    filterSpec = "\t"+filter.getFilterRegex()+"\t"+xsel.getXPath()+"\t"+xsel.getDesc()+"\t"+filter.getCaseSensitivity();
+	}
+	if(mdi.getUserData() != null){
+	    mdi.setUserData(mdi.getUserData().toString()+"\t"+conditionalOutputURL+filterSpec);
+	}
+	else{
+	    mdi.setUserData(conditionalOutputURL.toString()+filterSpec);
+	}
+    }
+
+    /**
      * Retrieves processing instructions embedded in Moby XML docs if they have the for <?seahawk attr="val"?>
      */
     public static String getSeahawkAttrFromDoc(URL docURL, String attrName) throws Exception{ 



From gordonp at dev.open-bio.org  Fri Apr  9 15:58:23 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 9 Apr 2010 11:58:23 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004091558.o39FwMVA001941@dev.open-bio.org>


gordonp
Fri Apr  9 11:58:22 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util
In directory dev.open-bio.org:/tmp/cvs-serv1902/src/main/ca/ucalgary/seahawk/util

Modified Files:
	DataFlowRecorder.java 
Log Message:
Added support for case sensitive searches, and 'previous input' conditional service execution
moby-live/Java/src/main/ca/ucalgary/seahawk/util DataFlowRecorder.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataFlowRecorder.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataFlowRecorder.java	2010/03/29 20:53:04	1.2
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataFlowRecorder.java	2010/04/09 15:58:22	1.3
@@ -31,6 +31,8 @@
     public static final String T2FLOW_DISPATCHXML = "ca/ucalgary/seahawk/resources/t2flowDispatchStack.xml";
     public static final String T2FLOW_REGEXFILTER_BEANSHELL = "ca/ucalgary/seahawk/resources/RegexFilterBeanShell";
     public static final String T2FLOW_XPATHFILTER_BEANSHELL = "ca/ucalgary/seahawk/resources/XPathFilterBeanShell";
+    public static final String T2FLOW_PASSFILTER_BEANSHELL = "ca/ucalgary/seahawk/resources/PassFilterBeanShell"; // = if condition
+    public static final String T2FLOW_LISTFLATTEN_BEANSHELL = "ca/ucalgary/seahawk/resources/FlattenListBeanShell";
 
     private Central mobyCentral;
     private Map<String,Integer> namesUsed;  // keep count of workflow element name usage so as not to duplicate an ID
@@ -39,9 +41,12 @@
     // Value is processor and port names
     private Map<String,String[]> filter2Processor;
     private Map<String,String[]> decomp2Processor; // reuse decomposition processors if same decomp done more than once on a given doc
+    private Map<String,String[]> input2Processor; // if same input use more than once, create only one input port
     private DocumentBuilder docBuilder;
     private static String regexFilterScript = null;
     private static String xpathFilterScript = null;
+    private static String passFilterScript = null;
+    private static String listFlattenScript = null;
     private static Element dispatchStack = null;
     private static Transformer nullTransformer = null;
     private static Logger logger = Logger.getLogger(DataFlowRecorder.class.getName());
@@ -57,8 +62,9 @@
 
 	namesUsed = new HashMap<String,Integer>();
 	url2Processor = new HashMap<String,String>();
-	filter2Processor = new HashMap<String,String[]>(); // key is compound:  url \n regex \n xpath
+	filter2Processor = new HashMap<String,String[]>(); // key is compound:  url \n regex \n xpath \n caseSensitivity
 	decomp2Processor = new HashMap<String,String[]>(); // key is url with xpath attached as ref (the way Seahawk generates them)
+	input2Processor = new HashMap<String,String[]>(); // key is input instance XML 
     }
 
     /**
@@ -154,6 +160,7 @@
 	url2Processor.clear();  // clear map of results already produced in backtracking (handling workflow forks)
 	filter2Processor.clear(); // ditto
 	decomp2Processor.clear(); // ditto
+	input2Processor.clear(); // ditto
 
 	// Generate all of the outputs requested by the call.  None should be intermediaries 
 	// of another (the backtracking done by addWorkflowElements will capture these).
@@ -162,7 +169,7 @@
 	    // Create the inputs, processors and data links required for the workflow to create the result doc
 	    String ultimateProcessorName = addWorkflowElements(result.getKey(), doc, inputPorts, processors, datalinks);
 	    
-	    // If there is a filter active on the currently displyed doc, we need to apply it here
+	    // If there is a filter active on the currently displayed doc, we need to apply it here
 	    FilterSearch filter = result.getValue();
 	    String[] regexProcessorAndPorts = null;
 	    String filterKey = null;
@@ -190,9 +197,11 @@
 		    }
 		    else{
 			regexProcessorAndPorts = createRegexFilter(filter.getFilterRegex().toString(), 
-								   filter.getSelectedXPath(), 
+								   filter.getSelectedXPath(),
+								   filter.getCaseSensitivity(),
 								   ultimateProcessorName,
-								   getPortName(outputParam, true), 
+								   getPortName(outputParam, true),
+								   1, // desired list dpeth
 								   processors, datalinks, doc);
 			filter2Processor.put(filterKey, regexProcessorAndPorts);
 		    }
@@ -275,6 +284,9 @@
 	MobyService service = DataUtils.getService(resultDom);
 	Registry registry = DataUtils.getRegistry(resultDom);
 	MobyDataJob sampleJob = DataUtils.getInputSample(resultDom, registry);
+	if(sampleJob == null){
+	    return "foo";  //todo: doc was a loaded Moby XML, not a service output or recognized data
+	}
 
 	Element processorElement = createProcessorElement(service, sampleJob, doc);
 	// add processor to workflow
@@ -297,111 +309,181 @@
 	    MobyPrimaryData sampleData = (MobyPrimaryData) sd;
 
 	    // has provenance info?
+	    String[] data = null;
+	    String[] condPassProcessorAndPorts = null;  //[procname, input port, outputport]
 	    if(sampleData.getUserData() != null){
-		// User data has the form srcURL#generalSelectionXPath <tab> actualInputDataXptr <tab> regexFilter 
-		// where the filter is optional 
-		String[] data = sampleData.getUserData().toString().split("\t");
+		// User data has the form 
+		// srcURL#generalSelectionXPath <tab> actualInputDataXptr <tab> regexFilter <tab> conditionalURL
+		// where the filter and conditionalURL are optional 
+		data = sampleData.getUserData().toString().split("\t");
+		//options: selection + filter + cond, selection + cond, or cond only
+		if(data.length == 11 || data.length == 7 || data.length == 5){
+		    System.err.println("Adding conditional for " + resultURLString);
+		    String conditionURL = data[data.length-5];
+		    String conditionRegex = data[data.length-4];
+		    XPathOption conditionXPath = new XPathOption(data[data.length-3], data[data.length-2]);
+		    boolean caseSensitivity = Boolean.parseBoolean(data[data.length-1]);
+		    condPassProcessorAndPorts = createServiceConditionFilter(new URL(conditionURL), conditionRegex, conditionXPath, caseSensitivity,
+									     doc, inputPorts, processors, datalinks);
+		    String[] conditionlessData = new String[data.length-5];
+		    System.arraycopy(data, 0, conditionlessData, 0, data.length-5);
+		    data = conditionlessData;
+		}
+		else{
+		    System.err.println("Skipping conditional, only " + data.length + 
+				       "members in provenance data for " + resultURLString);
+		}
+	    }
+
+	    // true means treat as a collection if that's what the sample data is
+	    String sinkPortName = getPortName(sampleData, true);
+	    if(data != null && data.length != 0){
 		URL dataSrcURL = null;
 		try{
 		    dataSrcURL = new URL(data[0]);
 		} catch(Exception e){
 		    logger.log(Level.WARNING, "Ignoring unexpected UserData in Moby DOM, was not " +
 			       "a provenance URL as expected URL (" + sampleData.getUserData().toString() + ")");
+		    continue;
 		}
-		if(dataSrcURL != null){
-		    // recursion for workflow creation by backtracking service input provenance
-		    String feedingProcessorName = null;
-		    String feedingProcessorPort = null;
-		    String dataSrcURLString = dataSrcURL.toString().replaceFirst("#.*$", ""); //get rid of ref part
-		    if(url2Processor.containsKey(dataSrcURLString)){
-			feedingProcessorName = url2Processor.get(dataSrcURLString);
+		// recursion for workflow creation by backtracking service input provenance
+		String feedingProcessorName = null;
+		String feedingProcessorPort = null;
+		String dataSrcURLString = dataSrcURL.toString().replaceFirst("#.*$", ""); //get rid of ref part
+		if(url2Processor.containsKey(dataSrcURLString)){
+		    feedingProcessorName = url2Processor.get(dataSrcURLString);
+		}
+		else{
+		    feedingProcessorName = addWorkflowElements(dataSrcURL, doc, inputPorts, processors, datalinks);
+		}
+		
+		// Take into account data[2..5] if they are present, 
+		// which filter the data by a regex before any other activities happen
+		// Format of spec is regex <tab> xpath <tab> xpathTextDesc <tab> booleanForCaseSensitivity
+		if(data.length == 6){
+		    String[] origFeederProcessorAndPort = getPortFromURLRef(dataSrcURL,
+									    sampleData,
+									    feedingProcessorName,
+									    null,
+									    processors, 
+									    datalinks,
+									    doc,
+									    false);
+		    
+		    // Lookup key is url \n regex \n xpath \n caseSensitivity
+		    String[] regexProcessorAndPorts = null;
+		    String filterKey = dataSrcURLString+"\n"+data[2]+"\n"+data[3]+"\n"+data[5];
+		    if(filter2Processor.containsKey(filterKey)){ // filter already exists from another branch
+			regexProcessorAndPorts = filter2Processor.get(filterKey);
 		    }
 		    else{
-			feedingProcessorName = addWorkflowElements(dataSrcURL, doc, inputPorts, processors, datalinks);
-		    }
-
-		    // true means treat as a collection if that's what the sample data is
-		    String sinkPortName = getPortName(sampleData, true);
-
-		    // Take into account data[2..4] if they are present, 
-		    // which filter the data by a regex before any other activities happen
-		    // Format of spec is regex <tab> xpath <tab> xpathTextDesc, so the earlier split gives use indices 1..3
-		    if(data.length == 5){
-			String[] origFeederProcessorAndPort = getPortFromURLRef(dataSrcURL,
-										sampleData,
-										feedingProcessorName,
-										null,
-										processors, 
-										datalinks,
-										doc,
-										false);
-
-			// Lookup key is url \n regex \n xpath
-			String[] regexProcessorAndPorts = null;
-			String filterKey = dataSrcURLString+"\n"+data[2]+"\n"+data[3];
-			if(filter2Processor.containsKey(filterKey)){ // filter already exists from another branch
-			    regexProcessorAndPorts = filter2Processor.get(filterKey);
-			}
-			else{
-			    regexProcessorAndPorts = createRegexFilter(data[2], 
-								       new XPathOption(data[3], data[4]), 
-								       origFeederProcessorAndPort[0], 
-								       origFeederProcessorAndPort[1], 
-								       processors, datalinks, doc);
-			    // New filter is applied to just this branch from a service for the moment...record the filter
-			    // so that if same filter criteria are applied to more than one branch, we only make one filter
-			    filter2Processor.put(dataSrcURLString+"\n"+data[2]+"\n"+data[3], regexProcessorAndPorts);
-			}
-			feedingProcessorName = regexProcessorAndPorts[0];
-			feedingProcessorPort = regexProcessorAndPorts[regexProcessorAndPorts.length-1];  //last one is output
+			regexProcessorAndPorts = createRegexFilter(data[2], 
+								   new XPathOption(data[3], data[4]),
+								   Boolean.parseBoolean(data[5]),
+								   origFeederProcessorAndPort[0], 
+								   origFeederProcessorAndPort[1],
+								   1, // desired list depth 
+								   processors, datalinks, doc);
+			// New filter is applied to just this branch from a service for the moment...record the filter
+			// so that if same filter criteria are applied to more than one branch, we only make one filter
+			filter2Processor.put(filterKey, regexProcessorAndPorts);
 		    }
-
-		    // getPortFromURLRef() may inject extra processors between the processorName and feedingProcessorName
-		    // in order to maintain type safety, etc. so the data link may change (based on last arg being set to true).
-		    String[] feederProcessorAndPort = getPortFromURLRef(dataSrcURL,
-									sampleData,
-									feedingProcessorName,
-									feedingProcessorPort, //if null, determined from urlref
-									processors, 
-									datalinks,
-									doc,
-									true); 
-		    datalinks.appendChild(createDataLinkElement(feederProcessorAndPort[0], feederProcessorAndPort[1],
-								processorName, sinkPortName, 
+		    feedingProcessorName = regexProcessorAndPorts[0];
+		    feedingProcessorPort = regexProcessorAndPorts[regexProcessorAndPorts.length-1];  //last one is output
+		}
+		
+		// getPortFromURLRef() may inject extra processors between the processorName and feedingProcessorName
+		// in order to maintain type safety, etc. so the data link may change (based on last arg being set to true).
+		String[] feederProcessorAndPort = getPortFromURLRef(dataSrcURL,
+								    sampleData,
+								    feedingProcessorName,
+								    feedingProcessorPort, //if null, determined from urlref
+								    processors, 
+								    datalinks,
+								    doc,
+								    true); 
+		if(condPassProcessorAndPorts != null){
+		    // inject condition filter between feeder service and current service 
+		    datalinks.appendChild(createDataLinkElement(feederProcessorAndPort[0],
+								feederProcessorAndPort[1],
+								condPassProcessorAndPorts[0], 
+								condPassProcessorAndPorts[1],
 								doc));
-		    
+		    feederProcessorAndPort[0] = condPassProcessorAndPorts[0];
+		    feederProcessorAndPort[1] = condPassProcessorAndPorts[2];
 		}
+
+		datalinks.appendChild(createDataLinkElement(feederProcessorAndPort[0], feederProcessorAndPort[1],
+							    processorName, sinkPortName, 
+							    doc));
+		
 	    }
 	    // Otherwise it's a workflow input the user will need to specify
 	    else{
-		String uniqueInputName = createUniqueName(getInputName(sampleData));
-		// todo: sample data may be of more specific type than service requires
-		inputPorts.appendChild(createWorkflowInputElement(uniqueInputName, sampleData, doc));
-		if(sampleData.getDataType().getName().equals(MobyTags.MOBYOBJECT)){
-		    String mobifyingProcessorName = addIdMobifyingProcessor(processors, datalinks, 
-									    sampleData, processorName, 
-									    inputName, doc);
-		    datalinks.appendChild(createWorkflowInputLinkElement(uniqueInputName, 
-									 mobifyingProcessorName, 
-									 "fileurl", 
-									 sampleData, 
-									 doc));
+		// pName is editable name for input processor target...
+		// allows injection of condition without affecting method's return value
+		String pName = processorName; 
+		if(condPassProcessorAndPorts != null){
+		    // inject condition filter between data creator and current service 
+		    datalinks.appendChild(createDataLinkElement(condPassProcessorAndPorts[0],
+								condPassProcessorAndPorts[2],
+								pName,
+								sinkPortName,
+								doc));
+		    pName = condPassProcessorAndPorts[0];
+		    sinkPortName = condPassProcessorAndPorts[1];
+		}
+		// The sample data may be used in more than one branch of the flow...avoid duplication
+		// Get the real data XML, to see if we've encountered it before as input (it'd be in the hash)
+		// Remember that sd is the loop's original MobyDataInstance before it's been coerced into a MobyPrimaryData, 
+		// which doesn't have XML modes, etc.
+		String inputKey = getInputKey(sd);
+		System.err.println("Input key for " + processorName + " is " + inputKey);
+
+		String[] mobifyingProcessorNameAndPorts = null;
+		if(input2Processor.containsKey(inputKey)){
+		    mobifyingProcessorNameAndPorts = input2Processor.get(inputKey);		    
 		}
 		else{
-		    // TODO: Need to build complex input from MOB rule or spreadsheet fields?
+		    if(sampleData.getDataType().getName().equals(MobyTags.MOBYOBJECT)){
+			mobifyingProcessorNameAndPorts = addIdMobifyingProcessor(processors, datalinks, inputPorts,
+										 sampleData, doc);
+			input2Processor.put(inputKey, mobifyingProcessorNameAndPorts);
+		    }
+		    else{
+			// TODO: Need to build complex input from MOB rule or spreadsheet fields?
+		    }
 		}
+		// link the created data to the workflow service
+		datalinks.appendChild(createDataLinkElement(mobifyingProcessorNameAndPorts[0], 
+							    mobifyingProcessorNameAndPorts[1], 
+							    pName, sinkPortName, 
+							    doc));
 	    }
+
 	}
 
 	return processorName;
     }
 
+    // returns the same value for moby sample data instances containing the same data in XML form
+    private String getInputKey(MobyDataInstance sd){
+	int oldXmlMode = sd.getXmlMode();
+	sd.setXmlMode(MobyDataInstance.SERVICE_XML_MODE);
+	String inputKey = sd.toXML();
+	sd.setXmlMode(oldXmlMode);
+
+	// get rid of the top-level article name, as this is immaterial to the 
+	// value equivalence of objects (only matters to the actual service call mechanism)
+	return inputKey.replaceFirst(MobyTags.ARTICLENAME+"\\s*=\\s*(['\"]).*?\\1", "");
+    }
+
     // Actually adds a few processors, but only one needs to be returned and connected to an input port.
     // The others are constant values.  By default we assume that you want to run a bunch of IDs 
     // in a file, we also link in a Taverna spreadsheet importer.
-    private String addIdMobifyingProcessor(Element processors, Element datalinks, 
-					   MobyPrimaryData sampleData, String targetProcessorName, 
-					   String targetProcessorPort, Document doc) throws Exception{
+    // Returns [spreadsheetReadingProcName, outputPort]
+    private String[] addIdMobifyingProcessor(Element processors, Element datalinks, Element dataFlowInputPorts,
+					     MobyPrimaryData sampleData, Document doc) throws Exception{
 	String processorName = "Create-" + sampleData.getDataType().getName();
 	MobyNamespace ns = null;
 	MobyNamespace[] nss = ((MobyPrimaryData) sampleData).getNamespaces();
@@ -518,7 +600,7 @@
 	Map<String,String> feeds = new HashMap<String,String>();  //what port on data creator it maps to
 	constants.put(ns.getName()+"-namespace-constant", ns.getName());
 	feeds.put(ns.getName()+"-namespace-constant", "namespace");
-	constants.put("article_name-constant", targetProcessorPort);
+	constants.put("article_name-constant", "unimportant");
 	feeds.put("article_name-constant", "article name");
 
 	for(Map.Entry<String,String> constant: constants.entrySet()){
@@ -632,19 +714,23 @@
 	port.setAttribute("name", "fileurl");
 	port.setAttribute("depth", "0");
 
+	String uniqueInputName = createUniqueName(getInputName(sampleData));
+	// todo: sample data may be of more specific type than service requires
+	dataFlowInputPorts.appendChild(createWorkflowInputElement(uniqueInputName, sampleData, doc));
+	datalinks.appendChild(createWorkflowInputLinkElement(uniqueInputName, 
+							     importerName, 
+							     "fileurl", 
+							     sampleData, 
+							     doc));
+
 	// link the spreadsheet reader to the Moby data creator 
 	datalinks.appendChild(createDataLinkElement(importerName, outputUniqueName,
 						    processorName, "id",
 						    doc));
 
-	// link the created data to the first workflow service, which takes an id
-	datalinks.appendChild(createDataLinkElement(processorName, "mobyData", 
-						    targetProcessorName, "Object("+targetProcessorPort+")", 
-						    doc));
-
-	// return the name of the spreadsheet reading processor so it can be hooked up
-	// to an input port for a Moby service
-	return importerName;
+	// return the name of the spreadsheet reading processor and output port so it can be hooked up
+	// to input ports for Moby services
+	return new String[]{processorName, portNames[portNames.length-1]};
     }
 
     private Element createConstantProcessor(String constantName, String constantValue, Document doc)
@@ -884,15 +970,86 @@
 				 processors, datalinks, doc);
     }
 
-    private String[] createRegexFilter(String regex, XPathOption xpath, String srcProcessor, String srcPort, 
+    // Make the continued use of data X in the workflow conditional on the results of running X through service f
+    // and passing the filter condition set on f.  Equivalent to if(f(X) matches f_filter){...}
+    // returns [proc name, input port, output port]
+    private String[] createServiceConditionFilter(URL conditionURL, String filterRegex, XPathOption filterXPath,
+						  boolean caseSensitive, Document doc,
+						  Element inputPorts, Element processors, Element datalinks)
+	throws Exception{
+
+	// Open the conditionURL, and find out what service result is used, and what filter applied
+ 	Document conditionDoc = docBuilder.parse(conditionURL.openStream());
+ 	MobyService service = DataUtils.getService(conditionDoc);
+ 	Document condServiceOutputDoc = DataUtils.getInputDoc(conditionDoc);
+
+	// The bits to run the service "f"
+
+ 	String dataSrcURLString = conditionURL.toString().replaceFirst("#.*$", ""); //get rid of ref part
+ 	String processorName = null;
+ 	// See if the service creating the input for the conditional service has already been added to the workflow
+ 	if(url2Processor.containsKey(dataSrcURLString)){
+ 	    processorName = url2Processor.get(dataSrcURLString);
+ 	}
+ 	else{
+	    processorName = addWorkflowElements(conditionURL, doc, inputPorts, processors, datalinks);
+ 	}
+
+ 	String filterKey = dataSrcURLString+"\n"+filterRegex+"\n"+filterXPath.getXPath()+"\n"+caseSensitive;
+ 	String[] regexFilterProcNameAndPort = null;
+ 	//todo: gimpy loop below, as more than one service output would cause a trampling of regex output ports
+ 	for(MobyPrimaryData outputParam: service.getPrimaryOutputs()){
+ 	    // See if the filter on the conditional service has already been used in the workflow
+ 	    if(filter2Processor.containsKey(filterKey)){
+ 		regexFilterProcNameAndPort = filter2Processor.get(filterKey);
+ 	    }
+ 	    else{
+ 		regexFilterProcNameAndPort = createRegexFilter(filterRegex, 
+ 							       filterXPath,
+							       caseSensitive, 
+ 							       processorName,
+ 							       getPortName(outputParam, true),
+							       0, //depth of list desired (will return match count)
+ 							       processors, datalinks, doc);
+ 		filter2Processor.put(filterKey, regexFilterProcNameAndPort);
+ 	    }
+ 	}
+
+	// We need to flatten the 2-deep list generated by the regex filter's cross product
+	String[] beanShellFlattenerProcNameAndPorts = addListFlattenBeanShell(processors, doc);
+
+	datalinks.appendChild(createDataLinkElement(regexFilterProcNameAndPort[0],
+						    regexFilterProcNameAndPort[1],
+						    beanShellFlattenerProcNameAndPorts[0], 
+						    beanShellFlattenerProcNameAndPorts[1],
+						    doc));
+
+	// Essentially an "if" condition, error if incoming value is empty, missing, or zero
+	String[] beanShellFilterProcNameAndPorts = addPassFilterBeanShell(processors, doc);
+
+	datalinks.appendChild(createDataLinkElement(beanShellFlattenerProcNameAndPorts[0],
+						    beanShellFlattenerProcNameAndPorts[2],
+						    beanShellFilterProcNameAndPorts[0], 
+						    beanShellFilterProcNameAndPorts[2],
+						    doc));
+
+	return new String[]{beanShellFilterProcNameAndPorts[0], 
+                            beanShellFilterProcNameAndPorts[1], 
+                            beanShellFilterProcNameAndPorts[3]};
+    }
+
+    private String[] createRegexFilter(String regex, XPathOption xpath, boolean caseSensitive, 
+				       String srcProcessor, String srcPort, int listDepth, 
  				       Element processors, Element datalinks, Document doc)
  	throws Exception{
 	String constantXPathName = createUniqueName(xpath.toString());
 	processors.appendChild(createConstantProcessor(constantXPathName, xpath.getXPath(), doc));
 	String constantRegexName = createUniqueName(regex);
 	processors.appendChild(createConstantProcessor(constantRegexName, regex, doc));
+	String constantCaseSensitivityName = createUniqueName("cs_"+caseSensitive);
+	processors.appendChild(createConstantProcessor(constantCaseSensitivityName, ""+caseSensitive, doc));
 
-	String[] beanShellFilterProcNameAndPorts = addRegexFilterBeanShell(processors, doc);
+	String[] beanShellFilterProcNameAndPorts = addRegexFilterBeanShell(listDepth, processors, doc);
 	
 	datalinks.appendChild(createDataLinkElement(srcProcessor,
 						    srcPort,
@@ -903,11 +1060,15 @@
 						    beanShellFilterProcNameAndPorts[0], 
 						    beanShellFilterProcNameAndPorts[2],
 						    doc)); 
-	datalinks.appendChild(createDataLinkElement(constantXPathName, "value",
+	datalinks.appendChild(createDataLinkElement(constantCaseSensitivityName, "value",
 						    beanShellFilterProcNameAndPorts[0], 
 						    beanShellFilterProcNameAndPorts[3],
 						    doc)); 
-	return new String[]{beanShellFilterProcNameAndPorts[0], beanShellFilterProcNameAndPorts[4]};	
+	datalinks.appendChild(createDataLinkElement(constantXPathName, "value",
+						    beanShellFilterProcNameAndPorts[0], 
+						    beanShellFilterProcNameAndPorts[4],
+						    doc)); 
+	return new String[]{beanShellFilterProcNameAndPorts[0], beanShellFilterProcNameAndPorts[5]};	
     }
     
     private String[] createXrefParser(MobyNamespace nsObj, String srcProcessor, String srcPort, 
@@ -1231,29 +1392,76 @@
 	}
     }
 
+   private String[] addListFlattenBeanShell(Element processors, Document doc) 
+	throws Exception{
+	String beanShellProcName = createUniqueName("Create_Pass_Fail_List");
+	
+	// Now do all the param-specific stuff below (inserts into various parts of the elements defined above)
+	Map<String,String> inputsMap = new LinkedHashMap<String,String>();  
+	// linked because order is important to line up port connections
+	Map<String,String> inputTypes = new LinkedHashMap<String,String>();
+	inputsMap.put("inputlist", "2");
+	inputTypes.put("inputlist", "text/plain");
+	Map<String,String> outputsMap = new LinkedHashMap<String,String>();
+	outputsMap.put("outputlist", "1");
+
+	return addBeanShell(beanShellProcName, "dot",
+			    inputsMap, inputTypes, outputsMap, 
+			    getListFlattenScript(), new String[]{}, 
+			    processors, doc);	
+    }    
+
+    private String[] addPassFilterBeanShell(Element processors, Document doc) 
+	throws Exception{
+	String beanShellProcName = createUniqueName("IfPassesContentFilter");
+	
+	// Now do all the param-specific stuff below (inserts into various parts of the elements defined above)
+	Map<String,String> inputsMap = new LinkedHashMap<String,String>();  
+	// linked because order is important to line up port connections
+	Map<String,String> inputTypes = new LinkedHashMap<String,String>();
+	inputsMap.put("dataToPassThrough", "1");
+	inputsMap.put("conditionResults", "1");
+	inputTypes.put("dataToPassThrough", "text/xml");
+	inputTypes.put("conditionResults", "text/plain");
+	Map<String,String> outputsMap = new LinkedHashMap<String,String>();
+	outputsMap.put("dataPassed", "1");
+
+	return addBeanShell(beanShellProcName, "cross",
+			    inputsMap, inputTypes, outputsMap, 
+			    getPassFilterScript(), new String[]{}, 
+			    processors, doc);	
+    }    
+
     // Returns the name of the bean shell processor and its ports, so we can create the data links in the caller
     // The input is the original moby xml, and the xpath to extract, and the regex to apply to the text contents of the xpath results.
     // The output is a list of moby xml docs, one for each mobyData that fit the xpath and regex criteria.
-    private String[] addRegexFilterBeanShell(Element processors, Document doc) 
+    private String[] addRegexFilterBeanShell(int listDepth, Element processors, Document doc) 
 	throws Exception{
-	String beanShellProcName = createUniqueName("Filter_By_Content");
+	String beanShellProcName = createUniqueName("Filter"+(listDepth == 0 ? "_Match_Count" : "_By_Content"));
 	
 	// Now do all the param-specific stuff below (inserts into various parts of the elements defined above)
 	Map<String,String> inputsMap = new LinkedHashMap<String,String>();  
-	// linked because order is importtant to line up port connections
+	// linked because order is important to line up port connections
 	Map<String,String> inputTypes = new LinkedHashMap<String,String>();
 	inputsMap.put("xml_text", "0");
 	inputsMap.put("regex", "0");
+        inputsMap.put("case_sensitive", "0");
 	inputsMap.put("xpath", "0");
 	inputTypes.put("xml_text", "text/xml");
 	inputTypes.put("xpath", "text/plain");
 	inputTypes.put("regex", "text/plain");
+	inputTypes.put("case_sensitive", "text/plain");
 	Map<String,String> outputsMap = new LinkedHashMap<String,String>();
-	outputsMap.put("nodelistAsXML", "1");
+	if(listDepth == 0){
+	    outputsMap.put("matchCount", "0");
+        }
+        else{
+            outputsMap.put("nodelistAsXML", ""+listDepth);
+        }
 
-	return addBeanShell(beanShellProcName,
+	return addBeanShell(beanShellProcName, "cross",
 			    inputsMap, inputTypes, outputsMap, 
-			    getRegexFilterScript(), new String[]{"dom4j:dom4j:1.6"}, 
+			    getRegexFilterScript(listDepth), new String[]{"dom4j:dom4j:1.6"}, 
 			    processors, doc);	
     }
 
@@ -1274,13 +1482,13 @@
 	Map<String,String> outputsMap = new HashMap<String,String>();
 	outputsMap.put("nodelistAsXML", "1");
 
-	return addBeanShell(beanShellProcName,
+	return addBeanShell(beanShellProcName, "cross",
 			    inputsMap, inputTypes, outputsMap, 
 			    getXPathFilterScript(), new String[]{"dom4j:dom4j:1.6"}, 
 			    processors, doc);
     }
 
-    private String[] addBeanShell(String beanShellProcName,
+    private String[] addBeanShell(String beanShellProcName, String vectorComboOp,
 				  Map<String,String> inputsMap, Map<String,String> inputTypes, 
 				  Map<String,String> outputsMap, String script, String[] dependencySpecs,
 				  Element processors, Document doc) throws Exception{
@@ -1345,8 +1553,11 @@
 	iterationStrategyStack.appendChild(iteration);
 	Element strategy = doc.createElementNS(T2FLOW_NS, "strategy");
 	iteration.appendChild(strategy);
-	Element cross = doc.createElementNS(T2FLOW_NS, "cross");
-	strategy.appendChild(cross);
+	Element vectorOp = null;
+        if(vectorComboOp != null){
+            vectorOp = doc.createElementNS(T2FLOW_NS, vectorComboOp);
+	    strategy.appendChild(vectorOp); // either cross or dot
+        }
 
 	// Lst processor name, input ports and output ports, in that order.
 	Vector<String> returnSpec = new Vector<String>();
@@ -1370,7 +1581,9 @@
 	    mimeTypes.appendChild(createElWithText(doc, "", "string", inputTypes.get(input.getKey())));
 
 	    Element port = doc.createElementNS(T2FLOW_NS, "port");
-	    cross.appendChild(port);
+	    if(vectorOp != null){
+                vectorOp.appendChild(port);
+            }
 	    port.setAttribute("depth", input.getValue());
 	    port.setAttribute("name", input.getKey());
 	}
@@ -1517,7 +1730,7 @@
     private String createUniqueName(String preferredName){
 	if(namesUsed.containsKey(preferredName)){
 	    namesUsed.put(preferredName, namesUsed.get(preferredName).intValue()+1); //increment
-	    preferredName += namesUsed.get(preferredName);
+	    preferredName += "_"+namesUsed.get(preferredName);
 	}
 	else{
 	    namesUsed.put(preferredName, 1); // will be auto-boxed to Integer
@@ -1528,8 +1741,6 @@
     // dataType(articleName) as required by the Taverna Moby plugin
     private String getPortName(MobyPrimaryData data, boolean asCollection){
 	if(data instanceof MobyPrimaryDataSet){
-	    // todo: Hmm...don't yet handle case where collections are passed from one service to another...
-	    // here we assume iterating over the collection
 	    if(asCollection){
 		return data.getDataType().getName()+"(Collection - '"+data.getName()+"')";
 	    }
@@ -1680,7 +1891,7 @@
 
 	    // Did we override the default value for the secondary param in the example input?
 	    Element stringValue = doc.createElementNS("", "string");
-	    if(sampleInput.containsKey(secParam.getName())){
+	    if(sampleInput != null && sampleInput.containsKey(secParam.getName())){
 		stringValue.appendChild(doc.createTextNode(((MobyDataSecondaryInstance) sampleInput.get(secParam.getName())).getValue()));
 	    }
 	    else{  // use the default defined in Moby Central
@@ -1739,6 +1950,28 @@
 	return central;
     }
 
+    private synchronized String getListFlattenScript() throws Exception{
+	if(listFlattenScript == null){
+	    URL scriptURL = getClass().getClassLoader().getResource(T2FLOW_LISTFLATTEN_BEANSHELL);
+	    if(scriptURL == null){
+		throw new Exception("Cannot find resource " + T2FLOW_LISTFLATTEN_BEANSHELL);
+	    }
+	    listFlattenScript = HTMLUtils.getURLContents(scriptURL);
+	}
+	return listFlattenScript;
+    }
+
+    private synchronized String getPassFilterScript() throws Exception{
+	if(passFilterScript == null){
+	    URL scriptURL = getClass().getClassLoader().getResource(T2FLOW_PASSFILTER_BEANSHELL);
+	    if(scriptURL == null){
+		throw new Exception("Cannot find resource " + T2FLOW_PASSFILTER_BEANSHELL);
+	    }
+	    passFilterScript = HTMLUtils.getURLContents(scriptURL);
+	}
+	return passFilterScript;
+    }
+
     private synchronized String getXPathFilterScript() throws Exception{
 	if(xpathFilterScript == null){
 	    URL scriptURL = getClass().getClassLoader().getResource(T2FLOW_XPATHFILTER_BEANSHELL);
@@ -1750,7 +1983,7 @@
 	return xpathFilterScript;
     }
 
-    private synchronized String getRegexFilterScript() throws Exception{
+    private synchronized String getRegexFilterScript(int listDepth) throws Exception{
 	if(regexFilterScript == null){
 	    URL scriptURL = getClass().getClassLoader().getResource(T2FLOW_REGEXFILTER_BEANSHELL);
 	    if(scriptURL == null){
@@ -1758,7 +1991,12 @@
 	    }
 	    regexFilterScript = HTMLUtils.getURLContents(scriptURL);
 	}
-	return regexFilterScript;
+	if(listDepth == 0){// list to scalar conversion
+	    return regexFilterScript+"\nString matchCount = \"\"+nodelistAsXML.size();";
+        }
+        else{
+ 	    return regexFilterScript;
+        }
     }
 
     private synchronized Element getDispatchStack(Document newOwnerDoc) throws Exception{



From gordonp at dev.open-bio.org  Fri Apr  9 16:58:14 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 9 Apr 2010 12:58:14 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004091658.o39GwEOB003781@dev.open-bio.org>


gordonp
Fri Apr  9 12:58:13 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/minnow
In directory dev.open-bio.org:/tmp/cvs-serv3745/src/main/ca/ucalgary/minnow

Modified Files:
	MinJarMaker.java 
Log Message:
got rid of annoying cvs-related files in secondary jars
moby-live/Java/src/main/ca/ucalgary/minnow MinJarMaker.java,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/minnow/MinJarMaker.java,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/minnow/MinJarMaker.java	2010/03/30 19:14:04	1.6
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/minnow/MinJarMaker.java	2010/04/09 16:58:13	1.7
@@ -812,7 +812,7 @@
 	       relativePath.equals("META-INF") || //this one causes null pointers in jarsigner 
 	       relativePath.equals("testdata") || 
 	       relativePath.equals("deployment") || 
-	       relativePath.equals("CVS")){
+	       relativePath.endsWith("CVS")){
 		//System.err.println("Skipping " + relativePath);
 		continue;
 	    }



From gordonp at dev.open-bio.org  Sat Apr 10 00:40:17 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 9 Apr 2010 20:40:17 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004100040.o3A0eH2E014912@dev.open-bio.org>


gordonp
Fri Apr  9 20:40:17 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources
In directory dev.open-bio.org:/tmp/cvs-serv14854/src/main/ca/ucalgary/seahawk/resources

Modified Files:
	RegexFilterBeanShell 
Log Message:
Added support for filter inversion (boolean negation)
moby-live/Java/src/main/ca/ucalgary/seahawk/resources RegexFilterBeanShell,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources/RegexFilterBeanShell,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources/RegexFilterBeanShell	2010/04/09 15:49:18	1.2
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources/RegexFilterBeanShell	2010/04/10 00:40:17	1.3
@@ -11,9 +11,12 @@
 List nodelist = document.selectNodes(xpath);
 
 ArrayList outputXmlList = new ArrayList();
+ArrayList outputXmlList_false = new ArrayList();
 int i = 1;
 Map collections = new LinkedHashMap();
 Map collectionsEnd = new HashMap();
+Map collections_false = new LinkedHashMap();
+Map collectionsEnd_false = new HashMap();
 Pattern pattern = Pattern.compile(regex, Pattern.MULTILINE | Pattern.DOTALL | (Boolean.parseBoolean(case_sensitive) ? 0 : Pattern.CASE_INSENSITIVE));
 for (Iterator iter = nodelist.iterator(); iter.hasNext();) {
         Node node = (Node) iter.next();
@@ -31,10 +34,17 @@
                         break;
                 default: break;
         }
-        if(!match){
-                continue;
-        }
 
+	Map cs = null;
+	Map csEnd = null;
+        if(match){
+		cs = collections;
+		csEnd = collectionsEnd;
+	}
+	else{
+		cs = collections_false;
+		csEnd = collectionsEnd_false;
+        }
         //go up the tree until we hit a mobyData...this is the unit we can forward
         StringBuilder collection = null;
         StringBuilder collectionEnd = null;
@@ -43,11 +53,11 @@
                    node.getParent().getName().equals("Collection")){
                         collection = new StringBuilder();  //start tracking parents
                         collectionEnd = new StringBuilder();
-                        if(!collections.containsKey(collection)){
-                                collections.put(collection, new Vector());
-                                collectionsEnd.put(collection, collectionEnd);
+                        if(!cs.containsKey(collection)){
+                                cs.put(collection, new Vector());
+                                csEnd.put(collection, collectionEnd);
                         }
-                        ((Vector)collections.get(collection)).add(node.asXML());
+                        ((Vector)cs.get(collection)).add(node.asXML());
                 }
                 node = node.getParent();
                 if(node != null && collection != null){
@@ -61,14 +71,17 @@
                         collectionEnd.append("</"+((Element) node).getQualifiedName()+">");
                 }
         }
-        if(node == null){
+        if(node == null){ // wasn't part of a mobyData block
                 continue;
         }
-        // At mobyData level if we got here
+        // At mobyData level if we got here, add if job not already present
         if(collection == null){
-                outputXmlList.add(
-                "<moby:MOBY xmlns:moby='http://www.biomoby.org/moby' xmlns='http://www.biomoby.org/moby'>"+
-                "<moby:mobyContent>"+node.asXML()+"</moby:mobyContent></moby:MOBY>");
+		String jobData = "<moby:MOBY xmlns:moby='http://www.biomoby.org/moby' xmlns='http://www.biomoby.org/moby'>"+
+                		 "<moby:mobyContent>"+node.asXML()+"</moby:mobyContent></moby:MOBY>";
+                List list = (match ? outputXmlList : outputXmlList_false);
+		if(!list.contains(jobData)){
+			list.add(jobData);
+		}
         }
 }
 
@@ -83,6 +96,16 @@
         }
         ((List) uniqueCollections.get(keyString)).addAll((List) collection.getValue());
 }
+Map uniqueCollections_false = new LinkedHashMap();
+Map uniqueCollectionsEnd_false = new LinkedHashMap();
+for(Map.Entry collection: collections_false.entrySet()){
+        String keyString = collection.getKey().toString();
+        if(!uniqueCollections_false.containsKey(keyString)){
+                uniqueCollections_false.put(keyString, new Vector());
+                uniqueCollectionsEnd_false.put(keyString, collectionsEnd_false.get(collection.getKey()));
+        }
+        ((List) uniqueCollections_false.get(keyString)).addAll((List) collection.getValue());
+}
 
 //Now concat the collection members that pass the filter
 for(Map.Entry collection: uniqueCollections.entrySet()){
@@ -99,6 +122,21 @@
 
         outputXmlList.add(block.toString());
 }
+for(Map.Entry collection: uniqueCollections_false.entrySet()){
+        StringBuilder block = new StringBuilder();
+        block.append("<moby:MOBY xmlns:moby='http://www.biomoby.org/moby' xmlns='http://www.biomoby.org/moby'>\n");
+        block.append("<moby:mobyContent>\n");
+        block.append(collection.getKey().toString());
+        for(String val: (List) collection.getValue()){
+                block.append(val);
+        }
+        block.append(uniqueCollectionsEnd_false.get(collection.getKey().toString()));  // closing tags
+        block.append("</moby:mobyContent>\n");
+        block.append("</moby:MOBY>\n");
+
+        outputXmlList_false.add(block.toString());
+}
 
-List nodelistAsXML=outputXmlList;
+List TRUE_nodelistAsXML=outputXmlList;
+List FALSE_nodelistAsXML=outputXmlList_false;
 



From gordonp at dev.open-bio.org  Sat Apr 10 00:40:17 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 9 Apr 2010 20:40:17 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004100040.o3A0eHik014894@dev.open-bio.org>


gordonp
Fri Apr  9 20:40:17 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv14854/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	FilterSearchWidget.java MobyContentPane.java 
Log Message:
Added support for filter inversion (boolean negation)
moby-live/Java/src/main/ca/ucalgary/seahawk/gui FilterSearchWidget.java,1.2,1.3 MobyContentPane.java,1.24,1.25
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/FilterSearchWidget.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/FilterSearchWidget.java	2010/04/09 15:50:09	1.2
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/FilterSearchWidget.java	2010/04/10 00:40:17	1.3
@@ -18,12 +18,18 @@
     private FilterSearch currentFilterSearch;
     private JLabel closeIcon;
     private JToggleButton caseButton;
+    private JButton inverseButton; // decides whether filter is "if" or "unless"
     private JTextField searchField;
     private JComboBox docPartOptions;
     private MobyContentPane contentPane;
     public static final String CASE_SENSITIVE_ICON_RESOURCE = "ca/ucalgary/seahawk/resources/images/case_sensitive.png";
     public static final String CASE_INSENSITIVE_ICON_RESOURCE = "ca/ucalgary/seahawk/resources/images/case_insensitive.png";
+    private static final String IF_TEXT = "<html><u>if</u></html>";
+    private static final String UNLESS_TEXT = "<html><u>unless</u></html>";
+    private static final String CASE_INSENSITIVE_MSG = "<html>The filter is case insensitive,<br>click to make case sensitive</html>";
+    private static final String CASE_SENSITIVE_MSG = "<html>The filter is case sensitive,<br>click to make case insensitive</html>";
     private static final String CASE_BUTTON_NAME = "case_sensitivity_button"; 
+    private static final String INVERSE_BUTTON_NAME = "boolean_button"; 
 
     private static Logger logger = Logger.getLogger(FilterSearchWidget.class.getName());
 
@@ -45,7 +51,7 @@
 	Dimension buttonSize = new Dimension(24,24);
 	caseButton = new JToggleButton(new ImageIcon(cl.getResource(CASE_SENSITIVE_ICON_RESOURCE)));
 	caseButton.setDisabledIcon(new ImageIcon(cl.getResource(CASE_INSENSITIVE_ICON_RESOURCE)));
-	caseButton.setToolTipText("Toggles the case sensitivity of the filter");
+	caseButton.setToolTipText(CASE_INSENSITIVE_MSG);
 	caseButton.setPreferredSize(buttonSize);
 	caseButton.setEnabled(true);
 	caseButton.setSelected(false);
@@ -53,12 +59,20 @@
 	caseButton.setMargin(new java.awt.Insets(2,2,2,2));
         caseButton.setName(CASE_BUTTON_NAME); // so test cases can find the component
 
+	inverseButton = new JButton(IF_TEXT);
+	inverseButton.setToolTipText("<html>Click to invert the selection between \"if\" and \"unless\"</html>");
+	inverseButton.setEnabled(true);
+	inverseButton.addActionListener(this);
+	inverseButton.setBorderPainted(false); // underline is hint enough that we can press it...looks cleaner
+        inverseButton.setName(INVERSE_BUTTON_NAME); // so test cases can find the component	
+
 	setLayout(new BoxLayout(this, BoxLayout.LINE_AXIS));
 	add(closeIcon);
 	add(Box.createRigidArea(new Dimension(5,0)));
 	add(caseButton);
 	add(Box.createRigidArea(new Dimension(5,0)));
-	add(new JLabel("Show data if "));
+	add(new JLabel("Show data "));
+	add(inverseButton);
 	add(Box.createRigidArea(new Dimension(5,0)));
 	searchField = new JTextField(25);
 	searchField.setToolTipText("A literal string, or a regular expression");
@@ -81,11 +95,15 @@
 	currentFilterSearch = null;
 	if(fs == null){
 	    caseButton.setEnabled(false);
+	    inverseButton.setEnabled(false);
 	    searchField.setEnabled(false);
 	    docPartOptions.setEnabled(false);
 	    return;
 	}
 
+	inverseButton.setEnabled(true);
+	inverseButton.setText(fs.getSelectionInversed() ? UNLESS_TEXT : IF_TEXT);
+
 	caseButton.setEnabled(true);
 	caseButton.setSelected(fs.getCaseSensitivity());
 
@@ -101,11 +119,30 @@
      * Called when the user has changed the xpath
      */
     public void actionPerformed(ActionEvent e){
-	if(e.getSource() == caseButton){
+	if(e.getSource() == inverseButton){
+	    // Toggle the label for the if/unless button
+	    if(inverseButton.getText().equals(IF_TEXT)){
+		inverseButton.setText(UNLESS_TEXT);
+		currentFilterSearch.setSelectionInversed(true);
+	    }
+	    else{
+		inverseButton.setText(IF_TEXT);
+		currentFilterSearch.setSelectionInversed(false);
+	    }
+	    contentPane.applyFilter(true);
+	    return;
+        }
+	else if(e.getSource() == caseButton){
 	    if(currentFilterSearch == null){
 	        return;
             }
             currentFilterSearch.setCaseSensitivity(caseButton.isSelected());
+	    if(caseButton.isSelected()){
+		caseButton.setToolTipText(CASE_SENSITIVE_MSG);
+	    }
+	    else{
+		caseButton.setToolTipText(CASE_INSENSITIVE_MSG);
+	    }
 	    contentPane.applyFilter(true);
 	    return;
         }
@@ -127,6 +164,7 @@
 	sb.replace(0, sb.length(), searchField.getText());
 	contentPane.applyFilter(true);
     }
+
     public void insertUpdate(DocumentEvent e){
 	if(currentFilterSearch == null){
 	    return;

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java,v
retrieving revision 1.24
retrieving revision 1.25
diff -u -r1.24 -r1.25
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java	2010/04/09 15:54:16	1.24
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java	2010/04/10 00:40:17	1.25
@@ -1239,7 +1239,6 @@
 	    popup.add(createServicePopupItem);
 	    popup.setVisible(true);	    
 	}
-	// todo: 
 	// The item below is mainly to allow X to be used in service Y if running service Z on X meets some filter criteria.
 	// This is a common task in bioinformatics workflows.
 	// Backtrack from data to input used for service that generated the data.
@@ -1510,12 +1509,15 @@
 	    }
 	}
 	
+	boolean inversed = fs.getSelectionInversed();
 	Map<String,Boolean> parentMatchingXPtrs = new LinkedHashMap<String,Boolean>();
 	for(String currXPtr: filterableNodes){
 	    for(Map.Entry<String,Boolean> matchingXPtr: matchingXPtrs.entrySet()){
 		if(matchingXPtr.getKey().startsWith(currXPtr+"/")){ // a parent of the matching data
 		    // No positive example yet?
-		    if(!parentMatchingXPtrs.containsKey(currXPtr) || !parentMatchingXPtrs.get(currXPtr).booleanValue()){
+		    if(!parentMatchingXPtrs.containsKey(currXPtr) || 
+		       !inversed && !parentMatchingXPtrs.get(currXPtr).booleanValue() ||
+		       inversed && parentMatchingXPtrs.get(currXPtr).booleanValue()){
 			System.err.println("Adding "+ matchingXPtr.getValue() + " for " + currXPtr);
 			parentMatchingXPtrs.put(currXPtr, matchingXPtr.getValue());
 		    }
@@ -1526,11 +1528,16 @@
 	matchingXPtrs.putAll(parentMatchingXPtrs);
 	for(String currXPtr: matchingXPtrs.keySet()){
 	    // Is part of the selection criteria, but doesn't match the regex
+	    boolean shouldFilter = false;
 	    if(!matchingXPtrs.get(currXPtr).booleanValue() &&
-	       // special condition: if "entire document" xpath is given, filter only at the job level
+	       // special condition: if "entire response" xpath is given, filter only at the job level
 	       (!currentSelectionXPath.equals(FilterSearch.SELECT_ALL_XPATH) || jobXPtrs.containsKey(currXPtr))){
-		filteredData.put(currXPtr, "todo");
+		shouldFilter = true;
 	    }
+	    if(!inversed && shouldFilter ||
+	       inversed && !shouldFilter){ 
+		filteredData.put(currXPtr, "todo");
+	    }	    
 	}
 
 	//todo: filter objects without the HAS field at all...



From gordonp at dev.open-bio.org  Sat Apr 10 00:40:18 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 9 Apr 2010 20:40:18 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004100040.o3A0eIZb014938@dev.open-bio.org>


gordonp
Fri Apr  9 20:40:17 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util
In directory dev.open-bio.org:/tmp/cvs-serv14854/src/main/ca/ucalgary/seahawk/util

Modified Files:
	DataFlowRecorder.java DataUtils.java FilterSearch.java 
Log Message:
Added support for filter inversion (boolean negation)
moby-live/Java/src/main/ca/ucalgary/seahawk/util DataFlowRecorder.java,1.3,1.4 DataUtils.java,1.2,1.3 FilterSearch.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataFlowRecorder.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataFlowRecorder.java	2010/04/09 15:58:22	1.3
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataFlowRecorder.java	2010/04/10 00:40:17	1.4
@@ -174,7 +174,8 @@
 	    String[] regexProcessorAndPorts = null;
 	    String filterKey = null;
 	    if(filter != null && filter.getFilterRegex().length() > 0){
-		filterKey = result.getKey()+"\n"+filter.getFilterRegex()+"\n"+filter.getSelectedXPath().getXPath();
+		filterKey = result.getKey()+"\n"+filter.getFilterRegex()+"\n"+
+		    filter.getSelectedXPath().getXPath()+"\n"+filter.getCaseSensitivity();
 	    }
 
 	    // Create the workflow output and data links
@@ -206,8 +207,10 @@
 			filter2Processor.put(filterKey, regexProcessorAndPorts);
 		    }
 
+		    // The proc has an output port for non-matches (penultimate index) and matches (ultimate index)
+		    int regexOutPort = regexProcessorAndPorts.length-(filter.getSelectionInversed() ? 2 : 1);
 		    datalinks.appendChild(createWorkflowOutputLinkElement(regexProcessorAndPorts[0],
-									  regexProcessorAndPorts[regexProcessorAndPorts.length-1],
+									  regexProcessorAndPorts[regexOutPort],
 									  uniqueOutputName,
 									  doc));
 		    break; // only one output when filter is attached: the XML doc
@@ -317,16 +320,18 @@
 		// where the filter and conditionalURL are optional 
 		data = sampleData.getUserData().toString().split("\t");
 		//options: selection + filter + cond, selection + cond, or cond only
-		if(data.length == 11 || data.length == 7 || data.length == 5){
+		if(data.length == 14 || data.length == 8 || data.length == 6){
 		    System.err.println("Adding conditional for " + resultURLString);
-		    String conditionURL = data[data.length-5];
-		    String conditionRegex = data[data.length-4];
-		    XPathOption conditionXPath = new XPathOption(data[data.length-3], data[data.length-2]);
-		    boolean caseSensitivity = Boolean.parseBoolean(data[data.length-1]);
-		    condPassProcessorAndPorts = createServiceConditionFilter(new URL(conditionURL), conditionRegex, conditionXPath, caseSensitivity,
+		    String conditionURL = data[data.length-6];
+		    String conditionRegex = data[data.length-5];
+		    XPathOption conditionXPath = new XPathOption(data[data.length-4], data[data.length-3]);
+		    boolean caseSensitivity = Boolean.parseBoolean(data[data.length-2]);
+		    boolean inverse = Boolean.parseBoolean(data[data.length-1]);
+		    condPassProcessorAndPorts = createServiceConditionFilter(new URL(conditionURL), conditionRegex, 
+									     conditionXPath, caseSensitivity, inverse,
 									     doc, inputPorts, processors, datalinks);
-		    String[] conditionlessData = new String[data.length-5];
-		    System.arraycopy(data, 0, conditionlessData, 0, data.length-5);
+		    String[] conditionlessData = new String[data.length-6];
+		    System.arraycopy(data, 0, conditionlessData, 0, data.length-6);
 		    data = conditionlessData;
 		}
 		else{
@@ -357,10 +362,10 @@
 		    feedingProcessorName = addWorkflowElements(dataSrcURL, doc, inputPorts, processors, datalinks);
 		}
 		
-		// Take into account data[2..5] if they are present, 
+		// Take into account data[2..6] if they are present, 
 		// which filter the data by a regex before any other activities happen
 		// Format of spec is regex <tab> xpath <tab> xpathTextDesc <tab> booleanForCaseSensitivity
-		if(data.length == 6){
+		if(data.length == 7){
 		    String[] origFeederProcessorAndPort = getPortFromURLRef(dataSrcURL,
 									    sampleData,
 									    feedingProcessorName,
@@ -370,9 +375,11 @@
 									    doc,
 									    false);
 		    
-		    // Lookup key is url \n regex \n xpath \n caseSensitivity
+		    // Lookup key is url \n regex \n xpath \n caseSensitivity 
+		    // (inverse selection uses same processor, different output port, so not part of the key)
 		    String[] regexProcessorAndPorts = null;
 		    String filterKey = dataSrcURLString+"\n"+data[2]+"\n"+data[3]+"\n"+data[5];
+		    boolean inversed = Boolean.parseBoolean(data[6]);
 		    if(filter2Processor.containsKey(filterKey)){ // filter already exists from another branch
 			regexProcessorAndPorts = filter2Processor.get(filterKey);
 		    }
@@ -389,7 +396,9 @@
 			filter2Processor.put(filterKey, regexProcessorAndPorts);
 		    }
 		    feedingProcessorName = regexProcessorAndPorts[0];
-		    feedingProcessorPort = regexProcessorAndPorts[regexProcessorAndPorts.length-1];  //last one is output
+		    // The proc has an output port for non-matches (penultimate index) and matches (ultimate index)
+		    int regexOutPort = regexProcessorAndPorts.length-(inversed ? 2 : 1);
+		    feedingProcessorPort = regexProcessorAndPorts[regexOutPort];  
 		}
 		
 		// getPortFromURLRef() may inject extra processors between the processorName and feedingProcessorName
@@ -921,6 +930,7 @@
 		// supertype of the output from the other service!		
 		if(namespace != null){
 		    MobyNamespace nsObj = MobyNamespace.getNamespace(namespace, getRegistryFromService(srcService));
+		    System.err.println("About to create namespace filter for "+ srcProcessor + " port " + portName + " when srcPort was " + srcPort);
 		    return createNamespaceFilter(nsObj, srcProcessor, portName, processors, datalinks, doc);
 		}
 		else if(xrefNs != null){
@@ -974,7 +984,7 @@
     // and passing the filter condition set on f.  Equivalent to if(f(X) matches f_filter){...}
     // returns [proc name, input port, output port]
     private String[] createServiceConditionFilter(URL conditionURL, String filterRegex, XPathOption filterXPath,
-						  boolean caseSensitive, Document doc,
+						  boolean caseSensitive, boolean inverse, Document doc,
 						  Element inputPorts, Element processors, Element datalinks)
 	throws Exception{
 
@@ -996,30 +1006,31 @@
  	}
 
  	String filterKey = dataSrcURLString+"\n"+filterRegex+"\n"+filterXPath.getXPath()+"\n"+caseSensitive;
- 	String[] regexFilterProcNameAndPort = null;
+ 	String[] regexFilterProcNameAndPorts = null;
  	//todo: gimpy loop below, as more than one service output would cause a trampling of regex output ports
  	for(MobyPrimaryData outputParam: service.getPrimaryOutputs()){
  	    // See if the filter on the conditional service has already been used in the workflow
  	    if(filter2Processor.containsKey(filterKey)){
- 		regexFilterProcNameAndPort = filter2Processor.get(filterKey);
+ 		regexFilterProcNameAndPorts = filter2Processor.get(filterKey);
  	    }
  	    else{
- 		regexFilterProcNameAndPort = createRegexFilter(filterRegex, 
+ 		regexFilterProcNameAndPorts = createRegexFilter(filterRegex, 
  							       filterXPath,
 							       caseSensitive, 
  							       processorName,
  							       getPortName(outputParam, true),
 							       0, //depth of list desired (will return match count)
  							       processors, datalinks, doc);
- 		filter2Processor.put(filterKey, regexFilterProcNameAndPort);
+ 		filter2Processor.put(filterKey, regexFilterProcNameAndPorts);
  	    }
  	}
 
 	// We need to flatten the 2-deep list generated by the regex filter's cross product
 	String[] beanShellFlattenerProcNameAndPorts = addListFlattenBeanShell(processors, doc);
 
-	datalinks.appendChild(createDataLinkElement(regexFilterProcNameAndPort[0],
-						    regexFilterProcNameAndPort[1],
+	int regexOutPort = regexFilterProcNameAndPorts.length-(inverse ? 2 : 1);
+	datalinks.appendChild(createDataLinkElement(regexFilterProcNameAndPorts[0],
+						    regexFilterProcNameAndPorts[regexOutPort],
 						    beanShellFlattenerProcNameAndPorts[0], 
 						    beanShellFlattenerProcNameAndPorts[1],
 						    doc));
@@ -1068,7 +1079,9 @@
 						    beanShellFilterProcNameAndPorts[0], 
 						    beanShellFilterProcNameAndPorts[4],
 						    doc)); 
-	return new String[]{beanShellFilterProcNameAndPorts[0], beanShellFilterProcNameAndPorts[5]};	
+	return new String[]{beanShellFilterProcNameAndPorts[0], 
+			    beanShellFilterProcNameAndPorts[5], // false (non-matching) output
+			    beanShellFilterProcNameAndPorts[6]}; // true (matching) output
     }
     
     private String[] createXrefParser(MobyNamespace nsObj, String srcProcessor, String srcPort, 
@@ -1090,6 +1103,7 @@
 	throws Exception{
 
 	String decompKey = srcProcessor+"\n"+srcPort+"\n"+xpath;
+	System.err.println("Decomp key is " + decompKey);
 	// Has this decomp already been created in another branch?
 	if(decomp2Processor.containsKey(decompKey)){
 	    return decomp2Processor.get(decompKey);
@@ -1108,7 +1122,7 @@
 						    beanShellFilterProcNameAndPorts[0], 
 						    beanShellFilterProcNameAndPorts[2],
 						    doc)); 
-	String[] procSpec =  new String[]{beanShellFilterProcNameAndPorts[0], beanShellFilterProcNameAndPorts[3]};
+	String[] procSpec = new String[]{beanShellFilterProcNameAndPorts[0], beanShellFilterProcNameAndPorts[3]};
 	decomp2Processor.put(decompKey, procSpec); //in case we need to reuse it in another branch
 	return procSpec;
     }
@@ -1453,10 +1467,12 @@
 	inputTypes.put("case_sensitive", "text/plain");
 	Map<String,String> outputsMap = new LinkedHashMap<String,String>();
 	if(listDepth == 0){
-	    outputsMap.put("matchCount", "0");
+	    outputsMap.put("FALSE_matchCount", "0");
+	    outputsMap.put("TRUE_matchCount", "0");
         }
         else{
-            outputsMap.put("nodelistAsXML", ""+listDepth);
+            outputsMap.put("FALSE_nodelistAsXML", ""+listDepth);
+            outputsMap.put("TRUE_nodelistAsXML", ""+listDepth);
         }
 
 	return addBeanShell(beanShellProcName, "cross",
@@ -1991,8 +2007,9 @@
 	    }
 	    regexFilterScript = HTMLUtils.getURLContents(scriptURL);
 	}
-	if(listDepth == 0){// list to scalar conversion
-	    return regexFilterScript+"\nString matchCount = \"\"+nodelistAsXML.size();";
+	if(listDepth == 0){// list to scalar conversions
+	    return regexFilterScript+"\nString TRUE_matchCount = \"\"+TRUE_nodelistAsXML.size();\n"+
+		                     "\nString FALSE_matchCount = \"\"+FALSE_nodelistAsXML.size();\n";
         }
         else{
  	    return regexFilterScript;

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataUtils.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataUtils.java	2010/04/09 15:57:46	1.2
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataUtils.java	2010/04/10 00:40:17	1.3
@@ -117,7 +117,8 @@
 		    if(newFilter != null){
 			XPathOption xsel = newFilter.getSelectedXPath();
 			newProvenanceData += "\t"+newFilter.getFilterRegex()+
-			    "\t"+xsel.getXPath()+"\t"+xsel.getDesc()+"\t"+newFilter.getCaseSensitivity();
+			    "\t"+xsel.getXPath()+"\t"+xsel.getDesc()+"\t"+
+			    newFilter.getCaseSensitivity()+"\t"+newFilter.getSelectionInversed();
 		    }
 		    pi.setData(attr_val[0]+"=\""+newProvenanceData+"\"");
 		}
@@ -640,7 +641,8 @@
 	
 	if(fs != null && fs.getFilterRegex().length() > 0){
 	    XPathOption xsel = fs.getSelectedXPath();
-	    userData.append("\t"+fs.getFilterRegex()+"\t"+xsel.getXPath()+"\t"+xsel.getDesc()+"\t"+fs.getCaseSensitivity());
+	    userData.append("\t"+fs.getFilterRegex()+"\t"+xsel.getXPath()+"\t"+xsel.getDesc()+"\t"+
+			    fs.getCaseSensitivity()+"\t"+fs.getSelectionInversed());
 	}
 	mobyData.setUserData(userData.toString());
     }
@@ -653,7 +655,8 @@
 	String filterSpec = "";
 	if(filter != null && filter.getFilterRegex().length() > 0){
 	    XPathOption xsel = filter.getSelectedXPath();
-	    filterSpec = "\t"+filter.getFilterRegex()+"\t"+xsel.getXPath()+"\t"+xsel.getDesc()+"\t"+filter.getCaseSensitivity();
+	    filterSpec = "\t"+filter.getFilterRegex()+"\t"+xsel.getXPath()+"\t"+xsel.getDesc()+"\t"+
+		filter.getCaseSensitivity()+"\t"+filter.getSelectionInversed();
 	}
 	if(mdi.getUserData() != null){
 	    mdi.setUserData(mdi.getUserData().toString()+"\t"+conditionalOutputURL+filterSpec);

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/FilterSearch.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/FilterSearch.java	2010/04/09 15:48:19	1.3
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/FilterSearch.java	2010/04/10 00:40:17	1.4
@@ -21,6 +21,7 @@
 
     private URL docURL;
     private boolean caseSensitivity = false;
+    private boolean inverseSelection = false;
     private StringBuffer filterRegex;
     private Vector<XPathOption> xpathOptions;
     private int xpathSelected = 0;
@@ -74,6 +75,14 @@
 	}
     }
 
+    public boolean getSelectionInversed(){
+	return inverseSelection;
+    }
+
+    public void setSelectionInversed(boolean inversed){
+	inverseSelection = inversed;
+    }
+
     public boolean getCaseSensitivity(){
 	return caseSensitivity;
     }



From gordonp at dev.open-bio.org  Sat Apr 10 22:42:09 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Sat, 10 Apr 2010 18:42:09 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004102242.o3AMg9nE014502@dev.open-bio.org>


gordonp
Sat Apr 10 18:42:09 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data
In directory dev.open-bio.org:/tmp/cvs-serv14466/src/main/org/biomoby/shared/data

Modified Files:
	MobyDataObject.java 
Log Message:
Improved equals() for base object equivalency...value not instance based
moby-live/Java/src/main/org/biomoby/shared/data MobyDataObject.java,1.26,1.27
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataObject.java,v
retrieving revision 1.26
retrieving revision 1.27
diff -u -r1.26 -r1.27
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataObject.java	2008/01/07 22:11:36	1.26
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataObject.java	2010/04/10 22:42:09	1.27
@@ -302,7 +302,7 @@
     public boolean equals(Object passedInObject) throws ClassCastException{
       Object ourObject = getObject();
       if(passedInObject != null && passedInObject instanceof MobyDataObject){
-	  if(((MobyDataObject) passedInObject).getDataType() == getDataType()){
+	  if(((MobyDataObject) passedInObject).getDataType().equals(getDataType())){
 	      // An object of the same class.  See if their XMLs are equivalent.
 	      int ourOldXMLMode = getXmlMode();
 	      int itsOldXMLMode = ((MobyDataObject) passedInObject).getXmlMode();



From gordonp at dev.open-bio.org  Sun Apr 11 01:58:05 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Sat, 10 Apr 2010 21:58:05 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004110158.o3B1w59N019017@dev.open-bio.org>


gordonp
Sat Apr 10 21:58:05 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services
In directory dev.open-bio.org:/tmp/cvs-serv18981/src/main/ca/ucalgary/seahawk/services

Modified Files:
	MobyClient.java 
Log Message:
Added regex support for IUPAC monosacchride residues (\M)
moby-live/Java/src/main/ca/ucalgary/seahawk/services MobyClient.java,1.25,1.26
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/MobyClient.java,v
retrieving revision 1.25
retrieving revision 1.26
diff -u -r1.25 -r1.26
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/MobyClient.java	2010/03/17 20:21:55	1.25
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/MobyClient.java	2010/04/11 01:58:05	1.26
@@ -1391,14 +1391,15 @@
 
     /**
      * Converts seahawk-specific regex syntax into generic Java syntax (e.g \N becomes a
-     * match for any IUPAC DNA character, \P any amino acid).  We pass in the member map so that
+     * match for any IUPAC DNA character, \P any amino acid, \M for any monosacchiride abbreviation).  
+     * We pass in the member map so that
      * this method can populate the last field of rules that inherit complex members (by virtue 
      * of using the capture group whose values is derived from \p{ruleName}), with ruleName 
      */
     protected String processRegExp(String regex, Map<String,String[]> membersMap) throws Exception{
 	String returnValue = regex.replaceAll("\\\\N", "[acgtunxACGTUNX]")
-	    .replaceAll("\\\\P", "[ARNDCQEGHILKMFPSTWYVBZXarndcqeghilkmfpstwyvbz*]");
-	
+	    .replaceAll("\\\\P", "[ARNDCQEGHILKMFPSTWYVBZXarndcqeghilkmfpstwyvbz*]")
+	    .replaceAll("\\\\M", "(?:Abe|IdoA|All|Lyx|Alt|Man|Api|Mur|Ara|Neu|Ara-ol|Neu5Ac|dRib|Neu2en5Ac|Fru|Neu5Gc|Fuc|Kdo|Fuc-ol|Rha|Gal|Rha3,4Me2|GalN|Psi|GalNAc|Qui|B-D-Galp4S|Rib|Glc|Rib5P|GlcN|Ribulo|Rul|GlcN3N|Sor|Glc-ol|Tag|GlcNAc|Tal|GlcA|Xyl|GlcpA6Et|Xylulo|Xul|Gul|Xyl2CMe|Ido)");
 	// Now see if there are any references to other patterns (by rule name) 
 	// with the \p{} syntax specific to Seahawk
 	Pattern charClassPattern = Pattern.compile("\\\\p\\{([A-Za-z0-9]+)\\}");



From gordonp at dev.open-bio.org  Sun Apr 11 02:00:02 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Sat, 10 Apr 2010 22:00:02 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004110200.o3B202wI019153@dev.open-bio.org>


gordonp
Sat Apr 10 22:00:02 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv19034/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	MobyObjectTransferHandler.java 
Log Message:
Added native support for primitive datatype recognition in text transfers
moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyObjectTransferHandler.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyObjectTransferHandler.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyObjectTransferHandler.java	2007/12/17 18:44:13	1.3
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyObjectTransferHandler.java	2010/04/11 02:00:02	1.4
@@ -218,7 +218,30 @@
 	for(String fieldName: acceptableData.keySet()){
 	    int itemCount = 1;
 	    MobyDataType desiredDataType = acceptableData.get(fieldName).getDataType();
+	    String dataTypeName = desiredDataType.getName();
 	    System.err.println("Checking text for field " + fieldName+ ", data type " + desiredDataType.getName());
+
+	    // trivial data creations first ...
+	    if(dataTypeName.equals(MobyTags.MOBYSTRING)){
+		foundData.put(fieldName+"#"+itemCount++, new MobyDataString(text));
+	    }
+	    else if(dataTypeName.equals(MobyTags.MOBYBOOLEAN) && 
+		    text.matches("(true|True|TRUE|1|yes|Yes|YES|false|False|FALSE|0|no|No|NO)")){
+		foundData.put(fieldName+"#"+itemCount++, 
+			      new MobyDataBoolean(text.matches("(true|True|TRUE|1|yes|Yes|YES)")));
+	    }
+	    else if(dataTypeName.equals(MobyTags.MOBYINTEGER) && 
+		    text.matches("\\d+")){
+		foundData.put(fieldName+"#"+itemCount++, new MobyDataInt("", text));
+	    }
+	    else if(dataTypeName.equals(MobyTags.MOBYFLOAT) && 
+		    text.matches("\\d+(?:\\.\\d*)?(?:[eE][\\-\\+]?\\d+)?")){
+		foundData.put(fieldName+"#"+itemCount++, new MobyDataFloat(text));
+	    }
+	    else if(dataTypeName.equals(MobyTags.MOBYFLOAT) && 
+		    text.matches("(?:19|20)\\d\\d-(?:0[1-9]|1[012])-([012][1-9]|3[01])")){
+		foundData.put(fieldName+"#"+itemCount++, new MobyDataDateTime(text));
+	    }
 	    MobyDataObject[] textData = client.getMobyObjects(text, desiredDataType);
 	    if(textData != null){
 		System.err.println("Found " + textData.length + " matches");



From gordonp at dev.open-bio.org  Sun Apr 11 02:20:46 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Sat, 10 Apr 2010 22:20:46 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004110220.o3B2Kkwu020079@dev.open-bio.org>


gordonp
Sat Apr 10 22:20:46 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources
In directory dev.open-bio.org:/tmp/cvs-serv20043/src/main/ca/ucalgary/seahawk/resources

Modified Files:
	mobyBuilderRules.xml 
Log Message:
Added LINUCS carbohydrate sequence recognition, for fun
moby-live/Java/src/main/ca/ucalgary/seahawk/resources mobyBuilderRules.xml,1.10,1.11
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources/mobyBuilderRules.xml,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources/mobyBuilderRules.xml	2010/03/17 20:21:55	1.10
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources/mobyBuilderRules.xml	2010/04/11 02:20:46	1.11
@@ -66,6 +66,16 @@
   <member value="Length" whitespace="strip">string-length('$1')</member>
 </object>
 
+<!-- \M is IUPAC monosaccharide residue shorthand -->
+<object>
+  <regex>\[\]\[\\S+\]\{.*?(?:([ab]-D-)?\M.?[\x20\(\)\[\]\-\+0-9\{\}]+){3,}</regex>
+  <datatype value="LINUCS"/>
+  <namespace>
+    <ns value="unknown">''</ns>
+  </namespace>
+  <member value="sequence" whitespace="strip">$0</member>
+</object>
+
 <!-- ABI sequence trace's magic signature at start of file -->
 <object>
   <regex>\AABIF.*\z</regex>



From gordonp at dev.open-bio.org  Sun Apr 11 02:22:07 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Sat, 10 Apr 2010 22:22:07 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004110222.o3B2M7Dc020123@dev.open-bio.org>


gordonp
Sat Apr 10 22:22:06 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv20087/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	MobyDataObjectWidget.java 
Log Message:
Better populated data field description
moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyDataObjectWidget.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyDataObjectWidget.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyDataObjectWidget.java	2007/12/06 17:26:26	1.3
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyDataObjectWidget.java	2010/04/11 02:22:06	1.4
@@ -18,6 +18,7 @@
  */
 public class MobyDataObjectWidget extends JLabel implements MobyObjectReceiver, MobyContentProducer{
     public static final int PARAM_TOOLTIP_WIDTH = 50;
+    public static final int MAX_DATA_DESC = 30;
     public static final Color INSTANTIATED_FG_COLOUR = Color.DARK_GRAY;
     public static final Color UNINSTANTIATED_FG_COLOUR = Color.RED;
     public static final String INSTANTIATED_ICON_RESOURCE = "ca/ucalgary/seahawk/resources/images/checkmark.gif";
@@ -150,7 +151,14 @@
 		labelText = name+": Collection("+dataType.getName()+") -- "+actualData.getName();
 	    }
 	    else{
-		labelText = name+": "+dataType.getName()+" -- "+actualData.getName();
+		String display = actualData.getName();
+		if(display == null || display.trim().length() == 0){
+		    display = ((MobyDataInstance) actualData).getObject().toString();
+		}
+		if(display.length() > MAX_DATA_DESC){
+		    display = display.substring(0, MAX_DATA_DESC-3)+"...";
+		}
+		labelText = name+": "+dataType.getName()+" -- "+display;
 	    }
 	    tipText = dataType.getDescription();
 	    if(tipText == null || tipText.length() == 0){



From gordonp at dev.open-bio.org  Sun Apr 11 02:25:03 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Sat, 10 Apr 2010 22:25:03 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004110225.o3B2P3eJ020209@dev.open-bio.org>


gordonp
Sat Apr 10 22:25:03 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv20173/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	MobyContentClipboard.java 
Added Files:
	DataImportChoiceDialog.java DataImportChoiceListener.java 
Log Message:
Improved data import to clipboard UI
moby-live/Java/src/main/ca/ucalgary/seahawk/gui DataImportChoiceDialog.java,NONE,1.1 DataImportChoiceListener.java,NONE,1.1 MobyContentClipboard.java,1.9,1.10
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentClipboard.java,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentClipboard.java	2010/04/09 15:51:53	1.9
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentClipboard.java	2010/04/11 02:25:03	1.10
@@ -6,6 +6,7 @@
 
 import org.biomoby.client.MobyRequestEventHandler;
 import org.biomoby.shared.MobyDataType;
+import org.biomoby.shared.MobyNamespace;
 import org.biomoby.shared.data.*;
 import org.biomoby.shared.parser.MobyTags;
 
@@ -20,12 +21,13 @@
 import java.io.FileOutputStream;
 import java.net.URL;
 import java.util.*;
+import java.util.regex.Pattern;
 
 /**
  * The clipboard is a special tab that holds a query with a MOBY Collection
  * that the user can add and subtract MobyDataInstances from.
  */
-public class MobyContentClipboard extends MobyContentPane{
+public class MobyContentClipboard extends MobyContentPane implements DataImportChoiceListener{
     public final static String CLEAR_CLIPBOARD_OPTION = "Clear Clipboard";
     public final static String CLIPBOARD_FILE_NAME = "SeaHawkClipboard";
     public final static String CLIPBOARD_COLLECTION_NAME = "Clipboard Collection";
@@ -41,7 +43,13 @@
     private File clipboardFile;
     private MobyDataJob query;  // lump all data into one query
     private MobyDataObjectSet collection;  // lump all data into one collection
-    private String previousImportDataType = null;
+    private MobyDataType previousImportDataType = null;
+    private MobyNamespace previousImportNS = null;
+
+    private Pattern commentRegex;
+    private Pattern scriptRegex;
+    private Pattern styleRegex;
+    private Pattern tagRegex;
 
     // Clipboard editing variables
     private JMenuItem deleteDataPopupItem;
@@ -88,6 +96,12 @@
 	setTransferHandler(new FileAndTextTransferHandler(cGUI, false)); // false = open data in current tab
 	editorPane.setTransferHandler(getTransferHandler());
 
+	// Setup regexes used for stripping HTML docs of their markup (for data pasting ops)
+	commentRegex = Pattern.compile("<!--.*?-->", Pattern.MULTILINE | Pattern.DOTALL);
+	scriptRegex = Pattern.compile("<script.*?</script>",  Pattern.MULTILINE | Pattern.DOTALL | Pattern.CASE_INSENSITIVE);
+	styleRegex = Pattern.compile("<style.*?</style>",  Pattern.MULTILINE | Pattern.DOTALL | Pattern.CASE_INSENSITIVE);
+	tagRegex = Pattern.compile("<.*?>", Pattern.MULTILINE | Pattern.DOTALL);
+
 	sGUI.setClipboard(this);	
     }
 
@@ -248,7 +262,11 @@
 	    logger.warn("Could not read contents of the URL to import to the clipboard ("+u+"):" +e);
 	    return;
 	}
-	
+	if(urlContents.indexOf("<html") != -1 || urlContents.indexOf("<HTML") != -1){
+	    urlContents = tagRegex.matcher(commentRegex.matcher(styleRegex.matcher(scriptRegex.matcher(urlContents).replaceAll("")).replaceAll("")).replaceAll("")).replaceAll("");
+	}
+	System.err.println(urlContents);
+
 	MobyDataType targetDataType = null;
 	if(collection != null){
 	    targetDataType = collection.getDataType();
@@ -277,47 +295,28 @@
 		return;
 	    }
 	}
-	// Otherwise we need to ask the user what data to import ("Paste as...")
-	// Implicitly...mobyDataFound.length > 1
-	String[] selectionValues = new String[mobyDataFound.length];
-	for(int i = 0; i < mobyDataFound.length; i++){
-	    selectionValues[i] = mobyDataFound[i].getDataType().getName();
-	    if(MobyTags.MOBYOBJECT.equals(selectionValues[i]) &&
-	       mobyDataFound[i].getPrimaryNamespace() != null){
-		selectionValues[i] += " (" + mobyDataFound[i].getPrimaryNamespace().getName() + ")";
-	    }
-	}
-	// Sort alphabetically
-	//Arrays.sort(selectionValues);
-	String initialSelectionValue = selectionValues[0];
-	if(previousImportDataType != null){
-	    for(String selectionValue: selectionValues){
-		if(previousImportDataType.equals(selectionValue)){
-		    initialSelectionValue = selectionValue;
-		    break;
-		}
-	    }
-	}
-	String selection = (String) JOptionPane.showInputDialog(this, 
-								"Paste data as...", 
-								"Data import choice", 
-								JOptionPane.PLAIN_MESSAGE, 
-								(Icon) null, 
-								selectionValues, 
-								initialSelectionValue);
-	if(selection == null){
-	    logger.warn("No data type for import selected, abandoning import");
+
+	// Otherwise we need the user to choose
+	new DataImportChoiceDialog(contentGUI, mobyDataFound, previousImportDataType, previousImportNS, this);
+    }
+
+    // Callback once user has selected the data to import from the DataImportChoiceDialog
+    public void importConfirmed(DataImportChoiceDialog dialog, MobyDataObject[] selectedData){	
+	if(selectedData == null){
+	    logger.warn("Got null for import selection, abandoning import");
 	    return;
 	}
-	for(int i = 0; i < selectionValues.length; i++){
-	    if(selection.equals(selectionValues[i])){
-		addCollectionData(mobyDataFound[i]);
-		previousImportDataType = selection;
-		return;
+	for(int i = 0; i < selectedData.length; i++){
+	    addCollectionData(selectedData[i], i == selectedData.length-1); // only update display on last import
+	    previousImportDataType = selectedData[i].getDataType();
+	    if(selectedData[i].getPrimaryNamespace() != null){
+		previousImportNS = selectedData[i].getPrimaryNamespace();
 	    }
 	}
     }
 
+    public void importCanceled(DataImportChoiceDialog dialog){}
+
     public boolean hasXMLSource(){
 	return true;
     }



From gordonp at dev.open-bio.org  Sun Apr 11 20:15:28 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Sun, 11 Apr 2010 16:15:28 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004112015.o3BKFS3Y017966@dev.open-bio.org>


gordonp
Sun Apr 11 16:15:28 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv17912/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	MobyContentPane.java 
Log Message:
Updates for proper support of data filtering when submitting to forward services
moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyContentPane.java,1.25,1.26
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java,v
retrieving revision 1.25
retrieving revision 1.26
diff -u -r1.25 -r1.26
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java	2010/04/10 00:40:17	1.25
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java	2010/04/11 20:15:28	1.26
@@ -532,7 +532,7 @@
 		isContentsXML = true;
 		// Is it the second stage of wrapping, where data results are being seen?
 		if(urlString.indexOf(WRAPPING_RESULTFILE_PREFIX) != -1){
-		    System.err.println("Wrapping service results");
+		    //System.err.println("Wrapping service results");
 		    isWrapping = true;
 		}
 		else{
@@ -1191,7 +1191,7 @@
 
 	// Complex case, load the doc fragment from the MOBY XML source file
 	if(docFragID != null && docFragID.length() > 0 && !targetURL.getHost().equals("moby")){
-	    return DataUtils.loadMobyDataFromXPointer(targetURL, filterHistory.get(getCurrentURL()));
+	    return DataUtils.loadMobyDataFromXPointer(targetURL, filteredData, filterHistory.get(getCurrentURL()));
 	}
 
 	// Simple case, build the object using the values encoded in the URL itself.
@@ -1256,8 +1256,13 @@
 
 	    // Get the input data for the *previous* service
 	    MobyDataJob inputData = DataUtils.getInputSample(srcDoc, SeahawkOptions.getRegistry());
+	    if(inputData == null){
+		// should only happen if Moby XML was loaded manually by a user, otherwise we've recorded this info...
+		logger.warn("No previous service info in Moby XML, 'previous input' option will not be displayed");
+		return;
+	    }
 	    for(MobyDataInstance previousMDI: inputData.getPrimaryData()){		
-		// add conditional of the current service as a criteria in user data for each previousMDI, 
+		    // add conditional of the current service as a criteria in user data for each previousMDI, 
 		// so PbE will properly reflect the logic of if(f1(x) matches filter){f2(x)}
 		DataUtils.addUserData(previousMDI, srcURL, getFilter());
 
@@ -1478,11 +1483,11 @@
                     }
 		else if(regex.matcher(((Element) node).getTextContent()).find()){
 		    matchingXPtrs.put(elementXPtr, Boolean.TRUE);
-		    System.err.println("Adding " + elementXPtr + " as " + matchingXPtrs.get(elementXPtr));
+		    //System.err.println("Adding " + elementXPtr + " as " + matchingXPtrs.get(elementXPtr));
 		}
 		else{
 		    matchingXPtrs.put(elementXPtr, Boolean.FALSE);
-		    System.err.println("Adding " + elementXPtr + " as " + matchingXPtrs.get(elementXPtr));
+		    //System.err.println("Adding " + elementXPtr + " as " + matchingXPtrs.get(elementXPtr));
 		}
 	    }
 	    else if(node instanceof Attr){
@@ -1494,12 +1499,12 @@
 		else if(regex.matcher(((Attr) node).getValue()).find()){
 		    // Mark the element to which the attribute belongs
 		    matchingXPtrs.put(attrParentXPtr, Boolean.TRUE);
-		    System.err.println("Adding " + attrParentXPtr + " attr parent as " + matchingXPtrs.get(attrParentXPtr));
+		    //System.err.println("Adding " + attrParentXPtr + " attr parent as " + matchingXPtrs.get(attrParentXPtr));
 		}
 		// so false doesn't override true for multi-attr elements
 		else if(!matchingXPtrs.containsKey(attrParentXPtr)){ 
 		    matchingXPtrs.put(attrParentXPtr, Boolean.FALSE);
-		    System.err.println("Adding " + attrParentXPtr + " attr parent as " + matchingXPtrs.get(attrParentXPtr));
+		    //System.err.println("Adding " + attrParentXPtr + " attr parent as " + matchingXPtrs.get(attrParentXPtr));
 		}
 		
 	    }
@@ -1518,7 +1523,7 @@
 		    if(!parentMatchingXPtrs.containsKey(currXPtr) || 
 		       !inversed && !parentMatchingXPtrs.get(currXPtr).booleanValue() ||
 		       inversed && parentMatchingXPtrs.get(currXPtr).booleanValue()){
-			System.err.println("Adding "+ matchingXPtr.getValue() + " for " + currXPtr);
+			//System.err.println("Adding "+ matchingXPtr.getValue() + " for " + currXPtr);
 			parentMatchingXPtrs.put(currXPtr, matchingXPtr.getValue());
 		    }
 		}
@@ -1732,7 +1737,7 @@
 	List<javax.swing.text.Element> links = new Vector<javax.swing.text.Element>();
 	for(int i = 0; i < el.getElementCount(); i++){
 	    javax.swing.text.Element childEl = el.getElement(i);
-	    System.err.println("Found child element " + childEl.getName());
+	    //System.err.println("Found child element " + childEl.getName());
 	    if(HTML.Tag.A.equals(childEl.getName())){
 		links.add(childEl);
 	    }
@@ -1979,10 +1984,10 @@
 	// normally it'd go to mouseDragged, but sometimes that's flakey so check manually for the 
 	// mouse button being down here.
 	if(overHyperlink && (e.getModifiersEx() & MouseEvent.BUTTON1_DOWN_MASK) == MouseEvent.BUTTON1_DOWN_MASK){
-	    System.err.println("Got wonky drag");
+	    //System.err.println("Got wonky drag");
 	    lastHyperlinkDragged = lastHyperlinkHovered;
 	    status.setText("Drop the hyperlink onto a Web form field to populate it");
-	    System.err.println("Dragging "+lastHyperlinkDragged);
+	    //System.err.println("Dragging "+lastHyperlinkDragged);
 	    getTransferHandler().exportAsDrag(this, e, TransferHandler.COPY);
 	}
 	else if(dragging){
@@ -1991,6 +1996,6 @@
     }
 
     public void lostOwnership(Clipboard clipboard, Transferable contents){
-	System.err.println("Lost clipboard ownership");
+	//System.err.println("Lost clipboard ownership");
     }
 }



From gordonp at dev.open-bio.org  Sun Apr 11 20:15:28 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Sun, 11 Apr 2010 16:15:28 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004112015.o3BKFSqr017948@dev.open-bio.org>


gordonp
Sun Apr 11 16:15:28 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util
In directory dev.open-bio.org:/tmp/cvs-serv17912/src/main/ca/ucalgary/seahawk/util

Modified Files:
	DataUtils.java 
Added Files:
	XPointerResolver.java 
Log Message:
Updates for proper support of data filtering when submitting to forward services
moby-live/Java/src/main/ca/ucalgary/seahawk/util XPointerResolver.java,NONE,1.1 DataUtils.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataUtils.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataUtils.java	2010/04/10 00:40:17	1.3
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataUtils.java	2010/04/11 20:15:28	1.4
@@ -450,7 +450,14 @@
 	}	
     }
 
-    public static MobyDataInstance loadMobyDataFromXPointer(URL targetURL, FilterSearch docFilter){
+    /**
+     * Get the data instance object associated with a given XPointer into a Moby XML doc
+     *
+     * @param targetURL of the form URLpath#/1/1/2/1 where /1/1/2/1 is an XPointer, or an standard xpath, to the part of the Moby XML doc to deserialize
+     * @param filteredXPtrs a map of the xpointers to data that should NOT be deserialized if children of the targetURL XPointer
+     * @param docFilter the current filter applied to the document in targetURL
+     */
+    public static MobyDataInstance loadMobyDataFromXPointer(URL targetURL, Map<String,String> filteredXPtrs, FilterSearch docFilter){
 	// Are we dealing with a simple object or a complex one?
 	MobyDataInstance mobyData = null;
 	
@@ -492,13 +499,35 @@
 	    return null;
 	}
 	
+	// Remove the filtered data from the doc before deserializing to a moby data instance
+	// That way the request actually reflects what is shown on the screen to the user.
+	if(filteredXPtrs != null){
+	    // Mark and sweep (if we just deleted as we found node, the XPointers could be 
+	    // wrong as they refer to ordinality)
+	    Vector<Node> nodesToDelete = new Vector<Node>();
+	    for(String xptr: filteredXPtrs.keySet()){
+		nodesToDelete.add(XPointerResolver.getNodeFromXPointer(domDoc, xptr));
+	    }
+
+	    // Delete
+	    for(Node nodeToDelete: nodesToDelete){
+		Node parent = nodeToDelete.getParentNode();
+		parent.removeChild(nodeToDelete);
+		// Get rid of Simple parents of deleted nodes, because empty Simple
+		// tags are not okay in Moby (causes parsing error)
+		if(MobyTags.SIMPLE.equals(parent.getLocalName())){
+		    parent.getParentNode().removeChild(parent);
+		}
+	    }
+	}
+
 	// Build and run the XPath statement
 	Element mobyObject = null;
 	NodeList idSearchResult = null;
 	Object xobject = null;
 	try{
 	    xobject = XPathFactory.newInstance().newXPath().evaluate(childXPath, 
-								     new InputSource(targetURL.openStream()), 
+								     domDoc, 
 								     XPathConstants.NODESET);
 						
 	    // Check the results



From gordonp at dev.open-bio.org  Wed Apr 14 22:02:05 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Wed, 14 Apr 2010 18:02:05 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004142202.o3EM252P007075@dev.open-bio.org>


gordonp
Wed Apr 14 18:02:04 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util
In directory dev.open-bio.org:/tmp/cvs-serv7013/src/main/ca/ucalgary/seahawk/util

Modified Files:
	DataUtils.java FilterSearch.java 
Added Files:
	MobyPayloadRequestListener.java MutableNodeList.java 
Log Message:
Changes to implement explicit 'for each' loops over Seahawk data lists (not quite functional yet, but compiles)
moby-live/Java/src/main/ca/ucalgary/seahawk/util MobyPayloadRequestListener.java,NONE,1.1 MutableNodeList.java,NONE,1.1 DataUtils.java,1.4,1.5 FilterSearch.java,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataUtils.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataUtils.java	2010/04/11 20:15:28	1.4
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataUtils.java	2010/04/14 22:02:04	1.5
@@ -4,6 +4,7 @@
 import java.net.URL;
 import java.util.*;
 import java.util.logging.*;
+import java.util.regex.*;
 import javax.xml.parsers.*;
 import javax.xml.transform.*;
 import javax.xml.transform.dom.DOMSource;
@@ -34,8 +35,12 @@
     public static final String TEMP_FILE_PREFIX = "seahawk";
     private static final String OUTPUT_SUFFIX = ".out.xml";
     private static final String INPUT_SUFFIX = ".in.xml";
-    private static DocumentBuilder docBuilder;
+    public static DocumentBuilder docBuilder;
     private static Transformer identityTransform;
+    public static XPathFactory xPathFactory;
+
+    public static final String ARTICLE_PEERS_MODE = "article_peers";
+    public static final String DATATYPE_PEERS_MODE = "datatype_peers";
 
     private static Logger logger = Logger.getLogger(DataUtils.class.getName());
 
@@ -54,6 +59,8 @@
 	} catch(Exception e){
 	    logger.log(Level.SEVERE, "Cannot get identity XSLT transform from configuration", e);
 	}
+
+	xPathFactory = XPathFactory.newInstance();
     }
 
     /**
@@ -176,7 +183,7 @@
 		// User data has the form srcURL#XpathSelectCriteria <tab> xptrActualDataSubmitted <tab> regexFilter 
 		// where the filter is optional 
 		String[] data = sampleData.getUserData().toString().split("\t");
-		System.err.println("Forward user data is " + sampleData.getUserData().toString());
+		//System.err.println("Forward user data is " + sampleData.getUserData().toString());
 		URL dataSrcURL = null;
 		try{
 		    dataSrcURL = new URL(data[0]);
@@ -437,7 +444,7 @@
 						"sync: the instance job '" + jobName + 
 						"' has no parameter '" + paramName + "'");
 			}
-			System.err.println("Setting user data val to " + attrValue + " for " + paramName);
+			//System.err.println("Setting user data val to " + attrValue + " for " + paramName);
       			contentInstance.get(jobName).get(paramName).setUserData(attrValue);		    
 		    }
 		    else{
@@ -451,24 +458,47 @@
     }
 
     /**
-     * Get the data instance object associated with a given XPointer into a Moby XML doc
+     * Loads targetURL, minus the nodes specified by the xpath keys in filteredXPtrs (map values are not currently used).
+     */
+    public static void filterDoc(Document domDoc, Map<String,String> filteredXPtrs){
+	 
+	if(domDoc == null){
+	    logger.log(Level.SEVERE, "Error: Could not get MOBY document as DOM (empty or malformed document?)");
+	    return;
+	}
+	
+	// Remove the filtered data from the doc before deserializing to a moby data instance
+	// That way the request actually reflects what is shown on the screen to the user.
+	if(filteredXPtrs != null){
+	    // Mark and sweep (if we just deleted as we found nodes, the XPointers could be 
+	    // wrong as they refer to ordinality)
+	    Vector<Node> nodesToDelete = new Vector<Node>();
+	    for(String xptr: filteredXPtrs.keySet()){
+		nodesToDelete.add(XPointerResolver.getNodeFromXPointer(domDoc, xptr));
+	    }
+
+	    // Delete
+	    for(Node nodeToDelete: nodesToDelete){
+		Node parent = nodeToDelete.getParentNode();
+		parent.removeChild(nodeToDelete);
+		// Get rid of Simple parents of deleted nodes, because empty Simple
+		// tags are not okay in Moby (causes parsing error)
+		if(MobyTags.SIMPLE.equals(parent.getLocalName())){
+		    parent.getParentNode().removeChild(parent);
+		}
+	    }
+	}
+    }
+
+    /**
+     * Get the data instance object associated with a given XPointer in a Moby XML doc.
      *
      * @param targetURL of the form URLpath#/1/1/2/1 where /1/1/2/1 is an XPointer, or an standard xpath, to the part of the Moby XML doc to deserialize
      * @param filteredXPtrs a map of the xpointers to data that should NOT be deserialized if children of the targetURL XPointer
      * @param docFilter the current filter applied to the document in targetURL
      */
     public static MobyDataInstance loadMobyDataFromXPointer(URL targetURL, Map<String,String> filteredXPtrs, FilterSearch docFilter){
-	// Are we dealing with a simple object or a complex one?
-	MobyDataInstance mobyData = null;
-	
-	// Find the DOM fragment corresponding to the MOBY ID anchor specified
-	// in the link URL by using an XPath statement on the source MOBY doc
-	//System.err.println("Retrieving complex object from XPointer " + targetURL);
-	
-	// A child Xpointer is of the form /1/2/1/1, specifying the DOM child 
-	// descent path from the root node to get to the target node.  The 
-	// equivalent XPath is /*[1]/*[2]/*[1]/*[1]
-	String childXPath = targetURL.getRef().replaceAll("/(\\d+)", "/*[$1]");
+
 	URL currentURL = null;
 	try{currentURL = new URL(targetURL.toString().replaceAll("#"+targetURL.getRef(), ""));}
 	catch(Exception e){
@@ -476,7 +506,6 @@
 	}
 
 	// Build the DOM
-	Element mobyDOMRoot = null;
 	Document domDoc = null;
 	try{
 	    domDoc = docBuilder.parse(targetURL.openStream());
@@ -489,46 +518,29 @@
 		       " could not be read (from " + targetURL + ")", ioe);
 	    return null;
 	}
+	// Does an in-place edit of domDoc
+	filterDoc(domDoc, filteredXPtrs);
+
+	// Are we dealing with a simple object or a complex one?
+	MobyDataInstance mobyData = null;
 	
-	if(domDoc != null){
-	    mobyDOMRoot = domDoc.getDocumentElement();
-	}
-	if(mobyDOMRoot == null){
-	    logger.log(Level.SEVERE, "Error: Could not get MOBY document as DOM from source URL " +
-		       targetURL + " (empty or malformed document?)");
-	    return null;
-	}
+	// Find the DOM fragment corresponding to the MOBY ID anchor specified
+	// in the link URL by using an XPath statement on the source MOBY doc
+	//System.err.println("Retrieving complex object from XPointer " + targetURL);
 	
-	// Remove the filtered data from the doc before deserializing to a moby data instance
-	// That way the request actually reflects what is shown on the screen to the user.
-	if(filteredXPtrs != null){
-	    // Mark and sweep (if we just deleted as we found node, the XPointers could be 
-	    // wrong as they refer to ordinality)
-	    Vector<Node> nodesToDelete = new Vector<Node>();
-	    for(String xptr: filteredXPtrs.keySet()){
-		nodesToDelete.add(XPointerResolver.getNodeFromXPointer(domDoc, xptr));
-	    }
-
-	    // Delete
-	    for(Node nodeToDelete: nodesToDelete){
-		Node parent = nodeToDelete.getParentNode();
-		parent.removeChild(nodeToDelete);
-		// Get rid of Simple parents of deleted nodes, because empty Simple
-		// tags are not okay in Moby (causes parsing error)
-		if(MobyTags.SIMPLE.equals(parent.getLocalName())){
-		    parent.getParentNode().removeChild(parent);
-		}
-	    }
-	}
+	// A child Xpointer is of the form /1/2/1/1, specifying the DOM child 
+	// descent path from the root node to get to the target node.  The 
+	// equivalent XPath is /*[1]/*[2]/*[1]/*[1]
+	String childXPath = targetURL.getRef().replaceAll("/(\\d+)", "/*[$1]");
 
 	// Build and run the XPath statement
 	Element mobyObject = null;
 	NodeList idSearchResult = null;
 	Object xobject = null;
 	try{
-	    xobject = XPathFactory.newInstance().newXPath().evaluate(childXPath, 
-								     domDoc, 
-								     XPathConstants.NODESET);
+	    xobject = xPathFactory.newXPath().evaluate(childXPath, 
+						       domDoc, 
+						       XPathConstants.NODESET);
 						
 	    // Check the results
 	    if(xobject != null){
@@ -603,7 +615,7 @@
      * Generalizes the element instance into an XPath retrieving it and all 
      * similarly nested elements (based on traversing the parent nodes and prepending their names)
      */
-    protected static String elementInContextToNameBasedXPath(Element targetElement){
+    public static String elementInContextToNameBasedXPath(Element targetElement){
 	String xpath = "";
 	
 	for(Element currentElement = targetElement; 
@@ -630,22 +642,20 @@
 		xpath = "/*[@"+MobyTags.OBJ_NAMESPACE + " = '" +
 		    currentElement.getAttribute(MobyTags.OBJ_NAMESPACE)+"']" + xpath;
 	    }
-	    else if(elName.equals(MobyTags.MOBYFLOAT) ||
-		    elName.equals(MobyTags.MOBYSTRING) ||
-		    elName.equals(MobyTags.MOBYBOOLEAN) ||
-		    elName.equals(MobyTags.MOBYINTEGER) ||
-		    elName.equals(MobyTags.MOBYDATETIME)){
+//	    else if(elName.equals(MobyTags.MOBYFLOAT) ||
+//		    elName.equals(MobyTags.MOBYSTRING) ||
+//		    elName.equals(MobyTags.MOBYBOOLEAN) ||
+//		    elName.equals(MobyTags.MOBYINTEGER) ||
+//		    elName.equals(MobyTags.MOBYDATETIME)){
 		// Assume that it isn't the primitive type, but rather the articleName
 		// that makes it appropriate to use.
-		xpath = "/*[@"+MobyTags.ARTICLENAME + " = '" +
-		    articleName+"']" + xpath;
-	    }
+//		xpath = "/*[@"+MobyTags.ARTICLENAME + " = '" +
+//		    articleName+"']" + xpath;
+//	    }
 	    else{
 		// It's a complex type.  Assume the type is why we are picking it.
 		// TODO: In future we may want to check if a parent type is allowed in 
-		// this slot, and generalize to that.  May also want to check that there isn't more
-		// than one member of this type at this level in a HAS relationship...
-		// in that case we probably want to go by articleName to catch the full semantics
+		// this slot, and generalize to that.  
 		xpath = "/"+elName + xpath;
 	    }
 	    if(!(currentElement.getParentNode() instanceof Element)){
@@ -696,6 +706,12 @@
     }
 
     /**
+     * Replace the selection xpath info in the data instance
+     */
+    public static void replaceUserData(MobyDataInstance mdi, String selectionXPath){
+    }
+
+    /**
      * Retrieves processing instructions embedded in Moby XML docs if they have the for <?seahawk attr="val"?>
      */
     public static String getSeahawkAttrFromDoc(URL docURL, String attrName) throws Exception{ 
@@ -777,4 +793,328 @@
 			    "any_namespace");
     }
       
+    // Recursively ascend the DOM tree and find out our place in its branching structure
+    public static String getXPtr(Node n){
+	if(n == null || n instanceof Document){
+	    return "";
+	}
+	Node parent = n.getParentNode();
+        if(parent == null && n instanceof Attr){
+	    parent = ((Attr) n).getOwnerElement();
+	}
+
+	NodeList children = parent.getChildNodes();
+	int nonElementCnt = 0;
+	for(int i = 0; i < children.getLength(); i++){
+	    if(!(children.item(i) instanceof Element)){
+		nonElementCnt++; 
+		continue;
+	    }
+	    if(n == children.item(i)){
+		return getXPtr(parent)+"/"+(i-nonElementCnt+1);
+	    }
+	}
+	return null;
+    }
+
+    /**
+     * If any moby object member is in a HAS relationship, add it to the list of filterable items
+     */
+    public static Boolean addHASXPtrs(List<String> filterList, Element object){
+	String tagName = object.getLocalName();
+	boolean isContainer = false;
+	MobyDataType mobyDataType = null;	
+	if(tagName.equals(MobyTags.MOBYDATA) || tagName.equals(MobyTags.COLLECTION) || tagName.equals(MobyTags.SIMPLE) ||
+	   tagName.equals(MobyTags.CROSSREFERENCE)){
+	    isContainer = true;
+	}
+	else{
+	    mobyDataType = MobyDataType.getDataType(tagName, SeahawkOptions.getRegistry());
+	    if(mobyDataType == null){
+		logger.log(Level.WARNING,
+                           "Found datatype unknown to the registry ("+object.getLocalName()+")");
+		return Boolean.FALSE;
+	    }
+	}
+
+	Boolean hasHAS = Boolean.FALSE; // does the object have a member with a HAS relationship?
+	NodeList members = object.getChildNodes();
+	for(int i = 0; i < members.getLength(); i++){
+	    if(!(members.item(i) instanceof Element)){
+		continue;
+	    }
+
+	    Element member = (Element) members.item(i);
+	    addHASXPtrs(filterList, member);
+
+	    if(!isContainer){
+		String memberName = member.getAttribute(MobyTags.ARTICLENAME);
+		MobyRelationship membership = mobyDataType.getChild(memberName);
+		//System.err.println("Relationship for " + tagName  + " member " + memberName + 
+		//		   " is " + (membership == null ? null : membership.getRelationshipType()));
+		if(membership != null && membership.getRelationshipType() == Central.iHAS){
+		    filterList.add(getXPtr(member));
+		    if(!hasHAS){
+			hasHAS = Boolean.TRUE;
+		    }
+		}
+	    }
+	}
+	return hasHAS;
+    }
+
+    /**
+     * For one-off filtering of a doc. Populates xPtrsToFilter, and returns the 
+     * whole doc which you can manipulate yourself (e.g. removing the nodes identified).
+     */
+    public static Document findFilteredNodes(URL targetURL, FilterSearch filter, 
+                                             Map<String,String> xPtrsToFilter){
+        Document unfilteredDoc = null;
+	try{
+	    unfilteredDoc = docBuilder.parse(targetURL.openStream());
+	} catch(Exception e){
+	    logger.log(Level.SEVERE,
+                       "Could not parse Moby document " + targetURL, e);
+	    return null;
+	}
+	findFilteredNodes(unfilteredDoc, filter, null, xPtrsToFilter, null, null, null, true);
+	return unfilteredDoc;
+    }
+
+    /**
+     * Returns a list of xptrs to filterable nodes in the targetDoc, an populates the list of 
+     * xptrs that should be filtered according to the provided filter.  In-place edited fields are
+     * xPtrsToFilter, jobXPtrs, currentSelectedData, and currentSelectionXPath 
+     * (for caching efficiency on multiple consecutive 
+     * calls to this method, such as a live typed search in the UI).  The latter three can be null if no caching is desired.
+     */
+    public static List<String> findFilteredNodes(Document targetDoc, FilterSearch filter, List<String> filterableXPtrs,
+		    		                 Map<String,String> xPtrsToFilter, Map<String,Boolean> jobXPtrs,
+                                                 MutableNodeList currentSelectedData, StringBuffer currentSelectionXPath, 
+						 boolean apply){
+	xPtrsToFilter.clear();
+
+	// Filter out any moby jobs, parameters, collection members or HAS members that aren't in the matchingNodes
+	if(filterableXPtrs == null){
+	    if(jobXPtrs == null){
+		jobXPtrs = new HashMap<String,Boolean>();
+            }
+            else{
+                jobXPtrs.clear();
+            }
+	    filterableXPtrs = new Vector<String>();
+	    NodeList nodes = targetDoc.getElementsByTagNameNS(MobyTags.MOBY_XML_NS, MobyTags.MOBYDATA);
+	    for(int i = 0; i < nodes.getLength(); i++){
+		String jobXPtr = getXPtr(nodes.item(i));		
+		filterableXPtrs.add(jobXPtr);
+		jobXPtrs.put(jobXPtr, addHASXPtrs(filterableXPtrs, (Element) nodes.item(i)));
+	    }
+		
+	    // Collections
+	    nodes = targetDoc.getElementsByTagNameNS(MobyTags.MOBY_XML_NS, MobyTags.COLLECTION);
+	    for(int i = 0; i < nodes.getLength(); i++){
+		String collectionXPtr = getXPtr(nodes.item(i));
+		NodeList collectionMembers = nodes.item(i).getChildNodes();
+		int nonElementCnt = 0;
+		for(int j = 0; j < collectionMembers.getLength(); j++){		    
+		    if(!(collectionMembers.item(j) instanceof Element)){
+			nonElementCnt++;
+			continue;
+		    }
+		    filterableXPtrs.add(collectionXPtr+"/"+(j-nonElementCnt+1)+"/1");
+		}
+	    }
+	}
+
+	if(!apply || filter == null || filter.getFilterRegex().toString().length() == 0){
+	    return filterableXPtrs;
+	}
+	// Otherwise make a list of xpointers to data that should be filtered
+	XPathOption xsel = filter.getSelectedXPath();
+	
+	// Find the applicable DOM nodes if not yet found, or if selection criteria have changed
+	if(currentSelectedData == null || currentSelectedData.isEmpty() || 
+           currentSelectionXPath == null || !currentSelectionXPath.toString().equals(xsel.getXPath())){
+            if(currentSelectionXPath == null){
+               currentSelectionXPath = new StringBuffer(xsel.getXPath());
+            }
+	    else{
+               currentSelectionXPath.replace(0, currentSelectionXPath.length(), xsel.getXPath());
+            }
+	    try{
+		if(currentSelectedData == null){
+                    currentSelectedData = new MutableNodeList();
+                }
+                else{
+                    currentSelectedData.clear();
+                }
+		currentSelectedData.addAll((NodeList) xPathFactory.newXPath().evaluate(currentSelectionXPath.toString(), 
+                                                                                       targetDoc, 
+                                                                                       XPathConstants.NODESET)); 
+	    } catch(Exception e){
+		logger.log(Level.SEVERE, 
+                           "Could not evaluate XPath (" + xsel.getXPath() + ")", e);
+		return filterableXPtrs;
+	    }
+	    //	    System.err.println("There are " + currentSelectedData.getLength() + 
+	    //		       " items selected in the document using XPath " + currentSelectionXPath);
+	}
+	
+	// Find just the data subset also matching the regex
+	Map<String,Boolean> matchingXPtrs = new LinkedHashMap<String,Boolean>();
+	// Build the FSA only once, for efficiency
+	Pattern regex = Pattern.compile(filter.getFilterRegex().toString(), 
+                                        Pattern.MULTILINE | Pattern.DOTALL | 
+                                         (filter.getCaseSensitivity() ? 0 : Pattern.CASE_INSENSITIVE));
+	for(int i = 0; i < currentSelectedData.getLength(); i++){
+	    Node node = currentSelectedData.item(i);	    
+	    if(node instanceof Element){
+		String elementXPtr = getXPtr(node);
+		if(matchingXPtrs.containsKey(elementXPtr) &&
+		   matchingXPtrs.get(elementXPtr).booleanValue()){
+		    	continue;  // already true, no 
+                    }
+		else if(regex.matcher(((Element) node).getTextContent()).find()){
+		    matchingXPtrs.put(elementXPtr, Boolean.TRUE);
+		    //System.err.println("Adding " + elementXPtr + " as " + matchingXPtrs.get(elementXPtr));
+		}
+		else{
+		    matchingXPtrs.put(elementXPtr, Boolean.FALSE);
+		    //System.err.println("Adding " + elementXPtr + " as " + matchingXPtrs.get(elementXPtr));
+		}
+	    }
+	    else if(node instanceof Attr){
+		String attrParentXPtr = getXPtr(((Attr) node).getOwnerElement());
+		if(matchingXPtrs.containsKey(attrParentXPtr) &&
+	 	   matchingXPtrs.get(attrParentXPtr).booleanValue()){
+		    continue;
+                }
+		else if(regex.matcher(((Attr) node).getValue()).find()){
+		    // Mark the element to which the attribute belongs
+		    matchingXPtrs.put(attrParentXPtr, Boolean.TRUE);
+		    //System.err.println("Adding " + attrParentXPtr + " attr parent as " + matchingXPtrs.get(attrParentXPtr));
+		}
+		// so false doesn't override true for multi-attr elements
+		else if(!matchingXPtrs.containsKey(attrParentXPtr)){ 
+		    matchingXPtrs.put(attrParentXPtr, Boolean.FALSE);
+		    //System.err.println("Adding " + attrParentXPtr + " attr parent as " + matchingXPtrs.get(attrParentXPtr));
+		}
+		
+	    }
+	    else{
+		logger.log(Level.WARNING, 
+			   "Found filter xpath result item that was not an Element or Attribute as expected ("+
+			    node.getClass().getName()+")");
+	    }
+	}
+	
+	boolean inversed = filter.getSelectionInversed();
+	Map<String,Boolean> parentMatchingXPtrs = new LinkedHashMap<String,Boolean>();
+	for(String currXPtr: filterableXPtrs){
+	    for(Map.Entry<String,Boolean> matchingXPtr: matchingXPtrs.entrySet()){
+		if(matchingXPtr.getKey().startsWith(currXPtr+"/")){ // a parent of the matching data
+		    // No positive example yet?
+		    if(!parentMatchingXPtrs.containsKey(currXPtr) || 
+		       !inversed && !parentMatchingXPtrs.get(currXPtr).booleanValue() ||
+		       inversed && parentMatchingXPtrs.get(currXPtr).booleanValue()){
+			//System.err.println("Adding "+ matchingXPtr.getValue() + " for " + currXPtr);
+			parentMatchingXPtrs.put(currXPtr, matchingXPtr.getValue());
+		    }
+		}
+	    }
+	}
+
+	matchingXPtrs.putAll(parentMatchingXPtrs);
+	for(String currXPtr: matchingXPtrs.keySet()){
+	    // Is part of the selection criteria, but doesn't match the regex
+	    boolean shouldFilter = false;
+	    if(!matchingXPtrs.get(currXPtr).booleanValue() &&
+	       // special condition: if "entire response" xpath is given, filter only at the job level
+	       (!currentSelectionXPath.toString().equals(FilterSearch.SELECT_ALL_XPATH) || jobXPtrs.containsKey(currXPtr))){
+		shouldFilter = true;
+	    }
+	    if(!inversed && shouldFilter ||
+	       inversed && !shouldFilter){ 
+		xPtrsToFilter.put(currXPtr, "todo");
+	    }	    
+	}
+
+	//todo: filter objects without the HAS field at all...
+	return filterableXPtrs;
+    }
+    // We need to enumerate the possible peer-sets for the selected data item.  Is the user interested in
+    // items in the same namespace, same data type, or same article name?
+    public static NodeList getPeerElements(Document doc, MobyDataInstance mobyData, String peerMode){
+        if(!(mobyData instanceof MobyPrimaryData)){
+            logger.log(Level.WARNING, "Tried to get peers of data that was not an instanceof MobyPrimaryData (was " + 
+                                      mobyData.getClass().getName()+ ")");
+	    return null;
+	}
+        MobyDataType dataTypeTemplate = ((MobyPrimaryData) mobyData).getDataType();
+
+	NodeList peerElements = null;
+        String peerGroupXPath = null;
+	if(mobyData.getUserData() != null){
+	    String[] userData = ((String) mobyData.getUserData()).split("\t");
+	    // first arg is url#nameBasedXPath 
+	    peerGroupXPath = userData[0].split("#", 2)[1];
+        }
+        else{
+	    // Fallback is to get all nodes with the same name...
+            // warning: need to set this in the userdata sent to the job, to jibe with taverna workflow export selection of nodes!
+	    logger.log(Level.WARNING, "No UserData for data instance, falling back to all peer elements of the same datatype");
+            peerGroupXPath = "//"+dataTypeTemplate.getName();
+	}
+
+        // just look at data type tag, regardless of nesting
+        if(DATATYPE_PEERS_MODE.equals(peerMode)){
+            peerGroupXPath = peerGroupXPath.replaceFirst("^.+/", "//"); 
+        }
+        else if(ARTICLE_PEERS_MODE.equals(peerMode)){ 
+            String xpathArticleCondition = "[@"+MobyTags.ARTICLENAME + "='" + mobyData.getName() +"']";
+            // Pass back modified selection xpath for userdata (enables PBE to capture the additonal semantics)
+            // This is done by replacing first tab delimited field url#selectionXPath with url#newXPath
+            String newUserData = mobyData.getUserData().toString().replaceFirst("^(.*?)#.*?(?=\\t)", 
+                                                                                "$1#"+peerGroupXPath+xpathArticleCondition);
+            mobyData.setUserData(newUserData);
+
+            // keep from job article name down
+            peerGroupXPath = peerGroupXPath.replaceFirst("^.*/(Collection|Simple)", "//*");
+	    // we want to go by articleName too to catch the full semantics of the peer group definition
+            peerGroupXPath += xpathArticleCondition;
+        }
+        else{
+            logger.log(Level.SEVERE, "Got unknown mode for peer selection, aborting (mode was "+peerMode+")");
+            return null;
+        }
+        // For xpaths given above, MOBY namespace is problem in XPath evaluation. 
+        // solution: eliminate Moby envelope path parts: full path doesn't resolve in xpath for unknown reasons
+        //.replaceAll("/(MOBY|mobyContent|mobyData|Collection|Simple)","/moby:$1"); //attempt 1
+        //.replaceAll("/([a-zA-Z_0-9\\-]+)(?=/|$)", "/*[local-name() = '$1']") //attempt 2
+        //.replaceAll("/([a-zA-Z_0-9\\-]+)\\[", "/*[local-name() = '$1' and "); //attempt 2 cont'd
+
+	try{
+            peerElements = (NodeList) xPathFactory.newXPath().evaluate(peerGroupXPath, 
+								       doc, 
+								       XPathConstants.NODESET);
+        } catch(Exception e){
+            logger.log(Level.SEVERE, "Could not evaluate UserData XPath "+peerGroupXPath, e);
+        }
+        System.err.println("Got " + peerElements.getLength() + " peers for " + peerGroupXPath);
+
+        return peerElements;
+    }
+
+    // given a node from a Moby XML dom, find the name of the mobyData job that's its parent
+    public static String findMobyJobName(Node n){
+        while(n != null && !n.getLocalName().equals(MobyTags.MOBYDATA)){
+            n = n.getParentNode();
+        }
+        if(n == null){
+            return null; // no mobyData parent
+        }
+        else{
+            return MobyPrefixResolver.getAttr((Element) n, MobyTags.QUERYID);
+        }
+    }
 }

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/FilterSearch.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/FilterSearch.java	2010/04/10 00:40:17	1.4
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/FilterSearch.java	2010/04/14 22:02:04	1.5
@@ -28,6 +28,20 @@
     public static final String SELECT_ALL_XPATH = "//* | //*/@*";
 
     /**
+     * A c-tor to manually populate the filter with a specific set of filter criteria.  
+     * No autopoulation of options is done.
+     */
+    public FilterSearch(String regex, XPathOption xpath, boolean case_sensitive, boolean inverse_selection){
+	filterRegex = new StringBuffer(regex);
+	xpathOptions = new Vector<XPathOption>();
+	xpathOptions.add(xpath);
+	setCaseSensitivity(case_sensitive);
+	setSelectionInversed(inverse_selection);
+    }
+
+    /**
+     * Autopopulates the possible search field values based on the incoming doc
+     *
      * @param docToFilter the document that will be used to determine what XPaths can be suggested
      * @param docBuilder the xml parser to use on the document
      *
@@ -106,4 +120,15 @@
     public Vector<XPathOption> getXPathOptions(){
 	return xpathOptions;
     }
+
+    public boolean equals(Object o){
+        if(o == null || !(o instanceof FilterSearch)){
+          return false;
+        }
+        FilterSearch other = (FilterSearch) o;
+        return filterRegex.toString().equals(other.filterRegex.toString()) &&
+               getSelectedXPath().getXPath().equals(other.getSelectedXPath().getXPath()) &&
+               caseSensitivity == other.caseSensitivity &&
+	       inverseSelection == other.inverseSelection;
+    }
 }



From gordonp at dev.open-bio.org  Wed Apr 14 22:02:04 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Wed, 14 Apr 2010 18:02:04 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004142202.o3EM24JD007053@dev.open-bio.org>


gordonp
Wed Apr 14 18:02:04 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv7013/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	MobyContentPane.java MobyServicesGUI.java 
Added Files:
	MobyPayloadCreator.java 
Log Message:
Changes to implement explicit 'for each' loops over Seahawk data lists (not quite functional yet, but compiles)
moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyPayloadCreator.java,NONE,1.1 MobyContentPane.java,1.26,1.27 MobyServicesGUI.java,1.17,1.18
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java,v
retrieving revision 1.26
retrieving revision 1.27
diff -u -r1.26 -r1.27
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java	2010/04/11 20:15:28	1.26
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java	2010/04/14 22:02:04	1.27
@@ -1,4 +1,3 @@
-
 package ca.ucalgary.seahawk.gui;
 
 // For external links
@@ -72,8 +71,8 @@
     public static final String SERVICE_CREATION_MSG = "Create a service returning this datatype";
     private static final int TAB_ICON_SPACER = 2;
 
-    private static String SEARCH_VISIBLE = "Search visible";
-    private static String SEARCH_HIDDEN = "Search hidden";
+    private static final String SEARCH_VISIBLE = "Search visible";
+    private static final String SEARCH_HIDDEN = "Search hidden";
 
     private static ImageIcon hourglassIcon; 
     private static ImageIcon failedIcon; 
@@ -105,10 +104,10 @@
     private Map<String,String> filteredData; //Map<xptrOfFilteredData,>
     private boolean filterChanged;
     private Document currentDoc; //the doc DOM being actively filtered
-    private NodeList currentSelectedData = null;
-    private String currentSelectionXPath = null;
-    private Map<String,Boolean> jobXPtrs = null;  // Map<xptr,has a HAS member>
+    private MutableNodeList currentSelectedData = null;
+    private StringBuffer currentSelectionXPath = null;
     private List<String> filterableNodes = null;  // List<xptr>
+    private Map<String,Boolean> jobXPtrs = null;  // Map<xptr,has a HAS member>
     private List<AttributeSet> origStyles = null;
     private boolean firstDocRendering = true;
 
@@ -141,20 +140,6 @@
     private final static String wsServletPath = "/SOAPServlet";
     private static Acme.Serve.Serve servletContainer;
     private static Map<String,MobyContentGUI> id2GuiMap;
-    private static DocumentBuilder docBuilder;
-    private static XPathFactory xPathFactory;
-
-    static{
-	xPathFactory = XPathFactory.newInstance();
-
-	DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
-	dbf.setNamespaceAware(true);
-	try{
-	    docBuilder = dbf.newDocumentBuilder();
-	} catch(Exception e){
-	    logger.warn("Cannot get XML parser from configuration", e);
-	}
-    }
 
     public MobyContentPane(MobyContentGUI cGUI, MobyServicesGUI sGUI, JTabbedPane parentComponent, DataFlowRecorder recorder, JLabel statusBar){
 	tabbedPane = parentComponent;
@@ -200,7 +185,9 @@
 	filterHistory = new HashMap<URL,FilterSearch>();
 	deletedFilters = new HashMap<URL,FilterSearch>();
 	xPtrsReferencedInNextService = new Vector<String>();
+        currentSelectedData = new MutableNodeList();
 	filteredData = new HashMap<String,String>();
+	jobXPtrs = new HashMap<String,Boolean>();
 
 	ClassLoader cl = getClass().getClassLoader();
 	if(cl == null){
@@ -738,9 +725,8 @@
 	// If this page has a filter associated with it before reload it
 	try{
 	    currentDoc = null;  // get rid of previous in-memory doc use for interactive filtering, if any
-	    currentSelectedData = null;
-	    currentSelectionXPath = null;
-	    jobXPtrs = null;
+	    currentSelectedData.clear();
+	    currentSelectionXPath = new StringBuffer();
 	    filterableNodes = null;
 	    origStyles = null;
 	    firstDocRendering = true;
@@ -1209,14 +1195,54 @@
 			       "not extract MOBY Data Object from " +targetURL);
 	    return;
 	}
+	if(!(mobyData instanceof MobyPrimaryData)){
+	    logger.warn("Cannot create MOBY service list for non-primary " +
+			"MOBY Data (was " +mobyData.getClass().getName()+")");
+	    return;
+	}
 
 	JPopupMenu popup = new DynamicJPopupMenu();
 	popup.setName(MOBY_SERVICE_POPUP_NAME);
 	addExtraMobyOptions(popup, mobyData, targetURL);
-	JMenuItem checkingLinksPopupItem = new JMenuItem("Check for services...");
+	JMenuItem checkingLinksPopupItem = new JMenuItem("Checking for services...");
 	popup.add(checkingLinksPopupItem);
 	popup.show(this, lastClickX+editorPane.getX(), lastClickY+editorPane.getY());
 	servicesGUI.addPopupOptions(mobyData, popup, true, getDefaultHandler()); // true = asynchronous
+
+	// It's possible that the current node clicked has peers that could also be submitted at the same time.
+	// In this case, create a "for each" option to submit all peers to the service.  We don't actually build
+	// the input data, but provde a callback listener to create the full submission envelope if the user 
+	// chooses the for each option.  The Moby data instance's userData gives us the current context, enabling us 
+        // to construct the correct payload in MobyPayloadCreator.createPayload() at any point in the future.
+        String origUserData = (String) mobyData.getUserData();
+        MobyPayloadRequestListener payloadCreator = new MobyPayloadCreator(this);
+        for(String peerMode: new String[]{DataUtils.ARTICLE_PEERS_MODE, DataUtils.DATATYPE_PEERS_MODE}){
+            // note that getPeerElements() will modify the userData to reflect the semantic of the requested peer mode
+            mobyData.setUserData(origUserData);
+            NodeList peerElements = DataUtils.getPeerElements(getCurrentDoc(), mobyData, peerMode);
+            if(peerElements.getLength() <= 1){
+                continue; // no 'for each' option if only one to process...
+            }
+            String each = "each <i>(" + peerElements.getLength() + " total)</i>";
+            if(peerMode.equals(DataUtils.ARTICLE_PEERS_MODE)){
+                each += " '"+mobyData.getName()+"'";
+            }
+            MobyDataType dataType = ((MobyPrimaryData) mobyData).getDataType();
+            if(mobyData instanceof MobyPrimaryDataSet){	 // Collection
+                servicesGUI.addPopupOptions((MobyPrimaryDataSet) mobyData, popup, true, getDefaultHandler(), payloadCreator, 
+					    (String) mobyData.getUserData(), each);
+            }
+            else if(MobyTags.MOBYOBJECT.equals(dataType.getName())){  
+                MobyNamespace namespace = null;
+                servicesGUI.addPopupOptions(namespace, popup, true, getDefaultHandler(), payloadCreator, 
+                                            (String) mobyData.getUserData(), each);
+            }
+            else{
+                servicesGUI.addPopupOptions(dataType, popup, true, getDefaultHandler(), payloadCreator, 
+                                            (String) mobyData.getUserData(), each);
+            }
+        }
+
 	status.setText("Shift+Click=Service in new tab, Ctrl+Click=Use default 2nd params");
 	if(popup.getSubElements().length > 0){
 	    popup.setSelected(null);
@@ -1228,6 +1254,15 @@
 	}
     }
 
+    Map<String,String> getFilteredData(){
+      return filteredData;
+    }
+
+    Map<String,Boolean> getJobXPtrs(){
+      return jobXPtrs;
+    }
+
+
     /**
      * Subclasses can use this method to expand the popup menu.  Be sure to call super.addExtraMobyOptions()
      */
@@ -1252,7 +1287,7 @@
 
 	//System.err.println("Should create a previous input menu item for " + mdi.getUserData());
 	try{
-	    Document srcDoc = docBuilder.parse(srcURL.openStream());
+	    Document srcDoc = DataUtils.docBuilder.parse(srcURL.openStream());
 
 	    // Get the input data for the *previous* service
 	    MobyDataJob inputData = DataUtils.getInputSample(srcDoc, SeahawkOptions.getRegistry());
@@ -1262,7 +1297,7 @@
 		return;
 	    }
 	    for(MobyDataInstance previousMDI: inputData.getPrimaryData()){		
-		    // add conditional of the current service as a criteria in user data for each previousMDI, 
+		// add conditional of the current service as a criteria in user data for each previousMDI, 
 		// so PbE will properly reflect the logic of if(f1(x) matches filter){f2(x)}
 		DataUtils.addUserData(previousMDI, srcURL, getFilter());
 
@@ -1271,6 +1306,7 @@
 	} catch(Exception e){
 	    logger.warn("Could not load previous service info, 'previous input' option will not be displayed", e);
 	}
+
     }
 
     /**
@@ -1392,231 +1428,41 @@
 	return null;
     }
 
-    /**
-     * Determine the parts of the XML document matching the FilterSearch criteria, and filter the view accordingly.
-     */
-    public void applyFilter(boolean apply){
-	if(!filterChanged){
-	    filterChanged = true;
-	}
-	filteredData.clear();
-
+    protected Document getCurrentDoc(){
 	if(currentDoc == null){  // parse the doc into memory if not already there
 	    try{
-		currentDoc = docBuilder.parse(getCurrentURL().openStream());
+		currentDoc = DataUtils.docBuilder.parse(getCurrentURL().openStream());
 	    } catch(Exception e){
 		logger.error("Could not parse Moby document " + getCurrentURL(), e);
-		return;
-	    }
-	}
-	// Filter out any moby jobs, parameters, collection members or HAS members that aren't in the matchingNodes
-	if(filterableNodes == null){
-	    jobXPtrs = new HashMap<String,Boolean>();
-	    filterableNodes = new Vector<String>();
-	    NodeList nodes = currentDoc.getElementsByTagNameNS(MobyTags.MOBY_XML_NS, MobyTags.MOBYDATA);
-	    for(int i = 0; i < nodes.getLength(); i++){
-		String jobXPtr = getXPtr(nodes.item(i));		
-		filterableNodes.add(jobXPtr);
-		jobXPtrs.put(jobXPtr, addHASXPtrs(filterableNodes, (Element) nodes.item(i)));
-	    }
-		
-	    // Collections
-	    nodes = currentDoc.getElementsByTagNameNS(MobyTags.MOBY_XML_NS, MobyTags.COLLECTION);
-	    for(int i = 0; i < nodes.getLength(); i++){
-		String collectionXPtr = getXPtr(nodes.item(i));
-		NodeList collectionMembers = nodes.item(i).getChildNodes();
-		int nonElementCnt = 0;
-		for(int j = 0; j < collectionMembers.getLength(); j++){		    
-		    if(!(collectionMembers.item(j) instanceof Element)){
-			nonElementCnt++;
-			continue;
-		    }
-		    filterableNodes.add(collectionXPtr+"/"+(j-nonElementCnt+1)+"/1");
-		}
+		return null;
 	    }
 	}
-
-	if(!apply || !filterHistory.containsKey(getCurrentURL()) ||
-	   (filterHistory.containsKey(getCurrentURL()) && 
-	    filterHistory.get(getCurrentURL()).getFilterRegex().toString().length() == 0)){
-	    // Show whole doc if no filter or if filter is blank, so nothing to do here
-	    if(firstDocRendering){
-		firstDocRendering = false;
-	    }
-	    else{
-		displayFilterEffect(); //need to cleanup previous state
-	    }
-	    return;
-	}
-	// Otherwise make a list of xpointers to data that should be grayed out
-	FilterSearch fs = filterHistory.get(getCurrentURL());
-	XPathOption xsel = fs.getSelectedXPath();
-	
-	// Find all the matching data
-	XPath xpath = xPathFactory.newXPath();
-	// Find the applicable DOM nodes if not yet found, or if selection criteria have changed
-	if(currentSelectedData == null || currentSelectionXPath == null || !currentSelectionXPath.equals(xsel.getXPath())){
-	    currentSelectionXPath = xsel.getXPath();
-	    try{
-		currentSelectedData = (NodeList) xpath.evaluate(currentSelectionXPath, currentDoc, XPathConstants.NODESET);
-	    } catch(Exception e){
-		logger.error("Could not evaluate XPath (" + xsel.getXPath() + ") over " + getCurrentURL(), e);
-		return;
-	    }
-	    //	    System.err.println("There are " + currentSelectedData.getLength() + 
-	    //		       " items selected in the document using XPath " + currentSelectionXPath);
-	}
-	
-	// Find just the data subset also matching the regex
-	Map<String,Boolean> matchingXPtrs = new LinkedHashMap<String,Boolean>();
-	// Build the FSA only once, for efficiency
-	Pattern regex = Pattern.compile(fs.getFilterRegex().toString(), 
-                                        Pattern.MULTILINE | Pattern.DOTALL | 
-                                         (fs.getCaseSensitivity() ? 0 : Pattern.CASE_INSENSITIVE));
-	for(int i = 0; i < currentSelectedData.getLength(); i++){
-	    Node node = currentSelectedData.item(i);	    
-	    if(node instanceof Element){
-		String elementXPtr = getXPtr(node);
-		if(matchingXPtrs.containsKey(elementXPtr) &&
-		   matchingXPtrs.get(elementXPtr).booleanValue()){
-		    	continue;  // already true, no 
-                    }
-		else if(regex.matcher(((Element) node).getTextContent()).find()){
-		    matchingXPtrs.put(elementXPtr, Boolean.TRUE);
-		    //System.err.println("Adding " + elementXPtr + " as " + matchingXPtrs.get(elementXPtr));
-		}
-		else{
-		    matchingXPtrs.put(elementXPtr, Boolean.FALSE);
-		    //System.err.println("Adding " + elementXPtr + " as " + matchingXPtrs.get(elementXPtr));
-		}
-	    }
-	    else if(node instanceof Attr){
-		String attrParentXPtr = getXPtr(((Attr) node).getOwnerElement());
-		if(matchingXPtrs.containsKey(attrParentXPtr) &&
-	 	   matchingXPtrs.get(attrParentXPtr).booleanValue()){
-		    continue;
-                }
-		else if(regex.matcher(((Attr) node).getValue()).find()){
-		    // Mark the element to which the attribute belongs
-		    matchingXPtrs.put(attrParentXPtr, Boolean.TRUE);
-		    //System.err.println("Adding " + attrParentXPtr + " attr parent as " + matchingXPtrs.get(attrParentXPtr));
-		}
-		// so false doesn't override true for multi-attr elements
-		else if(!matchingXPtrs.containsKey(attrParentXPtr)){ 
-		    matchingXPtrs.put(attrParentXPtr, Boolean.FALSE);
-		    //System.err.println("Adding " + attrParentXPtr + " attr parent as " + matchingXPtrs.get(attrParentXPtr));
-		}
-		
-	    }
-	    else{
-		logger.warn("Found filter xpath result item that was not an Element or Attribute as expected ("+
-			    node.getClass().getName()+")");
-	    }
-	}
-	
-	boolean inversed = fs.getSelectionInversed();
-	Map<String,Boolean> parentMatchingXPtrs = new LinkedHashMap<String,Boolean>();
-	for(String currXPtr: filterableNodes){
-	    for(Map.Entry<String,Boolean> matchingXPtr: matchingXPtrs.entrySet()){
-		if(matchingXPtr.getKey().startsWith(currXPtr+"/")){ // a parent of the matching data
-		    // No positive example yet?
-		    if(!parentMatchingXPtrs.containsKey(currXPtr) || 
-		       !inversed && !parentMatchingXPtrs.get(currXPtr).booleanValue() ||
-		       inversed && parentMatchingXPtrs.get(currXPtr).booleanValue()){
-			//System.err.println("Adding "+ matchingXPtr.getValue() + " for " + currXPtr);
-			parentMatchingXPtrs.put(currXPtr, matchingXPtr.getValue());
-		    }
-		}
-	    }
-	}
-
-	matchingXPtrs.putAll(parentMatchingXPtrs);
-	for(String currXPtr: matchingXPtrs.keySet()){
-	    // Is part of the selection criteria, but doesn't match the regex
-	    boolean shouldFilter = false;
-	    if(!matchingXPtrs.get(currXPtr).booleanValue() &&
-	       // special condition: if "entire response" xpath is given, filter only at the job level
-	       (!currentSelectionXPath.equals(FilterSearch.SELECT_ALL_XPATH) || jobXPtrs.containsKey(currXPtr))){
-		shouldFilter = true;
-	    }
-	    if(!inversed && shouldFilter ||
-	       inversed && !shouldFilter){ 
-		filteredData.put(currXPtr, "todo");
-	    }	    
-	}
-
-	//todo: filter objects without the HAS field at all...
-	
-	// apply gray out in the document display
-	displayFilterEffect();
+        return currentDoc;
     }
 
-    // If any moby object member is in a HAS relationship, add it to the list of filterable items
-    private Boolean addHASXPtrs(List<String> filterList, Element object){
-	String tagName = object.getLocalName();
-	boolean isContainer = false;
-	MobyDataType mobyDataType = null;	
-	if(tagName.equals(MobyTags.MOBYDATA) || tagName.equals(MobyTags.COLLECTION) || tagName.equals(MobyTags.SIMPLE) ||
-	   tagName.equals(MobyTags.CROSSREFERENCE)){
-	    isContainer = true;
-	}
-	else{
-	    mobyDataType = MobyDataType.getDataType(tagName, SeahawkOptions.getRegistry());
-	    if(mobyDataType == null){
-		logger.warn("Found datatype unknown to the registry ("+object.getLocalName()+")");
-		return Boolean.FALSE;
-	    }
+    /**
+     * Determine the parts of the XML document matching the FilterSearch criteria for the current doc, 
+     * and filter the view accordingly.  Used for interactive filtering in the display.
+     */
+    protected void applyFilter(boolean apply){
+	if(!filterChanged){
+	    filterChanged = true;
 	}
 
-	Boolean hasHAS = Boolean.FALSE; // does the object have a member with a HAS relationship?
-	NodeList members = object.getChildNodes();
-	for(int i = 0; i < members.getLength(); i++){
-	    if(!(members.item(i) instanceof Element)){
-		continue;
-	    }
-
-	    Element member = (Element) members.item(i);
-	    addHASXPtrs(filterList, member);
-
-	    if(!isContainer){
-		String memberName = member.getAttribute(MobyTags.ARTICLENAME);
-		MobyRelationship membership = mobyDataType.getChild(memberName);
-		//System.err.println("Relationship for " + tagName  + " member " + memberName + 
-		//		   " is " + (membership == null ? null : membership.getRelationshipType()));
-		if(membership != null && membership.getRelationshipType() == Central.iHAS){
-		    filterList.add(getXPtr(member));
-		    if(!hasHAS){
-			hasHAS = Boolean.TRUE;
-		    }
-		}
-	    }
+        FilterSearch filter = filterHistory.get(getCurrentURL());
+	filterableNodes = DataUtils.findFilteredNodes(getCurrentDoc(), filter, filterableNodes, filteredData, jobXPtrs,
+                                                      currentSelectedData, currentSelectionXPath, apply);
+ 
+	if((!apply || filter == null || filter.getFilterRegex().toString().length() == 0) && firstDocRendering){
+	    // Show whole doc if no filter or if filter is blank, so nothing to do here
+	    firstDocRendering = false;
 	}
-	return hasHAS;
+	// apply gray out in the document display, or need to cleanup previous state even if no filter now
+        else{
+	    displayFilterEffect();
+        }
     }
 
-    // Recursively ascend the DOM tree and find out our place in its branching structure
-    private String getXPtr(Node n){
-	if(n == null || n instanceof Document){
-	    return "";
-	}
-	Node parent = n.getParentNode();
-        if(parent == null && n instanceof Attr){
-	    parent = ((Attr) n).getOwnerElement();
-	}
-
-	NodeList children = parent.getChildNodes();
-	int nonElementCnt = 0;
-	for(int i = 0; i < children.getLength(); i++){
-	    if(!(children.item(i) instanceof Element)){
-		nonElementCnt++; 
-		continue;
-	    }
-	    if(n == children.item(i)){
-		return getXPtr(parent)+"/"+(i-nonElementCnt+1);
-	    }
-	}
-	return null;
-    }
 
     /**
      * Gray out parts of the HTML view if they are part of the filtered data.
@@ -1681,7 +1527,7 @@
 	// Gray out the mismatched textual data
 	for(Map.Entry<String,String> dataToFilter: filteredData.entrySet()){	    
 
-	    //System.err.println("Filtering "+dataToFilter.getKey());
+	    System.err.println("Filtering "+dataToFilter.getKey());
 	    javax.swing.text.AbstractDocument.AbstractElement htmlDiv = 
 		(javax.swing.text.AbstractDocument.AbstractElement) d.getElement(dataToFilter.getKey());
 	    if(htmlDiv == null){
@@ -1998,4 +1844,5 @@
     public void lostOwnership(Clipboard clipboard, Transferable contents){
 	//System.err.println("Lost clipboard ownership");
     }
+
 }

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java,v
retrieving revision 1.17
retrieving revision 1.18
diff -u -r1.17 -r1.18
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java	2010/04/09 15:55:48	1.17
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java	2010/04/14 22:02:04	1.18
@@ -1,11 +1,11 @@
 package ca.ucalgary.seahawk.gui;
 
 import ca.ucalgary.seahawk.services.MobyClient;
-import ca.ucalgary.seahawk.util.HTMLUtils;
-import ca.ucalgary.seahawk.util.SeahawkOptions;
+import ca.ucalgary.seahawk.util.*;
 
 import org.biomoby.shared.*;
 import org.biomoby.shared.data.*;
+import org.biomoby.shared.parser.MobyTags;
 import org.biomoby.client.CentralImpl;
 import org.biomoby.client.MobyRequest;
 import org.biomoby.client.MobyRequestEventHandler;
@@ -182,6 +182,7 @@
 	return handler;
     }
 
+    // synchronized so simultaneous requests don't get their input data mixed up
     public void setupServiceSecondaryData(MobyRequestEventHandler handler){
 	MobyDataInstance[] castInputs = new MobyDataInstance[primaryInput.length];
 	for(int i = 0; i < primaryInput.length; i++){
@@ -194,14 +195,17 @@
 	    castInputs[i] = (MobyDataInstance) primaryInput[i];
 	}
 
-	try{	    
-	    mobyRequest.setInput(castInputs);
-	    mobyRequest.setSecondaryInput(secondaryInputInstances);
-	} catch(MobyException me){
-	    me.printStackTrace();
-	    logger.warn("Error while trying to set service input: " + me);
-	}
-	executeService(handler);
+        // code from mobyRequest.setInput() to executeService() should always be synced to avoid input mixup between requests
+        synchronized(mobyRequest){
+	    try{	    
+	        mobyRequest.setInput(castInputs);
+	        mobyRequest.setSecondaryInput(secondaryInputInstances);
+	    } catch(MobyException me){
+	        me.printStackTrace();
+	        logger.warn("Error while trying to set service input: " + me);
+	    }
+	    executeService(handler);
+        }
     }
 
     protected void setupService(MobyService mobyService, MobyDataInstance mdi, int handlerHashCode, boolean useDefaultSecondaries){
@@ -217,18 +221,21 @@
 	System.arraycopy(primaryInputTemplate, 0, primaryInput, 0, primaryInput.length);
 
 	if(!hasSecondaryInput(mobyService)){
-	    try{
-		// Implement simple input (i.e. only one input argument)
-		mobyRequest.setInput(mdi, "");
-	    }
-	    catch(MobyException me){
-		logger.error("Failure in MOBY input, was not acceptable:" + me);
-		return;
-	    }
+            // code from mobyRequest.setInput() to executeService() should always be synced to avoid input mixup between requests
+            synchronized(mobyRequest){
+	        try{
+		    // Implement simple input (i.e. only one input argument)
+		    mobyRequest.setInput(mdi, "");
+	        }
+	        catch(MobyException me){
+		    logger.error("Failure in MOBY input, was not acceptable:" + me);
+		    return;
+	        }
 
-	    // No need for further info, just launch the request
-	    removePopupOptions();
-	    executeService(getHandlerByHashCode(handlerHashCode));
+	        // No need for further info, just launch the request
+	        removePopupOptions();
+	        executeService(getHandlerByHashCode(handlerHashCode));
+            }
 	}
 	else{
 	    // We need more info from the user to launch this service
@@ -502,7 +509,8 @@
     class OptionLoaderThread extends Thread{
 	Node targetNode = null;
 	MobyRequestEventHandler handler = null;
-	MobyDataInstance mobyData = null;
+	MobyPayloadRequestListener payloadCreator = null;
+	Object mobyData = null;
 	String extraMenuText = null;
 	JPopupMenu popupList;
 
@@ -513,11 +521,13 @@
 	    this.handler = handler;
 	}
 
-	public OptionLoaderThread(MobyDataInstance mobyData, JPopupMenu popupList, MobyRequestEventHandler handler, String extraMenuText){
+	public OptionLoaderThread(Object mobyData, JPopupMenu popupList, MobyRequestEventHandler handler, 
+                                  MobyPayloadRequestListener payloadCreator, String extraMenuText){
 	    super();
 	    this.mobyData = mobyData;
 	    this.popupList = popupList;
 	    this.handler = handler;
+            this.payloadCreator = payloadCreator;
 	    this.extraMenuText = extraMenuText;
 	}
 
@@ -526,7 +536,7 @@
 		addPopupOptions(targetNode, popupList, false, handler);
 	    }
 	    else if(mobyData != null){
-		addPopupOptions(mobyData, popupList, false, handler, extraMenuText);
+		addPopupOptions(mobyData, popupList, false, handler, payloadCreator, extraMenuText);
 	    }
 	    else{
 		logger.warn("Warning: OptionLoaderThread has no data to work with");
@@ -576,6 +586,30 @@
     }
 
     /**
+     * Creates a menu item based on the provided data type.  If a service is selected from here,
+     * a callback will be made to the MobyPayloadRequestListener for the actual submission data.
+     *
+     * @param payloadKey a key that will be used in the callback so the listener knows what payload the create
+     */
+    public void addPopupOptions(MobyDataType mobyDataType, JPopupMenu popupList, boolean asynchronous, 
+                                MobyRequestEventHandler handler, MobyPayloadRequestListener payloadCreator, 
+                                String payloadKey, String extraMenuText){
+        addPopupOptions(mobyDataType, popupList, asynchronous, handler, payloadCreator, extraMenuText);
+    }
+
+    public void addPopupOptions(MobyNamespace mobyNamespace, JPopupMenu popupList, boolean asynchronous, 
+                                MobyRequestEventHandler handler, MobyPayloadRequestListener payloadCreator, 
+                                String payloadKey, String extraMenuText){
+        addPopupOptions(mobyNamespace, popupList, asynchronous, handler, payloadCreator, extraMenuText);
+    }
+
+    public void addPopupOptions(MobyPrimaryDataSet collection, JPopupMenu popupList, boolean asynchronous, 
+                                MobyRequestEventHandler handler, MobyPayloadRequestListener payloadCreator, 
+                                String payloadKey, String extraMenuText){
+        addPopupOptions(collection, popupList, asynchronous, handler, payloadCreator, extraMenuText);
+    }
+
+    /**
      * Same as three arg addPopupOptions, but uses default response handler
      */
     public void addPopupOptions(MobyDataInstance mobyData, JPopupMenu popupList, boolean asynchronous){
@@ -586,13 +620,16 @@
      * Find the list of available services querying MobyCentral directly with a piece of data.
      */
     public void addPopupOptions(MobyDataInstance mobyData, JPopupMenu popupList, boolean asynchronous, MobyRequestEventHandler handler){
-	addPopupOptions(mobyData, popupList, asynchronous, handler, null);
+	addPopupOptions(mobyData, popupList, asynchronous, handler, null, null);
     }
 
     /**
      * Find the list of available services querying MobyCentral directly with a piece of data.
+     *
+     * @param mobyData a MobyDataInstance, or in the case of deferred data to be created by payloadCreator, a MobyDataType, MobyNamespace, or MobyPrimaryDataSet
      */
-    public void addPopupOptions(MobyDataInstance mobyData, JPopupMenu popupList, boolean asynchronous, MobyRequestEventHandler handler, String extraMenuText){
+    public void addPopupOptions(Object mobyData, JPopupMenu popupList, boolean asynchronous, 
+                                MobyRequestEventHandler handler, MobyPayloadRequestListener payloadCreator, String extraMenuText){
 
 	if(asynchronous){
 	    //Show the user that we're doing something...
@@ -605,7 +642,7 @@
 	    }
 
 	    // Call this method synchronously in a different thread
-	    OptionLoaderThread lt = new OptionLoaderThread(mobyData, popupList, handler, extraMenuText);
+	    OptionLoaderThread lt = new OptionLoaderThread(mobyData, popupList, handler, payloadCreator, extraMenuText);
 	    lt.start();
 	    return;
 	}
@@ -625,7 +662,9 @@
 	    popupList.setVisible(true);
 	}
 
-	addClipboardItem(submenu, mobyData);
+	if(mobyData instanceof MobyDataInstance){
+            addClipboardItem(submenu, (MobyDataInstance) mobyData);
+        }
 	submenu.add(getWaitItem(submenu));
 
  	MobyDataServiceAssocInstance serviceAssocObject = null;  
@@ -637,6 +676,15 @@
 	    else if(mobyData instanceof MobyDataObject){
 		serviceAssocObject = mobyClient.getServices((MobyDataObject) mobyData);
 	    }
+            // The data will be loaded later
+            else if(payloadCreator != null){
+                if(mobyData instanceof MobyPrimaryDataSet){
+                    //serviceAssocObject = mobyClient.getServices(new MobyDataObjectSetDeferred(mobyData, payloadCreator, requestKey));
+                }
+                else{
+                    //serviceAssocObject = mobyClient.getServices(new MobyDataObjectDeferred(mobyData, payloadCreator, requestKey));
+                }
+            }
 	    else{
 		logger.warn("Service options for objects other than MobyDataObject " +
 			    "and MobyDataObjectSet are not yet supported.");
@@ -1136,51 +1184,50 @@
 	return menu;
     }
 
-    public JMenu createObjectSubMenu(MobyDataInstance mdi, String extraMenuText){
-	if(!(mdi instanceof MobyPrimaryData)){
-	    logger.warn("Ignoring non-primary data object submitted to menu creation: " + mdi);
-	    return null;
-	}
-	
-	MobyPrimaryData targetData = (MobyPrimaryData) mdi;
-	String id = targetData.getId();
-	if(id == null){
-	    id = "";
-	}
-	else if(id.length() > MAX_ID_LEN+3){
-	    id = id.substring(0, MAX_ID_LEN)+"...";
-	}
-	
-	MobyDataType mobyDataType = targetData.getDataType();
-	String name = null;
-	if(mobyDataType == null){
-	    logger.warn("PG: Warning: no datatype associated with service " + 
-			targetData.getName());
-	}
-	else{
-	    name = mobyDataType.getName();
-	}
-	if("Object".equals(name)){
-	    MobyNamespace namespaces[] = targetData.getNamespaces();
-	    //System.err.println("Got base object with namespaces numbering " + namespaces.length);
-	    if(namespaces != null && namespaces.length > 0 && namespaces[0] != null){
-		//System.err.println("Checking namespace "+ namespaces[0].getName());
-		name = namespaces[0].getName();
+    /**
+     * Template object may be one of MobyPrimaryData, or in case of deferred content loading a 
+     * MobyNamespace, MobyDataType, or MobyPrimaryDataSet.
+     */
+    public JMenu createObjectSubMenu(Object templateObject, String extraMenuText){
+        String id = null;
+        MobyDataType mobyDataType = null;
+        String name = null;
+	MobyNamespace[] namespaces = null;
+	if(templateObject instanceof MobyPrimaryData){
+	    MobyPrimaryData targetData = (MobyPrimaryData) templateObject;
+	    mobyDataType = targetData.getDataType();
+	    namespaces = targetData.getNamespaces();
+	    id = targetData.getId();
+	    if(id == null){
+	        id = "";
 	    }
-	}
-	else{
-	    //System.err.println("Got complex object with datatype name " + name);
-	}
+	    else if(id.length() > MAX_ID_LEN+3){
+	        id = id.substring(0, MAX_ID_LEN)+"...";
+	    }
+	    if(MobyTags.MOBYOBJECT.equals(mobyDataType.getName()) &&
+               namespaces != null && namespaces.length > 0 && namespaces[0] != null){
+		name = namespaces[0].getName();
+            }
+            else{
+                name = mobyDataType.getName();
+            }
+        }
+        else if(templateObject instanceof MobyNamespace){
+            namespaces = new MobyNamespace[]{(MobyNamespace) templateObject};
+            mobyDataType = MobyDataType.getDataType(MobyTags.MOBYOBJECT, SeahawkOptions.getRegistry());
+            name = ((MobyNamespace) templateObject).getName();
+        }
+        else if(templateObject instanceof MobyDataType){
+            mobyDataType = (MobyDataType) templateObject;
+            name = ((MobyDataType) templateObject).getName();
+        }
+        else{
+            logger.error("Could not create submenu for object of unaccepted type "+templateObject.getClass().getName());
+        }
 	
-	// Make sure we have a fully documented data type object
-	mobyDataType = MobyDataType.getDataType(targetData.getDataType().getName(), SeahawkOptions.getRegistry());
 	String desc = null;
 	String datatype = null;
-	if(mobyDataType == null){
-	    logger.warn("PG: Warning (submenu): no datatype associated with service " + 
-			targetData.getName());
-	}
-	else{
+	if(mobyDataType != null){
 	    datatype = mobyDataType.getName();
 	    desc = mobyDataType.getDescription();
 	    if(desc == null || desc.length() == 0){
@@ -1189,19 +1236,12 @@
 	}
 	if(datatype != null && datatype.indexOf("objectclass:") != -1){ 
 	    //LSID type URN, truncate the prefix and keep the part a user would care about (last part, the class name)
-	    
 	    datatype = datatype.substring(datatype.indexOf("objectclass:")+12);
 	}
 
 	JMenu submenu = null;
-	MobyNamespace[] namespaces = targetData.getNamespaces();
 	// If not defined, derive a description from the Data Namespace
-	if(mobyDataType == null){
-	    desc = "Unknown datatype";
-	    submenu = new JMenu("Services for unknown datatype");
-	    assignMenuDataIndex(submenu);
-	}
-	else if("Object".equals(mobyDataType.getName())){
+	if(MobyTags.MOBYOBJECT.equals(mobyDataType.getName())){
 	    String mobydesc = "?";
 	    if(namespaces != null){
 		// Take the longest description
@@ -1214,20 +1254,30 @@
 		}
 	    }
 	    desc = "Record Identifier - " + mobydesc;
-	    submenu = new JMenu("Services for " + (extraMenuText == null ? "" : extraMenuText+" ")+datatype + ":" + id);
+	    if(templateObject instanceof MobyDataObjectSet){
+		datatype += " collection";
+	    }
+	    submenu = new JMenu("<html>Services for " + (extraMenuText == null ? "" : extraMenuText+" ") + 
+                                datatype + (id == null ? "" : ":" + id)+"</html>");
 	    assignMenuDataIndex(submenu);
 	}
-	else if("String".equals(mobyDataType.getName())){
-	    String sample = targetData.getName();
-	    if(sample == null){
-		sample = targetData.toString();
+	else if(MobyTags.MOBYSTRING.equals(mobyDataType.getName())){
+	    String sample = "";
+            if(templateObject instanceof MobyDataInstance){
+                sample = ((MobyDataInstance) templateObject).getName();
+                if(sample == null){
+		    sample = "\""+((MobyDataInstance) templateObject).toString()+"\"";
+	        }
+            }
+	    if(templateObject instanceof MobyDataObjectSet){
+		sample += " collection";
 	    }
 	    if(sample.length() > MAX_ID_LEN+3){
-		sample = sample.substring(0, MAX_ID_LEN)+"...";
+		sample = "\""+sample.substring(0, MAX_ID_LEN)+"...\"";
 	    }
 	    desc = "A piece of text";
-	    submenu = new JMenu("Services for "+(extraMenuText == null ? "" : extraMenuText+" ")+
-				"String \"" + sample + "\"");
+	    submenu = new JMenu("<html>Services for "+(extraMenuText == null ? "" : extraMenuText+" ")+
+				"String " + sample+"</html>");
 	    assignMenuDataIndex(submenu);
 	}
 	// Complex object
@@ -1240,17 +1290,18 @@
 		    desc += "["+namespaceDesc+"]";
 		}
 	    }
-	    if(targetData instanceof MobyDataObject && id != null && id.length() > 0){
+	    if(templateObject instanceof MobyDataObject && id != null && id.length() > 0){
 		objectLabel += ":" + id;
 	    }
-	    else if(targetData instanceof MobyDataObjectSet){
+	    else if(templateObject instanceof MobyDataObjectSet){
 		objectLabel += " collection";
 	    }
-	    submenu = new JMenu("Services for " + (extraMenuText == null ? "" : extraMenuText+" ")+objectLabel);
+	    submenu = new JMenu("<html>Services for " + (extraMenuText == null ? "" : extraMenuText+" ")+objectLabel+"</html>");
 	    assignMenuDataIndex(submenu);
 	}
 	desc = "Input data: " + desc;
 	desc = HTMLUtils.htmlifyToolTipText(desc, MAX_SERVICE_DESC_LEN);
+        System.err.println("New submenu has label " + submenu.getText());
 	submenu.setToolTipText(desc);
 	submenu.setName(SERVICE_SUBMENU_NAME);
 	return submenu;



From gordonp at dev.open-bio.org  Wed Apr 14 23:48:28 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Wed, 14 Apr 2010 19:48:28 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004142348.o3ENmSDf009599@dev.open-bio.org>


gordonp
Wed Apr 14 19:48:27 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util
In directory dev.open-bio.org:/tmp/cvs-serv9535/src/main/ca/ucalgary/seahawk/util

Modified Files:
	MobyPayloadRequestListener.java 
Added Files:
	MobyContentCreator.java MobyDataObjectDeferred.java 
	MobyDataObjectSetDeferred.java 
Log Message:
Additional commit related to initial implementation 'for each' in Seahawk service invocation
moby-live/Java/src/main/ca/ucalgary/seahawk/util MobyContentCreator.java,NONE,1.1 MobyDataObjectDeferred.java,NONE,1.1 MobyDataObjectSetDeferred.java,NONE,1.1 MobyPayloadRequestListener.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/MobyPayloadRequestListener.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/MobyPayloadRequestListener.java	2010/04/14 22:02:04	1.1
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/MobyPayloadRequestListener.java	2010/04/14 23:48:27	1.2
@@ -10,7 +10,10 @@
  */	
 public interface MobyPayloadRequestListener{
     /**
-     * @param requestKey the value given to the caller when the listener was registered (tells the listener what payload to create baesd on some internal naming convention for the listener)
+     * Assumes the listener knows what payload to create based on some internal context stored by the listener. 
+     * (i.e. you need to create a new listener specific to each deferred payload. 
+     *
+     * @param paramNameforJobs the name of the moby job  parameter to which each value should be assigned
      */
-    public org.biomoby.shared.data.MobyContentInstance createPayload(String requestKey, String paramNameforJobs); 
+    public org.biomoby.shared.data.MobyContentInstance createPayload(String paramNameforJobs); 
 }



From gordonp at dev.open-bio.org  Wed Apr 14 23:48:27 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Wed, 14 Apr 2010 19:48:27 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004142348.o3ENmRar009579@dev.open-bio.org>


gordonp
Wed Apr 14 19:48:27 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv9535/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	MobyContentPane.java MobyPayloadCreator.java 
	MobyServicesGUI.java 
Log Message:
Additional commit related to initial implementation 'for each' in Seahawk service invocation
moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyContentPane.java,1.27,1.28 MobyPayloadCreator.java,1.1,1.2 MobyServicesGUI.java,1.18,1.19
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java,v
retrieving revision 1.27
retrieving revision 1.28
diff -u -r1.27 -r1.28
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java	2010/04/14 22:02:04	1.27
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java	2010/04/14 23:48:27	1.28
@@ -1215,7 +1215,6 @@
 	// chooses the for each option.  The Moby data instance's userData gives us the current context, enabling us 
         // to construct the correct payload in MobyPayloadCreator.createPayload() at any point in the future.
         String origUserData = (String) mobyData.getUserData();
-        MobyPayloadRequestListener payloadCreator = new MobyPayloadCreator(this);
         for(String peerMode: new String[]{DataUtils.ARTICLE_PEERS_MODE, DataUtils.DATATYPE_PEERS_MODE}){
             // note that getPeerElements() will modify the userData to reflect the semantic of the requested peer mode
             mobyData.setUserData(origUserData);
@@ -1229,17 +1228,20 @@
             }
             MobyDataType dataType = ((MobyPrimaryData) mobyData).getDataType();
             if(mobyData instanceof MobyPrimaryDataSet){	 // Collection
-                servicesGUI.addPopupOptions((MobyPrimaryDataSet) mobyData, popup, true, getDefaultHandler(), payloadCreator, 
-					    (String) mobyData.getUserData(), each);
+                servicesGUI.addPopupOptions((MobyPrimaryDataSet) mobyData, popup, true, getDefaultHandler(), 
+					    new MobyPayloadCreator(this, (String) mobyData.getUserData()), 
+					    each);
             }
             else if(MobyTags.MOBYOBJECT.equals(dataType.getName())){  
                 MobyNamespace namespace = null;
-                servicesGUI.addPopupOptions(namespace, popup, true, getDefaultHandler(), payloadCreator, 
-                                            (String) mobyData.getUserData(), each);
+                servicesGUI.addPopupOptions(namespace, popup, true, getDefaultHandler(),
+					    new MobyPayloadCreator(this, (String) mobyData.getUserData()), 
+                                            each);
             }
             else{
-                servicesGUI.addPopupOptions(dataType, popup, true, getDefaultHandler(), payloadCreator, 
-                                            (String) mobyData.getUserData(), each);
+                servicesGUI.addPopupOptions(dataType, popup, true, getDefaultHandler(),
+					    new MobyPayloadCreator(this, (String) mobyData.getUserData()), 
+                                            each);
             }
         }
 
@@ -1301,7 +1303,7 @@
 		// so PbE will properly reflect the logic of if(f1(x) matches filter){f2(x)}
 		DataUtils.addUserData(previousMDI, srcURL, getFilter());
 
-		servicesGUI.addPopupOptions(previousMDI, popup, true, null, "previous input");
+		servicesGUI.addPopupOptions(previousMDI, popup, true, null, null, "previous input");
 	    }
 	} catch(Exception e){
 	    logger.warn("Could not load previous service info, 'previous input' option will not be displayed", e);

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyPayloadCreator.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyPayloadCreator.java	2010/04/14 22:02:04	1.1
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyPayloadCreator.java	2010/04/14 23:48:27	1.2
@@ -14,14 +14,16 @@
  */
 public class MobyPayloadCreator implements MobyPayloadRequestListener{
     private MobyContentPane srcPane;
+    private String requestKey;
 
     private static Logger logger = Logger.getLogger(MobyPayloadCreator.class.getName());
 
-    public MobyPayloadCreator(MobyContentPane pane){
+    public MobyPayloadCreator(MobyContentPane pane, String requestKey){
         srcPane = pane;
+	this.requestKey = requestKey;
     }
 
-    public MobyContentInstance createPayload(String requestKey, String targetJobArgName){
+    public MobyContentInstance createPayload(String targetJobArgName){
 	// The request key is the sample data's app context: 
         // url#xpath <tab> sample_xptr <tab> filter_regex <tab> filter_xpath <tab> xpath_desc <tab> case_sensitive_boolean <tab> inverse selection
         // from which we will build the peer dataset to submit.

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java,v
retrieving revision 1.18
retrieving revision 1.19
diff -u -r1.18 -r1.19
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java	2010/04/14 22:02:04	1.18
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java	2010/04/14 23:48:27	1.19
@@ -586,30 +586,6 @@
     }
 
     /**
-     * Creates a menu item based on the provided data type.  If a service is selected from here,
-     * a callback will be made to the MobyPayloadRequestListener for the actual submission data.
-     *
-     * @param payloadKey a key that will be used in the callback so the listener knows what payload the create
-     */
-    public void addPopupOptions(MobyDataType mobyDataType, JPopupMenu popupList, boolean asynchronous, 
-                                MobyRequestEventHandler handler, MobyPayloadRequestListener payloadCreator, 
-                                String payloadKey, String extraMenuText){
-        addPopupOptions(mobyDataType, popupList, asynchronous, handler, payloadCreator, extraMenuText);
-    }
-
-    public void addPopupOptions(MobyNamespace mobyNamespace, JPopupMenu popupList, boolean asynchronous, 
-                                MobyRequestEventHandler handler, MobyPayloadRequestListener payloadCreator, 
-                                String payloadKey, String extraMenuText){
-        addPopupOptions(mobyNamespace, popupList, asynchronous, handler, payloadCreator, extraMenuText);
-    }
-
-    public void addPopupOptions(MobyPrimaryDataSet collection, JPopupMenu popupList, boolean asynchronous, 
-                                MobyRequestEventHandler handler, MobyPayloadRequestListener payloadCreator, 
-                                String payloadKey, String extraMenuText){
-        addPopupOptions(collection, popupList, asynchronous, handler, payloadCreator, extraMenuText);
-    }
-
-    /**
      * Same as three arg addPopupOptions, but uses default response handler
      */
     public void addPopupOptions(MobyDataInstance mobyData, JPopupMenu popupList, boolean asynchronous){
@@ -678,16 +654,32 @@
 	    }
             // The data will be loaded later
             else if(payloadCreator != null){
-                if(mobyData instanceof MobyPrimaryDataSet){
-                    //serviceAssocObject = mobyClient.getServices(new MobyDataObjectSetDeferred(mobyData, payloadCreator, requestKey));
-                }
-                else{
-                    //serviceAssocObject = mobyClient.getServices(new MobyDataObjectDeferred(mobyData, payloadCreator, requestKey));
-                }
+                try{
+                    if(mobyData instanceof MobyPrimaryDataSet){
+			serviceAssocObject = mobyClient.getServices(new MobyDataObjectSetDeferred((MobyPrimaryDataSet) mobyData, 
+												  payloadCreator));
+		    }
+		    else if(mobyData instanceof MobyNamespace){
+			serviceAssocObject = mobyClient.getServices(new MobyDataObjectDeferred((MobyNamespace) mobyData, 
+											       payloadCreator));
+		    }
+		    else if(mobyData instanceof MobyDataType){
+			serviceAssocObject = mobyClient.getServices(new MobyDataObjectDeferred((MobyDataType) mobyData, 
+											       payloadCreator));
+		    }
+		    else{
+			logger.warn("Ignoring unrecognized template class (" + mobyData.getClass().getName()+
+				    ") for deferred data creation by a MobyPayloadRequestListener"); 
+			return;
+		    }
+		} catch(Exception e){
+		    logger.error("Could not create deferred Moby data object", e);
+		}
             }
 	    else{
 		logger.warn("Service options for objects other than MobyDataObject " +
-			    "and MobyDataObjectSet are not yet supported.");
+			    "and MobyDataObjectSet are not yet supported unless you " +
+			    "have defined a MobyPayloadRequestListener.");
 		return;
 	    }
 	} catch(Exception mobye){



From gordonp at dev.open-bio.org  Thu Apr 15 18:51:17 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Thu, 15 Apr 2010 14:51:17 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004151851.o3FIpHrB006441@dev.open-bio.org>


gordonp
Thu Apr 15 14:51:17 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data
In directory dev.open-bio.org:/tmp/cvs-serv6403/src/main/org/biomoby/shared/data

Modified Files:
	MobyContentInstance.java 
Log Message:
Made contents maintain insertion order by switching to LinkedHashMap for underlying Map storage
moby-live/Java/src/main/org/biomoby/shared/data MobyContentInstance.java,1.14,1.15
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyContentInstance.java,v
retrieving revision 1.14
retrieving revision 1.15
diff -u -r1.14 -r1.15
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyContentInstance.java	2008/01/14 22:54:19	1.14
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyContentInstance.java	2010/04/15 18:51:17	1.15
@@ -31,7 +31,7 @@
     private String serviceAuthURI = null;
     private String serviceNotes = null;
     private int xmlMode = MobyDataInstance.SERVICE_XML_MODE;
-    private HashMap<String, MobyDataJob> members;
+    private LinkedHashMap<String, MobyDataJob> members;
     private int autoID = 1;  // to name members without existing names
     private Vector<ServiceException> exceptions;
 
@@ -40,7 +40,7 @@
      * Useful if you are a client composing a query, or a server composing a response.
      */
     public MobyContentInstance(){
-	members = new HashMap<String, MobyDataJob>();
+	members = new LinkedHashMap<String, MobyDataJob>();
 	exceptions = new Vector<ServiceException>();
     }
 
@@ -106,7 +106,7 @@
 	    }
 	}
 	
-	members = new HashMap<String,MobyDataJob>();
+	members = new LinkedHashMap<String,MobyDataJob>();
 
 	// If we got this far, we're in the clear for the single envelope
 	// What we need to parse now is the one or more sets of data in the envelope



From gordonp at dev.open-bio.org  Fri Apr 16 17:29:21 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 16 Apr 2010 13:29:21 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004161729.o3GHTLfE014979@dev.open-bio.org>


gordonp
Fri Apr 16 13:29:21 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory dev.open-bio.org:/tmp/cvs-serv14943/src/main/org/biomoby/client

Modified Files:
	MobyRequest.java 
Log Message:
Fixed javadoc typo
moby-live/Java/src/main/org/biomoby/client MobyRequest.java,1.46,1.47
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java,v
retrieving revision 1.46
retrieving revision 1.47
diff -u -r1.46 -r1.47
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java	2010/03/29 20:42:48	1.46
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java	2010/04/16 17:29:21	1.47
@@ -238,7 +238,7 @@
 
     /**
      * This method will assign the provided secondary parameters to all primary input data currently
-     * in this object.  This is covenient if you are running 100 seqs through BLAST and only want to set
+     * in this object.  This is convenient if you are running 100 seqs through BLAST and only want to set
      * the parameters once.  If you instead want to set secondary input differently for all primary inputs, you'll
      * need to create a custom MobyContentInstance as input to setInput().
      *



From gordonp at dev.open-bio.org  Fri Apr 16 17:32:33 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 16 Apr 2010 13:32:33 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004161732.o3GHWXGF015279@dev.open-bio.org>


gordonp
Fri Apr 16 13:32:33 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services
In directory dev.open-bio.org:/tmp/cvs-serv15243/src/main/ca/ucalgary/seahawk/services

Modified Files:
	MobyClient.java 
Log Message:
Implemented proper logging, account for deferred data objects
moby-live/Java/src/main/ca/ucalgary/seahawk/services MobyClient.java,1.26,1.27
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/MobyClient.java,v
retrieving revision 1.26
retrieving revision 1.27
diff -u -r1.26 -r1.27
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/MobyClient.java	2010/04/11 01:58:05	1.26
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/MobyClient.java	2010/04/16 17:32:33	1.27
@@ -1,6 +1,6 @@
 package ca.ucalgary.seahawk.services;
 
-import ca.ucalgary.seahawk.util.SeahawkOptions;
+import ca.ucalgary.seahawk.util.*;
 
 import org.biomoby.client.*;
 import org.biomoby.registry.meta.*;
@@ -116,8 +116,8 @@
 	    docBuilder = dbf.newDocumentBuilder();
 	}
 	catch(ParserConfigurationException pce){
-	    System.err.println("Error: Could not find an XML parser, will not be able to use " +
-			       "MOBY xpath and regex mapper default behaviors: " + pce);
+	    logger.log(Level.SEVERE, "Error: Could not find an XML parser, will not be able to use " +
+		       "MOBY xpath and regex mapper default behaviors: ", pce);
 	}
 	ClassLoader cl = getClass().getClassLoader();
 	if(cl == null){
@@ -138,8 +138,8 @@
 	}
 	if(dataMappingXMLURL == null){
 	    if(rulesResource.length() != 0){ // if not left intentionally blank
-		System.err.println("Could not find MOBY data mapping resource '"+
-				   rulesResource+"'");
+		logger.log(Level.WARNING, "Could not find MOBY data mapping resource '"+
+				          rulesResource+"'");
 	    }
 	}
 	else{
@@ -147,7 +147,7 @@
 		addMappingsFromURL(dataMappingXMLURL);
 	    }
 	    catch(Exception e){
-		System.err.println("Error loading default data mapping rules ("+dataMappingXMLURL+"):" + e);
+		logger.log(Level.SEVERE, "Error loading default data mapping rules ("+dataMappingXMLURL+")", e);
                 e.printStackTrace();
 	    }
 	}
@@ -198,8 +198,8 @@
      */
     public void addMappingsFromURL(URL u) throws Exception{
 	if(docBuilder == null){
-	    System.err.println("Asked to add data mappings from file, " +
-			       "but no XML parser is available");
+	    logger.log(Level.SEVERE, "Asked to add data mappings from file, " +
+			             "but no XML parser is available");
 	    return;
 	}
 
@@ -229,13 +229,13 @@
 	}
 
 	if(nsContext.getNamespaceURI(prefix) != null){
-	    System.err.println("Prefix definition for " + prefix + " already exists, ignoring new definition");
+	    logger.log(Level.WARNING, "Prefix definition for " + prefix + " already exists, ignoring new definition");
 	    return;
 	}
 
 	String nsURI = e.getTextContent();
 	if(nsURI == null || nsURI.length() == 0){
-	    System.err.println("Prefix definition for " + prefix + " has a blank URI rule, ignoring");
+	    logger.log(Level.WARNING, "Prefix definition for " + prefix + " has a blank URI rule, ignoring");
 	    return;
 	}
 	nsContext.setPrefix(nsURI, prefix);	
@@ -264,7 +264,7 @@
 	    }
 
 	    if(!RULE_SET_TAG.equals(ruleSet.getLocalName())){
-		System.err.println("Skipping unexpected top level tag " + ruleSet.getLocalName());
+		logger.log(Level.WARNING, "Skipping unexpected top level tag " + ruleSet.getLocalName());
 		continue;
 	    }
 
@@ -304,18 +304,18 @@
 		}
 		else if(isArticleNameRule(ruleMember)){
 		    if(articleNameString != null && articleNameString.length() != 0){
-			System.err.println("Skipping unexpected article name definition node, " +
-					   "a valid article name rule has already been " +
-					   "created for this ruleset");
+			logger.log(Level.WARNING, "Skipping unexpected article name definition node, " +
+					          "a valid article name rule has already been " +
+					          "created for this ruleset");
 			continue;
 		    }
 		    articleNameString = ruleMember.getTextContent();
 		}
 		else if(isDataTypeRule(ruleMember)){
 		    if(dataTypeString != null && dataTypeString.length() != 0){
-			System.err.println("Skipping unexpected datatype definition node, " +
-					   "a valid datatype rule has already been " +
-					   "created for this ruleset");
+			logger.log(Level.WARNING, "Skipping unexpected datatype definition node, " +
+					          "a valid datatype rule has already been " +
+					          "created for this ruleset");
 			continue;
 		    }
 		    dataTypeString = getDataType(ruleMember);
@@ -328,15 +328,15 @@
 		}
 		// skip any Dublin Core metadata in validation
 		else if(!MobyPrefixResolver.DUBLIN_CORE_NAMESPACE.equals(ruleMember.getNamespaceURI())){
-		    System.err.println("Skipping unexpected "+RULE_SET_TAG+
-				       " child node " + ruleMember.getLocalName());
+		    logger.log(Level.WARNING, "Skipping unexpected "+RULE_SET_TAG+
+				              " child node " + ruleMember.getLocalName());
 		    continue;
 		} 
 	    }
 
 	    if(xpathStrings.size() == 0 && regexStrings.size() == 0 && urlRegexStrings.size() == 0){
-		System.err.println("Skipping namespace rule that has no xpath " +
-				   "url_regex or regex specs associated with it");
+		logger.log(Level.WARNING, "Skipping namespace rule that has no xpath " +
+				          "url_regex or regex specs associated with it");
 		// Next ruleset
 		continue;
 	    }
@@ -344,9 +344,9 @@
 	    // Simple object with just namespace & ID
 	    if(dataTypeString == null || dataTypeString.length() == 0){
 		if(memberMap.size() != 0){
-		    System.err.println("Warning: ignoring member rules, since " +
-				       "no datatype was defined for the ruleset " +
-				       "(base Object will be created)");
+		    logger.log(Level.WARNING, "Warning: ignoring member rules, since " +
+				              "no datatype was defined for the ruleset " +
+				              "(base Object will be created)");
 		}
 
 		for(int j = 0; j < xpathStrings.size(); j++){
@@ -362,8 +362,8 @@
 	    // Build complex object
 	    else{
 		if(memberMap.size() == 0){
-		    System.err.println("Complex datatype (" + dataTypeString + " was defined " +
-				       " in the ruleset, but no members were defined");
+		    logger.log(Level.WARNING, "Complex datatype (" + dataTypeString + " was defined " +
+				              " in the ruleset, but no members were defined");
 		}
 
 		for(int j = 0; j < xpathStrings.size(); j++){
@@ -465,7 +465,7 @@
 	    regexStrings.add(str);
 	}
 	else{
-	    System.err.println("Skipping blank regex rule"); 
+	    logger.log(Level.WARNING, "Skipping blank regex rule"); 
 	}
 
 	return str;
@@ -483,7 +483,7 @@
 	    urlRegexStrings.add(str);
 	}
 	else{
-	    System.err.println("Skipping blank url_regex rule"); 
+	    logger.log(Level.WARNING, "Skipping blank url_regex rule"); 
 	}
 
 	return str;
@@ -501,7 +501,7 @@
 	    xPathStrings.add(str);
 	}
 	else{
-	    System.err.println("Skipping blank XPath rule"); 
+	    logger.log(Level.WARNING, "Skipping blank XPath rule"); 
 	}
 
 	return str;
@@ -524,7 +524,7 @@
 	String memberNameKey = isPrimitiveDataType(dataTypeName) ? 
 	    MobyComplexBuilder.PRIMITIVE_VALUE_SENTINEL : memTag.getAttribute(DATATYPE_RULE_ATTR);
 	if(ruleValue == null || ruleValue.length() == 0){
-	    System.err.println("Object member " + memberNameKey + " has a blank value rule");
+	    logger.log(Level.WARNING, "Object member " + memberNameKey + " has a blank value rule");
 	}
 
 	String memberDataTypeSetting = memTag.getAttribute(DATATYPE_ATTR);
@@ -574,10 +574,10 @@
 		!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 (" + memberWhitespaceSetting + 
-			       "), overriding with default of " + WHITESPACE_ATTR_KEEP_VAL);
+	    logger.log(Level.WARNING, "Object member " + memberNameKey + 
+			              " has an unrecognized value for the " + WHITESPACE_ATTR +
+			              " attribute (" + memberWhitespaceSetting + 
+			              "), overriding with default of " + WHITESPACE_ATTR_KEEP_VAL);
 	    memberWhitespaceSetting = WHITESPACE_ATTR_KEEP_VAL;
 	}
 
@@ -587,14 +587,14 @@
 	}
 	else if(!memberEncodingSetting.equals(ENCODING_ATTR_NONE_VAL) &&
 		!memberEncodingSetting.equals(ENCODING_ATTR_BASE64_VAL)){
-	    System.err.println("Object member " + memberNameKey + 
-			       " has an unrecognized value for the " + ENCODING_ATTR +
-			       " attribute, overriding with default of " + ENCODING_ATTR_NONE_VAL);
+	    logger.log(Level.WARNING, "Object member " + memberNameKey + 
+			              " has an unrecognized value for the " + ENCODING_ATTR +
+			              " attribute, overriding with default of " + ENCODING_ATTR_NONE_VAL);
 	    memberWhitespaceSetting = ENCODING_ATTR_NONE_VAL;
 	}
 
 	if(membersMap.containsKey(memberNameKey)){
-	    System.err.println("Object member " + memberNameKey + " already exists, ignoring new definition");
+	    logger.log(Level.WARNING, "Object member " + memberNameKey + " already exists, ignoring new definition");
 	    return;
 	}
 
@@ -637,8 +637,8 @@
 					" cannot have empty children");
 		}
 		if(namespaceStrings.containsKey(keyName)){
-		    System.err.println("Ignoring duplicate namespace value rule for " +
-				       "namespace '" + keyName + "'");
+		    logger.log(Level.WARNING, "Ignoring duplicate namespace value rule for " +
+				              "namespace '" + keyName + "'");
 		    continue;
 		}
 		if(keyName != null && keyName.length() != 0){
@@ -649,7 +649,7 @@
 		}
 	    }
 	    else{
-		System.err.println("Skipping unexpected "+NAMESPACE_RULE_TAG+" child node " + specName);
+		logger.log(Level.WARNING, "Skipping unexpected "+NAMESPACE_RULE_TAG+" child node " + specName);
 		continue;
 	    }
 	}
@@ -716,13 +716,11 @@
 			    }
 			}
 			catch(MobyException me){
-			    System.err.println("Could not build Moby object from match:" + me);
-			    me.printStackTrace();
+			    logger.log(Level.SEVERE, "Could not build Moby object from match", me);
 			}
 		    }
 		} catch(Throwable t){  // Principally stack overflows
-		    System.err.println("Exception/Error ("+t+") while applying regex '"+pattern.pattern()+"' to text");
-		    t.printStackTrace(System.err);
+		    logger.log(Level.SEVERE, "Exception/Error ("+t+") while applying regex '"+pattern.pattern()+"' to text", t);
 		}
 	    }
 	}
@@ -765,11 +763,11 @@
 		// have the exact same contents as the same members who are their
 		// subtypes, as these are superfluous.
 
-		System.err.println("Multiple Moby objects were found in the text data, " +
-				   "but the request was to return a simple. " +
-				   "Only the first value in the collection has been returned.");
+		logger.log(Level.WARNING, "Multiple Moby objects were found in the text data, " +
+				          "but the request was to return a simple. " +
+				          "Only the first value in the collection has been returned.");
 		for(MobyDataObject result: results){
-		    System.err.println("Found object: " + result.getDataType().getName()); 
+		    logger.log(Level.WARNING, "Found object: " + result.getDataType().getName()); 
 		}
 		// TODO: should we instead return the one deepest in the hierarchy (or with the most members)?
 		return results.elementAt(0);
@@ -818,11 +816,11 @@
 		// have the exact same contents as the same members who are their
 		// subtypes, as these are superfluous.
 
-		System.err.println("Multiple Moby objects were found in the text data, " +
-				   "but the request was to return a simple. " +
-				   "Only the first value in the collection has been returned.");
+		logger.log(Level.WARNING, "Multiple Moby objects were found in the text data, " +
+				          "but the request was to return a simple. " +
+				          "Only the first value in the collection has been returned.");
 		for(MobyDataObject result: results){
-		    System.err.println("Found object: " + result.getDataType().getName()); 
+		    logger.log(Level.WARNING, "Found object: " + result.getDataType().getName()); 
 		}
 		// TODO: should we instead return the one deepest in the hierarchy (or with the most members)?
 		return results.elementAt(0);
@@ -916,11 +914,11 @@
 		// have the exact same contents as the same members who are their
 		// subtypes, as these are superfluous.
 
-		System.err.println("Multiple Moby objects were found in the text data, " +
-				   "but the request was to return a simple. " +
-				   "Only the first value in the collection has been returned.");
+		logger.log(Level.WARNING, "Multiple Moby objects were found in the text data, " +
+			                  "but the request was to return a simple. " +
+				          "Only the first value in the collection has been returned.");
 		for(MobyDataObject result: results){
-		    System.err.println("Found object: " + result.getDataType().getName()); 
+		    logger.log(Level.WARNING, "Found object: " + result.getDataType().getName()); 
 		}
 		// TODO: should we instead return the one deepest in the hierarchy (or with the most members)?
 		return results.elementAt(0);
@@ -994,12 +992,11 @@
 			    }
 			}
 			catch(MobyException me){
-			    System.err.println("Could not build Moby object from match:" + me);
-			    me.printStackTrace();
+			    logger.log(Level.SEVERE, "Could not build Moby object from match", me);
 			}
 		    }
 		} catch(Throwable t){ // Principally stack overflows
-		    System.err.println("Exception/Error ("+t+") while applying regex '"+pattern.pattern()+"' to binary data");
+		    logger.log(Level.SEVERE, "Exception/Error ("+t+") while applying regex '"+pattern.pattern()+"' to binary data", t);
 		}
 	    }
 	}
@@ -1050,7 +1047,7 @@
     public Map<String,MobyDataObject[]> getMobyObjectsURNMap(CharSequence textData, byte[] bytes){
 	Map results = new HashMap<String,MobyDataObject[]>();
 	if(regexMap.isEmpty()){
-	    System.out.println("The MOBY Client has not been provided any regex->moby data mappings!");
+	    logger.log(Level.WARNING, "The MOBY Client has not been provided any regex->moby data mappings!");
 	    return results;
 	}
 
@@ -1069,12 +1066,11 @@
 			}
 		    }
 		    catch(MobyException me){
-			System.err.println("Could not build Moby object from match (rule "+urn+"):" + me);
-			me.printStackTrace();
+			logger.log(Level.SEVERE, "Could not build Moby object from match (rule "+urn+")", me);
 		    }
 		}
 	    }catch(Throwable t){ // Principally stack overflows
-		System.err.println("Exception/Error ("+t+") while applying regex '"+pattern.pattern()+"' to text/binary");
+		logger.log(Level.SEVERE, "Exception/Error ("+t+") while applying regex '"+pattern.pattern()+"' to text/binary", t);
 	    }
 	    if(urn != null && !objectVector.isEmpty()){
 		results.put(urn, (MobyDataObject[]) objectVector.toArray(new MobyDataObject[objectVector.size()]));
@@ -1086,7 +1082,7 @@
 
     public MobyDataObject[] getMobyObjects(CharSequence textData, byte[] bytes){
 	if(regexMap.isEmpty()){
-	    System.out.println("The MOBY Client has not been provided any regex->moby data mappings!");
+	    logger.log(Level.WARNING, "The MOBY Client has not been provided any regex->moby data mappings!");
 	    return new MobyDataObject[0];
 	}
 
@@ -1109,12 +1105,11 @@
 			}
 		    }
 		    catch(MobyException me){
-			System.err.println("Could not build Moby object from match:" + me);
-			me.printStackTrace();
+			logger.log(Level.SEVERE, "Could not build Moby object from match", me);
 		    }
 		}
 	    }catch(Throwable t){ // Principally stack overflows
-		System.err.println("Exception/Error ("+t+") while applying regex '"+pattern.pattern()+"' to text/binary");
+		logger.log(Level.SEVERE, "Exception/Error ("+t+") while applying regex '"+pattern.pattern()+"' to text/binary", t);
 	    }
 	}
 
@@ -1142,7 +1137,7 @@
 
     public MobyDataObject[] getMobyObjects(URL url, String linkText, MobyDataType targetDataType){
 	if(urlRegexMap.isEmpty()){
-	    System.out.println("The MOBY Client has not been provided any url regex->moby data mappings!");
+	    logger.log(Level.WARNING, "The MOBY Client has not been provided any url regex->moby data mappings!");
 	    return new MobyDataObject[0];
 	}
 
@@ -1171,8 +1166,7 @@
 		    }
 		}
 		catch(MobyException me){
-		    System.err.println("Could not build Moby object from url regex match:" + me);
-		    me.printStackTrace();
+		    logger.log(Level.SEVERE, "Could not build Moby object from url regex match", me);
 		}
 	    }
 	}
@@ -1188,7 +1182,7 @@
 
 	// No xpaths to check
 	if(xpathMap.isEmpty()){
-	    System.out.println("The MOBY Client has not been provided any xpath->moby data mappings!");
+	    logger.log(Level.WARNING, "The MOBY Client has not been provided any xpath->moby data mappings!");
 	    return new MobyDataObject[0];
 	}
 	
@@ -1224,8 +1218,8 @@
 		    }
 		    
 		}catch(XPathExpressionException xpe2){
-		    System.err.println( "Warning: Cannot access resulting node list "+
-					"due to exception in its retrieval: " + xpe2);
+		    logger.log(Level.WARNING, "Warning: Cannot access resulting node list "+
+			       "due to exception in its retrieval: ", xpe2);
 		    return new Vector<MobyDataObject>();
 		}
 	    }
@@ -1241,9 +1235,9 @@
 		    }
 		}
 		else{ //not a node sequence
-		    System.out.println("Warning: the XPath expression ("+ xpath +
-				       ") did not return a node set, cannot select document elements."+
-				       " The returned object was of type "+ result.getClass().getName() );
+		    logger.log(Level.WARNING, "Warning: the XPath expression ("+ xpath +
+			                      ") did not return a node set, cannot select document elements."+
+				              " The returned object was of type "+ result.getClass().getName() );
 		    return new Vector<MobyDataObject>();
 		}
 	    }		
@@ -1253,8 +1247,8 @@
 	//xpe.printStackTrace();
 	    return new Vector<MobyDataObject>();
 	}catch(MobyException me){
-	    System.err.println("Warning: Cannot create objects from select nodes due " +
-			       " to exception in MOBY logic:" + me);
+	    logger.log(Level.WARNING, "Warning: Cannot create objects from select nodes due " +
+		       " to exception in MOBY logic:", me);
 	    return new Vector<MobyDataObject>();
 	}
 	
@@ -1270,7 +1264,7 @@
 
 	// No xpaths to check
 	if(xpathMap.isEmpty()){
-	    System.out.println("The MOBY Client has not been provided any xpath->moby data mappings!");
+	    logger.log(Level.WARNING, "The MOBY Client has not been provided any xpath->moby data mappings!");
 	    return results;
 	}
 	
@@ -1340,14 +1334,24 @@
 	    }
 
 	    if(mdos[i] instanceof MobyDataObject){
-		mobyDataServiceAssocInstances[i] = new MobyDataObjectSAI((MobyDataObject) mdos[i], mService);
+		if(mdos[i] instanceof MobyDataObjectDeferred){
+		    mobyDataServiceAssocInstances[i] = new MobyDataObjectDeferredSAI((MobyDataObjectDeferred) mdos[i], mService);
+		}
+		else{
+		    mobyDataServiceAssocInstances[i] = new MobyDataObjectSAI((MobyDataObject) mdos[i], mService);
+		}
 	    }
 	    else if(mdos[i] instanceof MobyDataObjectSet){
-		mobyDataServiceAssocInstances[i] = new MobyDataObjectSetSAI((MobyDataObjectSet) mdos[i], mService);
+		if(mdos[i] instanceof MobyDataObjectSetDeferred){
+		    mobyDataServiceAssocInstances[i] = new MobyDataObjectSetDeferredSAI((MobyDataObjectSetDeferred) mdos[i], mService);
+		}
+		else{
+		    mobyDataServiceAssocInstances[i] = new MobyDataObjectSetSAI((MobyDataObjectSet) mdos[i], mService);
+		}
 	    }
 	    else{
 		logger.log(Level.WARNING, "MobyClient could not handle service-associating an instance of " + mdos[i].getClass());
-		System.err.println("MobyClient could not handle service-associating an instance of " + mdos[i].getClass());
+		//System.err.println("MobyClient could not handle service-associating an instance of " + mdos[i].getClass());
 	    }
 	}
 	return mobyDataServiceAssocInstances; 
@@ -1363,7 +1367,7 @@
 
     public void addRegexMapping(String regexp, String[] mobyObj, String articleName, String urn){ //mobyObj<--mobyNamespaces
 	if(mobyObj == null){
-	    System.err.println("Ignoring empty namespace-only regex rule mappings");
+	    logger.log(Level.WARNING, "Ignoring empty namespace-only regex rule mappings");
 	    return;
 	}
 
@@ -1377,7 +1381,7 @@
 
     public void addURLRegexMapping(String url_regexp, String[] mobyObj, String articleName, String urn){ //mobyObj<--mobyNamespaces
 	if(mobyObj == null){
-	    System.err.println("Ignoring empty namespace-only url regex rule mappings");
+	    logger.log(Level.WARNING, "Ignoring empty namespace-only url regex rule mappings");
 	    return;
 	}
 
@@ -1466,7 +1470,7 @@
 
     protected void addRegexMapping(String regexp, Map<String,String> nsRules, String articleName, String ruleName, String urn){ //nsRules = Map<String ns, String regex_replacement>
 	if(nsRules == null || nsRules.size() == 0){
-	    System.err.println("Ignoring empty namespace-only regex rule mappings");
+	    logger.log(Level.WARNING, "Ignoring empty namespace-only regex rule mappings");
 	    return;
 	}
 
@@ -1475,7 +1479,7 @@
 
     protected void addURLRegexMapping(String url_regexp, Map<String,String> url_nsRules, String articleName, String urn){ //nsRules = Map<String ns, String regex_replacement>
 	if(url_nsRules == null || url_nsRules.size() == 0){
-	    System.err.println("Ignoring empty namespace-only url regex rule mappings");
+	    logger.log(Level.WARNING, "Ignoring empty namespace-only url regex rule mappings");
 	    return;
 	}
 
@@ -1517,8 +1521,8 @@
 	    if(memberRelationship.getRelationshipType() == Central.iHAS){
 		String[] rule = membersMap.get(memberRelationship.getName());
 		if(rule == null){
-		    System.err.println("Skipping HAS member "+memberRelationship.getName() + 
-				       " without an explicit rule (may be defined by inheritance?)");		    
+		    logger.log(Level.WARNING, "Skipping HAS member "+memberRelationship.getName() + 
+				              " without an explicit rule (may be defined by inheritance?)");		    
 		    continue;
 		}
 		Pattern pattern = Pattern.compile(newRegexp, Pattern.DOTALL | Pattern.COMMENTS);
@@ -1527,8 +1531,8 @@
 		    if(captured.containsKey(i)){ //autoboxed int
 			// Already encapsulated the capture group due to another
 			// HAS member, don't need to add anything
-			System.err.println("Skipping processing of capture group "+i+
-					   ", it's already been processed by another member in this rule");
+			logger.log(Level.WARNING, "Skipping processing of capture group "+i+
+					          ", it's already been processed by another member in this rule");
 			continue;
 		    }
 		    if(rule[0].matches("^.*\\$"+i+"(?=\\D.*|\\z)")){
@@ -1614,9 +1618,7 @@
 	    }
 
 	}catch(Exception e){
-	    System.err.println("Could not create regular expression statement from '" +
-			       regexp + "': " + e);
-	    e.printStackTrace();
+	    logger.log(Level.SEVERE, "Could not create regular expression statement from '" + regexp + "'", e);
 	}
     }
 
@@ -1651,15 +1653,15 @@
 		builderNameMap.put(urn, mcb);
 	    }
 	}catch(Exception e){
-	    System.err.println("Could not create URL regular expression statement from '" +
-			       url_regexp + "': " + e);
+	    logger.log(Level.SEVERE, "Could not create URL regular expression statement from '" +
+			             url_regexp + "': " + e);
 	    e.printStackTrace();
 	}
     }
 
     public void addXPathMapping(String xpath, String[] mobyObj){ //mobyObj<--mobyNamespaces
 	if(mobyObj == null){
-	    System.err.println("Ignoring empty namespace-only regex rule mappings");
+	    logger.log(Level.WARNING, "Ignoring empty namespace-only regex rule mappings");
 	    return;
 	}
 
@@ -1707,10 +1709,7 @@
 	}catch(Exception e){
 	    logger.log(Level.WARNING, 
 		       "Could not create XPath select statement from '" +
-			xpath_exp + "': " + e.getMessage());
-	    System.err.println("Could not create XPath select statement from '" +
-			       xpath_exp + "': " + e);
-
+		       xpath_exp + "': ", e);
 	}
     }
 
@@ -1773,8 +1772,8 @@
 		    else if(line.indexOf("\t") == 0){
 			String[] fields = line.trim().split(",");
 			if(fields.length != 2){ 
-			    System.err.println("Unrecognized line (not 2 comma delimited fields) " +
-					       "from ValidateService: " + line.trim());
+			    logger.log(Level.WARNING, "Unrecognized line (not 2 comma delimited fields) " +
+					              "from ValidateService: " + line.trim());
 			}
 			else if(fields[1].equals("true")){
 			    // service is okay, don't add to dead map
@@ -1783,8 +1782,8 @@
 			    isDeadMap.put(currentAuthority+":"+fields[0], "dead");
 			}
 			else{
-			    System.err.println("Unrecognized line (second field not 'true' or 'false') " +
-					       "from ValidateService: " + line.trim());			    
+			    logger.log(Level.WARNING, "Unrecognized line (second field not 'true' or 'false') " +
+					              "from ValidateService: " + line.trim());			    
 			}
 		    }
 		}



From gordonp at dev.open-bio.org  Fri Apr 16 17:33:26 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 16 Apr 2010 13:33:26 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004161733.o3GHXQBs015331@dev.open-bio.org>


gordonp
Fri Apr 16 13:33:25 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv15287/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	MobyContentPane.java MobyPayloadCreator.java 
	MobyServicesGUI.java 
Log Message:
First fully functional version of 'for each' service invocation in Seahawk
moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyContentPane.java,1.28,1.29 MobyPayloadCreator.java,1.2,1.3 MobyServicesGUI.java,1.19,1.20
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java,v
retrieving revision 1.28
retrieving revision 1.29
diff -u -r1.28 -r1.29
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java	2010/04/14 23:48:27	1.28
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java	2010/04/16 17:33:25	1.29
@@ -1175,9 +1175,23 @@
 
 	String docFragID = targetURL.getRef();  // We store the xpath in the anchor part of the URL
 
-	// Complex case, load the doc fragment from the MOBY XML source file
+	// Complex case, load the doc fragment from the MOBY XML source file 
+	// where the targetURL is url#xptr with xptr like /1/2/1/1
 	if(docFragID != null && docFragID.length() > 0 && !targetURL.getHost().equals("moby")){
-	    return DataUtils.loadMobyDataFromXPointer(targetURL, filteredData, filterHistory.get(getCurrentURL()));
+	    URL currentURL = null;
+	    try{currentURL = new URL(targetURL.toString().replaceAll("#"+targetURL.getRef(), ""));}
+	    catch(Exception e){
+		logger.error("Couldn't extract referenceless URL from " + targetURL, e);
+	    }
+	    // refers to currently loaded doc
+	    if(currentURL.equals(getCurrentURL())){
+		return DataUtils.loadMobyDataFromXPointer(currentURL, getCurrentDoc(), docFragID, 
+							  filteredData, filterHistory.get(getCurrentURL()));
+	    }
+	    // refers to another moby doc, let DataUtils resolve the doc for us
+	    else{
+		return DataUtils.loadMobyDataFromXPointer(targetURL, filteredData, filterHistory.get(getCurrentURL()));
+	    }
 	}
 
 	// Simple case, build the object using the values encoded in the URL itself.
@@ -1218,7 +1232,7 @@
         for(String peerMode: new String[]{DataUtils.ARTICLE_PEERS_MODE, DataUtils.DATATYPE_PEERS_MODE}){
             // note that getPeerElements() will modify the userData to reflect the semantic of the requested peer mode
             mobyData.setUserData(origUserData);
-            NodeList peerElements = DataUtils.getPeerElements(getCurrentDoc(), mobyData, peerMode);
+            NodeList peerElements = DataUtils.getPeerElements(getCurrentDoc(), mobyData, getFilteredData(), peerMode);
             if(peerElements.getLength() <= 1){
                 continue; // no 'for each' option if only one to process...
             }
@@ -1227,21 +1241,33 @@
                 each += " '"+mobyData.getName()+"'";
             }
             MobyDataType dataType = ((MobyPrimaryData) mobyData).getDataType();
+	    MobyNamespace[] namespaces = ((MobyPrimaryData) mobyData).getNamespaces();
             if(mobyData instanceof MobyPrimaryDataSet){	 // Collection
                 servicesGUI.addPopupOptions((MobyPrimaryDataSet) mobyData, popup, true, getDefaultHandler(), 
 					    new MobyPayloadCreator(this, (String) mobyData.getUserData()), 
 					    each);
             }
             else if(MobyTags.MOBYOBJECT.equals(dataType.getName())){  
-                MobyNamespace namespace = null;
-                servicesGUI.addPopupOptions(namespace, popup, true, getDefaultHandler(),
-					    new MobyPayloadCreator(this, (String) mobyData.getUserData()), 
-                                            each);
+		if(namespaces != null && namespaces.length > 0){
+		    servicesGUI.addPopupOptions(namespaces[0], popup, true, getDefaultHandler(),
+						new MobyPayloadCreator(this, (String) mobyData.getUserData()), 
+						each);
+		}
+		//else base object wth no namespace...useless!
             }
             else{
-                servicesGUI.addPopupOptions(dataType, popup, true, getDefaultHandler(),
-					    new MobyPayloadCreator(this, (String) mobyData.getUserData()), 
-                                            each);
+		// A non-base object, with a namespace too
+		if(namespaces != null && namespaces.length > 0){
+		    ((MobyPrimaryDataSimple) mobyData).setId(""); //anonymize
+		    servicesGUI.addPopupOptions((MobyPrimaryDataSimple) mobyData, popup, true, getDefaultHandler(),
+						new MobyPayloadCreator(this, (String) mobyData.getUserData()), 
+						each);
+		}
+		else{  //just the data type useful
+		    servicesGUI.addPopupOptions(dataType, popup, true, getDefaultHandler(),
+						new MobyPayloadCreator(this, (String) mobyData.getUserData()), 
+						each);
+		}
             }
         }
 
@@ -1286,13 +1312,21 @@
 	if(getFilter() == null){
 	    return;
 	}
+	String[] userData = mdi.getUserData() == null ? null : 
+	    mdi.getUserData().toString().split("\t");
+	// second user data arg is 
+	Node mdiNode = userData == null || userData.length < 2 ? null : 
+	    XPointerResolver.getNodeFromXPointer(getCurrentDoc(), userData[1]);
 
 	//System.err.println("Should create a previous input menu item for " + mdi.getUserData());
 	try{
 	    Document srcDoc = DataUtils.docBuilder.parse(srcURL.openStream());
 
+	    //System.err.println("Context node is "+mdiNode+ " from user data" + mdi.getUserData());
 	    // Get the input data for the *previous* service
-	    MobyDataJob inputData = DataUtils.getInputSample(srcDoc, SeahawkOptions.getRegistry());
+	    MobyDataJob inputData = DataUtils.getInputSample(srcDoc, 
+							     DataUtils.findMobyJobName(mdiNode), 
+							     SeahawkOptions.getRegistry());
 	    if(inputData == null){
 		// should only happen if Moby XML was loaded manually by a user, otherwise we've recorded this info...
 		logger.warn("No previous service info in Moby XML, 'previous input' option will not be displayed");
@@ -1529,7 +1563,7 @@
 	// Gray out the mismatched textual data
 	for(Map.Entry<String,String> dataToFilter: filteredData.entrySet()){	    
 
-	    System.err.println("Filtering "+dataToFilter.getKey());
+	    //System.err.println("Filtering "+dataToFilter.getKey());
 	    javax.swing.text.AbstractDocument.AbstractElement htmlDiv = 
 		(javax.swing.text.AbstractDocument.AbstractElement) d.getElement(dataToFilter.getKey());
 	    if(htmlDiv == null){

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyPayloadCreator.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyPayloadCreator.java	2010/04/14 23:48:27	1.2
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyPayloadCreator.java	2010/04/16 17:33:25	1.3
@@ -27,6 +27,7 @@
 	// The request key is the sample data's app context: 
         // url#xpath <tab> sample_xptr <tab> filter_regex <tab> filter_xpath <tab> xpath_desc <tab> case_sensitive_boolean <tab> inverse selection
         // from which we will build the peer dataset to submit.
+	System.err.println("Request key is " + requestKey);
 	String[] requestKeyFields = requestKey.split("\t");
 
 	String[] requestParts = requestKeyFields[0].split("#", 2);
@@ -50,20 +51,24 @@
 	Map<String,String> xptrsToFilter = new HashMap<String,String>();
 	FilterSearch filter = null;
 	// Was there a filter in the request?
-	if(requestKeyFields.length >= 6){
- 	    filter = new FilterSearch(requestKeyFields[1], 
-				      new XPathOption(requestKeyFields[2], requestKeyFields[3]), 
-                                      Boolean.parseBoolean(requestKeyFields[4]), 
-				      Boolean.parseBoolean(requestKeyFields[5]));
+	if(requestKeyFields.length >= 7){
+ 	    filter = new FilterSearch(requestKeyFields[2], 
+				      new XPathOption(requestKeyFields[3], requestKeyFields[4]), 
+                                      Boolean.parseBoolean(requestKeyFields[5]), 
+				      Boolean.parseBoolean(requestKeyFields[6]));
         }
 	Document doc = null;
         // Get the list of nodes to filter, using in-memory data if possible
 	if(targetURL.equals(srcPane.getCurrentURL())){
             doc = srcPane.getCurrentDoc();
 
-            if(filter.equals(srcPane.getFilter())){
+            if(filter == null){
+		xptrsToFilter = null;
+	    }
+	    else if(filter.equals(srcPane.getFilter())){
                 // no need to redo the filtering, it's the current display's filtering
-                xptrsToFilter = srcPane.getFilteredData(); 
+		System.err.println("Reusing current filter");
+                xptrsToFilter = srcPane.getFilteredData();
             }
             else{
                 // we have the doc loaded, but the filter has changed since
@@ -75,44 +80,33 @@
        	    doc = DataUtils.findFilteredNodes(targetURL, filter, xptrsToFilter);	    
         }
 
-	// Get the valid parts of the doc for forwarding.
-        if(!xptrsToFilter.isEmpty()){
-  	    if(doc == srcPane.getCurrentDoc()){
-                // clone, because it'll be edited below by the filter, and we don't want to mess up currentDoc...
-                doc = (Document) srcPane.getCurrentDoc().cloneNode(true);
-            }
-            DataUtils.filterDoc(doc, xptrsToFilter);
-        }
+	MobyDataInstance mobyDataContext = new MobyDataObject("whatever");
+	mobyDataContext.setUserData(requestKey);
+	NodeList peerElements = DataUtils.getPeerElements(doc, mobyDataContext, 
+							  xptrsToFilter, DataUtils.DATATYPE_PEERS_MODE);
 
-        // find the peers of templateElement and put them into a MobyContentInstance
+        // find the peers of defined by the userData selection constraints and put them into a MobyContentInstance
 	MobyContentInstance payload = new MobyContentInstance();
         Map<String,Integer> jobPrefixes = new LinkedHashMap<String,Integer>();
 
-        NodeList peerElements = null;
-        try{
-            peerElements = (NodeList) DataUtils.xPathFactory.newXPath().evaluate(selectionXPath, 
-                                                                                 doc, 
-                                                                                 XPathConstants.NODESET);
-        } catch(Exception e){
-            logger.log(Level.SEVERE, "Could not select nodes from "+targetURL+" with XPath " + selectionXPath, e);
-            return null;
-        }
+	System.err.println("Loading MobyContentInstance with "+peerElements.getLength()+" elements for xpath "+selectionXPath);
         for(int i = 0; i < peerElements.getLength(); i++){
             Element peerElement = (Element) peerElements.item(i);
 	    // Try to make the job names trackable to the inputs:
             // Name the jobs according to their original job + a iterated number suffix, e.g. originatingJob_1, originatingJob_2
             String jobKey = DataUtils.findMobyJobName(peerElement);
             if(!jobPrefixes.containsKey(jobKey)){
+                jobPrefixes.put(jobKey, new Integer(1));
                 if(peerElements.getLength() > 1){
                     jobKey += "_1"; // only add a suffix if multiple loop members for the job
                 }
-                jobPrefixes.put(jobKey, new Integer(1));
             }
             else{
                 int suffixCount = jobPrefixes.get(jobKey).intValue();
-                jobKey += "_"+suffixCount;
                 jobPrefixes.put(jobKey, new Integer(suffixCount+1));
+                jobKey += "_"+(suffixCount+1);
             }
+	    System.err.println("Adding job "+jobKey+" for "+peerElement.getLocalName());
             MobyDataInstance mdi  = null;
             try{
                 mdi = MobyDataObject.createInstanceFromDOM(peerElement, SeahawkOptions.getRegistry());

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java,v
retrieving revision 1.19
retrieving revision 1.20
diff -u -r1.19 -r1.20
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java	2010/04/14 23:48:27	1.19
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java	2010/04/16 17:33:25	1.20
@@ -182,9 +182,13 @@
 	return handler;
     }
 
-    // synchronized so simultaneous requests don't get their input data mixed up
+    /**
+     * Called when the 'Execute Service' button in the secondary input dialog in pushed.
+     * Section synchronized so simultaneous requests don't get their input data mixed up
+     */
     public void setupServiceSecondaryData(MobyRequestEventHandler handler){
 	MobyDataInstance[] castInputs = new MobyDataInstance[primaryInput.length];
+	MobyContentInstance mci = null;
 	for(int i = 0; i < primaryInput.length; i++){
 	    if(!(primaryInput[i] instanceof MobyDataInstance)){
 		logger.warn("Warning: setupServiceSecondaryData was called before the primary input" +
@@ -192,13 +196,34 @@
 			    " of class "+primaryInput[i].getClass().getName());
 		return;
 	    }
-	    castInputs[i] = (MobyDataInstance) primaryInput[i];
+	    // Is one of the params a 'for each'
+	    if(primaryInput[i] instanceof MobyContentCreator){
+		mci = ((MobyContentCreator) primaryInput[i]).getAllContents(primaryInput[i].getName());
+	    }
+	    else{
+		castInputs[i] = (MobyDataInstance) primaryInput[i];
+	    }
+	}
+	// Cross product of single value primary params with param that is a content creator array
+	if(mci != null){
+	    for(MobyDataJob job: mci.values()){
+		for(int i = 0; i < castInputs.length; i++){
+		    if(castInputs[i] != null){
+			job.put(castInputs[i].getName(), castInputs[i]);
+		    }
+		}
+	    }
 	}
 
         // code from mobyRequest.setInput() to executeService() should always be synced to avoid input mixup between requests
         synchronized(mobyRequest){
 	    try{	    
-	        mobyRequest.setInput(castInputs);
+	        if(mci != null){
+		    mobyRequest.setInput(mci);
+		}
+		else{
+		    mobyRequest.setInput(castInputs);
+		}
 	        mobyRequest.setSecondaryInput(secondaryInputInstances);
 	    } catch(MobyException me){
 	        me.printStackTrace();
@@ -224,8 +249,13 @@
             // code from mobyRequest.setInput() to executeService() should always be synced to avoid input mixup between requests
             synchronized(mobyRequest){
 	        try{
+		    if(mdi instanceof MobyContentCreator){
+			mobyRequest.setInput(((MobyContentCreator) mdi).getAllContents(primaryInput[0].getName()));
+		    }
 		    // Implement simple input (i.e. only one input argument)
-		    mobyRequest.setInput(mdi, "");
+		    else{
+			mobyRequest.setInput(mdi, "");
+		    }
 	        }
 	        catch(MobyException me){
 		    logger.error("Failure in MOBY input, was not acceptable:" + me);
@@ -539,7 +569,7 @@
 		addPopupOptions(mobyData, popupList, false, handler, payloadCreator, extraMenuText);
 	    }
 	    else{
-		logger.warn("Warning: OptionLoaderThread has no data to work with");
+		logger.warn("Warning: OptionLoaderThread has no data to work with", new Exception("Arrggh"));
 	    }
 	}
     }
@@ -646,27 +676,27 @@
  	MobyDataServiceAssocInstance serviceAssocObject = null;  
 // 	//Services for only the one piece of data
 	try{
-	    if(mobyData instanceof MobyDataObjectSet){
-		serviceAssocObject = mobyClient.getServices((MobyDataObjectSet) mobyData);
-	    }
-	    else if(mobyData instanceof MobyDataObject){
-		serviceAssocObject = mobyClient.getServices((MobyDataObject) mobyData);
-	    }
             // The data will be loaded later
-            else if(payloadCreator != null){
+            if(payloadCreator != null){
                 try{
                     if(mobyData instanceof MobyPrimaryDataSet){
 			serviceAssocObject = mobyClient.getServices(new MobyDataObjectSetDeferred((MobyPrimaryDataSet) mobyData, 
 												  payloadCreator));
 		    }
-		    else if(mobyData instanceof MobyNamespace){
-			serviceAssocObject = mobyClient.getServices(new MobyDataObjectDeferred((MobyNamespace) mobyData, 
+		    else if(mobyData instanceof MobyPrimaryDataSimple){  // pass in if datatype and namespace are useful
+			serviceAssocObject = mobyClient.getServices(new MobyDataObjectDeferred(((MobyPrimaryDataSimple) mobyData).getDataType(),
+											       ((MobyPrimaryDataSimple) mobyData).getNamespaces()[0],
 											       payloadCreator));
 		    }
 		    else if(mobyData instanceof MobyDataType){
 			serviceAssocObject = mobyClient.getServices(new MobyDataObjectDeferred((MobyDataType) mobyData, 
 											       payloadCreator));
 		    }
+		    else if(mobyData instanceof MobyNamespace){
+			System.err.println("Creating deferred dataset payload");
+			serviceAssocObject = mobyClient.getServices(new MobyDataObjectDeferred((MobyNamespace) mobyData, 
+											       payloadCreator));
+		    }
 		    else{
 			logger.warn("Ignoring unrecognized template class (" + mobyData.getClass().getName()+
 				    ") for deferred data creation by a MobyPayloadRequestListener"); 
@@ -675,6 +705,12 @@
 		} catch(Exception e){
 		    logger.error("Could not create deferred Moby data object", e);
 		}
+	    }
+	    else if(mobyData instanceof MobyDataObjectSet){
+		serviceAssocObject = mobyClient.getServices((MobyDataObjectSet) mobyData);
+	    }
+	    else if(mobyData instanceof MobyDataObject){
+		serviceAssocObject = mobyClient.getServices((MobyDataObject) mobyData);
             }
 	    else{
 		logger.warn("Service options for objects other than MobyDataObject " +
@@ -730,9 +766,6 @@
 		    logger.warn("Cannot add service options, cannot find " +
 				"parent moby object index for submenu " + 
 				submenu.getText());
-		    System.err.println("Cannot add service options, cannot find " +
-				"parent moby object index for submenu " + 
-				submenu.getText());
 		    return;
 		}
 		dataIndex = ((Integer) submenu2msIndex.get(parent)).intValue();
@@ -1250,7 +1283,7 @@
 		datatype += " collection";
 	    }
 	    submenu = new JMenu("<html>Services for " + (extraMenuText == null ? "" : extraMenuText+" ") + 
-                                datatype + (id == null ? "" : ":" + id)+"</html>");
+                                "<font color='red'>"+datatype + "</font>" + (id == null ? "" : ":" + id)+"</html>");
 	    assignMenuDataIndex(submenu);
 	}
 	else if(MobyTags.MOBYSTRING.equals(mobyDataType.getName())){
@@ -1269,7 +1302,7 @@
 	    }
 	    desc = "A piece of text";
 	    submenu = new JMenu("<html>Services for "+(extraMenuText == null ? "" : extraMenuText+" ")+
-				"String " + sample+"</html>");
+				"<font color='red'>String</font> " + sample+"</html>");
 	    assignMenuDataIndex(submenu);
 	}
 	// Complex object
@@ -1283,17 +1316,19 @@
 		}
 	    }
 	    if(templateObject instanceof MobyDataObject && id != null && id.length() > 0){
-		objectLabel += ":" + id;
+		objectLabel += "<font color='red'>"+objectLabel+"</font>:" + id;
 	    }
 	    else if(templateObject instanceof MobyDataObjectSet){
-		objectLabel += " collection";
+		objectLabel = "<font color='red'>"+objectLabel+" collection</font>";
+	    }
+	    else{
+		objectLabel = "<font color='red'>"+objectLabel+"</font>";
 	    }
 	    submenu = new JMenu("<html>Services for " + (extraMenuText == null ? "" : extraMenuText+" ")+objectLabel+"</html>");
 	    assignMenuDataIndex(submenu);
 	}
 	desc = "Input data: " + desc;
 	desc = HTMLUtils.htmlifyToolTipText(desc, MAX_SERVICE_DESC_LEN);
-        System.err.println("New submenu has label " + submenu.getText());
 	submenu.setToolTipText(desc);
 	submenu.setName(SERVICE_SUBMENU_NAME);
 	return submenu;



From gordonp at dev.open-bio.org  Fri Apr 16 17:33:26 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 16 Apr 2010 13:33:26 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004161733.o3GHXQvK015367@dev.open-bio.org>


gordonp
Fri Apr 16 13:33:26 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util
In directory dev.open-bio.org:/tmp/cvs-serv15287/src/main/ca/ucalgary/seahawk/util

Modified Files:
	DataFlowRecorder.java DataUtils.java FilterSearch.java 
	MobyDataObjectDeferred.java XPointerResolver.java 
Added Files:
	MobyDataObjectDeferredSAI.java 
	MobyDataObjectSetDeferredSAI.java 
Log Message:
First fully functional version of 'for each' service invocation in Seahawk
moby-live/Java/src/main/ca/ucalgary/seahawk/util MobyDataObjectDeferredSAI.java,NONE,1.1 MobyDataObjectSetDeferredSAI.java,NONE,1.1 DataFlowRecorder.java,1.4,1.5 DataUtils.java,1.5,1.6 FilterSearch.java,1.5,1.6 MobyDataObjectDeferred.java,1.1,1.2 XPointerResolver.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataFlowRecorder.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataFlowRecorder.java	2010/04/10 00:40:17	1.4
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataFlowRecorder.java	2010/04/16 17:33:26	1.5
@@ -321,7 +321,7 @@
 		data = sampleData.getUserData().toString().split("\t");
 		//options: selection + filter + cond, selection + cond, or cond only
 		if(data.length == 14 || data.length == 8 || data.length == 6){
-		    System.err.println("Adding conditional for " + resultURLString);
+		    //		    System.err.println("Adding conditional for " + resultURLString);
 		    String conditionURL = data[data.length-6];
 		    String conditionRegex = data[data.length-5];
 		    XPathOption conditionXPath = new XPathOption(data[data.length-4], data[data.length-3]);
@@ -334,10 +334,10 @@
 		    System.arraycopy(data, 0, conditionlessData, 0, data.length-6);
 		    data = conditionlessData;
 		}
-		else{
-		    System.err.println("Skipping conditional, only " + data.length + 
-				       "members in provenance data for " + resultURLString);
-		}
+// 		else{
+// 		    System.err.println("Skipping conditional, only " + data.length + 
+// 				       "members in provenance data for " + resultURLString);
+// 		}
 	    }
 
 	    // true means treat as a collection if that's what the sample data is
@@ -447,7 +447,7 @@
 		// Remember that sd is the loop's original MobyDataInstance before it's been coerced into a MobyPrimaryData, 
 		// which doesn't have XML modes, etc.
 		String inputKey = getInputKey(sd);
-		System.err.println("Input key for " + processorName + " is " + inputKey);
+		//		System.err.println("Input key for " + processorName + " is " + inputKey);
 
 		String[] mobifyingProcessorNameAndPorts = null;
 		if(input2Processor.containsKey(inputKey)){
@@ -930,7 +930,7 @@
 		// supertype of the output from the other service!		
 		if(namespace != null){
 		    MobyNamespace nsObj = MobyNamespace.getNamespace(namespace, getRegistryFromService(srcService));
-		    System.err.println("About to create namespace filter for "+ srcProcessor + " port " + portName + " when srcPort was " + srcPort);
+		    //		    System.err.println("About to create namespace filter for "+ srcProcessor + " port " + portName + " when srcPort was " + srcPort);
 		    return createNamespaceFilter(nsObj, srcProcessor, portName, processors, datalinks, doc);
 		}
 		else if(xrefNs != null){
@@ -1103,7 +1103,7 @@
 	throws Exception{
 
 	String decompKey = srcProcessor+"\n"+srcPort+"\n"+xpath;
-	System.err.println("Decomp key is " + decompKey);
+	//	System.err.println("Decomp key is " + decompKey);
 	// Has this decomp already been created in another branch?
 	if(decomp2Processor.containsKey(decompKey)){
 	    return decomp2Processor.get(decompKey);

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataUtils.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataUtils.java	2010/04/14 22:02:04	1.5
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataUtils.java	2010/04/16 17:33:26	1.6
@@ -166,6 +166,7 @@
 	Document resultDom = docBuilder.parse(serviceResultURL.openStream());
 	
 	Registry registry = getRegistry(resultDom);
+	//todo: check all jobs, not just a sample
 	MobyDataJob sampleJob = getInputSample(resultDom, registry);
 	    
 	// Trace the inputs that came from the current document 
@@ -343,6 +344,13 @@
      * @param responseDom the XML DOM for the answer from a Moby Web service called in Seahawk
      */
     public static MobyDataJob getInputSample(Document responseDom, Registry registry) throws Exception{
+	return getInputSample(responseDom, null, registry);
+    }
+
+    /**
+     * Same as two-arg, but retrieves a specific job's input (or null if not a job name found in the doc).
+     */
+    public static MobyDataJob getInputSample(Document responseDom, String jobName, Registry registry) throws Exception{
 	Document inputDoc = getInputDoc(responseDom);
 	if(inputDoc == null){
 	    return null;
@@ -360,11 +368,14 @@
 	    throw new Exception("Could not parse Moby output message from the given DOM");
 	}
 
+	if(jobName != null){
+	    return inputPayload.get(jobName);
+	}
 	// Pick a job that produced output, if given the choice of more that one
-	for(String jobName: inputPayload.keySet()){
-	    if(outputPayload.containsKey(jobName) &&
-	       outputPayload.get(jobName).size() > 0){
-		return inputPayload.get(jobName);
+	for(String jobID: inputPayload.keySet()){
+	    if(outputPayload.containsKey(jobID) &&
+	       outputPayload.get(jobID).size() > 0){
+		return inputPayload.get(jobID);
 	    }
 	}
 	return (MobyDataJob) inputPayload.values().iterator().next();
@@ -460,9 +471,9 @@
     /**
      * Loads targetURL, minus the nodes specified by the xpath keys in filteredXPtrs (map values are not currently used).
      */
-    public static void filterDoc(Document domDoc, Map<String,String> filteredXPtrs){
+    public static void filterNodes(Node rootNode, Map<String,String> filteredXPtrs){
 	 
-	if(domDoc == null){
+	if(rootNode == null){
 	    logger.log(Level.SEVERE, "Error: Could not get MOBY document as DOM (empty or malformed document?)");
 	    return;
 	}
@@ -474,7 +485,7 @@
 	    // wrong as they refer to ordinality)
 	    Vector<Node> nodesToDelete = new Vector<Node>();
 	    for(String xptr: filteredXPtrs.keySet()){
-		nodesToDelete.add(XPointerResolver.getNodeFromXPointer(domDoc, xptr));
+		nodesToDelete.add(XPointerResolver.getNodeFromXPointer(rootNode, xptr));
 	    }
 
 	    // Delete
@@ -497,86 +508,54 @@
      * @param filteredXPtrs a map of the xpointers to data that should NOT be deserialized if children of the targetURL XPointer
      * @param docFilter the current filter applied to the document in targetURL
      */
-    public static MobyDataInstance loadMobyDataFromXPointer(URL targetURL, Map<String,String> filteredXPtrs, FilterSearch docFilter){
-
-	URL currentURL = null;
-	try{currentURL = new URL(targetURL.toString().replaceAll("#"+targetURL.getRef(), ""));}
-	catch(Exception e){
-	    logger.log(Level.SEVERE, "Couldn't extract referenceless URL from " + targetURL, e);
-	}
-
-	// Build the DOM
-	Document domDoc = null;
-	try{
-	    domDoc = docBuilder.parse(targetURL.openStream());
-	} catch(org.xml.sax.SAXException saxe){
-	    logger.log(Level.SEVERE, "The document defining the MOBY data " +
-		       "could not be parsed", saxe);
-	    return null;
-	} catch(java.io.IOException ioe){
-	    logger.log(Level.SEVERE, "The document defining the MOBY data " +
-		       " could not be read (from " + targetURL + ")", ioe);
-	    return null;
-	}
-	// Does an in-place edit of domDoc
-	filterDoc(domDoc, filteredXPtrs);
-
+     public static MobyDataInstance loadMobyDataFromXPointer(URL targetURL, Map<String,String> filteredXPtrs, 
+							     FilterSearch docFilter){
+	 
+	 URL currentURL = null;
+	 try{currentURL = new URL(targetURL.toString().replaceAll("#"+targetURL.getRef(), ""));}
+	 catch(Exception e){
+	     logger.log(Level.SEVERE, "Couldn't extract referenceless URL from " + targetURL, e);
+	 }
+	 
+	 // Build the DOM
+	 Document domDoc = null;
+	 try{
+	     domDoc = docBuilder.parse(targetURL.openStream());
+	 } catch(org.xml.sax.SAXException saxe){
+	     logger.log(Level.SEVERE, "The document defining the MOBY data " +
+			"could not be parsed", saxe);
+	     return null;
+	 } catch(java.io.IOException ioe){
+	     logger.log(Level.SEVERE, "The document defining the MOBY data " +
+			" could not be read (from " + targetURL + ")", ioe);
+	     return null;
+	 }
+	 
+	 return loadMobyDataFromXPointer(currentURL, domDoc, targetURL.getRef(), filteredXPtrs, docFilter);
+    }
+    
+    public static MobyDataInstance loadMobyDataFromXPointer(URL docURL, Document domDoc, String targetXptr, 
+							    Map<String,String> filteredXPtrs, FilterSearch docFilter){
 	// Are we dealing with a simple object or a complex one?
 	MobyDataInstance mobyData = null;
 	
 	// Find the DOM fragment corresponding to the MOBY ID anchor specified
 	// in the link URL by using an XPath statement on the source MOBY doc
-	//System.err.println("Retrieving complex object from XPointer " + targetURL);
 	
 	// A child Xpointer is of the form /1/2/1/1, specifying the DOM child 
-	// descent path from the root node to get to the target node.  The 
-	// equivalent XPath is /*[1]/*[2]/*[1]/*[1]
-	String childXPath = targetURL.getRef().replaceAll("/(\\d+)", "/*[$1]");
-
-	// Build and run the XPath statement
-	Element mobyObject = null;
-	NodeList idSearchResult = null;
-	Object xobject = null;
-	try{
-	    xobject = xPathFactory.newXPath().evaluate(childXPath, 
-						       domDoc, 
-						       XPathConstants.NODESET);
-						
-	    // Check the results
-	    if(xobject != null){
-		idSearchResult = (NodeList) xobject;
-	    }
-	    else{
-		logger.log(Level.WARNING,"Could not find Moby object in document " + currentURL + 
-			   ", referred to by the reference ID in Moby link " + targetURL +
-			   " (document changed?)");
-		return null;
-	    }
-	}
-	catch(Exception e){// Syntax error
-	    logger.log(Level.SEVERE, "Error: Could not search Moby data instance for XPath " + 
-		       childXPath + ")",  e);
-	    return null;
-	}
+	// descent path from the root node to get to the target node. 
+	Element mobyObject = (Element) XPointerResolver.getNodeFromXPointer(domDoc, targetXptr);
 	
-	if(idSearchResult.getLength() == 0){
-	    logger.log(Level.WARNING, "Error: Could not find Moby data instance with XPath (" + childXPath + 
-		       " in " + targetURL);
-	    return null;
-	}
-	if(idSearchResult.getLength() > 1){
-	    logger.log(Level.WARNING, "Error: Moby data instance could not beresolved because " +
-		       "there are multiple elements with XPath " + childXPath + " in " +
-		       currentURL);
-	    return null;
-	}
-	if(!(idSearchResult.item(0) instanceof Element)){
-	    logger.log(Level.WARNING, "Error: Moby data instance with XPath " + childXPath + " in " +
-		       currentURL + " was not an element as required!");
-	    return null;
+	// Does an in-place edit of domDoc
+	// Check if the returned data was supposed to be filtered.  If so, don't filter.
+	if(filteredXPtrs != null && !filteredXPtrs.isEmpty() && !filteredXPtrs.containsKey(targetXptr)){
+	    // Otherwise filter, so child elements of the data to return reflect the current filter conditions 
+	    // (e.g. a collection may be filtered to just a subset based on namespace, so retrieving the collection should only 
+	    // return that subset of children).
+	    domDoc = (Document) domDoc.cloneNode(true); // true == deep
+	    filterNodes(domDoc, filteredXPtrs);
 	}
-	mobyObject = (Element) idSearchResult.item(0);
-	
+
 	// Create the Java MOBY API object based on the linked document DOM fragment
 	try{
 	    MobyDataInstance mdi = MobyDataObject.createInstanceFromDOM(mobyObject, SeahawkOptions.getRegistry());
@@ -587,8 +566,8 @@
 		mobyData = mdi;
 	    }
 	    else{
-		logger.log(Level.WARNING, "Error: Moby data instance retrieved with XPath " + childXPath + " in " +
-			   currentURL + " was not a primary MOBY input object as expected");
+		logger.log(Level.WARNING, "Error: Moby data instance retrieved with XPath " + targetXptr +
+			   " was not a primary MOBY input object as expected");
 		return null;
 	    }
 
@@ -600,8 +579,8 @@
 
 	    // For workflow creation, etc. associate the potential input data with its source generalized XPath
 	    // Also, if there is currently a filter on the doc, store it too as useful info for workflow creation.
-	    setUserData(mobyData, currentURL, elementInContextToNameBasedXPath(mobyObject), 
-			targetURL.getRef(), docFilter);
+	    setUserData(mobyData, docURL, elementInContextToNameBasedXPath(mobyObject), 
+			targetXptr, docFilter);
 	}
 	catch(MobyException mobye){  // Logic error
 	    logger.log(Level.SEVERE, "Error: Could not construct Moby data instance from document fragment: ", 
@@ -656,6 +635,7 @@
 		// It's a complex type.  Assume the type is why we are picking it.
 		// TODO: In future we may want to check if a parent type is allowed in 
 		// this slot, and generalize to that.  
+		// Also, account for namespace if present?
 		xpath = "/"+elName + xpath;
 	    }
 	    if(!(currentElement.getParentNode() instanceof Element)){
@@ -784,7 +764,7 @@
     /**
      * Find out which registry the service that created the reponse is registered in.
      * 
-     * @param responseURL the service response whose origin we should trace
+     * @param responseDoc the service response whose origin we should trace
      */
     public static Registry getRegistry(Document responseDoc) throws Exception{
         String endpointURL = getSeahawkAttrFromDoc(responseDoc, REGISTRY_ATTR);
@@ -1035,16 +1015,20 @@
 	    }
 	    if(!inversed && shouldFilter ||
 	       inversed && !shouldFilter){ 
-		xPtrsToFilter.put(currXPtr, "todo");
+		xPtrsToFilter.put(currXPtr, "whatever");
 	    }	    
 	}
 
 	//todo: filter objects without the HAS field at all...
 	return filterableXPtrs;
     }
-    // We need to enumerate the possible peer-sets for the selected data item.  Is the user interested in
-    // items in the same namespace, same data type, or same article name?
-    public static NodeList getPeerElements(Document doc, MobyDataInstance mobyData, String peerMode){
+
+    /**
+     * We need to enumerate the possible peer-sets for the selected data item.  Is the user interested in
+     * items in the same namespace/data type, or same article name?
+     */
+    public static NodeList getPeerElements(Document doc, MobyDataInstance mobyData, 
+					   Map<String,String> xPtrsToFilter, String peerMode){
         if(!(mobyData instanceof MobyPrimaryData)){
             logger.log(Level.WARNING, "Tried to get peers of data that was not an instanceof MobyPrimaryData (was " + 
                                       mobyData.getClass().getName()+ ")");
@@ -1054,10 +1038,13 @@
 
 	NodeList peerElements = null;
         String peerGroupXPath = null;
+	Node contextNode = null;
 	if(mobyData.getUserData() != null){
 	    String[] userData = ((String) mobyData.getUserData()).split("\t");
 	    // first arg is url#nameBasedXPath 
 	    peerGroupXPath = userData[0].split("#", 2)[1];
+	    contextNode = XPointerResolver.getNodeFromXPointer(doc, userData[1]);
+	    //System.err.println("Loaded context node " + userData[1] + " as " + contextNode);
         }
         else{
 	    // Fallback is to get all nodes with the same name...
@@ -1079,7 +1066,7 @@
             mobyData.setUserData(newUserData);
 
             // keep from job article name down
-            peerGroupXPath = peerGroupXPath.replaceFirst("^.*/(Collection|Simple)", "//*");
+            //peerGroupXPath = peerGroupXPath.replaceFirst("^.*?/(Collection|Simple)", "//*");
 	    // we want to go by articleName too to catch the full semantics of the peer group definition
             peerGroupXPath += xpathArticleCondition;
         }
@@ -1090,17 +1077,58 @@
         // For xpaths given above, MOBY namespace is problem in XPath evaluation. 
         // solution: eliminate Moby envelope path parts: full path doesn't resolve in xpath for unknown reasons
         //.replaceAll("/(MOBY|mobyContent|mobyData|Collection|Simple)","/moby:$1"); //attempt 1
-        //.replaceAll("/([a-zA-Z_0-9\\-]+)(?=/|$)", "/*[local-name() = '$1']") //attempt 2
-        //.replaceAll("/([a-zA-Z_0-9\\-]+)\\[", "/*[local-name() = '$1' and "); //attempt 2 cont'd
+        peerGroupXPath = peerGroupXPath.replaceAll("/([a-zA-Z_0-9\\-]+)", "/d:$1");
 
 	try{
-            peerElements = (NodeList) xPathFactory.newXPath().evaluate(peerGroupXPath, 
-								       doc, 
-								       XPathConstants.NODESET);
+	    XPath xpath = xPathFactory.newXPath();
+	    if(contextNode != null){
+		xpath.setNamespaceContext(new NamespaceContextImpl(contextNode, "d"));
+	    }
+            peerElements = (NodeList) xpath.evaluate(peerGroupXPath, 
+						     doc, 
+						     XPathConstants.NODESET);
         } catch(Exception e){
             logger.log(Level.SEVERE, "Could not evaluate UserData XPath "+peerGroupXPath, e);
         }
-        System.err.println("Got " + peerElements.getLength() + " peers for " + peerGroupXPath);
+        //System.err.println("Got " + peerElements.getLength() + " peers for " + peerGroupXPath);
+
+	// Remove peers that are currently filtered.  Seems to be quicker than cloning the doc, 
+	// filtering the node, then running the xpath.  Assumes you don't do much with peerElements
+	// afterwards, or you should apply the filter to remove errant children, etc.)
+	if(xPtrsToFilter != null && !xPtrsToFilter.isEmpty()){
+	    MutableNodeList filterPassedPeers = new MutableNodeList();
+	    for(int i = 0; i < peerElements.getLength(); i++){
+		boolean filtered = false;
+		String peerXPtr = getXPtr(peerElements.item(i));
+		// Check all ancestors to see if they are filtered
+		for(String ancestorXPtr = peerXPtr; 
+		    ancestorXPtr.length() > 0;
+		    ancestorXPtr = ancestorXPtr.replaceFirst("/\\d+$", "")){		
+		    if(xPtrsToFilter.containsKey(ancestorXPtr)){
+			filtered = true;
+			break;
+		    }
+		}
+		if(!filtered){
+		    Element peerElement = (Element) peerElements.item(i);
+		    // Now check if any child nodes need to be filtered
+		    Map<String,String> childrenToDelete = new HashMap<String,String>();
+		    for(String xptr: xPtrsToFilter.keySet()){
+			// is it a child of the peer about to be put in the "passed filter" list? 
+			if(xptr.indexOf(peerXPtr+"/") == 0){
+			    childrenToDelete.put(xptr.substring(peerXPtr.length()), "whatever");
+			}
+		    }
+		    if(!childrenToDelete.isEmpty()){
+			peerElement = (Element) peerElements.item(i).cloneNode(true); //true = deep copy
+			filterNodes(peerElement, childrenToDelete);
+		    }
+		    filterPassedPeers.add(peerElement);
+		}
+	    }
+	    peerElements = filterPassedPeers;
+	    //System.err.println("Got " + peerElements.getLength() + " peers that passed the filter");
+	}
 
         return peerElements;
     }

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/FilterSearch.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/FilterSearch.java	2010/04/14 22:02:04	1.5
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/FilterSearch.java	2010/04/16 17:33:26	1.6
@@ -121,11 +121,17 @@
 	return xpathOptions;
     }
 
+    public String toString(){
+	return filterRegex.toString()+"\t"+getSelectedXPath().getXPath()+"\t"+
+	    getSelectedXPath().getDesc()+"\t"+caseSensitivity+"\t"+inverseSelection;
+    }
+
     public boolean equals(Object o){
         if(o == null || !(o instanceof FilterSearch)){
           return false;
         }
         FilterSearch other = (FilterSearch) o;
+	//System.err.println("Comparing "+this+"\n\nand\n\n"+o);
         return filterRegex.toString().equals(other.filterRegex.toString()) &&
                getSelectedXPath().getXPath().equals(other.getSelectedXPath().getXPath()) &&
                caseSensitivity == other.caseSensitivity &&

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/MobyDataObjectDeferred.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/MobyDataObjectDeferred.java	2010/04/14 23:48:27	1.1
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/MobyDataObjectDeferred.java	2010/04/16 17:33:26	1.2
@@ -15,8 +15,8 @@
 	super(MobyDataType.getDataType(MobyTags.MOBYOBJECT, SeahawkOptions.getRegistry()), ns, "any_id");
 	dataCreator = listener;
     }
-    public MobyDataObjectDeferred(MobyDataType dt, MobyPayloadRequestListener listener){
-	super(dt);
+    public MobyDataObjectDeferred(MobyDataType dt, MobyPayloadRequestListener listener) throws Exception{
+	super(dt, new MobyNamespace("unknown"), "any_id");
 	dataCreator = listener;
     }
     public MobyDataObjectDeferred(MobyDataType dt, MobyNamespace ns, MobyPayloadRequestListener listener) throws Exception{

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/XPointerResolver.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/XPointerResolver.java	2010/04/11 20:15:28	1.1
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/XPointerResolver.java	2010/04/16 17:33:26	1.2
@@ -15,20 +15,24 @@
      * Note, this currently only works for stuff like /1/1/2/3/1/67, 
      * not all XPointers, which includes functions, etc.
      */
-    public static Node getNodeFromXPointer(Document d, String xptr){
-        if(d == null || xptr == null || xptr.length() < 2 || !xptr.startsWith("/1")){
+    public static Node getNodeFromXPointer(Node rootNode, String xptr){
+        if(rootNode == null || xptr == null || xptr.length() < 2){
 	    return null;
         }
-	Node currentNode = d.getDocumentElement();
+	Node currentNode = rootNode;
 	if(currentNode == null){
 	    return null;
 	}
-	if(xptr.equals("/1")){
-	    return currentNode;
-	}
+	if(rootNode instanceof Document){
+	    currentNode = ((Document) rootNode).getDocumentElement();
+	    if(xptr.equals("/1")){
+		return currentNode;
+	    }
         
-	// Get rid of leading "/1/"
-	String[] ordinal_steps = xptr.substring(3).split("/");
+	    // Get rid of leading "/1/"
+	    xptr = xptr.substring(3);
+	}
+	String[] ordinal_steps = xptr.split("/");
 	if(ordinal_steps.length == 0){
 	    return currentNode;
 	}    



From gordonp at dev.open-bio.org  Fri Apr 16 19:58:26 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 16 Apr 2010 15:58:26 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004161958.o3GJwQk7018588@dev.open-bio.org>


gordonp
Fri Apr 16 15:58:26 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services
In directory dev.open-bio.org:/tmp/cvs-serv18552/src/main/ca/ucalgary/seahawk/services

Modified Files:
	MobyClient.java 
Log Message:
Fixed logging messaages
moby-live/Java/src/main/ca/ucalgary/seahawk/services MobyClient.java,1.27,1.28
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/MobyClient.java,v
retrieving revision 1.27
retrieving revision 1.28
diff -u -r1.27 -r1.28
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/MobyClient.java	2010/04/16 17:32:33	1.27
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/MobyClient.java	2010/04/16 19:58:26	1.28
@@ -84,9 +84,7 @@
      * new registry will NOT be reflected here.
      */
     public MobyClient() throws MobyException{
-	this(SeahawkOptions.getRegistry() == null ? 
-	     RegistryCache.getDefaultRegistry() :
-	     SeahawkOptions.getRegistry());
+	this(SeahawkOptions.getRegistry());
     }
 
     /**



From gordonp at dev.open-bio.org  Fri Apr 16 19:59:01 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 16 Apr 2010 15:59:01 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004161959.o3GJx1sF018632@dev.open-bio.org>


gordonp
Fri Apr 16 15:59:01 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory dev.open-bio.org:/tmp/cvs-serv18596/src/main/org/biomoby/client

Modified Files:
	CentralImpl.java 
Log Message:
Fixed logging messages
moby-live/Java/src/main/org/biomoby/client CentralImpl.java,1.64,1.65
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java,v
retrieving revision 1.64
retrieving revision 1.65
diff -u -r1.64 -r1.65
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java	2010/03/29 19:48:28	1.64
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java	2010/04/16 19:59:01	1.65
@@ -131,7 +131,7 @@
     public static final String CENTRAL_IMPL_RESOURCE_NAME = "org.biomoby.client.CentralImpl";
     /** The class to use for getDefaultCentral if all else fails */
     public static final String DEFAULT_CENTRAL_IMPL_CLASSNAME = "org.biomoby.client.CentralDigestCachedImpl";
-    private static Logger logger = Logger.getLogger("org.biomoby.client.CentralImpl");
+    private static Logger logger = Logger.getLogger(CentralImpl.class.getName());
 
    /**
     * Thread local that gives each thread its own
@@ -1888,7 +1888,7 @@
 	ClassLoader classLoader = Thread.currentThread().getContextClassLoader();
 	URL resURL = classLoader.getResource("META-INF/services/"+CENTRAL_IMPL_RESOURCE_NAME);
 	if(resURL != null){
-	    System.err.println("Loading "+resURL);
+	    logger.log(Level.CONFIG, "Loading "+resURL);
 	    try{
 		LineNumberReader reader = new LineNumberReader(new InputStreamReader(resURL.openStream()));
 		for(String line = reader.readLine(); line != null; line = reader.readLine()){
@@ -1904,9 +1904,7 @@
 	    }
 	}
 	try{
-	    if(Boolean.getBoolean("moby.debug")){
-		System.err.println("Central class is  "+className+ " for " + reg);
-	    }
+	    logger.log(Level.CONFIG, "Central class is  "+className+ " for " + reg);
 	    Class clazz = Class.forName(className);
 	    if(reg == null){  // should use default nullary c-tor
 		defaultCentrals.put("", (CentralImpl) clazz.newInstance());



From gordonp at dev.open-bio.org  Fri Apr 16 20:36:17 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 16 Apr 2010 16:36:17 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004162036.o3GKaHua019856@dev.open-bio.org>


gordonp
Fri Apr 16 16:36:17 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv19820/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	MobyContentClipboard.java 
Log Message:
Switched to java.util.logging.*
moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyContentClipboard.java,1.10,1.11
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentClipboard.java,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentClipboard.java	2010/04/11 02:25:03	1.10
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentClipboard.java	2010/04/16 20:36:17	1.11
@@ -21,6 +21,7 @@
 import java.io.FileOutputStream;
 import java.net.URL;
 import java.util.*;
+import java.util.logging.*;
 import java.util.regex.Pattern;
 
 /**
@@ -54,7 +55,8 @@
     // Clipboard editing variables
     private JMenuItem deleteDataPopupItem;
     private MobyDataInstance itemToDelete;
-    private static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(MobyContentClipboard.class);
+    private static Logger logger = Logger.getLogger(MobyContentClipboard.class.getName());
+
     public MobyContentClipboard(MobyContentGUI cGUI, MobyServicesGUI sGUI, JTabbedPane parentComponent, 
 				DataFlowRecorder recorder, JLabel statusBar){
 	super(cGUI, sGUI, parentComponent, recorder, statusBar);
@@ -66,7 +68,7 @@
     	if(clipboardIcon == null){
 	    URL u = cl.getResource(CLIPBOARD_TAB_ICON_RESOURCE);
 	    if(u == null){
-		logger.warn("Could not find icon resource " + CLIPBOARD_TAB_ICON_RESOURCE);
+		logger.log(Level.WARNING, "Could not find icon resource " + CLIPBOARD_TAB_ICON_RESOURCE);
 	    }
 	    else{
 		clipboardIcon = new ImageIcon(u);
@@ -86,7 +88,7 @@
 	    clipboardFile = File.createTempFile(CLIPBOARD_FILE_NAME, ".xml");
 	}
 	catch(Exception e){
-	    logger.error("Clipboard failed to initialize, cannot create temp file:" + e);
+	    logger.log(Level.SEVERE, "Clipboard failed to initialize, cannot create temp file", e);
 	    return;
 	}
 	clipboardFile.deleteOnExit();
@@ -134,7 +136,7 @@
 	// (i.e. don't delete subparts of object)
 	if(!(mdi instanceof MobyDataObject) || !collection.contains(mdi)){
 	    mdi.setXmlMode(MobyDataInstance.SERVICE_XML_MODE);
-	    System.err.println("Skipping " + mdi.toXML());
+	    logger.log(Level.WARNING, "Skipping " + mdi.toXML());
 	    mdi.setXmlMode(MobyDataInstance.CENTRAL_XML_MODE);
 	    return;
 	}
@@ -160,7 +162,7 @@
 	    }
 	}
 	else{
-	    logger.warn("Clipboard: ignoring unrecognized source of event " + e);
+	    logger.log(Level.WARNING, "Clipboard: ignoring unrecognized source of event ", e);
 	}
     }
 
@@ -186,7 +188,7 @@
 
     public void addCollectionData(MobyDataInstance mdi, boolean updateDisplay){	
 	if(mdi == null){
-	    logger.warn("Cannot add null object to the clipboard.");
+	    logger.log(Level.WARNING, "Cannot add null object to the clipboard.");
 	    return;
 	}
 	if(!query.containsKey(CLIPBOARD_COLLECTION_NAME)){
@@ -200,9 +202,9 @@
 	    collection.add((MobyDataObject) mdi);
 	}
 	else{
-	    logger.warn("Cannot add object of class " + mdi.getClass() +
-			" to the clipboard, only MobyDataObject and MobyDataObjectSet" +
-			" are supported");
+	    logger.log(Level.WARNING, "Cannot add object of class " + mdi.getClass() +
+			              " to the clipboard, only MobyDataObject and MobyDataObjectSet" +
+			              " are supported");
 	    return;
 	}
 
@@ -246,26 +248,26 @@
 		return;
 	    }
 	} catch(Exception e){
-	    logger.warn("Could not transform binary file ("+u+"): " + e);
+	    logger.log(Level.WARNING, "Could not transform binary file ("+u+")", e);
 	}
 
 	// Not binary, see if it's text that's convertible to MOBY data
 	MobyClient client = servicesGUI.getMobyClient();
 	if(client == null){
-	    logger.warn("Could not get MOBY client from MOBY services GUI, " +
-			"cannot transform incoming clipboard data to MOBY objects");
+	    logger.log(Level.WARNING, "Could not get MOBY client from MOBY services GUI, " +
+			              "cannot transform incoming clipboard data to MOBY objects");
 	}
 	String urlContents = null;
 	try{
 	    urlContents = HTMLUtils.getURLContents(u);
 	} catch(Exception e){
-	    logger.warn("Could not read contents of the URL to import to the clipboard ("+u+"):" +e);
+	    logger.log(Level.WARNING, "Could not read contents of the URL to import to the clipboard ("+u+")", e);
 	    return;
 	}
 	if(urlContents.indexOf("<html") != -1 || urlContents.indexOf("<HTML") != -1){
 	    urlContents = tagRegex.matcher(commentRegex.matcher(styleRegex.matcher(scriptRegex.matcher(urlContents).replaceAll("")).replaceAll("")).replaceAll("")).replaceAll("");
 	}
-	System.err.println(urlContents);
+	logger.log(Level.FINE, urlContents);
 
 	MobyDataType targetDataType = null;
 	if(collection != null){
@@ -303,7 +305,7 @@
     // Callback once user has selected the data to import from the DataImportChoiceDialog
     public void importConfirmed(DataImportChoiceDialog dialog, MobyDataObject[] selectedData){	
 	if(selectedData == null){
-	    logger.warn("Got null for import selection, abandoning import");
+	    logger.log(Level.WARNING, "Got null for import selection, abandoning import");
 	    return;
 	}
 	for(int i = 0; i < selectedData.length; i++){
@@ -334,7 +336,7 @@
 	    return clipboardFile.toURI().toURL();
 	}
 	catch(java.net.MalformedURLException murle){
-	    logger.warn("Could not get clipboard file URL: " + murle);
+	    logger.log(Level.WARNING, "Could not get clipboard file URL from "+clipboardFile, murle);
 	    return null;
 	}
     }
@@ -348,8 +350,7 @@
 	    gotoURL(clipboardFile.toURI().toURL(), false);
 	}
 	catch(Exception e){
-	    logger.error("Clipboard failed to update the display, cannot write or load temp file:" + e);
-	    e.printStackTrace();
+	    logger.log(Level.SEVERE, "Clipboard failed to update the display, cannot write or load temp file", e);
 	    return;
 	}
 	tabbedPane.setTitleAt(tabbedPane.indexOfComponent(this), CLIPBOARD_TAB_NAME + 



From gordonp at dev.open-bio.org  Sun Apr 18 00:23:42 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Sat, 17 Apr 2010 20:23:42 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004180023.o3I0NgZd027546@dev.open-bio.org>


gordonp
Sat Apr 17 20:23:42 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util
In directory dev.open-bio.org:/tmp/cvs-serv27510/src/main/ca/ucalgary/seahawk/util

Modified Files:
	DataFlowRecorder.java 
Log Message:
Fixed so no problem when original data comes from the clipboard, or a saved moby xml file
moby-live/Java/src/main/ca/ucalgary/seahawk/util DataFlowRecorder.java,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataFlowRecorder.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataFlowRecorder.java	2010/04/16 17:33:26	1.5
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataFlowRecorder.java	2010/04/18 00:23:42	1.6
@@ -342,6 +342,7 @@
 
 	    // true means treat as a collection if that's what the sample data is
 	    String sinkPortName = getPortName(sampleData, true);
+	    // No user data means non-moby origin...backtracking stops.
 	    if(data != null && data.length != 0){
 		URL dataSrcURL = null;
 		try{
@@ -351,6 +352,16 @@
 			       "a provenance URL as expected URL (" + sampleData.getUserData().toString() + ")");
 		    continue;
 		}
+
+		// If srcService == null, the input source for this param was a Moby doc that wasn't a 
+		// service output, e.g. the clipboard or an old doc loaded from file.
+		MobyService srcService = DataUtils.getService(dataSrcURL);
+		if(srcService == null){
+		    addWorkflowInput(processorName, condPassProcessorAndPorts, sinkPortName, sampleData, 
+				     datalinks, processors, inputPorts, doc);
+		    continue;
+		}
+
 		// recursion for workflow creation by backtracking service input provenance
 		String feedingProcessorName = null;
 		String feedingProcessorPort = null;
@@ -429,52 +440,57 @@
 	    }
 	    // Otherwise it's a workflow input the user will need to specify
 	    else{
-		// pName is editable name for input processor target...
-		// allows injection of condition without affecting method's return value
-		String pName = processorName; 
-		if(condPassProcessorAndPorts != null){
-		    // inject condition filter between data creator and current service 
-		    datalinks.appendChild(createDataLinkElement(condPassProcessorAndPorts[0],
-								condPassProcessorAndPorts[2],
-								pName,
-								sinkPortName,
-								doc));
-		    pName = condPassProcessorAndPorts[0];
-		    sinkPortName = condPassProcessorAndPorts[1];
-		}
-		// The sample data may be used in more than one branch of the flow...avoid duplication
-		// Get the real data XML, to see if we've encountered it before as input (it'd be in the hash)
-		// Remember that sd is the loop's original MobyDataInstance before it's been coerced into a MobyPrimaryData, 
-		// which doesn't have XML modes, etc.
-		String inputKey = getInputKey(sd);
-		//		System.err.println("Input key for " + processorName + " is " + inputKey);
-
-		String[] mobifyingProcessorNameAndPorts = null;
-		if(input2Processor.containsKey(inputKey)){
-		    mobifyingProcessorNameAndPorts = input2Processor.get(inputKey);		    
-		}
-		else{
-		    if(sampleData.getDataType().getName().equals(MobyTags.MOBYOBJECT)){
-			mobifyingProcessorNameAndPorts = addIdMobifyingProcessor(processors, datalinks, inputPorts,
-										 sampleData, doc);
-			input2Processor.put(inputKey, mobifyingProcessorNameAndPorts);
-		    }
-		    else{
-			// TODO: Need to build complex input from MOB rule or spreadsheet fields?
-		    }
-		}
-		// link the created data to the workflow service
-		datalinks.appendChild(createDataLinkElement(mobifyingProcessorNameAndPorts[0], 
-							    mobifyingProcessorNameAndPorts[1], 
-							    pName, sinkPortName, 
-							    doc));
+		addWorkflowInput(processorName, condPassProcessorAndPorts, sinkPortName, sampleData, 
+				 datalinks, processors, inputPorts, doc);
 	    }
-
 	}
 
 	return processorName;
     }
 
+    private void addWorkflowInput(String pName, String[] condPassProcessorAndPorts, String sinkPortName, 
+				  MobyPrimaryData sampleData, Element datalinks, Element processors, 
+				  Element inputPorts, Document doc) throws Exception{
+	// pName is editable name for input processor target...
+	// allows injection of condition without affecting method's return value
+	if(condPassProcessorAndPorts != null){
+	    // inject condition filter between data creator and current service 
+	    datalinks.appendChild(createDataLinkElement(condPassProcessorAndPorts[0],
+							condPassProcessorAndPorts[2],
+							pName,
+							sinkPortName,
+							doc));
+	    pName = condPassProcessorAndPorts[0];
+	    sinkPortName = condPassProcessorAndPorts[1];
+	}
+	// The sample data may be used in more than one branch of the flow...avoid duplication
+	// Get the real data XML, to see if we've encountered it before as input (it'd be in the hash)
+	// Remember that sd is the loop's original MobyDataInstance before it's been coerced into a MobyPrimaryData, 
+	// which doesn't have XML modes, etc.
+	String inputKey = getInputKey((MobyDataInstance) sampleData);
+	//		System.err.println("Input key for " + processorName + " is " + inputKey);
+	
+	String[] mobifyingProcessorNameAndPorts = null;
+	if(input2Processor.containsKey(inputKey)){
+	    mobifyingProcessorNameAndPorts = input2Processor.get(inputKey);		    
+	}
+	else{
+	    if(sampleData.getDataType().getName().equals(MobyTags.MOBYOBJECT)){
+		mobifyingProcessorNameAndPorts = addIdMobifyingProcessor(processors, datalinks, inputPorts,
+									 sampleData, doc);
+		input2Processor.put(inputKey, mobifyingProcessorNameAndPorts);
+	    }
+	    else{
+		// TODO: Need to build complex input from MOB rule or spreadsheet fields?
+	    }
+	}
+	// link the created data to the workflow service
+	datalinks.appendChild(createDataLinkElement(mobifyingProcessorNameAndPorts[0], 
+						    mobifyingProcessorNameAndPorts[1], 
+						    pName, sinkPortName, 
+						    doc));	
+    }
+
     // returns the same value for moby sample data instances containing the same data in XML form
     private String getInputKey(MobyDataInstance sd){
 	int oldXmlMode = sd.getXmlMode();



From gordonp at dev.open-bio.org  Sun Apr 18 00:31:49 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Sat, 17 Apr 2010 20:31:49 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004180031.o3I0VnZ0028062@dev.open-bio.org>


gordonp
Sat Apr 17 20:31:49 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv28026/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	MobyServicesGUI.java 
Log Message:
Switched from Object to ID for basic object label, more intuitive for users
moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyServicesGUI.java,1.20,1.21
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java,v
retrieving revision 1.20
retrieving revision 1.21
diff -u -r1.20 -r1.21
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java	2010/04/16 17:33:25	1.20
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java	2010/04/18 00:31:49	1.21
@@ -693,7 +693,6 @@
 											       payloadCreator));
 		    }
 		    else if(mobyData instanceof MobyNamespace){
-			System.err.println("Creating deferred dataset payload");
 			serviceAssocObject = mobyClient.getServices(new MobyDataObjectDeferred((MobyNamespace) mobyData, 
 											       payloadCreator));
 		    }
@@ -1175,7 +1174,7 @@
     }
 
     public JMenu addOutputTypeSubMenu(JMenu parentMenu, MobyDataType type){
-	JMenu menu = new JMenu("Result type: " + type.getName());
+	JMenu menu = new JMenu("Result type: " + (type.getName().equals(MobyTags.MOBYOBJECT) ? "ID" : type.getName()));
 
 	MobyDataType[] typeLineage = type.getLineage();
 	String commonAncestorDesc = "";



From gordonp at dev.open-bio.org  Sun Apr 18 00:33:05 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Sat, 17 Apr 2010 20:33:05 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004180033.o3I0X5V4028106@dev.open-bio.org>


gordonp
Sat Apr 17 20:33:05 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv28070/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	MobySaveDialog.java 
Log Message:
Stripped seahawk preocessing instructions from saved XML as they can confuse on reload.  Workflow export is default save option now.
moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobySaveDialog.java,1.8,1.9
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobySaveDialog.java,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobySaveDialog.java	2010/03/29 19:53:16	1.8
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobySaveDialog.java	2010/04/18 00:33:05	1.9
@@ -92,11 +92,11 @@
 		    fileChooser.setName(FILE_CHOOSER_SAVE_TITLE);
 		    fileChooser.setFileHidingEnabled(false);
 		    fileChooser.setFileSelectionMode(JFileChooser.FILES_ONLY);
-		    fileChooser.addChoosableFileFilter(new DescriptiveFileFilter(HTML_EXT, HTML_DESC));
 		    if(document.hasXMLSource()){
 			fileChooser.addChoosableFileFilter(new DescriptiveFileFilter(T2FLOW_EXT, T2FLOW_DESC));
 			fileChooser.addChoosableFileFilter(new DescriptiveFileFilter(XML_EXT, XML_DESC));
 		    }
+		    fileChooser.addChoosableFileFilter(new DescriptiveFileFilter(HTML_EXT, HTML_DESC));
 		    fileChooser.setAcceptAllFileFilterUsed(false);
 		    if(lastDirOpened != null){
 			fileChooser.setCurrentDirectory(lastDirOpened);
@@ -318,7 +318,9 @@
 		    try {
 			OutputStream ostream = new FileOutputStream(f);
 			String xml = document.getXMLSource();
-			ostream.write(xml.getBytes());
+			// Before saving, strip out the Seahawk processing instructions, which will 
+			// confuse Seahawk if we reload the XML doc later.
+			ostream.write(xml.replaceAll("<\\?"+DataUtils.PI_TARGET+".*?\\?>","").getBytes());
 			ostream.flush();
 			ostream.close();
 		    } catch (Exception ex) {



From gordonp at dev.open-bio.org  Sun Apr 18 00:33:56 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Sat, 17 Apr 2010 20:33:56 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004180033.o3I0Xu7J028150@dev.open-bio.org>


gordonp
Sat Apr 17 20:33:56 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv28114/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	MobyPayloadCreator.java 
Log Message:
Cleaner logging
moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyPayloadCreator.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyPayloadCreator.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyPayloadCreator.java	2010/04/16 17:33:25	1.3
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyPayloadCreator.java	2010/04/18 00:33:56	1.4
@@ -27,7 +27,7 @@
 	// The request key is the sample data's app context: 
         // url#xpath <tab> sample_xptr <tab> filter_regex <tab> filter_xpath <tab> xpath_desc <tab> case_sensitive_boolean <tab> inverse selection
         // from which we will build the peer dataset to submit.
-	System.err.println("Request key is " + requestKey);
+	logger.log(Level.FINER, "Request key is " + requestKey);
 	String[] requestKeyFields = requestKey.split("\t");
 
 	String[] requestParts = requestKeyFields[0].split("#", 2);
@@ -67,7 +67,7 @@
 	    }
 	    else if(filter.equals(srcPane.getFilter())){
                 // no need to redo the filtering, it's the current display's filtering
-		System.err.println("Reusing current filter");
+		logger.log(Level.FINE, "Reusing current filter");
                 xptrsToFilter = srcPane.getFilteredData();
             }
             else{
@@ -89,7 +89,7 @@
 	MobyContentInstance payload = new MobyContentInstance();
         Map<String,Integer> jobPrefixes = new LinkedHashMap<String,Integer>();
 
-	System.err.println("Loading MobyContentInstance with "+peerElements.getLength()+" elements for xpath "+selectionXPath);
+	logger.log(Level.FINE, "Loading MobyContentInstance with "+peerElements.getLength()+" elements for xpath "+selectionXPath);
         for(int i = 0; i < peerElements.getLength(); i++){
             Element peerElement = (Element) peerElements.item(i);
 	    // Try to make the job names trackable to the inputs:
@@ -106,7 +106,7 @@
                 jobPrefixes.put(jobKey, new Integer(suffixCount+1));
                 jobKey += "_"+(suffixCount+1);
             }
-	    System.err.println("Adding job "+jobKey+" for "+peerElement.getLocalName());
+	    logger.log(Level.FINE, "Adding job "+jobKey+" for "+peerElement.getLocalName());
             MobyDataInstance mdi  = null;
             try{
                 mdi = MobyDataObject.createInstanceFromDOM(peerElement, SeahawkOptions.getRegistry());



From gordonp at dev.open-bio.org  Fri Apr 23 05:15:42 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 23 Apr 2010 01:15:42 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004230515.o3N5FglD024507@dev.open-bio.org>


gordonp
Fri Apr 23 01:15:42 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util
In directory dev.open-bio.org:/tmp/cvs-serv24471/src/main/ca/ucalgary/services/util

Modified Files:
	PBERecorder.java 
Log Message:
Truncate long example data abruptly if it has no whitespace
moby-live/Java/src/main/ca/ucalgary/services/util PBERecorder.java,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/PBERecorder.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/PBERecorder.java	2010/03/29 20:59:54	1.4
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/PBERecorder.java	2010/04/23 05:15:41	1.5
@@ -795,7 +795,10 @@
 	}
 
 	int end = text.length();
-	if(start + targetWord.length() + numChars < text.length()){
+	if(text.indexOf(" ") == -1){
+	    end = numChars;
+	}
+	else if(start + targetWord.length() + numChars < text.length()){
 	    end = start + targetWord.length() + numChars;
 	    // break at a word boundary
 	    while(end < text.length() && !Character.isWhitespace(text.charAt(end))){



From gordonp at dev.open-bio.org  Fri Apr 23 05:16:45 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 23 Apr 2010 01:16:45 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004230516.o3N5GjOm024551@dev.open-bio.org>


gordonp
Fri Apr 23 01:16:45 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services
In directory dev.open-bio.org:/tmp/cvs-serv24515/src/main/ca/ucalgary/seahawk/services

Modified Files:
	TextClient.java 
Log Message:
Better Dublin Core support, added getPossibleTextTypes() for drag and drop export
moby-live/Java/src/main/ca/ucalgary/seahawk/services TextClient.java,1.7,1.8
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/TextClient.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/TextClient.java	2009/06/09 19:22:21	1.7
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/TextClient.java	2010/04/23 05:16:45	1.8
@@ -8,13 +8,15 @@
 
 import org.w3c.dom.*;
 
-import javax.xml.transform.stream.*;
-import javax.xml.transform.*;
 import javax.xml.parsers.*;
+import javax.xml.transform.*;
+import javax.xml.transform.dom.DOMSource;
+import javax.xml.transform.stream.*;
 
 import java.io.*;
 import java.net.URL;
 import java.util.*;
+import java.util.logging.*;
 
 /**
  * This class uses XSLT rules to transform MOBY XML data representation
@@ -24,20 +26,26 @@
  */
 public class TextClient{
 
+    public static final String DATA_MAPPING_XSLT_RESOURCE = "ca/ucalgary/seahawk/resources/mobyRules.xsl";
+    public static final String RESOURCE_SYSTEM_PROPERTY = "seahawk.textrules";
+
     public final static String XSLT_NS = "http://www.w3.org/1999/XSL/Transform";
     public final static String XSLT_MODE_VAR = "selectedACDTypeTarget";
 
     private Vector<Transformer> moby2textConverters;  // XSLT engine
     private TransformerFactory transFactory;
     private DocumentBuilder docBuilder;
+    private URL dataMappingXSLTURL;
     //private Map<String,Transformer> id; //todo: unique xslt doc id (e.g. LSID or URL) -> transformer
 
     private Map<String, Vector<String>> typeTemplates;  //mobytype -> Vector(xsltrule1, xsltrule2,...)
     private Map<String, Vector<MobyNamespace>> typeNsRestrictions;  //mobytype -> Vector(mobynamespace1, ...)
     private Map<String, String> templateMode;
-    private String id;
+    private Map<String,String> templateIds; // template name -> URN
     private Registry registry;
 
+    private static Logger logger = Logger.getLogger(TextClient.class.getName());
+
     public TextClient() throws Exception{
 	this(SeahawkOptions.getRegistry() == null ? 
 	     RegistryCache.getDefaultRegistry() :
@@ -60,16 +68,95 @@
 	typeTemplates = new HashMap<String, Vector<String>>();
 	typeNsRestrictions = new HashMap<String, Vector<MobyNamespace>>();
 	templateMode = new HashMap<String, String>();
+	templateIds = new HashMap<String, String>();
+
+	ClassLoader cl = getClass().getClassLoader();
+	if(cl == null){
+	    cl = ClassLoader.getSystemClassLoader();
+	}
+        String rulesResource = System.getProperty(RESOURCE_SYSTEM_PROPERTY);
+        if(rulesResource == null){
+	  dataMappingXSLTURL = cl.getResource(DATA_MAPPING_XSLT_RESOURCE);
+        }
+	else if(rulesResource.length() != 0){
+	    // See if it's a URL
+	    try{
+		dataMappingXSLTURL = new URL(rulesResource);
+	    }
+	    catch(Exception e){
+		dataMappingXSLTURL = cl.getResource(rulesResource);
+	    }
+	}
+	if(dataMappingXSLTURL == null){
+	    if(rulesResource.length() != 0){ // if not left intentionally blank
+		logger.log(Level.WARNING, "Could not find MOBY to text mapping resource '"+
+				          rulesResource+"'");
+	    }
+	}
+	else{
+	    try{
+		addMappingsFromURL(dataMappingXSLTURL);
+	    }
+	    catch(Exception e){
+		logger.log(Level.SEVERE, "Error loading default data mapping rules ("+dataMappingXSLTURL+")", e);
+                e.printStackTrace();
+	    }
+	}
+    }
+
+    public String[] getPossibleTextTypes(MobyPrimaryData dataTemplate, boolean mustHaveURN){
+	Vector<String> possibleTypes = new Vector<String>();
+	// Search for templates matching the given type or one of its parent types,
+	// and see if they create the given text type (indicated by the template's mode attribute)
+	for(MobyDataType type = dataTemplate.getDataType();
+	    type != null;
+	    type = type.getParent()){
+	    if(typeTemplates.containsKey(type.getName())){
+		// These two vectors should be of the same length!
+		Vector<String> templateNames = typeTemplates.get(type.getName());
+		Vector<MobyNamespace> nsRestrictions = typeNsRestrictions.get(type.getName());
+		for(int i = 0; i < templateNames.size(); i++){
+		    String templateName = templateNames.elementAt(i);
+		    if(mustHaveURN && getTemplateURN(templateName) == null){
+			continue;
+		    }
+
+		    // the template input moby datatype is the same type as we have an instance of
+		    String textType = templateMode.get(templateName); // mode and text type name are one and the same
+		    // does set-ness match?
+		    if(dataTemplate instanceof MobyPrimaryDataSet){
+			if(templateName.startsWith("Collection-")){
+			    possibleTypes.add(textType);	
+			}
+		    }
+		    else{
+			if(!templateName.startsWith("Collection-")){
+			    possibleTypes.add(textType);
+			}
+		    }
+		    // Is there a namespace restriction on the transformation rule?
+		    MobyNamespace ns = nsRestrictions.elementAt(i);
+		    if(ns != null){
+			for(MobyNamespace n: dataTemplate.getNamespaces()){
+			    if(ns.equals(n)){
+				possibleTypes.add(textType);
+			    }
+			}
+		    }
+		}
+	    }
+	}
+	return possibleTypes.toArray(new String[possibleTypes.size()]);
+    }
+
+    public String getTemplateURN(String templateName){
+	return templateIds.get(templateName);
     }
 
     /**
      * @return the data format the xslt creates (the last template mode attribute in the file) 
      */
     public synchronized String addMappingsFromURL(URL xsltURL) throws Exception{
-        StreamSource stylesheet = new StreamSource(xsltURL.toString());
-	// Prepend to list, so later rules can override ones specified earlier
-	moby2textConverters.insertElementAt(transFactory.newTransformer(stylesheet), 0);
-
 	// We actually need to read in the XSLT file and keep track of the template
 	// names, modes, etc..  Currently, this will not follow links that
 	// import other stylesheets into the one being examined.
@@ -80,7 +167,6 @@
             throw new Exception("Error: Could not get XSLT document as DOM from source URL " 
 				+ xsltURL + " (empty or malformed document?)");
         }
-	getId(xsltDOMRoot);  // retrieve the dublin core metadata
 
 	String mode = null; // returned in the end
 
@@ -93,6 +179,9 @@
 		continue;
 	    }
 	    String templateName = template.getAttribute("name");
+
+	    templateIds.put(templateName, getId(template));
+
 	    String m = template.getAttribute("mode");
 	    if(m != null && m.trim().length() > 0){
 		mode = template.getAttribute("mode");
@@ -150,12 +239,16 @@
 	    typeNsRestrictions.get(templateNameParts[0]).insertElementAt(ns, 0);	    
 	}
 
+        DOMSource stylesheet = new DOMSource(domDoc);
+	// Prepend to list, so later rules can override ones specified earlier
+	moby2textConverters.insertElementAt(transFactory.newTransformer(stylesheet), 0);
+
 	//System.err.println("Mode returned by " + xsltURL + " is " + mode);
 	return mode; // return the last mode value in the file (useful when mapping XSLT -> data format)
     }
 
     // Looks for Dublin Core metadata
-    private void getId(Element xsltDOMRoot){
+    private String getId(Element xsltDOMRoot){
 	NodeList idElements = xsltDOMRoot.getElementsByTagNameNS(MobyPrefixResolver.DUBLIN_CORE_NAMESPACE,
 								 "identifier");
 	if(idElements.getLength() == 0){
@@ -163,13 +256,17 @@
 							     "source");
 	}
 	if(idElements.getLength() == 0){
-	    return;
+	    return null;
 	}
 	if(idElements.getLength() != 1){
 	    System.err.println("More than one Dublin Core identifier was found, cannot disambiguate.");
-	    return;
+	    return null;
 	}
-	id = idElements.item(0).getTextContent();
+	String id = idElements.item(0).getTextContent();
+	// remove child so id doesn't show up in the xslt output!
+	idElements.item(0).getParentNode().removeChild(idElements.item(0));
+	System.err.println("Found and removed "+id);
+	return id;
     }
 
    /**
@@ -374,17 +471,17 @@
 				e);
 	}	 
 	
-	if(client.id == null){
+	if(client.templateIds.isEmpty()){
 	    throw new Exception("Internal error: loaded the transformation rule (URI " + ruleURI + 
 				") from " + ruleSource + " but could not retrieve it from TextClient " +
 				"using the URI.  Make sure the transformation rule contains a Dublin Core " +
 				"identifier element specifying this URI.");
 	}
-	else if(!client.id.equals(ruleURI)){
+	else if(!client.templateIds.containsValue(ruleURI)){
 	    throw new Exception("Internal error: loaded the transformation rule (URI " + ruleURI + 
 				") from " + ruleSource + " but could not retrieve it from TextClient " +
 				"using the URI.  The given Dublin Core info for the rule actually loaded " +
-				"was " + client.id);
+				"was " + client.templateIds.values().iterator().next());
 	}
 	else{
 	    template = new MobyPrimaryDataSimple("templateRuleReturnedObject");
@@ -398,7 +495,7 @@
 	    if(dataTypeNames.size() > 1){
 		throw new Exception("Multiple TextClient rules were loaded from " + ruleSource +
 				    ", please separate them out into separate XSLT files to ensure " +
-				    "they can be referenced inidivudually and unambiguously.");
+				    "they can be referenced indivudually and unambiguously.");
 	    }
 	    MobyDataType type = MobyDataType.getDataType(dataTypeNames.toArray()[0].toString(), client.getRegistry());
 	    template.setDataType(type);



From gordonp at dev.open-bio.org  Fri Apr 23 05:17:28 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 23 Apr 2010 01:17:28 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004230517.o3N5HSKc024595@dev.open-bio.org>


gordonp
Fri Apr 23 01:17:28 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv24559/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	SeahawkTransferable.java 
Log Message:
Better complex object drag and drop export support
moby-live/Java/src/main/ca/ucalgary/seahawk/gui SeahawkTransferable.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java	2009/06/09 19:46:48	1.1
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java	2010/04/23 05:17:28	1.2
@@ -1,9 +1,15 @@
 package ca.ucalgary.seahawk.gui;
 
+import ca.ucalgary.seahawk.util.SeahawkOptions;
+import ca.ucalgary.seahawk.services.TextClient;
+
+import org.biomoby.shared.MobyPrimaryData;
 import org.biomoby.shared.data.*;
 
 import java.awt.datatransfer.*;
+import javax.swing.JOptionPane;
 import java.util.*;
+import java.util.logging.*;
 
 /**
  * This class handles the export of data from the Seahawk interface into other applications,
@@ -16,9 +22,20 @@
     private String lastPastedValue;
     private String lastTransformRuleURI;
 
+    private static TextClient textClient;
+    private static Logger logger = Logger.getLogger(SeahawkTransferable.class.getName());
+
     public SeahawkTransferable(MobyContentPane p){
 	pane = p;
     }
+    
+    private synchronized TextClient getTextClient() throws Exception{
+	if(textClient == null){
+	    textClient = new TextClient(SeahawkOptions.getRegistry());
+	    //auto populate the rules
+	}
+	return textClient;
+    }
 
     public Object getTransferData(DataFlavor flavor) 
 	throws UnsupportedFlavorException, java.io.IOException{
@@ -28,7 +45,7 @@
 	Class clazz = flavor.getRepresentationClass();
 	
 	// Essentially, we let the user drag Moby objects or submembers rather than substrings of members' text
-	// so that we can make simple rules for decomposition in programming-by-example.  OR an XSLT "DEM" rulew
+	// so that we can make simple rules for decomposition in programming-by-example.  OR an XSLT "DEM" rules
 	// could be applied to provide a particular format e.g. DNASequence -> FastA
 	String fieldString = null;
 	String transformRuleURI = null;
@@ -54,12 +71,38 @@
 	    fieldString = ((MobyDataObject) field).getValue().toString();
 	    transformRuleURI = "urn:lsid:bioxml.info:mobyLoweringSchemaMapping:DateTime2String";
 	}
-	else if(field instanceof MobyDataObjectVector){	    
-	}
-	else if(field instanceof MobyDataObjectSet){
+	else if(field instanceof MobyDataObjectVector){	
+	    //todo?
 	}
 	else if(field instanceof MobyDataComposite){
-	    // todo: Is there a DEM rule we can use?
+	    try{
+		// Is there a DEM rule we can use?
+		boolean ONLY_IF_HAS_URN = true;
+		String[] formatChoices = getTextClient().getPossibleTextTypes((MobyPrimaryData) field, ONLY_IF_HAS_URN);
+		String targetTextType = null;
+		if(formatChoices != null && formatChoices.length != 0){
+		    if(formatChoices.length == 1){
+			targetTextType = formatChoices[0];
+		    }
+		    else{
+			// Give the user a choice
+			targetTextType = formatChoices[0];
+			logger.log(Level.INFO, "Chose "+formatChoices[0]+" instead of "+formatChoices[1]);
+// 			targetTextType = (String) JOptionPane.showInputDialog(pane
+// 									      "Please select a text format to convert to",
+// 									      "Format choices available",
+// 									      JOptionPane.QUESTION_MESSAGE,
+// 									      null,
+// 									      formatChoices,
+// 									      formatChoices[0]);
+		    }
+		}
+		fieldString = getTextClient().getText(field, targetTextType);
+		transformRuleURI = getTextClient().getTemplateURN(targetTextType);
+	    } catch(Exception e){
+		pane.setStatus("Could not transform Moby object to text: " + e.getMessage());
+		logger.log(Level.SEVERE, "Could not transform Moby object to text: ", e);
+	    }
 	}
 	else{
 	    // Must be just a base MobyDataObject



From gordonp at dev.open-bio.org  Fri Apr 23 05:18:13 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 23 Apr 2010 01:18:13 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004230518.o3N5IDig024639@dev.open-bio.org>


gordonp
Fri Apr 23 01:18:13 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv24603/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	MobyServicesGUI.java 
Log Message:
Fixed duplication in complex object labels when they have namespaces too
moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyServicesGUI.java,1.21,1.22
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java,v
retrieving revision 1.21
retrieving revision 1.22
diff -u -r1.21 -r1.22
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java	2010/04/18 00:31:49	1.21
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java	2010/04/23 05:18:13	1.22
@@ -1315,7 +1315,7 @@
 		}
 	    }
 	    if(templateObject instanceof MobyDataObject && id != null && id.length() > 0){
-		objectLabel += "<font color='red'>"+objectLabel+"</font>:" + id;
+		objectLabel = "<font color='red'>"+objectLabel+"</font>:" + id;
 	    }
 	    else if(templateObject instanceof MobyDataObjectSet){
 		objectLabel = "<font color='red'>"+objectLabel+" collection</font>";



From gordonp at dev.open-bio.org  Fri Apr 23 05:19:10 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 23 Apr 2010 01:19:10 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004230519.o3N5JAnp024685@dev.open-bio.org>


gordonp
Fri Apr 23 01:19:10 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv24649/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	MobySaveDialog.java 
Log Message:
Removed redundant popup of single tab export if canceled
moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobySaveDialog.java,1.9,1.10
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobySaveDialog.java,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobySaveDialog.java	2010/04/18 00:33:05	1.9
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobySaveDialog.java	2010/04/23 05:19:10	1.10
@@ -92,11 +92,11 @@
 		    fileChooser.setName(FILE_CHOOSER_SAVE_TITLE);
 		    fileChooser.setFileHidingEnabled(false);
 		    fileChooser.setFileSelectionMode(JFileChooser.FILES_ONLY);
+		    fileChooser.addChoosableFileFilter(new DescriptiveFileFilter(HTML_EXT, HTML_DESC));
 		    if(document.hasXMLSource()){
-			fileChooser.addChoosableFileFilter(new DescriptiveFileFilter(T2FLOW_EXT, T2FLOW_DESC));
 			fileChooser.addChoosableFileFilter(new DescriptiveFileFilter(XML_EXT, XML_DESC));
+			fileChooser.addChoosableFileFilter(new DescriptiveFileFilter(T2FLOW_EXT, T2FLOW_DESC));
 		    }
-		    fileChooser.addChoosableFileFilter(new DescriptiveFileFilter(HTML_EXT, HTML_DESC));
 		    fileChooser.setAcceptAllFileFilterUsed(false);
 		    if(lastDirOpened != null){
 			fileChooser.setCurrentDirectory(lastDirOpened);
@@ -277,7 +277,8 @@
 
 	    // Waits until workflowConfirmed or workflowCanceled is called by the preview dialog
 	    dialog.available.acquire();
-	    return dialog.exportConfirmed;
+	    // Check choice, because if the user cancelled the dialog, don't show it again regardless
+	    return choice == 1 ? true : dialog.exportConfirmed;
 	} catch (Exception ex) {
 	    ex.printStackTrace();
 	    JOptionPane.showMessageDialog(null, "Cannot save the Seahawk tab history as a Taverna workflow: "+ex, 



From gordonp at dev.open-bio.org  Fri Apr 23 05:20:00 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 23 Apr 2010 01:20:00 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004230520.o3N5K0NK024729@dev.open-bio.org>


gordonp
Fri Apr 23 01:20:00 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv24693/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	MobyContentPane.java 
Log Message:
Fixed bug with support of plus sign in URLs to wrap as services
moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyContentPane.java,1.29,1.30
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java,v
retrieving revision 1.29
retrieving revision 1.30
diff -u -r1.29 -r1.30
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java	2010/04/16 17:33:25	1.29
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java	2010/04/23 05:20:00	1.30
@@ -273,6 +273,10 @@
 	}
     }
 
+    public void setStatus(String msg){
+	status.setText(msg);
+    }
+
     // servletPath is either the CGI or SOAP servlet
     private void createService(String servletPath){
 	// item name, set by MobyContentGUI's processResults(), is namedXPath#numericXPtr
@@ -459,7 +463,7 @@
 				   "Please manually launch a browser and go to the URL " +
 				   u);
 	    }
-	    desktop.browse(u.toURI());
+	    desktop.browse(new java.net.URI(u.toURI().toString().replace("+", "%2B")));
 	} catch (java.net.URISyntaxException urise){
 	    logger.error("Could not create URI from URL ("+u+"): " + urise);
 	} catch (java.io.IOException ioe){



From gordonp at dev.open-bio.org  Fri Apr 23 05:21:42 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 23 Apr 2010 01:21:42 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004230521.o3N5LgTu024871@dev.open-bio.org>


gordonp
Fri Apr 23 01:21:42 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources
In directory dev.open-bio.org:/tmp/cvs-serv24839/src/main/ca/ucalgary/seahawk/resources

Added Files:
	mobyRules.xsl 
Log Message:
Sibling of mobyRules.xsl in src/main/ca/ucalgary/services/resources, but with nicer format names and Dublin Core IDs for Daggoo wrapping
moby-live/Java/src/main/ca/ucalgary/seahawk/resources mobyRules.xsl,NONE,1.1


From gordonp at dev.open-bio.org  Sat Apr 24 17:23:27 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Sat, 24 Apr 2010 13:23:27 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004241723.o3OHNRQZ007370@dev.open-bio.org>


gordonp
Sat Apr 24 13:23:27 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv7331/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	MobySecondaryInputGUI.java MobyServicesGUI.java 
Added Files:
	ServiceChoiceListener.java ServiceSearchDialog.java 
Log Message:
Initial commit of service search dialog
moby-live/Java/src/main/ca/ucalgary/seahawk/gui ServiceChoiceListener.java,NONE,1.1 ServiceSearchDialog.java,NONE,1.1 MobySecondaryInputGUI.java,1.7,1.8 MobyServicesGUI.java,1.22,1.23
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobySecondaryInputGUI.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/gui/MobySecondaryInputGUI.java	2007/12/06 17:32:32	1.7
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobySecondaryInputGUI.java	2010/04/24 17:23:26	1.8
@@ -1,4 +1,3 @@
-
 package ca.ucalgary.seahawk.gui;
 
 import ca.ucalgary.seahawk.services.MobyClient;

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java,v
retrieving revision 1.22
retrieving revision 1.23
diff -u -r1.22 -r1.23
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java	2010/04/23 05:18:13	1.22
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java	2010/04/24 17:23:26	1.23
@@ -27,7 +27,7 @@
  * Implementation of the actually popup menu that lists services available, and invokes them.
  */
 
-public class MobyServicesGUI implements ActionListener, Comparator<MobyService>, PopupMenuListener{
+public class MobyServicesGUI implements ActionListener, Comparator<MobyService>, PopupMenuListener, ServiceChoiceListener{
     public final static int MAX_ID_LEN = 30;
     public final static String SERVICE_SUBMENU_NAME = "seahawkPopupSubMenuName";
 
@@ -35,6 +35,10 @@
     public final static int MAX_SERVICES_PER_SUBMENU = 12;  
     public final static int MAX_SERVICE_DESC_LEN = 50;
     public final static String CLIPBOARD_CMD = "clipboard";
+    public final static String SERVICESEARCH_CMD = "service_search";
+    public final static String SEARCH_LABEL = "Find service by keyword...";
+    public final static String CLIPBOARD_LABEL = "Add to clipboard";
+
     /** Always spring MOBY response in a new window if this modifier is present for a click */
     public final static int USE_DEFAULT_HANDLER_MASK  = ActionEvent.SHIFT_MASK;
     public final static int USE_DEFAULT_SECONDARIES_MASK  = ActionEvent.CTRL_MASK;
@@ -57,6 +61,7 @@
     int maxDataDesc = 22;
     // tracks nested submenus to root submenus of choices popup
     private Map<JMenu, JMenu> service2submenu; 
+    private Map<JMenuItem, JMenu> search2submenu; 
     private Map<JComponent,Integer> submenu2msIndex;
     private Map<JMenu,JMenuItem> submenu2waitItem;
     // for storing callbacks to other than the default response handler
@@ -75,6 +80,7 @@
 	submenu2msIndex = new HashMap<JComponent,Integer>();
 	submenu2waitItem = new HashMap<JMenu,JMenuItem>();
 	service2submenu = new HashMap<JMenu,JMenu>();
+	search2submenu = new HashMap<JMenuItem,JMenu>();
 	specificHandlers = new HashMap<Integer,WeakReference<MobyRequestEventHandler>>();
     }
 
@@ -124,6 +130,20 @@
 		}
 		return;
 	    }
+	    if(service.equals(SERVICESEARCH_CMD)){
+		synchronized(ms){
+		    if(ms[which_data] == null){
+			logger.warn("Ignoring searvice search in " + getClass().getName() +
+				    ", the data to add is currently null (index "+which_data+")"+
+				    ", from source " + e.getSource());
+			removePopupOptions(e.getSource());
+			return;
+		    }
+		    setupSearchData(search2submenu.get((JMenuItem) e.getSource()), ms[which_data]);
+		    removePopupOptions(e.getSource());
+		}
+		return;   
+	    }
 	    // Otherwise call a remote service
 	    int which_service = Integer.parseInt(service);
 
@@ -322,7 +342,7 @@
     }
 
     /**
-     * If the popup is cancelled, we want to remove any data we've stored, and kill any 
+     * If the popup is canceled, we want to remove any data we've stored, and kill any 
      * requests to MOBYCentral.
      */
     public void popupMenuCanceled(PopupMenuEvent e){
@@ -533,6 +553,7 @@
 	
 	for(int i = 0; i < submenus.length; i++){
 	    addServicesToSubMenu(submenus[i], serviceAssocObjects[i], handler);
+	    addSearchItem(submenus[i], 1);
 	}
     }
 
@@ -595,6 +616,7 @@
 		    //}}.start();
 	    }
 	    service2submenu.clear();
+	    search2submenu.clear();
 	    submenu2msIndex.clear();
 	    submenu2waitItem.clear();
 	    ms = new MobyDataServiceAssocInstance[0];
@@ -732,6 +754,7 @@
 	}
 
 	addServicesToSubMenu(submenu, serviceAssocObject, handler);
+        addSearchItem(submenu, 0);
     }
 
     protected synchronized void addServicesToSubMenu(JMenu submenu, MobyDataServiceAssocInstance msadi){
@@ -1333,6 +1356,15 @@
 	return submenu;
     }
 
+    public void serviceSelected(ServiceSearchDialog dialog, javax.swing.JMenuItem selectedServiceItem){
+	actionPerformed(new ActionEvent(selectedServiceItem, 1, selectedServiceItem.getActionCommand()));
+	removePopupOptions();
+    }
+
+    public void selectionCanceled(ServiceSearchDialog dialog){
+	removePopupOptions();  //cleanup stored data
+    }
+
     private synchronized int assignMenuDataIndex(JMenu submenu){
 	// Make the services array bigger, then copy over existing data, 
 	// leaving a blank at the end to be filled in by addServicesToSubMenu
@@ -1370,6 +1402,64 @@
 	}
     }
 
+    /**
+     * Removes the popup menu and replaces it with a window that has a filter widget
+     * over the list of services from the original popup.
+     */
+    protected void setupSearchData(JMenu objectMenu, MobyDataInstance mobyData){
+	// Setup the chooser dialog
+	ServiceSearchDialog searchDialog = new ServiceSearchDialog(null, 
+								   objectMenu.getText().replaceFirst("Services for", "Run "), 
+								   this);
+	addMenuOptionsToSearch(searchDialog, objectMenu);
+
+	searchDialog.initializeList();
+	searchDialog.pack();
+	searchDialog.setVisible(true);
+    }
+
+    private void addMenuOptionsToSearch(ServiceSearchDialog searchDialog, MenuElement menuElement){
+	if(menuElement instanceof JPopupMenu || menuElement instanceof JMenu){
+	    for(MenuElement subMenuElement: menuElement.getSubElements()){
+		addMenuOptionsToSearch(searchDialog, subMenuElement);
+	    }
+	}
+	else if(menuElement instanceof JMenuItem){ // leaf defining a service
+	    JMenuItem serviceItem = (JMenuItem) menuElement;
+	    String label = serviceItem.getText();
+	    if(label.equals(SEARCH_LABEL) || label.equals(CLIPBOARD_LABEL)){
+		return; // not real services
+	    }
+	    serviceItem.setText(label.replaceFirst("Run ", ""));
+	    searchDialog.addOption(serviceItem, false);
+	}
+	else{
+	    System.err.println("Got dead end with "+menuElement.getClass().getName());
+	}
+    }
+
+    public void addSearchItem(JMenu menu, int location){
+	if(menu == null){
+	    logger.warn("Cannot add service search option, menu reference passed in was null");
+	    return;
+	}
+
+	if(!submenu2msIndex.containsKey(menu)){
+	    logger.warn("Cannot add service search option, cannot find " +
+			"moby object list index for menu " + 
+			menu.getText());
+	    return;
+	}
+
+
+	int dataIndex = ((Integer) submenu2msIndex.get(menu)).intValue();
+	JMenuItem searchItem = new JMenuItem(SEARCH_LABEL);
+	searchItem.setActionCommand("MOBY:"+dataIndex+":"+SERVICESEARCH_CMD);
+	searchItem.addActionListener(this);
+	menu.add(searchItem, location);	
+	search2submenu.put(searchItem, menu);
+    }
+
     public void addClipboardItem(JMenu menu, MobyDataInstance mobyData){
 	if(menu == null){
 	    logger.warn("Cannot add clipboard option, menu reference passed in was null");
@@ -1408,11 +1498,11 @@
 	}
 	else{
 	    logger.warn("Clipboard option for objects other than MobyDataObject " +
-			       "and MobyDataObjectSet are not yet supported:"+mobyData);
+			"and MobyDataObjectSet are not yet supported:"+mobyData);
 	    return;
 	}
 
-	JMenuItem clipItem = new JMenuItem("Add to clipboard");
+	JMenuItem clipItem = new JMenuItem(CLIPBOARD_LABEL);
 	clipItem.setActionCommand("MOBY:"+dataIndex+":"+CLIPBOARD_CMD);
 	clipItem.addActionListener(this);
 	menu.add(clipItem);



From gordonp at dev.open-bio.org  Mon Apr 26 16:25:36 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Mon, 26 Apr 2010 12:25:36 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004261625.o3QGPasj025559@dev.open-bio.org>


gordonp
Mon Apr 26 12:25:36 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util
In directory dev.open-bio.org:/tmp/cvs-serv25523/src/main/ca/ucalgary/seahawk/util

Modified Files:
	DataUtils.java 
Log Message:
Ensured that moby namepsace is defined for xpath
moby-live/Java/src/main/ca/ucalgary/seahawk/util DataUtils.java,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataUtils.java,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataUtils.java	2010/04/16 17:33:26	1.6
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataUtils.java	2010/04/26 16:25:36	1.7
@@ -1044,7 +1044,7 @@
 	    // first arg is url#nameBasedXPath 
 	    peerGroupXPath = userData[0].split("#", 2)[1];
 	    contextNode = XPointerResolver.getNodeFromXPointer(doc, userData[1]);
-	    //System.err.println("Loaded context node " + userData[1] + " as " + contextNode);
+	    System.err.println("Loaded context node " + userData[1] + " as " + contextNode);
         }
         else{
 	    // Fallback is to get all nodes with the same name...
@@ -1082,13 +1082,16 @@
 	try{
 	    XPath xpath = xPathFactory.newXPath();
 	    if(contextNode != null){
-		xpath.setNamespaceContext(new NamespaceContextImpl(contextNode, "d"));
+		NamespaceContextImpl nsContext = new NamespaceContextImpl(contextNode, "d");
+		nsContext.setPrefix(MobyPrefixResolver.MOBY_XML_NAMESPACE, "d");
+		xpath.setNamespaceContext(nsContext);
 	    }
             peerElements = (NodeList) xpath.evaluate(peerGroupXPath, 
 						     doc, 
 						     XPathConstants.NODESET);
         } catch(Exception e){
             logger.log(Level.SEVERE, "Could not evaluate UserData XPath "+peerGroupXPath, e);
+	    return null;
         }
         //System.err.println("Got " + peerElements.getLength() + " peers for " + peerGroupXPath);
 



From gordonp at dev.open-bio.org  Mon Apr 26 16:26:18 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Mon, 26 Apr 2010 12:26:18 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004261626.o3QGQIZl025603@dev.open-bio.org>


gordonp
Mon Apr 26 12:26:18 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv25567/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	ServiceSearchDialog.java 
Log Message:
Case insensitive service name highlighting during search
moby-live/Java/src/main/ca/ucalgary/seahawk/gui ServiceSearchDialog.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/ServiceSearchDialog.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/ServiceSearchDialog.java	2010/04/24 17:23:27	1.1
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/ServiceSearchDialog.java	2010/04/26 16:26:18	1.2
@@ -127,6 +127,10 @@
 						Pattern.DOTALL | Pattern.CASE_INSENSITIVE | Pattern.MULTILINE);
 	activeChoices.clear();
 	for(JMenuItem serviceChoice: serviceChoices){
+	    if(serviceChoice.getText() == null){
+		continue;
+	    }
+	    
 	    String label = serviceChoice.getText().replaceAll("<.*?>", "").replaceAll("see description", "");
 	    // get rid of any coloring
 
@@ -134,12 +138,15 @@
 	    if(searchTerm == null || searchTerm.trim().length() == 0){
 		serviceChoice.setText(label);
 		activeChoices.addElement(serviceChoice);
+		continue;
 	    }
+	    Matcher matcher = searchPattern.matcher(label);
 	    // In the label?
-	    else if(serviceChoice.getText() != null &&
-		    searchPattern.matcher(label).find()){
-		label = label.replaceAll("("+searchTerm+")", "<font color='red'>$1</font>");
-		serviceChoice.setText("<html>"+label+"</html>");
+	    if(matcher.find()){
+		label = label.substring(0, matcher.start())+"<font color='red'>" +
+		    matcher.group(0) + "</font>" +
+		    (matcher.end() >= label.length() ? "" : label.substring(matcher.end()));
+		serviceChoice.setText("<html>" + label + "</html>");
 		activeChoices.addElement(serviceChoice);
 	    }
 	    // In the tooltip?



From gordonp at dev.open-bio.org  Mon Apr 26 16:27:31 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Mon, 26 Apr 2010 12:27:31 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004261627.o3QGRVV6025647@dev.open-bio.org>


gordonp
Mon Apr 26 12:27:31 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv25611/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	MobyServicesGUI.java 
Log Message:
Better UI refresh
moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyServicesGUI.java,1.23,1.24
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java,v
retrieving revision 1.23
retrieving revision 1.24
diff -u -r1.23 -r1.24
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java	2010/04/24 17:23:26	1.23
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java	2010/04/26 16:27:31	1.24
@@ -554,6 +554,7 @@
 	for(int i = 0; i < submenus.length; i++){
 	    addServicesToSubMenu(submenus[i], serviceAssocObjects[i], handler);
 	    addSearchItem(submenus[i], 1);
+	    refreshMenu(submenus[i]);
 	}
     }
 
@@ -755,6 +756,7 @@
 
 	addServicesToSubMenu(submenu, serviceAssocObject, handler);
         addSearchItem(submenu, 0);
+	refreshMenu(submenu);
     }
 
     protected synchronized void addServicesToSubMenu(JMenu submenu, MobyDataServiceAssocInstance msadi){
@@ -1121,7 +1123,9 @@
 	    }
 	    submenu.add(mobyItem);
 	}
+    }
 
+    protected void refreshMenu(JMenu submenu){
 	// Causes resizing based on new items
 	if(submenu.isPopupMenuVisible()){
 	    submenu.setPopupMenuVisible(false);



From gordonp at dev.open-bio.org  Mon Apr 26 16:28:11 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Mon, 26 Apr 2010 12:28:11 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004261628.o3QGSB9E025691@dev.open-bio.org>


gordonp
Mon Apr 26 12:28:11 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv25655/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	FilterSearchWidget.java 
Log Message:
Proper update of selected XPath when search restored
moby-live/Java/src/main/ca/ucalgary/seahawk/gui FilterSearchWidget.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/FilterSearchWidget.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/FilterSearchWidget.java	2010/04/10 00:40:17	1.3
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/FilterSearchWidget.java	2010/04/26 16:28:11	1.4
@@ -112,6 +112,7 @@
 
 	docPartOptions.setEnabled(true);
 	docPartOptions.setModel(new DefaultComboBoxModel(fs.getXPathOptions()));
+	docPartOptions.setSelectedItem(fs.getSelectedXPath());
 	currentFilterSearch = fs;  // done in this order so no feedback as DocumentEvents while setting fields programmatically
     }
 



From gordonp at dev.open-bio.org  Mon Apr 26 16:29:13 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Mon, 26 Apr 2010 12:29:13 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004261629.o3QGTD4M025779@dev.open-bio.org>


gordonp
Mon Apr 26 12:29:13 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv25739/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	MobyContentPane.java MobyPayloadCreator.java 
Log Message:
Account for possibility of null peer elements list
moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyContentPane.java,1.30,1.31 MobyPayloadCreator.java,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java,v
retrieving revision 1.30
retrieving revision 1.31
diff -u -r1.30 -r1.31
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java	2010/04/23 05:20:00	1.30
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java	2010/04/26 16:29:13	1.31
@@ -1237,7 +1237,7 @@
             // note that getPeerElements() will modify the userData to reflect the semantic of the requested peer mode
             mobyData.setUserData(origUserData);
             NodeList peerElements = DataUtils.getPeerElements(getCurrentDoc(), mobyData, getFilteredData(), peerMode);
-            if(peerElements.getLength() <= 1){
+            if(peerElements == null || peerElements.getLength() <= 1){
                 continue; // no 'for each' option if only one to process...
             }
             String each = "each <i>(" + peerElements.getLength() + " total)</i>";

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyPayloadCreator.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyPayloadCreator.java	2010/04/18 00:33:56	1.4
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyPayloadCreator.java	2010/04/26 16:29:13	1.5
@@ -85,8 +85,12 @@
 	NodeList peerElements = DataUtils.getPeerElements(doc, mobyDataContext, 
 							  xptrsToFilter, DataUtils.DATATYPE_PEERS_MODE);
 
-        // find the peers of defined by the userData selection constraints and put them into a MobyContentInstance
 	MobyContentInstance payload = new MobyContentInstance();
+	if(peerElements == null){
+	    return payload;
+	}
+
+        // find the peers of defined by the userData selection constraints and put them into a MobyContentInstance
         Map<String,Integer> jobPrefixes = new LinkedHashMap<String,Integer>();
 
 	logger.log(Level.FINE, "Loading MobyContentInstance with "+peerElements.getLength()+" elements for xpath "+selectionXPath);



From gordonp at dev.open-bio.org  Mon Apr 26 17:50:34 2010
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Mon, 26 Apr 2010 13:50:34 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201004261750.o3QHoXg0029187@dev.open-bio.org>


gordonp
Mon Apr 26 13:50:33 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv29151/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	FilterSearchWidget.java 
Log Message:
Kung foo with semaphores to let search filter only apply every 600ms or so when typing a longer string
moby-live/Java/src/main/ca/ucalgary/seahawk/gui FilterSearchWidget.java,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/FilterSearchWidget.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/FilterSearchWidget.java	2010/04/26 16:28:11	1.4
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/FilterSearchWidget.java	2010/04/26 17:50:33	1.5
@@ -5,6 +5,7 @@
 import java.awt.Dimension;
 import java.awt.event.*;
 import java.net.URL;
+import java.util.concurrent.*;
 import java.util.logging.*;
 import javax.swing.*;
 import javax.swing.event.*; 
@@ -22,6 +23,8 @@
     private JTextField searchField;
     private JComboBox docPartOptions;
     private MobyContentPane contentPane;
+    private Semaphore semaphore; // for search update delays in multikeystroke
+
     public static final String CASE_SENSITIVE_ICON_RESOURCE = "ca/ucalgary/seahawk/resources/images/case_sensitive.png";
     public static final String CASE_INSENSITIVE_ICON_RESOURCE = "ca/ucalgary/seahawk/resources/images/case_insensitive.png";
     private static final String IF_TEXT = "<html><u>if</u></html>";
@@ -48,6 +51,8 @@
 	closeIcon.addMouseListener(new Closer(this));
 	closeIcon.setToolTipText("Remove filter criteria");
 
+	semaphore = new Semaphore(1);  //1 search update for a given timeframe
+
 	Dimension buttonSize = new Dimension(24,24);
 	caseButton = new JToggleButton(new ImageIcon(cl.getResource(CASE_SENSITIVE_ICON_RESOURCE)));
 	caseButton.setDisabledIcon(new ImageIcon(cl.getResource(CASE_INSENSITIVE_ICON_RESOURCE)));
@@ -162,8 +167,10 @@
 	    return;
 	}
 	StringBuffer sb = currentFilterSearch.getFilterRegex();
-	sb.replace(0, sb.length(), searchField.getText());
-	contentPane.applyFilter(true);
+	synchronized(searchField){
+	    sb.replace(0, sb.length(), searchField.getText());
+	}
+	applyFilterWhenSuitable();
     }
 
     public void insertUpdate(DocumentEvent e){
@@ -171,8 +178,10 @@
 	    return;
 	}
 	StringBuffer sb = currentFilterSearch.getFilterRegex();
-	sb.replace(0, sb.length(), searchField.getText());
-	contentPane.applyFilter(true);
+	synchronized(searchField){
+	    sb.replace(0, sb.length(), searchField.getText());
+	}
+	applyFilterWhenSuitable();
     }
 
     public void removeUpdate(DocumentEvent e){
@@ -180,10 +189,53 @@
 	    return;
 	}
 	StringBuffer sb = currentFilterSearch.getFilterRegex();
-	sb.replace(0, sb.length(), searchField.getText());
-	contentPane.applyFilter(true);
+	synchronized(searchField){
+	    sb.replace(0, sb.length(), searchField.getText());
+	}
+	applyFilterWhenSuitable();
     }
 
+    // Waits 600 milliseconds to see if the user is typing a phrase, rather than 
+    // filtering for each letter added, which can be slow
+    private void applyFilterWhenSuitable(){
+	try{
+	    final Semaphore sem = semaphore;
+	    final MobyContentPane pane = contentPane;
+	    final JTextField sf = searchField;
+	    if(sem.tryAcquire()){
+		new Thread(){
+		    public void run(){
+			try{
+			    Thread.sleep(500);
+			}
+			catch(Exception e){
+			    logger.log(Level.WARNING, 
+				       "Delay less than 400ms on search input due to interrupt", 
+				       e);
+			}
+			synchronized(sf){
+			    try{
+				// Give 100ms for other threads past sb.replace() in DocumentListener callbacks to 
+				// try to acquire a permit, avoiding redundant applyFiolter call
+				Thread.sleep(100);
+			    }
+			    catch(Exception e){
+				logger.log(Level.WARNING, 
+					   "Delay less than 100ms on search input due to interrupt", 
+					   e);
+			    }
+			    pane.applyFilter(true);	
+			    sem.release();
+			}
+		    }
+		}.start();
+	    }
+	}catch(Exception e){
+	    logger.log(Level.SEVERE, "Search result updater was interrupted while waiting for a semaphore," +
+		                     "GUI may not reflect search field", e);
+	}
+	// else, it's going to be updated soon anyway with the latest string buffer...just return
+    }
 
     class Closer extends MouseAdapter{
 	boolean active = false;