Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362011-06-03T19:12:21ZEcoinformatics Redmine
Redmine Bug #5420 (Resolved): Two types of NPE issues when 2.2.0 installed and run by a non-admin windows...https://projects.ecoinformatics.org/ecoinfo/issues/54202011-06-03T19:12:21ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>In Windows XP I installed 2.2.0 using a non-admin user account and get NPEs when trying to do a component search or when clicking on the Sources button.</p>
<p>As background: during installation you're prompted as to which user you want to install as. I installed as this non-admin user, and since this user can't write to Program Files, I installed into a directory in this user's home dir (Documents and Settings\etc). Also, XP gives you an option to "protect my computer and data from unauthorized program activity" when installing -- I unchecked this, in hopes of avoiding any issues.</p>
<p>As this non-admin user, I also tried installing in a different way - when prompted on which user to install as, I installed into Program Files as an admin user. Surprisingly the two types of NPEs still occur.</p>
<p>When you try to do a Component Search, you get:</p>
<p>java.lang.NullPointerException<br /> at org.kepler.gui.SimpleLibrarySearcher.search(SimpleLibrarySearcher.java:172)<br /> at org.kepler.gui.ComponentLibraryTab$SearchButtonActionHandler.actionPerformed(ComponentLibraryTab.java:437)<br /> at org.kepler.gui.SimpleSearchUIPane$1.actionPerformed(SimpleSearchUIPane.java:91)<br /> at javax.swing.JTextField.fireActionPerformed(Unknown Source)<br /> at javax.swing.JTextField.postActionEvent(Unknown Source)<br /> at javax.swing.JTextField$NotifyAction.actionPerformed(Unknown Source)<br /> at javax.swing.SwingUtilities.notifyAction(Unknown Source)<br /> at javax.swing.JComponent.processKeyBinding(Unknown Source)<br /> at javax.swing.JComponent.processKeyBindings(Unknown Source)<br /> at javax.swing.JComponent.processKeyEvent(Unknown Source)<br /> at java.awt.Component.processEvent(Unknown Source)<br /> at java.awt.Container.processEvent(Unknown Source)<br /> at java.awt.Component.dispatchEventImpl(Unknown Source)<br /> at java.awt.Container.dispatchEventImpl(Unknown Source)<br /> at java.awt.Component.dispatchEvent(Unknown Source)<br /> at java.awt.KeyboardFocusManager.redispatchEvent(Unknown Source)<br /> at java.awt.DefaultKeyboardFocusManager.dispatchKeyEvent(Unknown Source)<br /> at java.awt.DefaultKeyboardFocusManager.preDispatchKeyEvent(Unknown Source)<br /> at java.awt.DefaultKeyboardFocusManager.typeAheadAssertions(Unknown Source)<br /> at java.awt.DefaultKeyboardFocusManager.dispatchEvent(Unknown Source)<br /> at java.awt.Component.dispatchEventImpl(Unknown Source)<br /> at java.awt.Container.dispatchEventImpl(Unknown Source)<br /> at java.awt.Window.dispatchEventImpl(Unknown Source)<br /> at java.awt.Component.dispatchEvent(Unknown Source)<br /> at java.awt.EventQueue.dispatchEventImpl(Unknown Source)<br /> at java.awt.EventQueue.access$000(Unknown Source)<br /> at java.awt.EventQueue$1.run(Unknown Source)<br /> at java.awt.EventQueue$1.run(Unknown Source)<br /> at java.security.AccessController.doPrivileged(Native Method)<br /> at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)<br /> at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)<br /> at java.awt.EventQueue$2.run(Unknown Source)<br /> at java.awt.EventQueue$2.run(Unknown Source)<br /> at java.security.AccessController.doPrivileged(Native Method)<br /> at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)<br /> at java.awt.EventQueue.dispatchEvent(Unknown Source)<br /> at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)<br /> at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)<br /> at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)<br /> at java.awt.EventDispatchThread.pumpEvents(Unknown Source)<br /> at java.awt.EventDispatchThread.pumpEvents(Unknown Source)<br /> at java.awt.EventDispatchThread.run(Unknown Source)</p>
<p>When you click the Sources button, you get:</p>
<p>Could not create data pane.: null<br />null</p>
<p>java.lang.NullPointerException<br /> at org.kepler.objectmanager.repository.RepositoryManager.<init>(RepositoryManager.java:129)<br /> at org.kepler.objectmanager.repository.RepositoryManager.getInstance(RepositoryManager.java:242)<br /> at org.kepler.gui.ComponentLibraryPreferencesTab.initializeTab(ComponentLibraryPreferencesTab.java:131)<br /> at org.kepler.gui.PreferencesTabFactory.createPreferencesTabs(PreferencesTabFactory.java:115)<br /> at org.kepler.gui.PreferencesFrame.initTabs(PreferencesFrame.java:126)<br /> at org.kepler.gui.PreferencesFrame.<init>(PreferencesFrame.java:100)<br /> at org.kepler.gui.PreferencesFrame.<init>(PreferencesFrame.java:75)<br /> at org.kepler.gui.PreferencesAction.actionPerformed(PreferencesAction.java:92)<br /> at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)<br /> at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)<br /> at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)<br /> at javax.swing.DefaultButtonModel.setPressed(Unknown Source)<br /> at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source)<br /> at java.awt.Component.processMouseEvent(Unknown Source)<br /> at javax.swing.JComponent.processMouseEvent(Unknown Source)<br /> at java.awt.Component.processEvent(Unknown Source)<br /> at java.awt.Container.processEvent(Unknown Source)<br /> at java.awt.Component.dispatchEventImpl(Unknown Source)<br /> at java.awt.Container.dispatchEventImpl(Unknown Source)<br /> at java.awt.Component.dispatchEvent(Unknown Source)<br /> at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)<br /> at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)<br /> at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)<br /> at java.awt.Container.dispatchEventImpl(Unknown Source)<br /> at java.awt.Window.dispatchEventImpl(Unknown Source)<br /> at java.awt.Component.dispatchEvent(Unknown Source)<br /> at java.awt.EventQueue.dispatchEventImpl(Unknown Source)<br /> at java.awt.EventQueue.access$000(Unknown Source)<br /> at java.awt.EventQueue$1.run(Unknown Source)<br /> at java.awt.EventQueue$1.run(Unknown Source)<br /> at java.security.AccessController.doPrivileged(Native Method)<br /> at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)<br /> at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)<br /> at java.awt.EventQueue$2.run(Unknown Source)<br /> at java.awt.EventQueue$2.run(Unknown Source)<br /> at java.security.AccessController.doPrivileged(Native Method)<br /> at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)<br /> at java.awt.EventQueue.dispatchEvent(Unknown Source)<br /> at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)<br /> at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)<br /> at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)<br /> at java.awt.EventDispatchThread.pumpEvents(Unknown Source)<br /> at java.awt.EventDispatchThread.pumpEvents(Unknown Source)<br /> at java.awt.EventDispatchThread.run(Unknown Source)</p> Bug #5396 (Resolved): rename ptolemy-8.1.0 module for the kepler 2.2 releasehttps://projects.ecoinformatics.org/ecoinfo/issues/53962011-05-05T23:44:11ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Christopher mentioned that the next ptolemy release might be called 8.1, and so he'd prefer kepler-2.2 name the included ptolemy module ptolemy-8.0.2 (why 8.0.2 and not 8.0.1, Christopher?).</p> Bug #5352 (Resolved): build-area-2.1 is not working and build-area-2.2 is needed for kepler-2.2 r...https://projects.ecoinformatics.org/ecoinfo/issues/53522011-03-15T20:56:47Zjianwu jianwujianwu@sdsc.edu
<p>I didn't see build-area-2.2 module for kepler-2.2 at <a class="external" href="https://code.kepler-project.org/code/kepler/releases/release-branches/">https://code.kepler-project.org/code/kepler/releases/release-branches/</a> or <a class="external" href="https://code.kepler-project.org/code/kepler/releases/released/">https://code.kepler-project.org/code/kepler/releases/released/</a>. When I tried to use <a class="external" href="https://code.kepler-project.org/code/kepler/releases/release-branches/build-area-2.1/">https://code.kepler-project.org/code/kepler/releases/release-branches/build-area-2.1/</a>, I got the following exception. Since kepler trunk is ever changing, we'd better have a build-area-2.2 module for kepler 2.2 release.</p>
<p>kepler:build-area-2.1 jianwu$ svn info<br />Path: .<br />URL: <a class="external" href="https://code.kepler-project.org/code/kepler/releases/release-branches/build-area-2.1">https://code.kepler-project.org/code/kepler/releases/release-branches/build-area-2.1</a><br />Repository Root: <a class="external" href="https://code.kepler-project.org/code/kepler">https://code.kepler-project.org/code/kepler</a><br />Repository UUID: edc41a2b-3e5c-0410-9d3f-8540a70682f1<br />Revision: 27291<br />Node Kind: directory<br />Schedule: normal<br />Last Changed Author: welker<br />Last Changed Rev: 26871<br />Last Changed Date: 2011-01-31 14:25:53 -0800 (Mon, 31 Jan 2011)</p>
<p>kepler:build-area-2.1 jianwu$ ant<br />Buildfile: /Users/jianwu/Kepler/repository/kepler/kepler-branch-2.2/build-area-2.1/build.xml</p>
<p>BUILD FAILED<br />/Users/jianwu/Kepler/repository/kepler/kepler-branch-2.2/build-area-2.1/build.xml:4: The following error occurred while executing this line:<br />/Users/jianwu/Kepler/repository/kepler/kepler-branch-2.2/build-area-2.1/settings/taskdefs.xml:5: typedef class org.kepler.build.Get cannot be found<br /> using the classloader AntClassLoader[]</p>
<p>Total time: 0 seconds</p> Bug #5346 (Resolved): Kepler 2.2r3 Mac OS 64-bit Matlab demo fails with 'no suitable image found'https://projects.ecoinformatics.org/ecoinfo/issues/53462011-03-09T01:49:28ZChristopher Brookscxh@eecs.berkeley.edu
<p>Under the Kepler-2.2r3 dmg installer, Mac OS X 10.5 with 64bit Java,<br />The Matlab demo at<br />Help <del>> Kepler Documentation -> background information about Ptolemy<br /></del>> Documentation -> Complete list of demos -> SDF -> Matlab<br />fails.</p>
<p>My ~/.MacOSX/environment.plist contains:</p>
<p>{<br /> "DYLD_LIBRARY_PATH" = "/Users/cxh/ptII/vendors/misc/dbxml-2.5.16/install/lib:/Applications/MATLA\<br />B_R2009b.app/sys/os/maci64/:/Applications/MATLAB_R2009b.app/sys/os/maci";<br /> "New item" = "";<br /> PATH = "/Users/cxh/ptII/vendors/misc/dbxml-2.5.16/install/bin:/Users/cxh/bin:/Users/cxh/ptII/bin\<br />:/usr/local/apache-maven/bin:/opt/subversion/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/texbi\<br />n:/usr/X11/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/texbin:/usr/local/texlive/2007/bin";<br />}</p>
<p>Tools -> Check System Variables says:</p>
<p>java.version = 1.6.0_22<br />java.vm.info = mixed mode<br />java.vm.name = Java HotSpot(TM) 64-Bit Server VM</p>
<p>The error is:</p>
ptolemy.kernel.util.IllegalActionException: There was a problem invoking the Ptolemy II Matlab interface.<br />The interface has been tested under Linux, Mac OS X, and Windows.<br />The interface requires that Matlab be installed on the local machine and that the ptmatlab shared library available.
<ul>
<li>Under Linux, you must have the LD_LIBRARY_PATH environment variable set to include the directories that contain libmx.so and libptmatlab.so.</li>
<li>Under Mac OS X, you must have the DYLD_LIBRARY_PATH environment variable set to include the directories that contain libmx.dylib and libptmatlab.jnilib.</li>
<li>Under Windows, you must have your PATH set to include the Matlab bin/win32 or equivalent directory so that libmex.dll is found and the directory that contains libptmatlab.dll. In addition, if you are running under Windows from the Cygwin bash prompt, then you must start Vergil with the -jni argument: $PTII/bin/vergil -jni. For details, see $PTII/jni/package.html.<br />Refer to $PTII/ptolemy/matlab/makefile for more information.<br /> in .MatlabExpression.MatlabExpression<br />Because:<br />/Applications/Kepler-2.2rc3/Kepler.app/Contents/Resources/Java/common-2.2.0/lib/ptolemy/matlab/libptmatlab.jnilib: no suitable image found. Did find: /Applications/Kepler-2.2rc3/Kepler.app/Contents/Resources/Java/common-2.2.0/lib/ptolemy/matlab/libptmatlab.jnilib: unknown required load command 0x80000022<br /> at ptolemy.matlab.Expression.preinitialize(Expression.java:263)<br /> at ptolemy.actor.Director.preinitialize(Director.java:1010)<br /> at ptolemy.actor.Director.preinitialize(Director.java:991)<br /> at ptolemy.domains.sdf.kernel.SDFDirector.preinitialize(SDFDirector.java:647)<br /> at ptolemy.actor.CompositeActor.preinitialize(CompositeActor.java:1735)<br /> at ptolemy.actor.Manager.preinitializeAndResolveTypes(Manager.java:983)<br /> at ptolemy.actor.Manager.initialize(Manager.java:643)<br /> at ptolemy.actor.Manager.execute(Manager.java:340)<br /> at ptolemy.actor.Manager.run(Manager.java:1164)<br /> at ptolemy.actor.Manager$3.run(Manager.java:1217)<br />Caused by: java.lang.UnsatisfiedLinkError: /Applications/Kepler-2.2rc3/Kepler.app/Contents/Resources/Java/common-2.2.0/lib/ptolemy/matlab/libptmatlab.jnilib: no suitable image found. Did find: /Applications/Kepler-2.2rc3/Kepler.app/Contents/Resources/Java/common-2.2.0/lib/ptolemy/matlab/libptmatlab.jnilib: unknown required load command 0x80000022<br /> at java.lang.ClassLoader$NativeLibrary.load(Native Method)<br /> at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1823)<br /> at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1699)<br /> at java.lang.Runtime.load0(Runtime.java:770)<br /> at java.lang.System.load(System.java:1020)<br /> at ptolemy.data.expr.UtilityFunctions._loadLibrary(UtilityFunctions.java:1985)<br /> at ptolemy.data.expr.UtilityFunctions.loadLibrary(UtilityFunctions.java:847)<br /> at ptolemy.matlab.Engine.<clinit>(Engine.java:176)<br /> at ptolemy.matlab.Expression.preinitialize(Expression.java:260)<br /> ... 9 more<br />Caused by: java.lang.UnsatisfiedLinkError: /Applications/Kepler-2.2rc3/Kepler.app/Contents/Resources/Java/common-2.2.0/lib/ptolemy/matlab/libptmatlab.jnilib: no suitable image found. Did find: /Applications/Kepler-2.2rc3/Kepler.app/Contents/Resources/Java/common-2.2.0/lib/ptolemy/matlab/libptmatlab.jnilib: unknown required load command 0x80000022<br /> at java.lang.ClassLoader$NativeLibrary.load(Native Method)<br /> at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1823)<br /> at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1699)<br /> at java.lang.Runtime.load0(Runtime.java:770)<br /> at java.lang.System.load(System.java:1020)<br /> at ptolemy.data.expr.UtilityFunctions._loadLibrary(UtilityFunctions.java:1985)<br /> at ptolemy.data.expr.UtilityFunctions.loadLibrary(UtilityFunctions.java:847)<br /> at ptolemy.matlab.Engine.<clinit>(Engine.java:176)<br /> at ptolemy.matlab.Expression.preinitialize(Expression.java:260)<br /> at ptolemy.actor.Director.preinitialize(Director.java:1010)<br /> at ptolemy.actor.Director.preinitialize(Director.java:991)<br /> at ptolemy.domains.sdf.kernel.SDFDirector.preinitialize(SDFDirector.java:647)<br /> at ptolemy.actor.CompositeActor.preinitialize(CompositeActor.java:1735)<br /> at ptolemy.actor.Manager.preinitializeAndResolveTypes(Manager.java:983)<br /> at ptolemy.actor.Manager.initialize(Manager.java:643)<br /> at ptolemy.actor.Manager.execute(Manager.java:340)<br /> at ptolemy.actor.Manager.run(Manager.java:1164)<br /> at ptolemy.actor.Manager$3.run(Manager.java:1217)</li>
</ul> Bug #5334 (Resolved): 2.2 rc3: kepler.sh file is not executable by default in Kepler.app/Contents...https://projects.ecoinformatics.org/ecoinfo/issues/53342011-03-01T23:52:08Zjianwu jianwujianwu@sdsc.edu
<p>I think many users need to use kepler.sh or kepler.bat to get console information. But in my installation on mac, Kepler.app/Contents/Resources/Java/kepler.sh is not executable. I have to change mode to run it.</p> Bug #5331 (Resolved): Errors in Help->Kepler Documentation page at kepler 2.2 rc3.https://projects.ecoinformatics.org/ecoinfo/issues/53312011-03-01T19:23:43Zjianwu jianwujianwu@sdsc.edu
<p>Two errors in the page:<br />1) The user mailing list at the end of the first paragraph should be <a class="email" href="mailto:kepler-users@kepler-project.org">kepler-users@kepler-project.org</a>, not <a class="email" href="mailto:kepler-users@ecoinformatics.org">kepler-users@ecoinformatics.org</a>. <br />2) contributors after 2007-09-25 are not included.</p> Bug #5328 (Resolved): 2.2rc2 - standalone module manager won't starthttps://projects.ecoinformatics.org/ecoinfo/issues/53282011-02-26T01:40:00ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>On mac 10.6 and windows XP, both with java 1.6, I can't get the standalone module manager application to start. On windows I tried both shortcuts and the executable itself. I didn't have this problem in the last rc.</p> Bug #5326 (Resolved): 2.2rc2 - upgrade config file bug workaround moves KeplerData/modules to Kep...https://projects.ecoinformatics.org/ecoinfo/issues/53262011-02-25T22:03:56ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>The workflow-around for the configuration file bug is to move a user's existing KeplerData/modules to KeplerData/modules.old during the first launch of 2.2. However I think we should instead just do something along the lines of moving each module's configuration dir to a configuration.old. The issue is that more than just config files reside in KeplerData/modules. E.g. the coreDB and provenance databases.</p> Bug #5325 (Resolved): 2.2rc2 - documentation problemshttps://projects.ecoinformatics.org/ecoinfo/issues/53252011-02-25T21:26:09ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>1) Most links in the pdfs don't work - you just see blue text.</p>
<p>2) User Manual Section 6 doesn't include changes to 6.0WorkingWithDatasets.doc. My guess is you didn't build the user manual from the individual chapters but instead edited a copy of the 2.1.0 version (?). If you're taking that route, you'll have to be careful with keeping TOC in sync and include changes from other files more recent than 2.1.0 docs:</p>
<p><del>rw-r--r-</del> 1 derik derik 28614618 Sep 28 13:13 KeplerUserManual-2.1.0.pdf<br /><del>rw-r--r-</del> 1 derik derik 27385066 Sep 28 13:13 KeplerUserManual-2.1.0.doc<br /><del>rw-r--r-</del>@ 1 derik derik 2173091 Jan 11 13:53 6.0WorkingWithDatasets.doc<br /><del>rw-r--r-</del> 1 derik derik 214528 Jan 19 13:07 A.BModules.doc<br /><del>rw-r--r-</del> 1 derik derik 28160 Feb 22 17:15 Title Page.doc</p>
<p>3) Remote Copy links of Getting Started Guide and Actor Reference link to 1.0.0 versions.</p>
<p>4) Copyright link to copyright.htm is 2003-2010. Should update to 2011.</p> Bug #5318 (Resolved): 2.2.0 release testinghttps://projects.ecoinformatics.org/ecoinfo/issues/53182011-02-23T00:03:50ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>David asked me to create a list of less obvious things to test for 2.2. Obviously this isn't comprehensive; please test other things as you go.</p>
<p>Note: you have to download the installer for 2.2; upgrading to 2.2 via the module manager within 2.1 or 2.0 will not work. Also note the 2.2 installer includes a standalone Module Manager app.</p>
<p>Test Kepler 2.0.0 to 2.2.0 transition:<br />---------------<br />Developers, remove any trunk generated artifacts: rm -rf ~/.keeper ~/KeplerData;<br />Start Kepler-2.0.0 installed on your machine from the 2.0 installer.<br />Components=>Sources=>check-mark the kepler repository as a Search item. This will cause a write of ~/KeplerData/modules/repository/configuration/configuration.xml.<br />Test Components search. Use <a class="external" href="http://kepler-dev.nceas.ucsb.edu/kepler/">http://kepler-dev.nceas.ucsb.edu/kepler/</a> to verify your results.<br />Test Data search. E.g. for aphid. Drag out a data source.<br />Create a simple workflow, e.g. SDF w/ 1 iteration, String Constant=>Display. Execute. Save to kar. Export to xml.<br />Quit 2.0.0. <br />Install 2.2.0 from the 2.2 installer.<br />Launch 2.2.0, click the Sources button. Verify this dialog comes up, and that your old, incompatible config file(s) in KeplerData have been moved out of the way, into a separate directory.<br />Navigate to Sources=>Preferences=>KAR Preferences and select strict.<br />Attempt to open the kar you saved in 2.0.0. Obligue the dialog, restart into 2.0.0.<br />A known limitation is that to return to 2.2.0 you should not use the Module Manager inside Kepler, use the standalone Module Manager application that ships with 2.2.0 to restart into 2.2.0.</p>
<p>Test Kepler 2.1.0 to 2.2.0 transition.<br />--------------------<br />Similar to above, but first upgrade your installed version of 2.0.0 to kepler-2.1.0 and/or reporting-2.1.0 via the 2.0.0 module manager. <br />Create a reporting 2.1.0 kar by exporting a run from the Workflow Run Manager. Attempt to open this kar from 2.2.0 in Strict mode, etc.</p>
Misc 2.2 tests:<br />----------------
<ul>
<li>Test the built in Module Manager.</li>
<li>Test each OS Installer.</li>
<li>Test all outreach demos.</li>
<li>Check Help=>About version number. Check Help=>Kepler Documentation -- test all links.</li>
<li>Create, save, right-click rename on canvas, export, run and open a workflow.</li>
<li>Search the Kepler repository via Components tab.</li>
<li>Search for remote data using Data tab.</li>
<li>Right-click on a kar and upload to the Kepler repository -- ideally the workflow has documentation, serves as a good example, and may be left on the repository for users, otherwise subsequently delete it. Contact myself, jing or ben for help deleting.</li>
<li>Outline tab - drag a workflow component out to canvas. Then delete it.</li>
</ul> Bug #5312 (Resolved): updating windowsXP installed 2.0.0 straight to 2.2.0 renders Kepler unable ...https://projects.ecoinformatics.org/ecoinfo/issues/53122011-02-15T22:57:34ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>On Windows XP, I had a Kepler-2.0 installed version. Using the module manager, I updated to kepler-2.2.0, skipping kepler-2.1.0. The modules downloaded, and kepler quit, and now I'm unable to start kepler again.</p> Bug #5311 (Resolved): 2.2.0rc1 - remote data sources don't workhttps://projects.ecoinformatics.org/ecoinfo/issues/53112011-02-15T21:56:43ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>In 2.2.0rc1 installed from the installer, remote data sources don't work. <br />I discovered this when trying to open PythonGenericDialog.xml demo workflow.<br />It also happens when you search the Data tab and try to drag out a data source.</p>
<p>The error message you see comes from EcogridDataCacheItem and is:<br />There has been a problem accessing the remote data<br />java.lang.String cannot be cast to [B</p>
<p>This doesn't appear to happen from trunk, or from 2.2.0 launched from the module manager. I'm not clear on why this is...</p> Bug #5310 (Resolved): 2.2.0rc1 - Documentation link problemshttps://projects.ecoinformatics.org/ecoinfo/issues/53102011-02-15T21:36:57ZDerik Barseghianbarseghian@nceas.ucsb.edu
Some issues with Help->Documentation in 2.2.0rc1:
<ul>
<li>None of the Local Copy links to documentation (at Help->Kepler Documentation) work.</li>
<li>The Remote Copy links point to 1.0 docs.</li>
<li>The workflow links don't work</li>
</ul> Bug #5309 (Resolved): 2.2.0rc1 - Preferences and Components Search (configuration) issuehttps://projects.ecoinformatics.org/ecoinfo/issues/53092011-02-15T21:34:41ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>I've given the mac installer a try and I've run into the configuration file issue - my ~/KeplerData/repository/configuration/configuration.xml does not contain the new properties authorizationPath or authenticatedquerypath and I get errors as a result. I also don't see old versions of my configuration files -- I believe the workaround that you implemented for <a class="external" href="http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5129">http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5129</a> was that the old configs are supposed to be moved out of the way on the first startup of 2.2.</p>
<p>Here's what I did:<br />cd ~/kepler.modules/build-area/; ant clean-all; rm -rf ~/KeplerData;<br />Start up previously installed Kepler 2.1.0 from Applications<br />Change my Components Sources to search the Kepler repository<br />Change Kar Preferences to Strict<br />Search for sdf. Create and run a simple workflow<br />Quit<br />Start installer 2.2.0rc1 from Applications<br />Clicking on the Sources button gives the below error. Attempting to search Components also gives an error.</p> Bug #5098 (Resolved): Save Archive (KAR)... will have exception when internet is not accessible.https://projects.ecoinformatics.org/ecoinfo/issues/50982010-07-19T22:30:21Zjianwu jianwujianwu@sdsc.edu
<p>Found by Chris Weed, I can reproduce it.</p>
<p>It happens when I right-click the actor, choose 'Save Archive (KAR)...' and try to save its kar file, no matter whether I choose 'Add Semantic Types' or not. </p>
<pre><code>[null] done writing KAR file to C:\Users\jianwu\KeplerData\workflows\MyWorkflows\ttt.kar<br /> [null] java.net.UnknownHostException: ptolemy.eecs.berkeley.edu<br /> [null] at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:177)<br /> [null] at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:366)<br /> [null] at java.net.Socket.connect(Socket.java:529)<br /> [null] at java.net.Socket.connect(Socket.java:478)<br /> [null] at sun.net.NetworkClient.doConnect(NetworkClient.java:163)<br /> [null] at sun.net.www.http.HttpClient.openServer(HttpClient.java:394)<br /> [null] at sun.net.www.http.HttpClient.openServer(HttpClient.java:529)<br /> [null] at sun.net.www.http.HttpClient.&lt;init&gt;(HttpClient.java:233)<br /> [null] at sun.net.www.http.HttpClient.New(HttpClient.java:306)<br /> [null] at sun.net.www.http.HttpClient.New(HttpClient.java:323)<br /> [null] at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:860)<br /> [null] at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:801)<br /> [null] at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:726)<br /> [null] at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1049)<br /> [null] at org.apache.xerces.impl.XMLEntityManager.setupCurrentEntity(Unknown Source)<br /> [null] at org.apache.xerces.impl.XMLEntityManager.startEntity(Unknown Source)<br /> [null] at org.apache.xerces.impl.XMLEntityManager.startDTDEntity(Unknown Source)<br /> [null] at org.apache.xerces.impl.XMLDTDScannerImpl.setInputSource(Unknown Source)<br /> [null] at org.apache.xerces.impl.XMLDocumentScannerImpl$DTDDispatcher.dispatch(Unknown Source)<br /> [null] at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)<br /> [null] at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)<br /> [null] at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)<br /> [null] at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)<br /> [null] at org.apache.xerces.parsers.DOMParser.parse(Unknown Source)<br /> [null] at org.apache.xerces.jaxp.DocumentBuilderImpl.parse(Unknown Source)<br /> [null] at org.kepler.moml.KeplerMetadataExtractor.extractActorMetadata(KeplerMetadataExtractor.java:101)<br /> [null] at org.kepler.objectmanager.cache.ActorCacheObject.&lt;init&gt;(ActorCacheObject.java:141)<br /> [null] at org.kepler.kar.handlers.ActorMetadataKAREntryHandler.cache(ActorMetadataKAREntryHandler.java:169)<br /> [null] at org.kepler.kar.KARFile.cache(KARFile.java:876)<br /> [null] at org.kepler.kar.KARFile.cacheKARContents(KARFile.java:591)<br /> [null] at org.kepler.kar.SaveKAR.saveToCache(SaveKAR.java:184)<br /> [null] at org.kepler.gui.kar.ExportArchiveAction.actionPerformed(ExportArchiveAction.java:344)<br /> [null] at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995)<br /> [null] at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318)<br /> [null] at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)<br /> [null] at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)<br /> [null] at javax.swing.AbstractButton.doClick(AbstractButton.java:357)<br /> [null] at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1223)<br /> [null] at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1264)<br /> [null] at java.awt.Component.processMouseEvent(Component.java:6263)<br /> [null] at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)<br /> [null] at java.awt.Component.processEvent(Component.java:6028)<br /> [null] at java.awt.Container.processEvent(Container.java:2041)<br /> [null] at java.awt.Component.dispatchEventImpl(Component.java:4630)<br /> [null] at java.awt.Container.dispatchEventImpl(Container.java:2099)<br /> [null] at java.awt.Component.dispatchEvent(Component.java:4460)<br /> [null] at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4574)<br /> [null] at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238)<br /> [null] at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168)<br /> [null] at java.awt.Container.dispatchEventImpl(Container.java:2085)<br /> [null] at java.awt.Window.dispatchEventImpl(Window.java:2478)<br /> [null] at java.awt.Component.dispatchEvent(Component.java:4460)<br /> [null] at java.awt.EventQueue.dispatchEvent(EventQueue.java:599)<br /> [null] at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)<br /> [null] at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)<br /> [null] at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)<br /> [null] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)<br /> [null] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)<br /> [null] at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)<br /> [null] Error parsing Actor KAR DOM "<?xml version="1.0"?><br /> [null] &lt;!DOCTYPE entity PUBLIC "-//UC Berkeley//DTD MoML 1//EN" <br /> [null] "http://ptolemy.e...": ptolemy.eecs.berkeley.edu<br /> [null] WARN (org.kepler.objectmanager.cache.CacheManager:insertObject:237)<br /> KAREntry has no lsid: null</code></pre>
<pre><code>It has similar exception when proxy is needed to access internet. The problem Chris found is as follows.</code></pre>
<p>I think the problem I am having is that it is trying to validate the XML against<br /><a class="external" href="http://ptolemy.eecs.berkeley.edu/xml/dtd/MoML_1.dtd">http://ptolemy.eecs.berkeley.edu/xml/dtd/MoML_1.dtd</a>, and my proxy<br />is probably in the way. Although I set the proxy in the kepler.bat file on the<br />command-line. I am not sure why it isn't going through.<br />Chris</p>
<p>[null] java.net.ConnectException: Connection timed out: connect<br />[null] at java.net.PlainSocketImpl.socketConnect(Native Method)<br />[null] at java.net.PlainSocketImpl.doConnect(Unknown Source)<br />[null] at java.net.PlainSocketImpl.connectToAddress(Unknown Source)<br />[null] at java.net.PlainSocketImpl.connect(Unknown Source)<br />[null] at java.net.SocksSocketImpl.connect(Unknown Source)<br />[null] at java.net.Socket.connect(Unknown Source)<br />[null] at java.net.Socket.connect(Unknown Source)<br />[null] at sun.net.NetworkClient.doConnect(Unknown Source)<br />[null] at sun.net.www.http.HttpClient.openServer(Unknown Source)<br />[null] at sun.net.www.http.HttpClient.openServer(Unknown Source)<br />[null] at sun.net.www.http.HttpClient.<init>(Unknown Source)<br />[null] at sun.net.www.http.HttpClient.New(Unknown Source)<br />[null] at sun.net.www.http.HttpClient.New(Unknown Source)<br />[null] at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(<br />Unknown Source)<br />[null] at sun.net.www.protocol.http.HttpURLConnection.plainConnect(Unkn<br />own Source)<br />[null] at sun.net.www.protocol.http.HttpURLConnection.connect(Unknown S<br />ource)<br />[null] at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Un<br />known Source)<br />[null] at org.apache.xerces.impl.XMLEntityManager.setupCurrentEntity(Un<br />known Source)<br />[null] at org.apache.xerces.impl.XMLEntityManager.startEntity(Unknown S<br />ource)<br />[null] at org.apache.xerces.impl.XMLEntityManager.startDTDEntity(Unknow<br />n Source)<br />[null] at org.apache.xerces.impl.XMLDTDScannerImpl.setInputSource(Unkno<br />wn Source)<br />[null] at org.apache.xerces.impl.XMLDocumentScannerImpl$DTDDispatcher.d<br />ispatch(Unknown Source)<br />[null] at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDoc<br />ument(Unknown Source)<br />[null] at org.apache.xerces.parsers.XML11Configuration.parse(Unknown So<br />urce)<br />[null] at org.apache.xerces.parsers.XML11Configuration.parse(Unknown So<br />urce)<br />[null] at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)<br />[null] at org.apache.xerces.parsers.DOMParser.parse(Unknown Source)<br />[null] at org.apache.xerces.jaxp.DocumentBuilderImpl.parse(Unknown Sour<br />ce)<br />[null] at org.kepler.moml.KeplerMetadataExtractor.extractActorMetadata(<br />KeplerMetadataExtractor.java:101)<br />[null] at org.kepler.objectmanager.cache.ActorCacheObject.<init>(ActorC<br />acheObject.java:141)<br />[null] at org.kepler.kar.handlers.ActorMetadataKAREntryHandler.cache(Ac<br />torMetadataKAREntryHandler.java:169)<br />[null] at org.kepler.kar.KARFile.cache(KARFile.java:876)<br />[null] at org.kepler.kar.KARFile.cacheKARContents(KARFile.java:591)<br />[null] at org.kepler.kar.SaveKAR.saveToCache(SaveKAR.java:184)<br />[null] at org.kepler.gui.kar.ExportArchiveAction.actionPerformed(Export<br />ArchiveAction.java:344)<br />[null] at javax.swing.AbstractButton.fireActionPerformed(Unknown Source<br />)<br />[null] at javax.swing.AbstractButton$Handler.actionPerformed(Unknown So<br />urce)<br />[null] at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown So<br />urce)<br />[null] at javax.swing.DefaultButtonModel.setPressed(Unknown Source)<br />[null] at javax.swing.AbstractButton.doClick(Unknown Source)<br />[null] at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source<br />)<br />[null] at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(<br />Unknown Source)<br />[null] at java.awt.Component.processMouseEvent(Unknown Source)<br />[null] at javax.swing.JComponent.processMouseEvent(Unknown Source)<br />[null] at java.awt.Component.processEvent(Unknown Source)<br />[null] at java.awt.Container.processEvent(Unknown Source)<br />[null] at java.awt.Component.dispatchEventImpl(Unknown Source)<br />[null] at java.awt.Container.dispatchEventImpl(Unknown Source)<br />[null] at java.awt.Component.dispatchEvent(Unknown Source)<br />[null] at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Sou<br />rce)<br />[null] at java.awt.LightweightDispatcher.processMouseEvent(Unknown Sour<br />ce)<br />[null] at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)<br />[null] at java.awt.Container.dispatchEventImpl(Unknown Source)<br />[null] at java.awt.Window.dispatchEventImpl(Unknown Source)<br />[null] at java.awt.Component.dispatchEvent(Unknown Source)<br />[null] at java.awt.EventQueue.dispatchEvent(Unknown Source)<br />[null] at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown S<br />ource)<br />[null] at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Sour<br />ce)<br />[null] at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown S<br />ource)<br />[null] at java.awt.EventDispatchThread.pumpEvents(Unknown Source)<br />[null] at java.awt.EventDispatchThread.pumpEvents(Unknown Source)<br />[null] at java.awt.EventDispatchThread.run(Unknown Source)<br />[null] Error parsing Actor KAR DOM "<?xml version="1.0"?><br />[null] <!DOCTYPE entity PUBLIC "-//UC Berkeley//DTD MoML 1//EN" <br />[null] "http://ptolemy.e...": Connection timed out: connect<br />[null] WARN (org.kepler.objectmanager.cache.CacheManager:insertObject:237)<br />KAREntry has no lsid: null</p>