Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362010-02-19T01:18:40ZEcoinformatics Redmine
Redmine 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> 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> 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> 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> 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> Bug #4613 (New): EML 2 Dataset automatically updating to latest package doesn't trigger "workflow...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> Bug #4591 (New): ImageJ creating folders based on file paths from prior executions saved in the MOMLhttps://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> 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 #4429 (New): EML 2 Dataset requires File Extension Filter parameterhttps://projects.ecoinformatics.org/ecoinfo/issues/44292009-09-30T20:43:38ZOliver Soongsoong@nceas.ucsb.edu
<p>I'm not 100% sure this isn't just a lack of documentation. When using EML 2 Dataset on a compressed data table (so using the As UnCompressed File Name Data Output Format), EML 2 Dataset will not function properly without a value in the File Extension Filter parameter. There does not seem to be a way to get all the files, regardless of extension, nor does there seem to be a way to get multiple extension types.</p>
<p>Personally, I'd be happy if the actor returned all files if the File Extension Parameter is blank.</p> Bug #4360 (New): Kepler gets slow under XPhttps://projects.ecoinformatics.org/ecoinfo/issues/43602009-08-31T23:33:06ZOliver Soongsoong@nceas.ucsb.edu
<p>I've been holding off on this, because it's hard to demonstrate, OS-specific, and quite difficult to debug, but it's getting to be problematic. Kepler slows significantly under XP. It's noticeable following the example of <a class="external" href="http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4359">http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4359</a>. This particular bug may exacerbate the problem, but it has been noticeable in other unrelated situations. I'd quote duration statistics, but much of the time is spent in the Preinitializing and Wrapping Up which aren't included in the duration.</p>
<p>I'd argue for the importance of this for the release. My understanding is that most devs use macs, while much of our user-base (at least in South Africa, but likely elsewhere as well) uses XP.</p>
<p>It's possible this is related to the Java VM version, but I'm not certain about that.</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 #3973 (New): Additional information for 64-bit users installing 1.0.0https://projects.ecoinformatics.org/ecoinfo/issues/39732009-04-10T23:12:04ZOliver Soongsoong@nceas.ucsb.edu
<p>Kepler 1.0.0 on 64-bit Windows systems seems to require a 32-bit java install, which is not the default provided by java.com. The error claims Java 1.5.0 could not be found, even if 1.5.0 is installed and even though it works with Java 1.6.0. At the very least, a note indicating such at kepler-project.org would help, and this seems to affect both XP and Vista.</p> Bug #3803 (New): Cannot open a workflow through the command prompt, open with, or send to menushttps://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>