Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362012-12-05T23:30:58ZEcoinformatics Redmine
Redmine Bug #5760 (In Progress): saving xml to existing file asks twice on machttps://projects.ecoinformatics.org/ecoinfo/issues/57602012-12-05T23:30:58ZDaniel Crawldanielcrawl@gmail.com
<p>On Mac, when saving a workflow as XML to an existing file, there are two dialogs that ask to overwrite the existing file. This occurs in Vergil, too.</p> Bug #5444 (In Progress): Kepler can't run workflow if two instances exist at same timehttps://projects.ecoinformatics.org/ecoinfo/issues/54442011-07-30T00:21:27ZJing Taotao@nceas.ucsb.edu
<p>Both vanilla and reporting suites (2.3) have problems. But the behaviors are different:<br />1. Vanilla kepler:</p>
<p>Start a kepler then start antoher one. The second one runs a workflow. Then close the first kepler. Finally close the second one, it shows the error:<br />java.sql.SQLException: Connection is broken: java.io.EOFException<br />at org.hsqldb.jdbc.Util.sqlException(Unknown Source)<br />at org.hsqldb.jdbc.jdbcStatement.fetchResult(Unknown Source)<br />at org.hsqldb.jdbc.jdbcStatement.execute(Unknown Source)<br />at org.kepler.util.sql.DatabaseType._executeSQL(DatabaseType.java:930)<br />at org.kepler.util.sql.HSQL.disconnect(HSQL.java:79)<br />at org.kepler.objectmanager.lsid.LSIDGenerator.closeDatabase(LSIDGenerator.java:400)<br />at org.kepler.module.core.Shutdown.shutdownModule(Shutdown.java:48)<br />at org.kepler.Kepler._initializeModules(Kepler.java:572)<br />at org.kepler.Kepler.access$100(Kepler.java:81)<br />at org.kepler.Kepler$Shutdown.shutdown(Kepler.java:663)<br />at org.kepler.util.ShutdownNotifier.shutdown(ShutdownNotifier.java:48)<br />at org.kepler.gui.KeplerGraphFrame.dispose(KeplerGraphFrame.java:1146)</p>
<p>2. Reporting kepler.<br />Two kepers are running. One runs a workflow and get an error:<br /><jing> ptolemy.kernel.util.IllegalActionException: Error recording workflow structure: Error connecting or initializing database.
{DB User Name=sa, Password=, DB Host=, DB Name=provenanceDB, DB Type=HSQL, DB Port=9002, DB Table Prefix=, JDBC URL=}<br />The database is already in use by another process: lockFile: org.hsqldb.persist.LockFile@aef9f24b[file =/home/tao/KeplerData/modules/provenance/db-2.3/provenanceDB.lck, exists=true, locked=false, valid=false, ] method: checkHeartbeat read: 2011-07-28 13:32:04.979 heartbeat - read: -8463 ms.<br />in .testWithReport.TOP Provenance Recorder<br />Because:<br />Error connecting or initializing database.
{DB User Name=sa, Password=, DB Host=, DB Name=provenanceDB, DB Type=HSQL, DB Port=9002, DB Table Prefix=, JDBC URL=}<br />The database is already in use by another process: lockFile: org.hsqldb.persist.LockFile@aef9f24b[file =/home/tao/KeplerData/modules/provenance/db-2.3/provenanceDB.lck, exists=true, locked=false, valid=false, ] method: checkHeartbeat read: 2011-07-28 13:32:04.979 heartbeat - read: -8463 ms.<br />at org.kepler.provenance.ProvenanceRecorder._recordWorkflowContents(ProvenanceRecorder.java:2618)<br />at org.kepler.provenance.ProvenanceRecorder.preinitialize(ProvenanceRecorder.java:583)<br />at ptolemy.actor.CompositeActor.preinitialize(CompositeActor.java:1682)<br />at ptolemy.actor.Manager.preinitializeAndResolveTypes(Manager.java:930)<br />at ptolemy.actor.Manager.initialize(Manager.java:636)<br />at ptolemy.actor.Manager.execute(Manager.java:340)<br />at ptolemy.actor.Manager.run(Manager.java:1111)<br />at ptolemy.actor.Manager$PtolemyRunThread.run(Manager.java:1641)</p> Bug #5249 (In Progress): test kepler for memory leakshttps://projects.ecoinformatics.org/ecoinfo/issues/52492010-11-30T22:50:17Zjianwu jianwujianwu@sdsc.edu
<p>a separate bug only for memory leak fixing for Kepler suite. bug 5095 depends on it.</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 #5048 (In Progress): Can't clean (or do other build system operations) offlinehttps://projects.ecoinformatics.org/ecoinfo/issues/50482010-06-14T21:57:22ZSean Riddleswriddle@gmail.com
<p>When I try to run "ant clean" from the sensor-view suite, I get the exception below. The module kepler-2.0.^ is not referenced by the modules.txt file, directly or otherwise, but is referenced in the modules.txt of an inactive module that is downloaded.</p>
<p>clean:<br /> [clean] Transforming arrow name for get: kepler-2.0.^<br /> [clean] java.lang.NullPointerException<br /> [clean] at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:105)<br /> [clean] at org.kepler.build.modules.Module.readPublished(Module.java:226)<br /> [clean] at org.kepler.build.modules.Module.tranformArrowNameForGet(Module.java:280)<br /> [clean] at org.kepler.build.modules.Module.transformName(Module.java:312)<br /> [clean] at org.kepler.build.modules.Module.<init>(Module.java:144)<br /> [clean] at org.kepler.build.modules.Module.<init>(Module.java:192)<br /> [clean] at org.kepler.build.modules.Suite.<init>(Suite.java:79)<br /> [clean] at org.kepler.build.modules.ModulesTxt.readHelper(ModulesTxt.java:148)<br /> [clean] at org.kepler.build.modules.ModulesTxt.read(ModulesTxt.java:120)<br /> [clean] at org.kepler.build.modules.Module.getModulesTxt(Module.java:604)<br /> [clean] at org.kepler.build.modules.ModuleUtil.getCurrentSuiteName(ModuleUtil.java:220)<br /> [clean] at org.kepler.build.modules.ModuleTree.<init>(ModuleTree.java:56)<br /> [clean] at org.kepler.build.modules.ModuleTree.init(ModuleTree.java:98)<br /> [clean] at org.kepler.build.modules.ModuleTree.instance(ModuleTree.java:86)<br /> [clean] at org.kepler.util.DotKeplerManager.initialize(DotKeplerManager.java:141)<br /> [clean] at org.kepler.util.DotKeplerManager.getInstance(DotKeplerManager.java:114)<br /> [clean] at org.kepler.build.project.ProjectLocator.getCacheFile(ProjectLocator.java:60)<br /> [clean] at org.kepler.build.UpdatePresentTxt.run(UpdatePresentTxt.java:64)<br /> [clean] at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:101)<br /> [clean] at org.kepler.build.modules.Module.readPresent(Module.java:215)<br /> [clean] at org.kepler.build.modules.Module.transformName(Module.java:303)<br /> [clean] at org.kepler.build.modules.Module.<init>(Module.java:144)<br /> [clean] at org.kepler.build.modules.Module.<init>(Module.java:192)<br /> [clean] at org.kepler.build.modules.Suite.<init>(Suite.java:79)<br /> [clean] at org.kepler.build.modules.ModulesTxt.readHelper(ModulesTxt.java:148)<br /> [clean] at org.kepler.build.modules.ModulesTxt.read(ModulesTxt.java:120)<br /> [clean] at org.kepler.build.modules.Module.getModulesTxt(Module.java:604)<br /> [clean] at org.kepler.build.modules.ModuleUtil.getCurrentSuiteName(ModuleUtil.java:220)<br /> [clean] at org.kepler.build.modules.ModuleTree.<init>(ModuleTree.java:56)<br /> [clean] at org.kepler.build.modules.ModuleTree.init(ModuleTree.java:98)<br /> [clean] at org.kepler.build.modules.ModulesTask.init(ModulesTask.java:86)<br /> [clean] at org.apache.tools.ant.ComponentHelper.createComponent(ComponentHelper.java:223)<br /> [clean] at org.apache.tools.ant.UnknownElement.makeObject(UnknownElement.java:414)<br /> [clean] at org.apache.tools.ant.UnknownElement.maybeConfigure(UnknownElement.java:160)<br /> [clean] at org.apache.tools.ant.Task.perform(Task.java:347)<br /> [clean] at org.apache.tools.ant.Target.execute(Target.java:357)<br /> [clean] at org.apache.tools.ant.Target.performTasks(Target.java:385)<br /> [clean] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1337)<br /> [clean] at org.apache.tools.ant.Project.executeTarget(Project.java:1306)<br /> [clean] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)<br /> [clean] at org.apache.tools.ant.Project.executeTargets(Project.java:1189)<br /> [clean] at org.apache.tools.ant.Main.runBuild(Main.java:758)<br /> [clean] at org.apache.tools.ant.Main.startAnt(Main.java:217)<br /> [clean] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:257)<br /> [clean] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:104)<br /> [clean] Caused by: java.lang.NullPointerException<br /> [clean] at org.kepler.build.PublishedTask.trimOlderNames(PublishedTask.java:49)<br /> [clean] at org.kepler.build.UpdatePublishedTxt.run(UpdatePublishedTxt.java:53)<br /> [clean] at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:101)<br /> [clean] ... 44 more<br /> [clean] --- Nested Exception ---<br /> [clean] java.lang.NullPointerException<br /> [clean] at org.kepler.build.PublishedTask.trimOlderNames(PublishedTask.java:49)<br /> [clean] at org.kepler.build.UpdatePublishedTxt.run(UpdatePublishedTxt.java:53)<br /> [clean] at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:101)<br /> [clean] at org.kepler.build.modules.Module.readPublished(Module.java:226)<br /> [clean] at org.kepler.build.modules.Module.tranformArrowNameForGet(Module.java:280)<br /> [clean] at org.kepler.build.modules.Module.transformName(Module.java:312)<br /> [clean] at org.kepler.build.modules.Module.<init>(Module.java:144)<br /> [clean] at org.kepler.build.modules.Module.<init>(Module.java:192)<br /> [clean] at org.kepler.build.modules.Suite.<init>(Suite.java:79)<br /> [clean] at org.kepler.build.modules.ModulesTxt.readHelper(ModulesTxt.java:148)<br /> [clean] at org.kepler.build.modules.ModulesTxt.read(ModulesTxt.java:120)<br /> [clean] at org.kepler.build.modules.Module.getModulesTxt(Module.java:604)<br /> [clean] at org.kepler.build.modules.ModuleUtil.getCurrentSuiteName(ModuleUtil.java:220)<br /> [clean] at org.kepler.build.modules.ModuleTree.<init>(ModuleTree.java:56)<br /> [clean] at org.kepler.build.modules.ModuleTree.init(ModuleTree.java:98)<br /> [clean] at org.kepler.build.modules.ModuleTree.instance(ModuleTree.java:86)<br /> [clean] at org.kepler.util.DotKeplerManager.initialize(DotKeplerManager.java:141)<br /> [clean] at org.kepler.util.DotKeplerManager.getInstance(DotKeplerManager.java:114)<br /> [clean] at org.kepler.build.project.ProjectLocator.getCacheFile(ProjectLocator.java:60)<br /> [clean] at org.kepler.build.UpdatePresentTxt.run(UpdatePresentTxt.java:64)<br /> [clean] at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:101)<br /> [clean] at org.kepler.build.modules.Module.readPresent(Module.java:215)<br /> [clean] at org.kepler.build.modules.Module.transformName(Module.java:303)<br /> [clean] at org.kepler.build.modules.Module.<init>(Module.java:144)<br /> [clean] at org.kepler.build.modules.Module.<init>(Module.java:192)<br /> [clean] at org.kepler.build.modules.Suite.<init>(Suite.java:79)<br /> [clean] at org.kepler.build.modules.ModulesTxt.readHelper(ModulesTxt.java:148)<br /> [clean] at org.kepler.build.modules.ModulesTxt.read(ModulesTxt.java:120)<br /> [clean] at org.kepler.build.modules.Module.getModulesTxt(Module.java:604)<br /> [clean] at org.kepler.build.modules.ModuleUtil.getCurrentSuiteName(ModuleUtil.java:220)<br /> [clean] at org.kepler.build.modules.ModuleTree.<init>(ModuleTree.java:56)<br /> [clean] at org.kepler.build.modules.ModuleTree.init(ModuleTree.java:98)<br /> [clean] at org.kepler.build.modules.ModulesTask.init(ModulesTask.java:86)<br /> [clean] at org.apache.tools.ant.ComponentHelper.createComponent(ComponentHelper.java:223)<br /> [clean] at org.apache.tools.ant.UnknownElement.makeObject(UnknownElement.java:414)<br /> [clean] at org.apache.tools.ant.UnknownElement.maybeConfigure(UnknownElement.java:160)<br /> [clean] at org.apache.tools.ant.Task.perform(Task.java:347)<br /> [clean] at org.apache.tools.ant.Target.execute(Target.java:357)<br /> [clean] at org.apache.tools.ant.Target.performTasks(Target.java:385)<br /> [clean] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1337)<br /> [clean] at org.apache.tools.ant.Project.executeTarget(Project.java:1306)<br /> [clean] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)<br /> [clean] at org.apache.tools.ant.Project.executeTargets(Project.java:1189)<br /> [clean] at org.apache.tools.ant.Main.runBuild(Main.java:758)<br /> [clean] at org.apache.tools.ant.Main.startAnt(Main.java:217)<br /> [clean] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:257)<br /> [clean] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:104)<br /> [clean] Module Directory could not be created</p> Bug #5045 (In Progress): Add a menu to add and configure new remote kepler servershttps://projects.ecoinformatics.org/ecoinfo/issues/50452010-06-09T18:33:14ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Figure 6 (<a class="external" href="https://kepler-project.org/developers/incubation/kepler-engineering-view-for-reap/engineering-view-plans">https://kepler-project.org/developers/incubation/kepler-engineering-view-for-reap/engineering-view-plans</a> ) shows Servers (Server1, Server2) in the Scheduled Workflows section on the left on the Workflow Scheduler view. We need a way for a user to add and configure these servers (address, username, password, database name, port, etc). I believe we've discussed extending the Sources (aka Preferences) menu to add an additional tab for this.</p>
<p>When a user clicks on a workflow listed on one of these servers, a new instance of Workflow Run Manager needs to be created and needs to connect to that server to show the runs, and in order to do this, it needs to access these connection parameters.</p> Bug #4978 (In Progress): Create additional 'module' property for any menu entries that are insert...https://projects.ecoinformatics.org/ecoinfo/issues/49782010-05-05T00:21:51ZSean Riddleswriddle@gmail.com
<p>As of revision r24221 and r24222-3 on the branch, there's a way to avoid those errors that look like:</p>
<pre><code>[run] ERROR (org.kepler.gui.MenuMapper:getActionFor:271) Exception trying to create an Action for classname: &lt;org.kepler.tagging.TagManagerAction&gt;:<br /> [run] null (java.lang.ClassNotFoundException: org.kepler.tagging.TagManagerAction)</code></pre>
<p>Those come from modules inserting menu entry information into the persistent gui module configuration and then the user removing that module from their active configuration. The system still tries to create that entry, which references a class that is no longer available. If a property named 'module' is created as a peer to 'name' and 'value', then the menu entry will only be generated if a module by that name is in the active configuration. See org.kepler.module.tagging.Initialize from the tagging module for an example of how to do this without hardwiring the module name.</p>
<p>So in order to eliminate error messages like the above, these additional properties need to be created when the menu entry is added to the gui configuration.</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 #4869 (In Progress): changes made to workflows during dialogs before committing (Edit Paramet...https://projects.ecoinformatics.org/ecoinfo/issues/48692010-03-04T19:04:24ZOliver Soongsoong@nceas.ucsb.edu
<p>When I make changes to an actor through the dialog, it seems like the changes are made to the workflow immediately, before the "Commit" button is clicked.</p>
<p>For example, create a workflow with an EML 2 Dataset actor. Make sure Kepler has not already authenticated with KNB. Now edit the EML 2 Dataset actor to reference a data package that requires authentication. The KNB login window will immediately pop up, even though no changes have been committed. Dismiss the window in some way. Now click the Help button and close the help window. The dialog will have disappeared. Open the actor dialog again, and the change will be there.</p>
<p>I should point out that the "Cancel" button does seem to work, but I suspect (based on debugging comments and comments in code) that this acts by reverting the changes already made.</p>
<p>I've seen this for sure on EML 2 Dataset and RExpression, since changes to one trigger visual feedback and I've mucked around in the code of the other. I suspect this is a general problem, though, and it may be a result of the underlying ptolemy design.</p> Bug #4859 (In Progress): GDALTranslate does not work on Windows 7 (64bit)https://projects.ecoinformatics.org/ecoinfo/issues/48592010-03-02T15:41:15ZTom Parrisparris@isciences.com
<p>GDALJniGlue fails to intialize on Windows 64bit operating systems.</p>
<p>ptolemy.kernel.util.IllegalActionException: in .GDAL_Translate_test_oak.manager<br />Because:<br />Could not initialize class org.ecoinformatics.seek.gis.gdal.GDALJniGlue<br />at ptolemy.actor.Manager.execute(Manager.java:472)<br />at ptolemy.actor.Manager.run(Manager.java:1119)<br />at ptolemy.actor.Manager$3.run(Manager.java:1160)<br />Caused by: java.lang.NoClassDefFoundError: Could not initialize class org.ecoinformatics.seek.gis.gdal.GDALJniGlue<br />at org.ecoinformatics.seek.gis.gdal.GDALTranslateActor.fire(GDALTranslateActor.java:207)<br />at ptolemy.actor.AtomicActor.iterate(AtomicActor.java:469)<br />at ptolemy.actor.sched.StaticSchedulingDirector.fire(StaticSchedulingDirector.java:188)<br />at ptolemy.actor.CompositeActor.fire(CompositeActor.java:458)<br />at ptolemy.actor.Manager.iterate(Manager.java:714)<br />at ptolemy.actor.Manager.execute(Manager.java:349)<br />... 2 more<br />Caused by: java.lang.NoClassDefFoundError: Could not initialize class org.ecoinformatics.seek.gis.gdal.GDALJniGlue<br />at org.ecoinformatics.seek.gis.gdal.GDALTranslateActor.fire(GDALTranslateActor.java:207)<br />at ptolemy.actor.AtomicActor.iterate(AtomicActor.java:469)<br />at ptolemy.actor.sched.StaticSchedulingDirector.fire(StaticSchedulingDirector.java:188)<br />at ptolemy.actor.CompositeActor.fire(CompositeActor.java:458)<br />at ptolemy.actor.Manager.iterate(Manager.java:714)<br />at ptolemy.actor.Manager.execute(Manager.java:349)<br />at ptolemy.actor.Manager.run(Manager.java:1119)<br />at ptolemy.actor.Manager$3.run(Manager.java:1160)</p> Bug #4811 (In Progress): No "Get Metadata" item on right-click menu after dragging an EML actor t...https://projects.ecoinformatics.org/ecoinfo/issues/48112010-02-18T21:42:45ZJing Taotao@nceas.ucsb.edu
<p>After dragging an EML actor from search result panel to canvas, there was a right-click menu item named "Get Metadata" on Kepler 1.0. User can use the menu item to review eml metadata. However, the "Get Metadata" menu item has gone on kepler 2.0.</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 #4700 (In Progress): Reminder Update Wiki information to reflect Kepler 2.0 release.https://projects.ecoinformatics.org/ecoinfo/issues/47002010-01-27T22:40:59Zdebi staggsstaggs@nceas.ucsb.edu
<p>Update the information on the Wiki to include changes to Kepler in the 2.0 release. Remove any information in the Wiki that is now outdated or inaccurate.</p> Bug #4699 (In Progress): Reminder Bug Update FAQ to reflect Kepler 2.0 releasehttps://projects.ecoinformatics.org/ecoinfo/issues/46992010-01-27T22:39:11Zdebi staggsstaggs@nceas.ucsb.edu
<p>Update the FAQ with the 2.0 release features. Remove any statements in the FAQ that are outdated or no longer accurate.</p> Bug #4667 (In Progress): New documentation on modules and extension points for moduleshttps://projects.ecoinformatics.org/ecoinfo/issues/46672010-01-13T22:49:25ZChad Berkleyberkley@nceas.ucsb.edu
<p>Should include information on the config system, karentryhandlers, viewpanes,<br />adding icons to the config, etc. See the Initialize methods of wrm and provenance for more info.</p>