<retrieveService>
<Service authURI="authority.URI.here" serviceName="MyService"/>
- <retrieveService>
+ </retrieveService>
<Service authURI="authority.URI.here" serviceName="MyService"
lsid='urn:lsid:authority.uri:serviceinstance:id'>
- <![CDATA[WSDL document here]]
+ <![CDATA[WSDL document here]]>
</Service>
From gordonp at dev.open-bio.org Thu Jun 7 19:55:42 2007
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Thu, 7 Jun 2007 19:55:42 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200706072355.l57Ntg5u025474@dev.open-bio.org>
gordonp
Thu Jun 7 19:55:42 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory dev.open-bio.org:/tmp/cvs-serv25439/src/main/org/biomoby/client
Modified Files:
CentralCachedCallsImpl.java
Log Message:
First stage commit of update: now concurrent requests for the sameCentral call are blocked, excepted for the first one
moby-live/Java/src/main/org/biomoby/client CentralCachedCallsImpl.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralCachedCallsImpl.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralCachedCallsImpl.java 2006/07/07 04:12:39 1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralCachedCallsImpl.java 2007/06/07 23:55:42 1.2
@@ -1,13 +1,15 @@
/**
* Implements the functionality of caching by reusing identical calls to
* MOBY central (e.g. asking multiple times what services take a DNA
- * sequence in the gi namespace).
+ * sequence in the gi namespace). This is an in-memory cache in CentralImpl,
+ * but a filesystem cache backs it up here, so calls can be cached between
+ * JVM instances.
*/
package org.biomoby.client;
import org.biomoby.shared.MobyException;
-import java.util.Properties;
+import java.util.*;
public class CentralCachedCallsImpl extends CentralImpl{
@@ -15,6 +17,8 @@
protected static final long THE_EPOCH = 0; // don't care when the call is made, it shouldn't affect the onto mapping of calls to IDs
protected static final Properties PROPERTIES = null; // don't have any properties for the call
+ protected Map$1<"); } - //else{ + else{ // Break up any really long DNA/AA stretches - htmlContents = htmlContents.replaceAll("([a-zA-Z]{60,})", "
$1"); - htmlContents = htmlContents.replaceAll("([a-zA-Z]{60})", "$1\n"); - //} + System.err.println("Trying to break up long streches"); + htmlContents = htmlContents.replaceAll("([a-zA-Z]{60})", "\n
"+
+ getInputStreamContents(url.openStream()).replaceAll("&", "&").replaceAll("<","<")+
+ "");
+ editorPane.setText(resultBuffer.toString());
}
else{
editorPane.setText(resultBuffer.toString());
@@ -322,6 +322,8 @@
}
// Regardless of the doc, scroll to a reference called "start:" if available.
// By default the pane will annoyingly scroll to the bottom when new data is loaded.
+ try{Thread.sleep(1000);} // Give it time to paint before scrolling
+ catch(Exception te){}
editorPane.scrollToReference("start");
}
catch (java.io.IOException ioe) {
@@ -385,11 +387,19 @@
* Called by MOBYRequest when the service request is being sent. We
* can create the GUI and wait message here.
*/
- public void start(MobyRequest request, int requestID){
+ public void start(MobyRequestEvent requestEvent){
hasFailed = false;
tabbedPane.setSelectedComponent(this);
- tabbedPane.setTitleAt(tabbedPane.indexOfComponent(this), ""+requestID+"-"+request.getService().getName());
+ tabbedPane.setTitleAt(tabbedPane.indexOfComponent(this),
+ ""+requestEvent.getID()+"-"+requestEvent.getService().getName());
setWaitScreen();
+ // Store the request being sent (w/ 2ndary params and all),
+ // for reference (e.g. when exporting a workflow)
+ try{
+ dataRecorder.saveInputData(requestEvent);
+ } catch(Exception e){
+ e.printStackTrace();
+ }
}
public void stop(MobyRequest request, int requestID){
@@ -474,6 +484,20 @@
return hasFailed;
}
+ public String toScufl() throws Exception{
+ URL[] historyToExport = (URL[]) history.toArray(new URL[history.size()]);
+ if(historyIndex != historyToExport.length-1){
+ // Shorten the array if we aren't cuurently on the last doc (i.e.
+ // we don't want to export documents forward in the history)
+ URL[] truncatedHistory = new URL[historyIndex];
+ System.arraycopy(historyToExport, 0, truncatedHistory, 0, historyIndex);
+ historyToExport = truncatedHistory;
+ }
+ ByteArrayOutputStream output = new ByteArrayOutputStream();
+ dataRecorder.exportWorkflow(historyToExport, output, DataRecorder.TAVERNA15);
+ return output.toString();
+ }
+
// Save the MOBY data to a file, then tell NewBrowser to load that local file URL
protected void loadDataInBrowser(MobyRequestEvent mre){
@@ -509,21 +533,12 @@
}
try {
- // Create temp file.
- File temp = File.createTempFile(serviceToFilePrefix(mobyRequest.getService()), ".xml");
-
- // Delete temp file when program exits.
- temp.deleteOnExit();
-
- // Write to temp file
- FileWriter out = new FileWriter(temp);
- out.write(mre.getContentsXML());
- out.close();
- gotoURL(temp.toURL(), true);
- } catch (IOException ioe) {
+ URL outputURL = dataRecorder.saveOutputData(mre);
+ gotoURL(outputURL, true);
+ } catch (Exception e) {
failed("Could not write a local file");
- editorPane.setText("ERROR: Could not write temporary file for MOBY results: " + ioe);
- ioe.printStackTrace();
+ editorPane.setText("ERROR: Could not write temporary file for MOBY results: " + e);
+ e.printStackTrace();
return;
}
succeeded(responseType);
@@ -821,12 +836,12 @@
}
if(mobyString != null){
- mobyData = new MobyDataString("", mobyString);
+ mobyData = new MobyDataString("", mobyString, SeahawkOptions.getRegistry());
}
else{
- mobyData = new MobyDataObject("");
+ mobyData = new MobyDataObject("", SeahawkOptions.getRegistry());
}
- mobyData.addNamespace(MobyNamespace.getNamespace(namespace));
+ mobyData.addNamespace(MobyNamespace.getNamespace(namespace, SeahawkOptions.getRegistry()));
if(mobyID != null){
mobyData.setId(mobyID);
@@ -952,8 +967,8 @@
* This method tries to figure out what kinds of MOBY Data could be
* created from the string given. e.g. Keywords, DNASequence, etc.
*/
- protected MobyDataInstance[] loadMobyDataFromString(String data, boolean reverseSelected){
- return MobyUtils.convertStringToObjects(data, reverseSelected);
+ protected MobyDataInstance[] loadMobyDataFromString(String data){
+ return MobyUtils.convertStringToObjects(data);
}
public boolean isMobyURL(URL u){
@@ -964,8 +979,8 @@
// MouseListener interface implementation
public void mouseClicked(MouseEvent e){
// Allow middle button paste
- if(e.getButton() == MouseEvent.BUTTON3 ||
- e.getButton() == MouseEvent.BUTTON2 && e.isAltDown()){
+ if(e.getButton() == MouseEvent.BUTTON2 ||
+ e.getButton() == MouseEvent.BUTTON3 && e.isAltDown()){
paste();
}
}
@@ -999,7 +1014,7 @@
if(selectedTextData == null){
return;
}
- MobyDataInstance[] mobyData = loadMobyDataFromString(selectedTextData, mark > dot);
+ MobyDataInstance[] mobyData = loadMobyDataFromString(selectedTextData);
if(mobyData == null || mobyData.length == 0){
logger.warn("No MobyData could be made from the selected text");
return;
@@ -1066,111 +1081,6 @@
status.setText("Click your selection to use as MOBY data!");
}
- private MobyService getService(int index) throws Exception{
- String filename = ((URL) history.elementAt(index)).getPath();
- if(filename.lastIndexOf('/') != -1){
- filename = filename.substring(filename.lastIndexOf('/')+1);
- }
- return filePrefixToService(filename);
- }
-
- private String getScuflProcessor(int index) throws Exception{
- MobyService service = getService(index);
-
- if(service == null){ //data was loaded from file, not from a service
- return "";
- }
-
- StringBuffer secondaryParams = new StringBuffer();
- // example input + The easiest way to create data is to simply drag a file, text selection, or Web link + onto the Seahawk interface. Seahawk will try to display the data you drop. +
+Click the folder/Web icon on the bottom toolbar will give you the option of @@ -64,14 +70,13 @@ With the mouse, you can highlight arbitrary sections of text in the Seahawk display. Clicking within selected text will raise a popup menu showing MOBY service options. Seahawk will try to determine the type of data highlighted are - potentially show services for the selection as a: + potentially show services for the selection as a, among other things:
+Please help us improve Seahawk by completing a user survey! +