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 #4809 (New): Kepler storing authenticated search resultshttps://projects.ecoinformatics.org/ecoinfo/issues/48092010-02-18T20:18:18ZOliver Soongsoong@nceas.ucsb.edu
<p>From a clean cache, start Kepler and search using authenticated sources. Authenticate and Kepler will return search results. Restart Kepler and perform the same search again. Kepler will not ask for credentials. Try instantiating a dataset that requires authentication, and Kepler will ask for credentials. Restart Kepler and perform a search for a different term and Kepler will ask for credentials.</p>
<p>It looks like the search results are cached. Since access to new data requires authentication, new searches require authentication, and access to previously cached authenticated data does not, this may not be a problem.</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 #4764 (New): ProvenanceRecorder.changeExecuted slow after workflow runhttps://projects.ecoinformatics.org/ecoinfo/issues/47642010-02-06T02:19:48ZOliver Soongsoong@nceas.ucsb.edu
<p>If I run any of the tpc workflows (e.g., tpc09), any subsequent changes to Kepler (say changing workflow parameters) cause Java to peg one of my CPU cores. This includes canceling changes to RExpression. I've seen this behavior on Windows XP and 7. While I haven't seen it under linux or OS X, I haven't tested those as extensively. I have tried small test workflows, and haven't seen a particularly noticeable slowdown, so it may be related to the size of the workflow run. I have to restart Kepler to get things back up to speed, and it's bad enough that I'm actually restarting Kepler after every run.</p>
<p>I'm not sure it's a memory thing. java.exe is about maxed out on memory (~0.5 GB) in the Task Manager, but the Check System Settings window says I have 46% free. I was watching jstat, and changes don't seem to trigger a flurry of garbage collection.</p> Kepler - Bug #4642 (New): memory usage & slowdownshttps://projects.ecoinformatics.org/ecoinfo/issues/46422009-12-19T03:45:53ZOliver Soongsoong@nceas.ucsb.edu
<p>I just hit a big slowdown caused by OOM problems. This bug is mostly a place to put down some of the stuff I found out. I used jmap to produce histograms when Kepler was crawling and immediately after a fresh restart. When Kepler was slow, there was a single workflow open with 4 actors and the Check System Settings window. The fresh Kepler retained the wrm and cache content, but discarded the 4 actors and all the accumulated memory leaking cruft.</p>
<p>A few things jump out at me, and I'd say I'm pretty uninformed. I've formatted as Object: stale #, fresh #.</p>
<p>org.kepler.util.WorkflowRun: 39206, 29<br />javax.swing.JMenuItem: 3411, 96<br />java.util.HashMap: 689643, 22885<br />org.kepler.objectmanager.lsid.KeplerLSID: 120115, 1339<br />java.util.LinkedList: 95565, 4468<br />ptolemy.kernel.util.Location: 1837, 45</p>
<p>Interestingly enough, I have 28 wrm entries. I think something's up with the wrm, but also a lot of GUI objects seem to be hanging around as well, so there may be other things going on as well.</p>
<p>And on a side note, jps -> jmap -> jhat produces some pretty cool results.</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 #4564 (New): Model Reference throws error with workflows in the same folder, but sti...https://projects.ecoinformatics.org/ecoinfo/issues/45642009-11-20T03:11:08ZOliver Soongsoong@nceas.ucsb.edu
<p>If I have a referring model (referring.xml) and a referred model (referred.xml) in the same folder, I have difficulty running the workflow. I get an error message that states "Not a file: file:/C:/Documents%20and%20Settings/soong/Desktop/kepler/referred.xml", even though both workflows are located at C:/tmp.</p>
<p>However, if I Skip element, both workflows execute as expected. Alternatively, if I refer to the referred document as ../tmp/referred.xml, both workflows also execute as expected.</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>