Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362010-09-16T00:43:48ZEcoinformatics Redmine
Redmine Bug #5177 (New): Enhance displaying workflow in kepler server library skinhttps://projects.ecoinformatics.org/ecoinfo/issues/51772010-09-16T00:43:48ZJing Taotao@nceas.ucsb.edu
<p>This bug is the secondary stag of bug 5145.</p>
<p>Here are from matt:</p>
<p>If you are in the process of revamping this stylesheet and presentation, its<br />probably worthwhile to also consider improving the presentation style. Please<br />review some other sites that display workflows on the web, including:</p>
<p>MyExperiment:<br /> Workflow: <a class="external" href="http://www.myexperiment.org/workflows/23.html">http://www.myexperiment.org/workflows/23.html</a><br /> Resultset: <a class="external" href="http://www.myexperiment.org/tags/49.html?type=workflows">http://www.myexperiment.org/tags/49.html?type=workflows</a></p>
<p>CrowdLabs:<br /> Workflow: <a class="external" href="http://www.crowdlabs.org/vistrails/workflows/details/119/">http://www.crowdlabs.org/vistrails/workflows/details/119/</a></p> Bug #5018 (New): Items with the same LSID show with the same name in the Components Libraryhttps://projects.ecoinformatics.org/ecoinfo/issues/50182010-05-19T23:36:20ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>If you have two items within a KAR that have different filenames but the same LSID, they show as one item in the components tree, even though the KAR actually contains two files (and the View Manifest reflects this). If the two items with the same LSID are in different KARs, the components tree will show one in each KAR, but they will share the same name, even if the filenames are different.</p> Bug #4869 (In Progress): changes made to workflows during dialogs before committing (Edit Paramet...https://projects.ecoinformatics.org/ecoinfo/issues/48692010-03-04T19:04:24ZOliver Soongsoong@nceas.ucsb.edu
<p>When I make changes to an actor through the dialog, it seems like the changes are made to the workflow immediately, before the "Commit" button is clicked.</p>
<p>For example, create a workflow with an EML 2 Dataset actor. Make sure Kepler has not already authenticated with KNB. Now edit the EML 2 Dataset actor to reference a data package that requires authentication. The KNB login window will immediately pop up, even though no changes have been committed. Dismiss the window in some way. Now click the Help button and close the help window. The dialog will have disappeared. Open the actor dialog again, and the change will be there.</p>
<p>I should point out that the "Cancel" button does seem to work, but I suspect (based on debugging comments and comments in code) that this acts by reverting the changes already made.</p>
<p>I've seen this for sure on EML 2 Dataset and RExpression, since changes to one trigger visual feedback and I've mucked around in the code of the other. I suspect this is a general problem, though, and it may be a result of the underlying ptolemy design.</p> Bug #4561 (New): icon overlays not showing up for actors in the components treehttps://projects.ecoinformatics.org/ecoinfo/issues/45612009-11-19T22:35:13ZOliver Soongsoong@nceas.ucsb.edu
<p>RExpression used to have the little R icon show up in the components tree (it was an easy way to find the RExpression actor without actually reading the labels). It's not there anymore. Not a problem per se, but it is a change in behavior.</p> Bug #4532 (New): have to manually click Build to rename repositorieshttps://projects.ecoinformatics.org/ecoinfo/issues/45322009-11-05T17:56:47ZOliver Soongsoong@nceas.ucsb.edu
<p>If I open the Components Sources dialog and change the name of one of the sources, then click Ok, the changes are not applied, which isn't the normal behavior of Ok. I have to click Build first, then Ok. Since Build is triggered when clicking Ok after adding or removing a repository, it seems like there just needs to be some improvements made to the change detection logic.</p>
<p>For that matter, do we really need a separate Build and Ok button? Maybe an Ok and Apply button, where the Apply is the current Build button. That would be more in line with a typical dialog.</p> Bug #4273 (New): Ctrl+E operates on mouse position, not selectionhttps://projects.ecoinformatics.org/ecoinfo/issues/42732009-07-27T20:50:27ZOliver Soongsoong@nceas.ucsb.edu
<p>This is a UI concern, but if I select an actor, then move the mouse over a different actor, then Ctrl+E, it will open the settings for the actor under the mouse, not the selected actor.</p> Bug #4113 (New): Kepler changes property position in XML but keeps valueshttps://projects.ecoinformatics.org/ecoinfo/issues/41132009-05-28T00:30:18ZOliver Soongsoong@nceas.ucsb.edu
<p>This doesn't affect the operation of Kepler, but it makes it a major pain to diff workflows and causes large portions of workflows to be sent by e-mail every time minor changes are made. If xml tags nested at the same level were simply sorted, this would make version control of the xml that much more effective.</p> Bug #3943 (New): error importing more than one actor created in one suite using kepler-1.0https://projects.ecoinformatics.org/ecoinfo/issues/39432009-04-04T01:13:50ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Procedure: Follow the new kepler-1.0 hello-world tutorial to create an actor in a hello-world suite. Create a second actor in this suite. Launch Kepler, instantiate both actors, export each to a kar, and then try to import each. I get an "Error inserting the kar file into the cache: Id already exists in the cache" when trying to import the second.</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 #3220 (New): "Save" from TextEditor interferes with workflow save-before-closing prompthttps://projects.ecoinformatics.org/ecoinfo/issues/32202008-04-14T19:15:08Zben leinfelderleinfelder@nceas.ucsb.edu
<p>While editing an RExpression script using the built-in TextEditor ("Open Actor"), Kevin Drury found that if he used "Save" from within the text editor window to save the contents of the script, closed that editor window, then closed the workflow window (that contained other unsaved changes), Kepler would not prompt him for a confirmation to save before closing the workflow. All changes would then be lost.<br />I've reproduced this behavior (we are both on a Mac).</p> Bug #3149 (New): cannot add arbitrary jars when exporting archivehttps://projects.ecoinformatics.org/ecoinfo/issues/31492008-02-14T19:31:46ZDan Higginshiggins@nceas.ucsb.edu
<p>The "Export Archive (kar)" popup menu asks if the class file of an actor should be included in the kar, but there is no way to add other classes/jars. ie jar libraries that may be needed by the actor. (One specific example - python actor needs the jython.jar to execute)</p>
<p>Need to add a dialog to let the user add arbitrary number of additional jars to a kar file.</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>