Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362009-03-24T00:11:16ZEcoinformatics Redmine
Redmine Bug #3915 (New): The error dialogue won't go away.https://projects.ecoinformatics.org/ecoinfo/issues/39152009-03-24T00:11:16Zjianwu jianwujianwu@sdsc.edu
<p>Workflow: There are two composite actors, one called CompositeActor1 on the top level, another called CompositeActor2, in CompositeActor1. There are two String Parameters: one called p1 on the top level, another called p2 with value '$p1/l', in CompositeActor1. p2 is used in actors in CompositeActor1, such as expression, file open.</p>
<p>Steps: <br />1) Open the whole workflow,<br />2) Open CompositeActor1,<br />3) Open CompositeActor2,<br />4) Close CompositeActor2,<br />5) Delete CompositeActor2,<br />6) Change the value of p1.</p>
<p>There will be an error saying that: "Error evaluating expression: $p1/l in .CompositeActor2.p2 Because The ID p1 is undefined."</p>
<p>There is no way to close the error except closing Kepler by force, which will lost all unsaved modification.</p>
<p>I found the bug with Kepler version 16865 and ptolemy version 52661, but I think this bug is always there.</p>
<p>I attached the workflow and error dialogue.</p> Bug #3555 (New): enhancements to Trace File view in provenance browserhttps://projects.ecoinformatics.org/ecoinfo/issues/35552008-10-23T00:25:07ZTimothy McPhillipsmcphillips@ecoinformatics.org
<p>The provenance browser allows one to view the raw trace file (in XML format) of the run currently loaded in the browser. It would be very nice if one could navigate the other provenance graphs by clicking on XML elements in this Trace File view, and have the details for the selected element appear in the left-hand panels, etc, similar to what happens when one clicks on the data, collections, and invocation items in the Dependency History and Collection History views. Clicking on these graphical views could highlight the corresponding lines in the trace file view as well. (Clicking on a token, object, or invocation id in the XML might also take you to the referenced item.)</p>
<p>A second very helpful feature would be color-coding of the XML in the Trace File view. Not color-coding to emphasize the XML syntax, but rather to highlight what XML elements comprise Collections, Data elements, metadata/annotations, and provenance records, say.</p>
<p>I think these enhancements would make it easier to make sense of the trace and provenance information stored in it.</p> Bug #3552 (In Progress): Annotation elements in trace file do not appear in details pane of prove...https://projects.ecoinformatics.org/ecoinfo/issues/35522008-10-22T20:07:51ZTimothy McPhillipsmcphillips@ecoinformatics.org
<p>The provenance browser shows the details for the selected data or collection element of a trace in the lower left-hand panel. When the element selected has been annotated with one or more Metadata elements, these appear as name-value pairs under the heading "Annotations" in that panel. However, if an <strong>Annotation</strong> element has been applied to the selected element, it is not displayed.</p>
<p>Annotation and Metadata elements should both appear in the details panel, probably under two distinct headings, 'Metadata' and 'Annotations'.</p>
<p>(Note that the distinction between metadata and annotations in COMAD is that the former are reserved for things that have always been true about the item it is associated with, while the former can be used for any purpose. Consequently, Metadata elements cannot be deleted or replaced during a COMAD workflow run, while Annotation elements can be.)</p> Bug #3546 (New): Automatically load trace for a completed run into the provenance browserhttps://projects.ecoinformatics.org/ecoinfo/issues/35462008-10-22T17:40:53ZTimothy McPhillipsmcphillips@ecoinformatics.org
<p>At present, viewing the trace of a workflow run via the provenance browser (the one in the provenance-apps module) requires either running the provenance browser from the command line or navigating to the trace for the latest workflow run in the MyTraces subtree in the Traces panel of the Workspace pane in Kepler. I almost always want to see the trace immediately on running a workflow.</p>
<p>Could we provide an option to load the trace of the current run automatically when it completes?</p> Bug #3388 (New): error running simihofi.xml workflow in Kepler 1.0.0https://projects.ecoinformatics.org/ecoinfo/issues/33882008-06-09T20:17:43ZKirsten Menger-Andersonkma500@hotmail.com
<p>I get the following error when I first open the simihofi.xml workflow (though the workflow does run):</p>
<p>Error encountered in: <property name="timeResolution" class="ptolemy.actor.parameters.SharedParameter" value="1E-10"> ptolemy.actor.parameters.SharedParameter</p> Bug #3361 (In Progress): parameters lose their Display Name when copy and pastedhttps://projects.ecoinformatics.org/ecoinfo/issues/33612008-06-04T00:23:06ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>It may be this is the 'proper' behavior, but it doesn't seem so to me (cxh?).</p>
<p>steps to reproduce:<br />- Drag Parameter to canvas<br />- Right click, Customize Name<br />- type in a New Name: new_name, and a Display Name: display_name<br />- Commit<br />- copy and paste the Parameter</p>
<pre><code>The second Parameter has New name: new_name2, and Display name: new_name2, but I think Display name should be: display_name2.</code></pre>
<p>This affects:</p>
<p>GriddlesParameter<br />ColorParameter<br />FileParameter<br />Parameter<br />PortParameter<br />RequireVersion<br />SemanticTypeParameter <br />StringParameter</p> Bug #3295 (New): Python/Ptolemnizer welcome text does not displayhttps://projects.ecoinformatics.org/ecoinfo/issues/32952008-05-13T18:43:06ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>A minor annoyance, but the SampleDelay actor's "Welcome to the..." text is not displaying in the InteractiveShell as the annotation states. <br />I also notice the SampleDelay actor in this workflow looks different than the one found in the library...</p> Bug #3292 (New): ENM/GDAL_h1K_NS workflow giving an exceptionhttps://projects.ecoinformatics.org/ecoinfo/issues/32922008-05-13T01:04:17ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>I upgraded to ubuntu 8.04 today, and now the GDAL_h1K_NS workflow is giving an exception (i'm using java 1.5.0_13).</p>
<p>ptolemy.kernel.util.IllegalActionException: in .GDAL_h1K_NS.manager<br />Because:<br />/home/barseghian/Kepler-1.0.0/lib/libgdalactor.so: Can't load IA 32-bit .so on a IA 32-bit platform</p>
<p>Maybe this workflow just needs an annotation warning like the other ENM ones? After a few attempts the Exception changes to a java.lang.NoClassDefFoundError</p> Bug #3291 (New): IPCC_ChangeNightlyBuildTest got an exceptionhttps://projects.ecoinformatics.org/ecoinfo/issues/32912008-05-09T21:57:31ZJing Taotao@nceas.ucsb.edu
<p>Running work-flow, demos/ENM/IPCC_Change_NightlyBuildTest.xml, got an exception. The supposed result is "true", but the result is not. So Nonstrict Test actor threw an exception.</p> Bug #3266 (In Progress): ENM/GARP_MultipleSpecies-V.xml problemshttps://projects.ecoinformatics.org/ecoinfo/issues/32662008-05-02T18:02:43ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>ENM/GARP_MultipleSpecies-V.xml crashes Ubuntu Kepler. <br />On mac execution completes but just gives ImageJ "Unrecognized comand: ASC TextReader" messages.</p> Bug #3226 (New): Eval: subplots from RExpression overly condensedhttps://projects.ecoinformatics.org/ecoinfo/issues/32262008-04-16T22:42:19ZKevin Drurydrury@nceas.ucsb.edu
<p>Using nightly build 14 Apr 08 under WinXP. The code below generates a publication-quality graphic when run from the R command line. When run in an RExpression actor, however the results are pretty unattractive.</p>
<p>Case 1: With an imageJ actor connected, the resulting RExpressionNUM.png is extremely compressed. i.e., there is lots of white space and the subplots are cramped.</p>
<p>Case 2: With no imageJ actor, and the "Automatically display graphics" button checked, the resulting pdf is less cramped than the png, but still not as well-proportioned as that coming directly from R.</p>
<p>Note: resizing the graphic does not help - proportions remain the same</p>
<ol>
<li>test code for RExpression actor subplot generation</li>
<li>get data and variables in order...<br />library(MASS) ;<br />names(wtloss) ; attach(wtloss) ;<br />w<-Weight ; d<-Days ;</li>
<li>set up stacked subplotting environment, plot top fig<br />par(mfrow=c(2,1)) ; plot(w~d) ; <br />res<-lm(w~d) ; abline(res) ;</li>
<li>plot bottom fig<br />r<-residuals(res) ; plot(d,r) ;</li>
<li>return to default graphics, clean up<br />par(mfrow=c(1,1)) ;<br />detach(wtloss) ;</li>
</ol> Bug #3204 (New): Kepler should have FSM exampleshttps://projects.ecoinformatics.org/ecoinfo/issues/32042008-04-02T21:15:37ZChristopher Brookscxh@eecs.berkeley.edu
<p>Finite State Machines are very powerful, there should<br />be a Kepler-specific scientific workflow that <br />illustrates FSMs.</p> Bug #3143 (New): dataFrame_R cache problem under parallelshttps://projects.ecoinformatics.org/ecoinfo/issues/31432008-02-11T20:26:29ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>I'm currently getting the following error with the demos/R/dataFrame_R.xml workflow when trying to run it under Parallels:</p>
<p>Error in file(file, "r") : unable to open connection<br />In addition: Warning message:<br />cannot open file '////.PSF//.Home//.kepler//cache////cachedata//urn.lsid.localhost.7a976669.0.0', reason 'Invalid argument' <br />Execution halted</p>
<p>All other R demos work fine. I've tried deleting .kepler and restarting to no avail. Others have reported success under Parallels.</p> Bug #1997 (New): Support Getting Metadata for Darwin Core search result itemhttps://projects.ecoinformatics.org/ecoinfo/issues/19972005-03-01T18:49:40ZJing Taotao@nceas.ucsb.edu
<p>In data search result panel, we add a new right click button for getting<br />metadata for the item. But currently we only support eml200 and eml201. We need<br />also support DarwinCore search result too. First we need create a style sheet to<br />transfer Darwincore xml to html.</p> Bug #1914 (In Progress): Implement the 'most recently used' concept for workflows and actorshttps://projects.ecoinformatics.org/ecoinfo/issues/19142005-01-24T18:45:25ZDan Higginshiggins@nceas.ucsb.edu