Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362015-08-16T22:50:16ZEcoinformatics Redmine
Redmine Bug #6831 (Closed): saving/loading window properties for multiple graphs/models in BasicGraphFramehttps://projects.ecoinformatics.org/ecoinfo/issues/68312015-08-16T22:50:16ZDaniel Crawldanielcrawl@gmail.com
<p>BasicGraphFrame saves properties such as center, zoom, size, etc., for the open frame. However, it assumes the frame only contains a single JGraph and model. Attached is an updated BasicGraphFrame that allows derived classes to save/load window properties for multiple JGraphs and models.</p> Bug #6829 (Closed): ant change-to fails under Windows Server 2012 R2 with Cygwinhttps://projects.ecoinformatics.org/ecoinfo/issues/68292015-08-12T23:39:08ZChristopher Brookscxh@eecs.berkeley.edu
<p>Under Windows Server 2012 R2 with Cygwin, I ran<br /><pre>
mkdir kepler.modules
cd kepler.modules
svn co https://code.kepler-project.org/code/kepler/trunk/modules/build-area
cd build-area
</pre></p>
<p>and then ant change-to failed:</p>
<pre>
$ ant change-to -Dsuite=kepler
Buildfile: C:\Users\cxh\src\kepler.modules\build-area\build.xml
change-to:
[change-to] Copying 1 file to C:\Users\cxh\src\kepler.modules\build-area
[change-to] Retrieving modules....
[change-to]
[change-to] kepler:
[change-to] Downloading (if necessary) kepler...
[change-to] svn co -r head https://code.kepler-project.org/code/kepler/trunk/modules/kepler C:\Users\cxh\src\kep\
ler.modules\kepler
[change-to] svn: E000002: Can't make directory '/cygdrive/c/Users/cxh/src/kepler.modules/build-area/C:\Users\cxh\
\src\kepler.modules\kepler': No such file or directory
[change-to]
BUILD FAILED
C:\Users\cxh\src\kepler.modules\build-area\build.xml:104: ERROR: It appears that the command did not execute pro\
perly and exited with an exit code of: 1
Total time: 1 second
cxh@AMPERE ~/src/kepler.modules/build-area
$
</pre>
<p>I can give out accounts on ampere.eecs.berkele.edu if necessary.</p> Bug #6634 (Closed): Error message popup not generated when saving to a write protected directory.https://projects.ecoinformatics.org/ecoinfo/issues/66342014-12-17T17:21:21ZArtur Szostakaszostak@partner.eso.org
<p>In the Kepler GUI a message popup window should appear when the saving of a file fails.<br />To reproduce the problem, run the following commands in a POSIX terminal (on Fedora 20 in this case):</p>
<pre><code>curl <a class="external" href="https://code.kepler-project.org/code/kepler/releases/installers/2.4/kepler-2.4-linux.tar.gz">https://code.kepler-project.org/code/kepler/releases/installers/2.4/kepler-2.4-linux.tar.gz</a> | tar xzf -<br /> mkdir my_workspace<br /> chmod -w my_workspace<br /> cp ./kepler-2.4/common-2.4.0/configs/ptolemy/configs/kepler/configuration.xml original_configuration.xml<br /> cat original_configuration.xml | head -n 257 > ./kepler-2.4/common-2.4.0/configs/ptolemy/configs/kepler/configuration.xml<br /> echo " &lt;property name=\"_alternateDefaultOpenDirectory\" value=\"`pwd`/my_workspace\" class=\"ptolemy.kernel.util.StringAttribute\"/&gt;" >> ./kepler-2.4/common-2.4.0/configs/ptolemy/configs/kepler/configuration.xml<br /> cat original_configuration.xml | tail -n 1 >> ./kepler-2.4/common-2.4.0/configs/ptolemy/configs/kepler/configuration.xml<br /> ./kepler-2.4/kepler.sh</code></pre>
<p>Once Kepler has started (you might have to close the initial "welcome"/"upgrade" popup windows), follow these instructions:</p>
<pre><code>Click on the "File->Save" item from the menu bar.<br /> Click on the "OK" button in the "Please enter a name for this workflow" pupup window.<br /> Click on the "Save" button in the "Save" popup window.</code></pre>
<p>No error message popup appears, even though there is a log message in the terminal about "permission denied".</p> Bug #6629 (Closed): type resolution problem when using RecordAssemblerhttps://projects.ecoinformatics.org/ecoinfo/issues/66292014-12-02T00:04:25ZDaniel Crawldanielcrawl@gmail.com
<p>Using RecordAssembler can cause type resolution to fail. Attached are two models that demonstrate the problem.</p>
<p>In rec-assembler-1.xml, a type resolution error will usually, but not always, occur when you run it.</p>
<p>In rec-assembler-2.xml, the second RecordAssembler actor is replaced with an Expression actor that constructs the same record, and no type resolution error occurs.</p> Bug #6467 (Closed): data tab no longer workshttps://projects.ecoinformatics.org/ecoinfo/issues/64672014-03-17T17:42:22ZDaniel Crawldanielcrawl@gmail.com
<p>Searching for "datos" in the data tab generates exceptions:</p>
<pre><code>[null] ERROR (org.ecoinformatics.seek.datasource.EcogridQueryDataCacheItem:doWork:110) The exception in query is <br /> [null] AxisFault<br /> [null] faultCode: {http://xml.apache.org/axis/}HTTP<br /> [null] faultSubcode: <br /> [null] faultString: (301)Moved Permanently<br /> [null] faultActor: <br /> [null] faultNode: <br /> [null] faultDetail: <br /> [null] {}:return code: 301<br /> [null] &lt;!DOCTYPE HTML PUBLIC &quot;-//IETF//DTD HTML 2.0//EN&quot;&gt;<br /> [null] &lt;html&gt;&lt;head&gt;<br /> [null] &lt;title&gt;301 Moved Permanently&lt;/title&gt;<br /> [null] &lt;/head&gt;&lt;body&gt;<br /> [null] &lt;h1&gt;Moved Permanently&lt;/h1&gt;<br /> [null] &lt;p&gt;The document has moved &lt;a href=&quot;<a class="external" href="https://knb.ecoinformatics.org/knb/services/QueryService&quot;&gt;here&lt;/a&gt;.&lt;/p">https://knb.ecoinformatics.org/knb/services/QueryService&amp;quot;&amp;gt;here&amp;lt;/a&amp;gt;.&amp;lt;/p</a>&gt;<br /> [null] &lt;hr&gt;<br /> [null] &lt;address&gt;Apache/2.2.14 (Ubuntu) Server at ecogrid.ecoinformatics.org Port 80&lt;/address&gt;<br /> [null] &lt;/body&gt;&lt;/html&gt;<br /> [null] <br /> [null] {http://xml.apache.org/axis/}HttpErrorCode:301<br /> [null] <br /> [null] (301)Moved Permanently<br /> [null] at org.apache.axis.transport.http.HTTPSender.readFromSocket(HTTPSender.java:744)<br /> [null] at org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:144)<br /> [null] at org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java:32)<br /> [null] at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118)<br /> [null] at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83)<br /> [null] at org.apache.axis.client.AxisClient.invoke(AxisClient.java:165)<br /> [null] at org.apache.axis.client.Call.invokeEngine(Call.java:2784)<br /> [null] at org.apache.axis.client.Call.invoke(Call.java:2767)<br /> [null] at org.apache.axis.client.Call.invoke(Call.java:2443)<br /> [null] at org.apache.axis.client.Call.invoke(Call.java:2366)<br /> [null] at org.apache.axis.client.Call.invoke(Call.java:1812)<br /> [null] at org.ecoinformatics.ecogrid.queryservice.stub.QueryServiceStub.query(Unknown Source)<br /> [null] at org.ecoinformatics.ecogrid.queryservice.QueryServiceClient.query(Unknown Source)<br /> [null] at org.ecoinformatics.seek.datasource.EcogridQueryDataCacheItem.doWork(EcogridQueryDataCacheItem.java:101)<br /> [null] at org.kepler.objectmanager.cache.DataCacheObject.run(DataCacheObject.java:422)<br /> [null] at java.lang.Thread.run(Thread.java:695)</code></pre> Bug #6439 (Closed): Double rounding fails in some cases while evaluating Expressionshttps://projects.ecoinformatics.org/ecoinfo/issues/64392014-03-04T12:24:32ZOwsiak Michalmichal.owsiak@man.poznan.pl
<p>It seems that addition of doubles can produce values slightly different than they should to be.</p>
<p>Please take a look at attached workflow (simple_error.xml).</p>
<p>Condition that should be satisfied to escape the loop is: 1.7 > 1.5 + 0.1</p>
<p>However, loop is interrupted sooner, because of incorrect calculation of doubles. Value of "p" is set to: 1.6000000000000003</p>
<p>This, of course, makes it impossible to use doubles as check points for the loops.</p>
<p>However, it seems that casting to string and back works fine (take a look at second workflow - simple.xml)</p>
<p>Cheers</p>
<p>Michal</p> Bug #6000 (Closed): parameter copy-paste exception on console.https://projects.ecoinformatics.org/ecoinfo/issues/60002013-06-07T23:58:42Zjianwu jianwujianwu@sdsc.edu
<p>This workflow (see attachment) has two parameters. The first one, called datadir, is Parameter type and the second one, called outputdir, is StringParameter type. The second one use the first one's as part of its value: $datadir/output. When I copy and paste parameter outputdir on the canvas, no error dialog pop up. But the console has an exception messages.</p>
<p>ptolemy.kernel.util.IllegalActionException: Warning:, there was a problem propagating "outputdir".<br /> [run] in .auto.outputdir<br /> [run] Because:<br /> [run] Error evaluating expression: $datadir/output<br /> [run] in .auto.outputdir<br /> [run] Because:<br /> [run] The ID datadir is undefined.<br /> [run] at ptolemy.data.expr.Variable._propagate(Variable.java:1789)<br /> [run] at ptolemy.data.expr.Variable.validate(Variable.java:1460)<br /> [run] at ptolemy.moml.MoMLParser.endDocument(MoMLParser.java:802)<br /> [run] at com.microstar.xml.XmlParser.doParse(XmlParser.java:162)<br /> [run] at com.microstar.xml.XmlParser.parse(XmlParser.java:132)<br /> [run] at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1556)<br /> [run] at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1512)<br /> [run] at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1655)<br /> [run] at ptolemy.moml.MoMLVariableChecker.checkCopy(MoMLVariableChecker.java:112)<br /> [run] at ptolemy.moml.MoMLVariableChecker.checkCopy(MoMLVariableChecker.java:81)<br /> [run] at ptolemy.vergil.basic.BasicGraphFrame.copy(BasicGraphFrame.java:341)<br /> [run] at ptolemy.vergil.basic.BasicGraphFrame$CopyAction.actionPerformed(BasicGraphFrame.java:3477)<br /> [run] at javax.swing.JComponent$ActionStandin.actionPerformed(JComponent.java:3376)<br /> [run] at javax.swing.SwingUtilities.notifyAction(SwingUtilities.java:1645)<br /> [run] at javax.swing.JComponent.processKeyBinding(JComponent.java:2859)<br /> [run] at javax.swing.KeyboardManager.fireBinding(KeyboardManager.java:267)<br /> [run] at javax.swing.KeyboardManager.fireKeyboardAction(KeyboardManager.java:216)<br /> [run] at javax.swing.JComponent.processKeyBindingsForAllComponents(JComponent.java:2936)<br /> [run] at javax.swing.JComponent.processKeyBindings(JComponent.java:2928)<br /> [run] at javax.swing.JComponent.processKeyEvent(JComponent.java:2822)<br /> [run] at java.awt.Component.processEvent(Component.java:6159)<br /> [run] at java.awt.Container.processEvent(Container.java:2083)<br /> [run] at java.awt.Component.dispatchEventImpl(Component.java:4744)<br /> [run] at java.awt.Container.dispatchEventImpl(Container.java:2141)<br /> [run] at java.awt.Component.dispatchEvent(Component.java:4572)<br /> [run] at java.awt.KeyboardFocusManager.redispatchEvent(KeyboardFocusManager.java:1856)<br /> [run] at java.awt.DefaultKeyboardFocusManager.dispatchKeyEvent(DefaultKeyboardFocusManager.java:722)<br /> [run] at java.awt.DefaultKeyboardFocusManager.preDispatchKeyEvent(DefaultKeyboardFocusManager.java:1000)<br /> [run] at java.awt.DefaultKeyboardFocusManager.typeAheadAssertions(DefaultKeyboardFocusManager.java:865)<br /> [run] at java.awt.DefaultKeyboardFocusManager.dispatchEvent(DefaultKeyboardFocusManager.java:686)<br /> [run] at java.awt.Component.dispatchEventImpl(Component.java:4616)<br /> [run] at java.awt.Container.dispatchEventImpl(Container.java:2141)<br /> [run] at java.awt.Window.dispatchEventImpl(Window.java:2489)<br /> [run] at java.awt.Component.dispatchEvent(Component.java:4572)<br /> [run] at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:710)<br /> [run] at java.awt.EventQueue.access$400(EventQueue.java:82)<br /> [run] at java.awt.EventQueue$2.run(EventQueue.java:669)<br /> [run] at java.awt.EventQueue$2.run(EventQueue.java:667)<br /> [run] at java.security.AccessController.doPrivileged(Native Method)<br /> [run] at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)<br /> [run] at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)<br /> [run] at java.awt.EventQueue$3.run(EventQueue.java:683)<br /> [run] at java.awt.EventQueue$3.run(EventQueue.java:681)<br /> [run] at java.security.AccessController.doPrivileged(Native Method)<br /> [run] at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)<br /> [run] at java.awt.EventQueue.dispatchEvent(EventQueue.java:680)<br /> [run] at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)<br /> [run] at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)<br /> [run] at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)<br /> [run] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)<br /> [run] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)<br /> [run] at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)<br /> [run] Caused by: ptolemy.kernel.util.IllegalActionException: Error evaluating expression: $datadir/output<br /> [run] in .auto.outputdir<br /> [run] Because:<br /> [run] The ID datadir is undefined.<br /> [run] at ptolemy.data.expr.Variable._evaluate(Variable.java:1691)<br /> [run] at ptolemy.data.expr.Variable._propagate(Variable.java:1767)<br /> [run] ... 51 more<br /> [run] Caused by: ptolemy.data.expr.UndefinedConstantOrIdentifierException: The ID datadir is undefined.<br /> [run] at ptolemy.data.expr.ParseTreeEvaluator.visitLeafNode(ParseTreeEvaluator.java:723)<br /> [run] at ptolemy.data.expr.ASTPtLeafNode.visit(ASTPtLeafNode.java:125)<br /> [run] at ptolemy.data.expr.ParseTreeEvaluator._evaluateChild(ParseTreeEvaluator.java:1360)<br /> [run] at ptolemy.data.expr.ParseTreeEvaluator._evaluateAllChildren(ParseTreeEvaluator.java:1314)</p> Bug #5894 (Closed): Clone problems in NamedObjIdhttps://projects.ecoinformatics.org/ecoinfo/issues/58942013-03-19T19:07:23ZChristopher Brookscxh@eecs.berkeley.edu
<p>Checking the configuration results in messages about clone problems in NamedObjId:</p>
<p>The valueListeners java.util.Vector field<br /> in the clone of "org.kepler.moml.NamedObjId" <br /> does not point to an object distinct from the master. <br /> This may cause problems with actor oriented classes.<br /> The clone(Workspace) method should have a line like:<br /> newObject.valueListeners = (Vector)newObject<br /> /* Get the object method or null? <strong>/ valueListeners;<br />The _id org.kepler.objectmanager.lsid.KeplerLSID field<br /> in the clone of "org.kepler.moml.NamedObjId" <br /> does not point to an object distinct from the master. <br /> This may cause problems with actor oriented classes.<br /> The clone(Workspace) method should have a line like:<br /> newObject._id = (KeplerLSID)newObject<br /> /</strong> Get the object method or null? */ _id;</p>
<p>To replicate:<br />1) Start Kepler<br />2) Click on the Documentation link<br />3) Click on "Background information about Ptolemy" <br />4) Click on the Copyright link<br />5) Click on the Copyright link at the bottom (Other copyrights ...)<br />6) Click on "other" information about this configuration at the bottom<br />7) Click on "about:configuration"</p>
<p>The text above will appear.</p>
<p>The issue with cloning could be causing problems with actor oriented classes.</p>
<p>This class should have a clone(Workspace) method added.</p> Bug #5893 (Closed): During installation, Kepler takes a long time to start up under Windowshttps://projects.ecoinformatics.org/ecoinfo/issues/58932013-03-19T14:51:33ZChristopher Brookscxh@eecs.berkeley.edu
<p>With Kepler-2.4RC3 under Windows2008R2 64-bit, the user is asked if they want to start up Kepler. I chose "yes" and nothing happened, so I completed the installation.</p>
<p>Then, I started up Kepler from the menu and it took a long time (over a minute?) to start up.</p>
<p>Then, it seemed like there were two Kepler instances?</p>
<p>It seems like Kepler took a long time to start, which is why when Kepler was starting during the installation, it seemed like nothing was happening.</p> Bug #5754 (Closed): unable to open TestSSHWithDisplay 2.3 run-kar from keplerRepository with WRM ...https://projects.ecoinformatics.org/ecoinfo/issues/57542012-11-30T21:47:36ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Need to look into why trying to force open this run-kar to see the workflow does nothing.</p> Bug #5659 (Closed): Kepler CaseGraphFrame and CaseGraphTableau have duplicated Ptolemy code.https://projects.ecoinformatics.org/ecoinfo/issues/56592012-08-06T23:45:27ZChristopher Brookscxh@eecs.berkeley.edu
<p>./gui/src/org/kepler/gui/frame/CaseGraphFrame.java<br />FIXME: Refactor!<br /> Duplicate of ptolemy/src/ptolemy/vergil/modal/CaseGraphFrame.java<br /> The Kepler version extends the Kepler-specific MultiCompositeGraphFrame which extends KeplerGraphFrame</p>
<ol>
<li><br />./gui/src/org/kepler/gui/frame/CaseGraphTableau.java<br />FIXME: Refactor!<br /> Probably like CaseGraphFrame above.</li>
</ol> Bug #5601 (Closed): Can still lose report design when saving to KARhttps://projects.ecoinformatics.org/ecoinfo/issues/56012012-05-07T23:15:32ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>It's still possible to lose your report design when you save to a KAR -- there's at least one scenario where you can see your report design in the Designer, save to KAR, and the ROML does not end up in the KAR.</p> Bug #4189 (Closed): Report Designer - Dynamic Report Item labels are not rendering correctlyhttps://projects.ecoinformatics.org/ecoinfo/issues/41892009-06-26T19:22:28Zdebi staggsstaggs@nceas.ucsb.edu
<p>After the labels are filled in, and then re-ordered, the dynamic report item panels are not rendering the labels correctly.</p> Bug #1898 (Closed): Redesign the web service harvester and create design documentationhttps://projects.ecoinformatics.org/ecoinfo/issues/18982005-01-20T19:56:04ZIlkay Altintasaltintas@sdsc.edu
<p>A document on how to do the harvesting to fit inn with the new dynamic actor<br />loading, annotation, etc. The harvested services should not be kept in the<br />repository, and they should be updated everytime the Kepler client is loaded. We<br />probably need to have a metarepository in the end to keep track of the<br />repositories and keywords that were searched and also collect some information<br />on the user's interest.</p>