Ecoinformatics Redmine: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362010-03-12T18:53:40ZEcoinformatics Redmine
Redmine Kepler - Bug #4881 (New): RExpression outputs [false] for any matrix of booleanshttps://projects.ecoinformatics.org/ecoinfo/issues/48812010-03-12T18:53:40ZOliver Soongsoong@nceas.ucsb.edu
<p>In an RExpression, add an output port "out" and use this R script:</p>
<p>out <- matrix(c(TRUE, FALSE, TRUE, FALSE), 2)</p>
<p>I get [false] as the output token, which seems to be because RExpression.java on line 1108 says:</p>
<p>mt = new BooleanMatrixToken();</p>
<p>instead of:</p>
<p>mt = new BooleanMatrixToken(valS);</p>
<p>or something similar. I'm not actually sure such a constructor exists, but it seems like it should given the other constructors in the lines before.</p> Kepler - Bug #4880 (New): RExpression cannot output matrix of stringshttps://projects.ecoinformatics.org/ecoinfo/issues/48802010-03-12T18:45:03ZOliver Soongsoong@nceas.ucsb.edu
<p>Create an RExpression with the output port "out" and for the script, use:</p>
<p>out <- matrix(letters, 2)</p>
<p>Looking at the code, it seems as if a matrix of strings was never really considered. Commas in the strings would likely cause problems, and I don't actually know if there's a StringMatrixToken.</p> Kepler - Bug #4879 (New): RExpression replaces ) in string vectors with } when outputting to a porthttps://projects.ecoinformatics.org/ecoinfo/issues/48792010-03-12T18:37:49ZOliver Soongsoong@nceas.ucsb.edu
<p>In an RExpression, create the output port "out" and in the R script, use:</p>
<p>out <- c("(", ")")</p>
<p>Hooking this to a Display actor, I get {"(", "}"}. This is because RExpression.java line 1139 (I think) has:</p>
<p>temp = temp.replace(')', '}');</p>
<p>which replaces all occurrences of ), even within the string.</p> Kepler - Bug #4870 (New): searching for packages with the same name from multiple sources sometim...https://projects.ecoinformatics.org/ecoinfo/issues/48702010-03-04T22:23:52ZOliver Soongsoong@nceas.ucsb.edu
<p>I have packages soong.4.14 and soong.28.5 on DEV and soong.4.15 and soong.28.9 on KNB. They all have the same title. The DEV packages require authentication to access the data but not to search. The KNB packages require authentication to search and access the data. If I search authenticated KNB or authenticated DEV individually, I see 2 entries. If I search authenticated KNB and authenticated DEV at the same time, I only see 3. I think this is caused by the way search records are "uniquely" named.</p> Kepler - Bug #4812 (New): local repository KAR [right click]->Delete fails when file does not existhttps://projects.ecoinformatics.org/ecoinfo/issues/48122010-02-19T01:18:40ZOliver Soongsoong@nceas.ucsb.edu
<p>Save a KAR to a local repository, then delete the file outside Kepler, then from the components tree right click the KAR and Delete. It will fail with an error to the console and the entry will not be removed from the tree. This could be handled better.</p> Kepler - Bug #4810 (New): [right click]->Save Archive (KAR) on composite actor borks port attributeshttps://projects.ecoinformatics.org/ecoinfo/issues/48102010-02-18T21:40:38ZOliver Soongsoong@nceas.ucsb.edu
<p>Open the example MOML and save the composite actor as a KAR file. If you extract the MOML from the KAR, you'll see extra properties:</p>
<p><property name="isMultiport" value="true" class="ptolemy.kernel.util.StringAttribute"/><br /><property name="isMultiport" class="ptolemy.kernel.util.StringAttribute" value="false"><br /></property></p>
<p>and</p>
<pre><code>&lt;property name="dataType" value="unknown" class="ptolemy.kernel.util.StringAttribute"/&gt;<br /> &lt;property name="isMultiport" class="ptolemy.kernel.util.StringAttribute" value="false"&gt;<br />&lt;/property&gt;</code></pre>
<p>This causes problems.</p> Kepler - Bug #4806 (New): add output port to Throw Exceptionhttps://projects.ecoinformatics.org/ecoinfo/issues/48062010-02-18T00:11:32ZOliver Soongsoong@nceas.ucsb.edu
<p>In some of my workflows, I have an actor that checks that certain components are installed and working before trying to run the workflow. If things are missing, it uses the Throw Exception actor to stop execution and display an error message. Right now, it's possible for the director to schedule the entire workflow before the error check, even if I use the "check" actor as a trigger. I just want some way to convince the director that needs to fire the Throw Exception actor before the rest of the workflow.</p> Kepler - Bug #4795 (New): RExpression & cache cleaninghttps://projects.ecoinformatics.org/ecoinfo/issues/47952010-02-13T00:15:09ZOliver Soongsoong@nceas.ucsb.edu
<p>My .kepler cache bloats pretty quickly because of RExpression's temporary files. Can we have RExpression clear it's cache folder on initialize? This way, if we need to inspect those temporary files after Kepler closes, we still can, but we'll inhibit cache bloat. I suggest doing this automatically because, while I might know what's safe to delete, I've been operating under the assumption that end users aren't expected to learn the internal structure and dependencies of .kepler.</p> Kepler - Bug #4639 (New): add support for -Drev to ant change-tohttps://projects.ecoinformatics.org/ecoinfo/issues/46392009-12-18T23:18:03ZOliver Soongsoong@nceas.ucsb.edu
<p>Doesn't happen very often, but I often am not checking out the head revision, and so it would be nice if ant change-to -Dsuite=wrp -Drev=22258 worked in the logical fashion. Not at all important, but probably not very hard.</p> Kepler - Bug #4613 (New): EML 2 Dataset automatically updating to latest package doesn't trigger ...https://projects.ecoinformatics.org/ecoinfo/issues/46132009-12-09T01:43:12ZOliver Soongsoong@nceas.ucsb.edu
<p>I have a saved workflow that uses judithk.40.47 in an EML 2 Dataset actor. It also has "Check for latest version" checked. The LSID is urn:lsid:gamma.msi.ucsb.edu/OpenAuth/:965:34:50. judithk.40 is currently at judithk.40.48. When I open Kepler, it prompts to update the actor to use the latest version. When closing Kepler, it doesn't prompt to save changes. If I let Kepler update the workflow to use judithk.40.48 and save, the LSID is not updated.</p> Kepler - Bug #4591 (New): ImageJ creating folders based on file paths from prior executions saved...https://projects.ecoinformatics.org/ecoinfo/issues/45912009-12-01T19:05:29ZOliver Soongsoong@nceas.ucsb.edu
<p>Not a hugely important bug and unlikely to cause any actual problems, but a bug nonetheless.</p>
<p>If I generate a workflow with an ImageJ actor, run it, then save it, the last image's path and filename will be saved into the MOML for the ImageJ actor.</p>
<p>If I take this workflow to another computer and open it, an empty file will be created at that saved path and filename, as long as Kepler has write permissions.</p>
<p>When transporting the workflow across platforms, it means folders can end up in weird places. I've seen home/soong/.kepler/... show up in a temp folder, on my desktop, and at the drive root, among other places.</p> Kepler - 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> Kepler - 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> Kepler - Bug #4407 (New): RExpression problems with named non-numeric vectorshttps://projects.ecoinformatics.org/ecoinfo/issues/44072009-09-24T15:12:50ZOliver Soongsoong@nceas.ucsb.edu
<p>RExpression seems to have a problem outputting named non-numeric vectors that is not present with named numeric vectors.</p>
<p>See attached workflow for examples.</p> Kepler - Bug #3803 (New): Cannot open a workflow through the command prompt, open with, or send t...https://projects.ecoinformatics.org/ecoinfo/issues/38032009-01-30T01:04:24ZOliver Soongsoong@nceas.ucsb.edu
<p>XP Pro x64 SP2, Java 1.6.0_11, Kepler 1.0.0 from kepler-project.org</p>
<p>If I right click a workflow file and select Open With->Kepler, I get an error.</p>
<p>If I add a shortcut to Kepler to my SendTo menu, then right click the workflow file and use the Send To link, I get the same error.</p>
<p>If I call Kepler from the command prompt with the workflow as the only argument, I get the same error.</p>
<p>An image of the error is at the URL.</p>
<p>I think this feature is available under linux: <br /><a class="external" href="https://dev.kepler-project.org/developers/reference/executing-kepler-from-the-command-line">https://dev.kepler-project.org/developers/reference/executing-kepler-from-the-command-line</a></p>