Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362010-03-05T22:14:10ZEcoinformatics Redmine
Redmine Bug #4872 (Resolved): listen to director throws errorhttps://projects.ecoinformatics.org/ecoinfo/issues/48722010-03-05T22:14:10ZOliver Soongsoong@nceas.ucsb.edu
<p>Add an SDF Director and the Tools->Listen to Director. An error pops up on the console:</p>
<p>Error creating action for class: org.kepler.gui.RunWithFeedbackChkBoxAction : null<br />Error creating action for class: org.kepler.gui.RunWithFeedbackChkBoxAction</p>
<p>I'm not sure if this causes problems or not.</p> Bug #4846 (Resolved): error opening kar from local repositoryhttps://projects.ecoinformatics.org/ecoinfo/issues/48462010-02-25T22:50:11ZOliver Soongsoong@nceas.ucsb.edu
<p>This is with wrp at r23202. I deleted .kepler and KeplerData. I create a trivial workflow (default SDF and RExpression) and save it as a KAR in the default local repository. On restarting Kepler, the KAR and local repository are not listed in the components pane. If I go into Sources and manually trigger a re-build of the component library, I can see the KAR, but nothing happens when I attempt to open it (right-click menu) except an error in the console:</p>
<p>org.kepler.objectmanager.cache.CacheException: Exception occurred while deserializing object<br /> at org.kepler.objectmanager.cache.CacheManager.getObject(CacheManager.java:529)<br /> at org.kepler.kar.handlers.ActorMetadataKAREntryHandler.open(ActorMetadataKAREntryHandler.java:206)<br /> at org.kepler.kar.KARFile.open(KARFile.java:889)<br /> at org.kepler.kar.KARFile.openKARContents(KARFile.java:665)<br /> at org.kepler.gui.kar.OpenArchiveAction.openKAR(OpenArchiveAction.java:162)<br /> at org.kepler.gui.kar.OpenArchiveAction.actionPerformed(OpenArchiveAction.java:143)<br /> at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995)<br /> at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318)<br /> at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)<br /> at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)<br /> at javax.swing.AbstractButton.doClick(AbstractButton.java:357)<br /> at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1223)<br /> at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1264)<br /> at java.awt.Component.processMouseEvent(Component.java:6263)<br /> at javax.swing.JComponent.processMouseEvent(JComponent.java:3255)<br /> at java.awt.Component.processEvent(Component.java:6028)<br /> at java.awt.Container.processEvent(Container.java:2041)<br /> at java.awt.Component.dispatchEventImpl(Component.java:4630)<br /> at java.awt.Container.dispatchEventImpl(Container.java:2099)<br /> at java.awt.Component.dispatchEvent(Component.java:4460)<br /> at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4574)<br /> at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238)<br /> at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168)<br /> at java.awt.Container.dispatchEventImpl(Container.java:2085)<br /> at java.awt.Window.dispatchEventImpl(Window.java:2475)<br /> at java.awt.Component.dispatchEvent(Component.java:4460)<br /> at java.awt.EventQueue.dispatchEvent(EventQueue.java:599)<br /> at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)<br /> at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)<br /> at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)<br /> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)<br /> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)<br /> at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)<br />Caused by: java.io.IOException: Error in ActorCacheObject(ReadExternal): null<br /> at org.kepler.objectmanager.cache.ActorCacheObject.readExternal(ActorCacheObject.java:250)<br /> at java.io.ObjectInputStream.readExternalData(ObjectInputStream.java:1792)<br /> at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1751)<br /> at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1329)<br /> at java.io.ObjectInputStream.readObject(ObjectInputStream.java:351)<br /> at org.kepler.objectmanager.cache.CacheManager.getObject(CacheManager.java:517)<br /> ... 32 more</p> Bug #4832 (Resolved): python actor outputting to disconnected composite output throws errorhttps://projects.ecoinformatics.org/ecoinfo/issues/48322010-02-24T21:07:44ZOliver Soongsoong@nceas.ucsb.edu
<p>I have a composite actor with an output port. Inside, I have an Expression passing a token to the default python actor, which repeats the token to the composite output port. The composite output port is disconnected. I get an error:</p>
<p>ptolemy.kernel.util.IllegalActionException: Error in invoking the fire method:<br />line 7, in fire<br /> at java.util.Arrays$ArrayList.<init>(Arrays.java:3357)</p>
<pre><code>at java.util.Arrays.asList(Arrays.java:3343)</code></pre>
<pre><code>at org.kepler.provenance.PortConnector.sendIdToConnections(PortConnector.java:242)</code></pre>
<pre><code>at org.kepler.provenance.sql.SQLRecordingV8._recordPortEvent(SQLRecordingV8.java:1974)</code></pre>
<pre><code>at org.kepler.provenance.sql.SQLRecording.portEvent(SQLRecording.java:584)</code></pre>
<pre><code>at org.kepler.provenance.ProvenanceRecorder.portEvent(ProvenanceRecorder.java:819)</code></pre>
<pre><code>at ptolemy.actor.IOPort._notifyPortEventListeners(IOPort.java:4130)</code></pre>
<pre><code>at ptolemy.actor.IOPort.broadcast(IOPort.java:261)</code></pre>
<pre><code>at ptolemy.actor.TypedIOPort.broadcast(TypedIOPort.java:238)</code></pre>
<pre><code>at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)</code></pre>
<pre><code>at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)</code></pre>
<pre><code>at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)</code></pre>
<pre><code>at java.lang.reflect.Method.invoke(Method.java:597)</code></pre>
<p>java.lang.NullPointerException: java.lang.NullPointerException</p>
<pre><code>in .tpc03-veld-condition-herbs.Prepare Data.Spatial Join Landtypes.Herbaceous Site Landtypes.Spatial Join.Synchronize<br />Because:<br />Traceback (innermost last):<br /> File "&lt;string&gt;", line 7, in fire<br /> at java.util.Arrays$ArrayList.&lt;init&gt;(Arrays.java:3357)</code></pre>
<pre><code>at java.util.Arrays.asList(Arrays.java:3343)</code></pre>
<pre><code>at org.kepler.provenance.PortConnector.sendIdToConnections(PortConnector.java:242)</code></pre>
<pre><code>at org.kepler.provenance.sql.SQLRecordingV8._recordPortEvent(SQLRecordingV8.java:1974)</code></pre>
<pre><code>at org.kepler.provenance.sql.SQLRecording.portEvent(SQLRecording.java:584)</code></pre>
<pre><code>at org.kepler.provenance.ProvenanceRecorder.portEvent(ProvenanceRecorder.java:819)</code></pre>
<pre><code>at ptolemy.actor.IOPort._notifyPortEventListeners(IOPort.java:4130)</code></pre>
<pre><code>at ptolemy.actor.IOPort.broadcast(IOPort.java:261)</code></pre>
<pre><code>at ptolemy.actor.TypedIOPort.broadcast(TypedIOPort.java:238)</code></pre>
<pre><code>at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)</code></pre>
<pre><code>at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)</code></pre>
<pre><code>at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)</code></pre>
<pre><code>at java.lang.reflect.Method.invoke(Method.java:597)</code></pre>
<p>java.lang.NullPointerException: java.lang.NullPointerException</p>
<pre><code>at ptolemy.actor.lib.python.PythonScript._reportScriptError(PythonScript.java:604)<br /> at ptolemy.actor.lib.python.PythonScript._invokeMethod(PythonScript.java:560)<br /> at ptolemy.actor.lib.python.PythonScript.fire(PythonScript.java:254)<br /> at ptolemy.actor.AtomicActor.iterate(AtomicActor.java:469)<br /> at ptolemy.actor.sched.StaticSchedulingDirector.fire(StaticSchedulingDirector.java:188)<br /> at ptolemy.actor.CompositeActor.fire(CompositeActor.java:458)<br /> at ptolemy.actor.Manager.iterate(Manager.java:714)<br /> at ptolemy.actor.Manager.execute(Manager.java:349)<br /> at ptolemy.actor.Manager.run(Manager.java:1119)<br /> at ptolemy.actor.Manager$3.run(Manager.java:1160)<br />Caused by: Traceback (innermost last):<br /> File "&lt;string&gt;", line 7, in fire<br /> at java.util.Arrays$ArrayList.&lt;init&gt;(Arrays.java:3357)</code></pre>
<pre><code>at java.util.Arrays.asList(Arrays.java:3343)</code></pre>
<pre><code>at org.kepler.provenance.PortConnector.sendIdToConnections(PortConnector.java:242)</code></pre>
<pre><code>at org.kepler.provenance.sql.SQLRecordingV8._recordPortEvent(SQLRecordingV8.java:1974)</code></pre>
<pre><code>at org.kepler.provenance.sql.SQLRecording.portEvent(SQLRecording.java:584)</code></pre>
<pre><code>at org.kepler.provenance.ProvenanceRecorder.portEvent(ProvenanceRecorder.java:819)</code></pre>
<pre><code>at ptolemy.actor.IOPort._notifyPortEventListeners(IOPort.java:4130)</code></pre>
<pre><code>at ptolemy.actor.IOPort.broadcast(IOPort.java:261)</code></pre>
<pre><code>at ptolemy.actor.TypedIOPort.broadcast(TypedIOPort.java:238)</code></pre>
<pre><code>at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)</code></pre>
<pre><code>at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)</code></pre>
<pre><code>at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)</code></pre>
<pre><code>at java.lang.reflect.Method.invoke(Method.java:597)</code></pre>
<p>java.lang.NullPointerException: java.lang.NullPointerException</p>
<pre><code>at org.python.core.Py.JavaError(Unknown Source)<br /> at org.python.core.Py.JavaError(Unknown Source)<br /> at org.python.core.PyReflectedFunction.__call__(Unknown Source)<br /> at org.python.core.PyMethod.__call__(Unknown Source)<br /> at org.python.core.PyObject.__call__(Unknown Source)<br /> at org.python.core.PyInstance.invoke(Unknown Source)<br /> at org.python.pycode._pyx21.fire$2(&lt;string&gt;:7)<br /> at org.python.pycode._pyx21.call_function(&lt;string&gt;)<br /> at org.python.core.PyTableCode.call(Unknown Source)<br /> at org.python.core.PyTableCode.call(Unknown Source)<br /> at org.python.core.PyTableCode.call(Unknown Source)<br /> at org.python.core.PyFunction.__call__(Unknown Source)<br /> at org.python.core.PyMethod.__call__(Unknown Source)<br /> at org.python.core.PyObject.__call__(Unknown Source)<br /> at ptolemy.actor.lib.python.PythonScript._invokeMethod(PythonScript.java:512)<br /> ... 8 more<br />Caused by: Traceback (innermost last):<br /> File "&lt;string&gt;", line 7, in fire<br /> at java.util.Arrays$ArrayList.&lt;init&gt;(Arrays.java:3357)</code></pre>
<pre><code>at java.util.Arrays.asList(Arrays.java:3343)</code></pre>
<pre><code>at org.kepler.provenance.PortConnector.sendIdToConnections(PortConnector.java:242)</code></pre>
<pre><code>at org.kepler.provenance.sql.SQLRecordingV8._recordPortEvent(SQLRecordingV8.java:1974)</code></pre>
<pre><code>at org.kepler.provenance.sql.SQLRecording.portEvent(SQLRecording.java:584)</code></pre>
<pre><code>at org.kepler.provenance.ProvenanceRecorder.portEvent(ProvenanceRecorder.java:819)</code></pre>
<pre><code>at ptolemy.actor.IOPort._notifyPortEventListeners(IOPort.java:4130)</code></pre>
<pre><code>at ptolemy.actor.IOPort.broadcast(IOPort.java:261)</code></pre>
<pre><code>at ptolemy.actor.TypedIOPort.broadcast(TypedIOPort.java:238)</code></pre>
<pre><code>at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)</code></pre>
<pre><code>at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)</code></pre>
<pre><code>at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)</code></pre>
<pre><code>at java.lang.reflect.Method.invoke(Method.java:597)</code></pre>
<p>java.lang.NullPointerException: java.lang.NullPointerException</p>
<pre><code>at org.python.core.Py.JavaError(Unknown Source)<br /> at org.python.core.Py.JavaError(Unknown Source)<br /> at org.python.core.PyReflectedFunction.__call__(Unknown Source)<br /> at org.python.core.PyMethod.__call__(Unknown Source)<br /> at org.python.core.PyObject.__call__(Unknown Source)<br /> at org.python.core.PyInstance.invoke(Unknown Source)<br /> at org.python.pycode._pyx21.fire$2(&lt;string&gt;:7)<br /> at org.python.pycode._pyx21.call_function(&lt;string&gt;)<br /> at org.python.core.PyTableCode.call(Unknown Source)<br /> at org.python.core.PyTableCode.call(Unknown Source)<br /> at org.python.core.PyTableCode.call(Unknown Source)<br /> at org.python.core.PyFunction.__call__(Unknown Source)<br /> at org.python.core.PyMethod.__call__(Unknown Source)<br /> at org.python.core.PyObject.__call__(Unknown Source)<br /> at ptolemy.actor.lib.python.PythonScript._invokeMethod(PythonScript.java:512)<br /> at ptolemy.actor.lib.python.PythonScript.fire(PythonScript.java:254)<br /> at ptolemy.actor.AtomicActor.iterate(AtomicActor.java:469)<br /> at ptolemy.actor.sched.StaticSchedulingDirector.fire(StaticSchedulingDirector.java:188)<br /> at ptolemy.actor.CompositeActor.fire(CompositeActor.java:458)<br /> at ptolemy.actor.Manager.iterate(Manager.java:714)<br /> at ptolemy.actor.Manager.execute(Manager.java:349)<br /> at ptolemy.actor.Manager.run(Manager.java:1119)<br /> at ptolemy.actor.Manager$3.run(Manager.java:1160)</code></pre> Bug #4807 (Resolved): GetMetadata does nothinghttps://projects.ecoinformatics.org/ecoinfo/issues/48072010-02-18T19:49:26ZOliver Soongsoong@nceas.ucsb.edu
<p>Search for any data, right click on a search result, and select the only option, "GetMetadata". This does not seem to do anything, and there are no errors on the console. There should probably also be a space in the label as well.</p> Bug #4804 (Resolved): copy/paste relation changes width from Auto to 1https://projects.ecoinformatics.org/ecoinfo/issues/48042010-02-17T23:26:36ZOliver Soongsoong@nceas.ucsb.edu
<p>Drag 2 actors to the canvas and join them with a relation. Copy the actors and relation and immediately paste it. The relation width changes from Auto to 1. This is only a problem when the relation joins 2 multiports, but that will happen when a composite actor has a multiport.</p>
<p>This could be a ptolemy problem.</p> Bug #4767 (Resolved): error instantiating actor with port types from KARhttps://projects.ecoinformatics.org/ecoinfo/issues/47672010-02-06T02:52:36ZOliver Soongsoong@nceas.ucsb.edu
<p>Create an Expression actor, give it an input port of type boolean, save it as a KAR into a local repository, then try and drag it onto the canvas. I get an error:</p>
<p>ptolemy.kernel.util.IllegalActionException: TypeAttribute can only be contained by instances of TypedIOPort.<br /> in .Expression.kepler:input and ._type</p> Bug #4709 (Resolved): error updating ptolemy/srchttps://projects.ecoinformatics.org/ecoinfo/issues/47092010-01-29T01:49:13ZOliver Soongsoong@nceas.ucsb.edu
<p>Mark was trying the latest Kepler and ran into a problem with the build system. I believe he did a full checkout of the trunk (or maybe just modules). ant change-to -Dsuite=wrp found all the modules it needed. ant update failed at the ptolemy module, because ptolemy/src doesn't exist in the stub. It might be nice to check whether the ptolemy folder is degenerate when updating.</p> Bug #4671 (Resolved): cannot export workflow runs when workflow has actors with <> in the nameshttps://projects.ecoinformatics.org/ecoinfo/issues/46712010-01-15T01:25:58ZOliver Soongsoong@nceas.ucsb.edu
<p>Title says it all. This is at r22494.</p> Bug #4669 (Resolved): report layout changes, but text field displays previous contenthttps://projects.ecoinformatics.org/ecoinfo/issues/46692010-01-15T00:50:04ZOliver Soongsoong@nceas.ucsb.edu
<p>This is at r22494. I create a trivial workflow (SDF only, 1 iteration) and a report with a text field. I enter some text into field and run. The report looks normal. I then go back to the layout, change the text, and run again. The debug output on the console indicates reporting is picking up the previous text, and that's what I see if I view the report. The report layout and viewer re-sync if I run again.</p> Bug #4660 (Resolved): Clicking in a section header highlights all the text.https://projects.ecoinformatics.org/ecoinfo/issues/46602010-01-12T19:16:05ZOliver Soongsoong@nceas.ucsb.edu
<p>I have a section header with some text in it and I want to change that text. If I click on it, it highlights all of the text. If I click on it again, it highlights all of the text again. There seems to be no way to move the editing cursor to a specific location with the mouse. I can use the keyboard arrow keys, but this behavior of the section header is different from the text item and the label parts of the dynamic items.</p> Bug #4548 (Resolved): string tokens with newlines print the escape sequenceshttps://projects.ecoinformatics.org/ecoinfo/issues/45482009-11-13T23:11:17ZOliver Soongsoong@nceas.ucsb.edu
<p>This was first noticed when viewing an RExpression's "output" port. The output port emits a string token containing a section of the RExpression's stdout stream, with newlines encoded in the relevant OS's format. The report will then display literal "\n" or "\r\n" in the report, rather than the appropriate newlines.</p>
<p>While much of reporting ignores newlines (text boxes, for example), it might be useful to respect them here, since the RExpression output is less useful without them.</p> Bug #4526 (Resolved): multi-line entries can be put into text items in reports, but they are disp...https://projects.ecoinformatics.org/ecoinfo/issues/45262009-11-04T02:59:57ZOliver Soongsoong@nceas.ucsb.edu
<p>I'm not sure if this is a bug or an enhancement request. I guess it depends on what the intention was. Are text boxes supposed to be a single "line" like <P></P> in HTML, or are they supposed to be more powerful?</p>
<p>I can live with either way, but the interface should be consistent, and it would be nice to know what I'm supposed to be doing.</p> Bug #4524 (Resolved): no prompt to save a changed reporthttps://projects.ecoinformatics.org/ecoinfo/issues/45242009-11-04T02:34:45ZOliver Soongsoong@nceas.ucsb.edu
<p>If I change the report, don't save, and close the window, I get no prompt to save it.</p> Bug #4357 (Resolved): Workflow Run Manager does not mark last failed execution redhttps://projects.ecoinformatics.org/ecoinfo/issues/43572009-08-31T21:41:30ZOliver Soongsoong@nceas.ucsb.edu
<p>The workflow run manager is supposed to highlight failed executions in red. If I run a workflow and it fails, though, it is not highlighted. If I run it again, then the first failure is highlighted but not the second. If I run it again, then the first two are highlighted, but not the third. If I close and re-open Kepler, all failures are highlighted. It seems that highlighting is not updated after an execution.</p> Bug #3801 (Resolved): open dialog, common places pane has white box instead of texthttps://projects.ecoinformatics.org/ecoinfo/issues/38012009-01-29T23:58:59ZOliver Soongsoong@nceas.ucsb.edu
<p>XP Pro x64 SP2, Java 1.6.0_11, Kepler 1.0.0 from kepler-project.org.</p>
<p>When I go to File->Open File..., the common places pane on the left has five icons and five white boxes where the icon labels are supposed to be.</p>
<p>Image at the URL.</p>