Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362014-08-21T16:52:36ZEcoinformatics Redmine
Redmine Feature #6587 (New): summarize missing actorshttps://projects.ecoinformatics.org/ecoinfo/issues/65872014-08-21T16:52:36ZDaniel Crawldanielcrawl@gmail.com
<p>If a workflow is opened that contains actors that are not present in the class path, an error dialog is displayed for each actor. It would be nice if a list of all the missing actors were displayed.</p>
<p>Attached is a modified MoMLParser.java (based on ptolemy-kepler-2.4 sources) from Philippe Huyhn that displays the missing actors. The list of missing actors is written to stdout. Using MessageHandler would be preferred since it displays a dialog, but MessageHandler appears to not allow copy and paste.</p> Bug #5691 (New): parameter choices are not savedhttps://projects.ecoinformatics.org/ecoinfo/issues/56912012-08-20T23:27:06ZDaniel Crawldanielcrawl@gmail.com
<p>The choices for Parameter.addChoice() are not written when the model is saved.</p> Bug #5689 (New): remove configs/.../configuration.xml overridehttps://projects.ecoinformatics.org/ecoinfo/issues/56892012-08-18T02:44:23ZDaniel Crawldanielcrawl@gmail.com
<p>The Ptolemy Configuration MoML for Kepler is in:</p>
<p>common/configs/ptolemy/configs/kepler/configuration.xml</p>
<p>This is overridden in several modules:</p>
<p>ddp-common/configs/ptolemy/configs/kepler/configuration.xml<br />fault-tolerance/configs/ptolemy/configs/kepler/configuration.xml<br />map-reduce/configs/ptolemy/configs/kepler/configuration.xml</p>
<p>As with other overrides, the problem is that when the master version changes, the copies need to be updated.</p>
<p>The difference is small:</p>
<p>diff common/configs/ptolemy/configs/kepler/configuration.xml fault-tolerance/configs/ptolemy/configs/kepler/configuration.xml <br />181a182</p>
<blockquote>
<p><input source="ptolemy/configs/kepler/contingencyTableauFactory.xml"/></p>
</blockquote>
<p>diff common/configs/ptolemy/configs/kepler/configuration.xml ddp-common/configs/ptolemy/configs/kepler/configuration.xml<br />181a182</p>
<blockquote>
<p><input source="ptolemy/configs/kepler/executionChoiceTableauFactory.xml"/></p>
</blockquote> Bug #5670 (New): see if runtimemonitor module can be deleted, contains duplicate codehttps://projects.ecoinformatics.org/ecoinfo/issues/56702012-08-10T01:45:49ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>The runtimemonitor module contains these classes:</p>
<p>./runtimemonitor/FigureUpdater.java<br />./runtimemonitor/MonitorAttribute.java<br />./runtimemonitor/MonitoredStatus.java<br />./runtimemonitor/MonitorIcon.java<br />./runtimemonitor/ProcessCentral.java<br />./runtimemonitor/ProcessCentralWindow.java<br />./runtimemonitor/RuntimeMonitor.java<br />./runtimemonitor/TableData.java</p>
<p>Everything but ProcessCentral, ProcessCentralWindow, and TableData are near duplicates of code now in gui.</p>
<p>fsaresh worked on this. Is this code used? Should the module be removed? I don't know if anything is using it anymore. Sensor-view and vanilla don't, so this bug isn't high priority.</p>
<p>I also see at r17463 dzinn also checked in duplicates of these classes to the pws module, which I don't know anything about.</p> Bug #5631 (New): PortParameters cannot be drag-instantiated from Outline/Items of Interest treeshttps://projects.ecoinformatics.org/ecoinfo/issues/56312012-06-19T20:23:27ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>You cannot drag out a PortParameter from the Outline/Items of Interest trees. The reason is ptolemy change r57732 to ParameterPort to avoid bug#4915:<br /> Parameter notDraggable = new Parameter(this, "_notDraggable");<br /> notDraggable.setPersistent(false);</p>
<p>This change should be removed and bug#4915 properly fixed. As part of this, we need to ensure proper behavior when dragged out from the Outline tab, and the Items of Interest panes in both Reporting and Plotting.</p> Bug #5628 (New): possible to get NPE when right-clicking on kar in Components treehttps://projects.ecoinformatics.org/ecoinfo/issues/56282012-06-15T23:25:41ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>It's possible to get this NPE when right-clicking on a KAR in the Components pane. I don't have a replication procedure yet. I think this is the first time I've seen this, so it's either new or uncommon.</p>
<p>Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException<br /> at java.io.File.<init>(File.java:222)<br /> at org.kepler.gui.popups.KARPopup.<init>(KARPopup.java:64)<br /> at org.kepler.gui.popups.LibraryPopupListener.handlePopupOutsideKar(LibraryPopupListener.java:116)<br /> at org.kepler.gui.popups.LibraryPopupListener.maybeShowPopup(LibraryPopupListener.java:235)<br /> at org.kepler.gui.popups.LibraryPopupListener.mouseReleased(LibraryPopupListener.java:66)<br /> at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:273)<br /> at java.awt.Component.processMouseEvent(Component.java:6375)<br /> at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)<br /> at java.awt.Component.processEvent(Component.java:6140)<br /> at java.awt.Container.processEvent(Container.java:2083)<br /> at java.awt.Component.dispatchEventImpl(Component.java:4737)<br /> at java.awt.Container.dispatchEventImpl(Container.java:2141)<br /> at java.awt.Component.dispatchEvent(Component.java:4565)<br /> at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4619)<br /> at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4280)<br /> at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4210)<br /> at java.awt.Container.dispatchEventImpl(Container.java:2127)<br /> at java.awt.Window.dispatchEventImpl(Window.java:2482)<br /> at java.awt.Component.dispatchEvent(Component.java:4565)<br /> at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:684)<br /> at java.awt.EventQueue.access$000(EventQueue.java:85)<br /> at java.awt.EventQueue$1.run(EventQueue.java:643)<br /> at java.awt.EventQueue$1.run(EventQueue.java:641)<br /> at java.security.AccessController.doPrivileged(Native Method)<br /> at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)<br /> at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)<br /> at java.awt.EventQueue$2.run(EventQueue.java:657)<br /> at java.awt.EventQueue$2.run(EventQueue.java:655)<br /> at java.security.AccessController.doPrivileged(Native Method)<br /> at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)<br /> at java.awt.EventQueue.dispatchEvent(EventQueue.java:654)<br /> at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)<br /> at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)<br /> at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)<br /> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)<br /> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)<br /> at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)</p> Bug #5333 (New): 2.2 rc3: getenv("") doesn't work for mac installation.https://projects.ecoinformatics.org/ecoinfo/issues/53332011-03-01T23:46:41Zjianwu jianwujianwu@sdsc.edu
<p>getenv is to get environment variable value in Kepler. It works for me in my installation on windows. On mac, it doesn't work if I start Kepler using Kepler.app. It only works if I start using Kepler.app/Contents/Resources/Java/kepler.sh.</p> Bug #5276 (New): component search performance is poorhttps://projects.ecoinformatics.org/ecoinfo/issues/52762011-01-24T22:21:07ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Searching for remote KARs through the Components pane is very slow -- search downloads and deals with karXML, each generally about twice as big as the kar it represents. During search the GUI is locked, and there is no progress indicator letting you know search is happening.</p>
<p>The query and related code probably need to be refactored to only download and utilize the bare minimum to show the results. This refactoring may necessitate some changes to what actions are possible on items in the results tree.</p>
<p>Jing and Matt will discuss this bug.</p> Bug #5170 (New): uploading a workflow requires a refreshhttps://projects.ecoinformatics.org/ecoinfo/issues/51702010-09-03T19:48:36ZDaniel Crawldanielcrawl@gmail.com
<p>When a workflow is uploaded to a remote repository, the component tree must be searched again before the workflow appears. It'd be nice if the workflow appeared when the upload completed.</p> Bug #5129 (In Progress): adding and removing configuration properties could be made easierhttps://projects.ecoinformatics.org/ecoinfo/issues/51292010-08-06T21:21:25ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Now that we've shipped 2.0, if a developer wants to add a new configuration property to a config file, they must first check if the user's config file has the property before accessing it, and add it if not. This is a minor hassle if your code tries to use this property in a number of places, each of which might be reached first during the user's kepler session...you have to do the check and possible add at each place. Instead, maybe the configuration manager could, during startup, run through all active modules config files and add properties if necessary to the user's copies in KeplerData. Handing removing properties would be harder -- if we remove a property, and then a user reverts to an older version of Kepler, this CM method would have to know to add the property back for that version.</p> Bug #4953 (In Progress): Remote Components category sticks around sometimeshttps://projects.ecoinformatics.org/ecoinfo/issues/49532010-04-21T00:51:03ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>If I search KeplerDevRepository for "run2", I currently get back one result: run2-mclaughlin_par,kar, inside the new category of Remote Components.<br />If I right-click on the kar and select Download, and then clear my search by, on the mac, hitting the little x button, or by hitting the Cancel button, the Remote Components category stills shows up in the tree. If you don't select download, the Remote Components category disappears, as I believe is intended.</p> Bug #4801 (In Progress): out of memoryhttps://projects.ecoinformatics.org/ecoinfo/issues/48012010-02-17T22:13:10ZOliver Soongsoong@nceas.ucsb.edu
<p>ERROR: RecordingException: Unable to query data table: out of memory</p>
<p>I opened tpc01, ran it, closed it, opened tpc03-herbs, ran it, closed it, opened tpc03-large-herbivores, ran it, closed it, opened tpc03-woody, ran it, closed it, opened tpc09, ran it, and hit the above out of memory error. I have 68 runs in the wrm, but 63 of them are various iterations of the small test workflow for bug 4789. I also have those 5 Kruger KARs in a local repository and all the data for them is cached. I can start Kepler and run any of those workflows by themselves. I started Kepler with an ant run, so the jvm should have a 512MB memory max.</p>
<p>Kruger workflows: <a class="external" href="https://code.ecoinformatics.org/code/kruger/trunk/workflows">https://code.ecoinformatics.org/code/kruger/trunk/workflows</a><br />Kruger: r439<br />Kepler: wrp r23080</p>
<p>It may be worth looking at bug 4642.</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 #4139 (In Progress): port names are displayed twicehttps://projects.ecoinformatics.org/ecoinfo/issues/41392009-06-09T02:20:31ZOliver Soongsoong@nceas.ucsb.edu
<p>When I choose to show port names, they are displayed once next to the port as expected and once in the upper left corner of the actor in a bold-looking font. This appears in both XP and linux.</p> Bug #3903 (New): Use Java logging utilities instead of Apache commons logging facilityhttps://projects.ecoinformatics.org/ecoinfo/issues/39032009-03-18T19:21:30ZChristopher Brookscxh@eecs.berkeley.edu
<p>ersonally, I'd like to switch to the logging utilities that<br />now ship with Java, see<br /><a class="external" href="http://java.sun.com/j2se/1.4.2/docs/guide/util/logging/">http://java.sun.com/j2se/1.4.2/docs/guide/util/logging/</a><br />The advantage is that it would be one less jar file to ship.<br />A quick search finds 144 files that use the apache logging facility.<br />Most of these changes could be handled automatically by a script.</p>
<p>Notes about the logging system can be found at<br /><a class="external" href="https://kepler-project.org/developers/reference/using-commons-logging">https://kepler-project.org/developers/reference/using-commons-logging</a></p>