Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362010-03-17T23:00:19ZEcoinformatics Redmine
Redmine Bug #4888 (Resolved): Runs with 1 error don't highlight red in WRMhttps://projects.ecoinformatics.org/ecoinfo/issues/48882010-03-17T23:00:19ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Looks like the code for dealing with errors is a little broken after the recent refactor of WorkflowRun: Runs with 1 error don't highlight red in the WRM because getErrorMessages always returns 0.</p> Bug #4851 (Resolved): KarEntryAttributes not saved in MANIFEST.MF/KarXMLhttps://projects.ecoinformatics.org/ecoinfo/issues/48512010-02-26T23:09:08Zben leinfelderleinfelder@nceas.ucsb.edu
<p>I'm trying to add some key metadata entries to the KAREntries I provide in the ReportInstanceKAREntryHandler. I can see them added successfully to the KAREntry, but they do not end up in the MANIFEST.MF. I believe they would show up in the KarXML if I could actually generate it on my current system, but I'm having difficulties getting report instances to export/upload from the WRM...</p> Bug #4802 (Resolved): KARs in KeplerData/workflows are being parsed on startuphttps://projects.ecoinformatics.org/ecoinfo/issues/48022010-02-17T22:13:34Zben leinfelderleinfelder@nceas.ucsb.edu
<p>When I launch Kepler with a clean cache but with a workflow sitting in my local workflow directory that uses protected KNB data, I am prompted to authenticate.<br />We should not be prompting people for authentication credentials on startup - only if I try to open the kar file should it be processed.<br />This used to happen, then it was fixed, now it is back again.</p> Bug #4682 (Resolved): losing reports from KARshttps://projects.ecoinformatics.org/ecoinfo/issues/46822010-01-21T01:10:30Zben leinfelderleinfelder@nceas.ucsb.edu
<p>I'm losing reports (still? again? I don't even know anymore). I'm<br />running r22544, with the modification to RExpression.java that I<br />e-mailed you about. I opened the tpc09 KAR (r430), and tried to<br />remove the <> signs (3 actors in the structure/analysis composite<br />actor). I deleted the <> signs, then changed the display name to put<br />them back. I then saved the KAR, and lost the report. The first<br />time, I had tried exporting a run archive (forgot about the <><br />problem), then made the <> name changes and tried saving them. I then<br />restarted Kepler, made the same <> name changes, and then tried saving<br />them and lost the report a second time. I don't have time today to<br />try it one more time, and I wouldn't be particularly surprised if it<br />worked the third or fourth time. However, the console log isn't<br />helpful. I've attached the log and the bogus KAR. You can check out<br />the starting KAR, which has the report, from svn.</p> Bug #4600 (Resolved): Changing workflow & running causes "execution history not found" message to...https://projects.ecoinformatics.org/ecoinfo/issues/46002009-12-04T01:21:03ZOliver Soongsoong@nceas.ucsb.edu
<p>This uses the example workflow in bug 4598.</p>
<p>Run the workflow. Change "Figure Number" to 12 and run again. Now view the report. The "No execution history found" message should appear. The displayed report is the old one.</p>
<p>This may be related to bug 4599.</p> Bug #4590 (Resolved): Workflow Run Manager - Export Archive can give errorhttps://projects.ecoinformatics.org/ecoinfo/issues/45902009-12-01T18:42:25ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Export Archive from WRM has problems again, I think with the recent changes to Cache. Yesterday fixed an out of range error in CacheManager in r21929, but there's now an error about adding to library.</p> Bug #4529 (Resolved): NPE while saving KAR crashes Keplerhttps://projects.ecoinformatics.org/ecoinfo/issues/45292009-11-04T06:19:39ZOliver Soongsoong@nceas.ucsb.edu
<p>While exploring another bug, I encountered this NPE, and it entirely killed Kepler. This happened after saving a workflow into a local repository. I don't know specifically how to replicate it, though.</p>
<p>done writing KAR file to C:\Documents and Settings\visitor\Desktop\kepler\workflows\test1.kar<br />java.lang.NullPointerException<br /> at org.kepler.kar.handlers.ActorMetadataKAREntryHandler.open(ActorMetadataKAREntryHandler.java:217)<br />[...]<br />ERROR (org.kepler.kar.handlers.ActorMetadataKAREntryHandler:open:235) error opening the workflow: null<br /> at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)</p> Bug #4527 (Resolved): reports cannot be loaded when InstanceAuthNamespace changeshttps://projects.ecoinformatics.org/ecoinfo/issues/45272009-11-04T03:39:51ZOliver Soongsoong@nceas.ucsb.edu
<p>Generate a report and save the KAR. Close Kepler, clean-all, delete the configuration folder, LastObjectID, and .ptolemy-compiled (I think that's almost everything that Kepler generates). Run Kepler again, and open the KAR. The report layout should be there. Now close Kepler and delete only InstanceAuthNamespace. Run Kepler again and open the KAR. The report should not be there.</p>
<p>This makes it hard to transport a KAR file to another computer or even another build of Kepler.</p> Bug #4512 (Resolved): missing entries with multiple copies of the same KAR file in a single repos...https://projects.ecoinformatics.org/ecoinfo/issues/45122009-10-28T22:43:23ZOliver Soongsoong@nceas.ucsb.edu
<p>Things don't seem to work right if I have multiple copies of the same KAR file in a single local repository. I think this is related to only one entry for an LSID being allowed in a repository.</p>
<p>If I make a file system copy of the KAR file, only one copy (the oldest?) will show up in Kepler, which could be reasonable if potentially confusing and inconvenient. I presume this is because the KAR files have identical LSIDs.</p>
<p>However, if I open the KAR in Kepler and Save Archive to create a copy, that copy will show up in Kepler, will appear to be empty (lacking XML and ROML entries), but can be opened. The original remains as before. I think this is because the KAR files have different LSIDs, but the XML and ROML files have the same.</p>
<p>Maybe this is as intended, but it's certainly confusing because the KARs look empty and the folder/KAR listing does not accurately reflect the file system structure.</p> Bug #4510 (Resolved): can't add local repository if its name begins with the name of another loca...https://projects.ecoinformatics.org/ecoinfo/issues/45102009-10-28T19:24:57ZOliver Soongsoong@nceas.ucsb.edu
<p>If I've added C:\Documents and Settings\soong\Desktop\kruger as a local repository, I can't add C:\Documents and Settings\soong\Desktop\kruger2. It complains that one is a subdirectory of the other, even though they are not.</p> Bug #4477 (Resolved): Grey out "undraggables"https://projects.ecoinformatics.org/ecoinfo/issues/44772009-10-16T19:17:34Zben leinfelderleinfelder@nceas.ucsb.edu
<p>In the Components tree we now have non-workflow items (items contained in KARs). These should be marked as different so that it's clear that we are mixing metaphors.</p> Bug #4475 (Resolved): Order context menu items consistentlyhttps://projects.ecoinformatics.org/ecoinfo/issues/44752009-10-16T19:15:36Zben leinfelderleinfelder@nceas.ucsb.edu
<p>There is a mix of options, sure, but options that appear across different context menus (ie "Open") should appear in similar locations on the list.</p> Bug #4457 (Resolved): Workflow Run Manager - past Report Layouts don't openhttps://projects.ecoinformatics.org/ecoinfo/issues/44572009-10-15T00:13:46ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>If in WRP you create a report layout, run the workflow, quit and restart kepler, and then "Open Workflow in New Window" for this run, the workflow and report for will be viewable, but the report layout does not show up.</p> Bug #4410 (Resolved): Cannot open KARs from arbitrary location on diskhttps://projects.ecoinformatics.org/ecoinfo/issues/44102009-09-24T18:12:15ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>You cannot open a KAR from an arbitrary location on disk, it must reside in a local repository.</p>
<p>One work-around is to create a dialog that prompts the user to move such a KAR into a local repo when they try to open it.</p>
<p>If we're going to keep this restriction in place, I would also think the Save Archive dialog shouldn't allow, or at least make difficult, the saving of KARs in locations besides local repositories.</p> Bug #4362 (Resolved): component search performancehttps://projects.ecoinformatics.org/ecoinfo/issues/43622009-09-01T20:27:55ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>For awhile now I've noticed the first search of the library has become much slower than it used to be, subsequent searches seemed to be fine, at least in the same window.</p>
<p>Just recently I've noticed the more Kepler windows I have open, the slower component search becomes. If I have 2 windows open when using WRP suite w/ my eclipse build on mac w/ 4gb ram, doing a search for "string" in the second window will generally crash Kepler with errors about Java heap space:<br />Exception in thread "AWT-EventQueue-0" java.lang.OutOfMemoryError: Java heap space<br /> at java.util.LinkedList.addBefore(LinkedList.java:634)<br /> at java.util.LinkedList.add(LinkedList.java:196)<br /> at ptolemy.kernel.CompositeEntity.entityList(CompositeEntity.java:788)<br /> at ptolemy.moml.EntityLibrary.entityList(EntityLibrary.java:357)</p>
<p>I've also seen this occasionally, though I'm not sure if it's related:<br />2009-09-01 13:04:36.530 java[50021:80f] Apple AWT Startup Exception : *** Collection <NSCFArray: 0x19e18d10> was mutated while being enumerated.<br />2009-09-01 13:04:36.531 java[50021:80f] Apple AWT Restarting Native Event Thread</p>
<p>On my linux cmd line build, just using kepler suite, I also notice performace issues, though it takes more windows for them to become severe. Once I have 7 kepler windows open, search for "string" takes about 12 seconds.</p>