Ecoinformatics Redmine: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362012-10-01T22:48:19ZEcoinformatics Redmine
Redmine Kepler - Bug #5721 (New): Add ModelRepaintController to the Kepler libraryhttps://projects.ecoinformatics.org/ecoinfo/issues/57212012-10-01T22:48:19ZSean Riddleswriddle@gmail.com
<p>This is a bug split off of 4903. ModelRepaintController is not in the Kepler actor library and should be added.</p> Kepler - Bug #5126 (Resolved): Determine whether we need to make installers for all minor releaseshttps://projects.ecoinformatics.org/ecoinfo/issues/51262010-08-04T19:29:26ZSean Riddleswriddle@gmail.com
<p>It seemed like a foregone conclusion that installers would be made for all minor and major releases. On the other hand, minor releases are the smallest level of release that allows the addition of new features (patches are supposed to be bug fixes only), and the generation of installers is still not fully automated. Perhaps a different policy on when installers are made should be considered.</p> Kepler - Bug #5125 (Resolved): Add feature to do a one-step revert of a botched update from outsi...https://projects.ecoinformatics.org/ecoinfo/issues/51252010-08-04T19:27:10ZSean Riddleswriddle@gmail.com
<p>If a patch does not work correctly, it is possible that Kepler will fail to restart after the patch's installation. The way to handle this (which will be made simpler in the future) is to run the module manager standalone and use it to restore to a working configuration.</p>
<p>The module manager should have an easy way to rollback the last patch that was applied, returning the user to the working configuration they were just in.</p>
<p>This should probably also disable automatic updates.</p> Kepler - Bug #5124 (Resolved): Add/fix the ability to patch a suitehttps://projects.ecoinformatics.org/ecoinfo/issues/51242010-08-04T19:23:40ZSean Riddleswriddle@gmail.com
<p>Currently, when you attempt to patch a suite using the instructions on the wiki, you get an error.</p>
<p>Example:</p>
<p>nceas-macbook05:build-area derik$ ant patch -Dtest=true -Dsuite=workflow-run-manager-2.0<br />Buildfile: build.xml</p>
<p>patch:<br />[patch-module] Error: You have failed to specify -Dmodule=<module.name> which is required.</p> Kepler - Bug #5123 (New): Create an ant task to display commits since last patch of a given modulehttps://projects.ecoinformatics.org/ecoinfo/issues/51232010-08-04T19:19:53ZSean Riddleswriddle@gmail.com
<p>Patches of modules are distributed as a zip containing the entire module. This means that someone can release a patch that accidentally includes someone else's work, if that someone had been committing their changes to the release branch of the same module (possibly working on a different patch). Before issuing a patch, it is handy to look at the version control log and see if there are any suspect commits that you might be inadvertently including.</p>
<p>The new ant task would execute 'svn log' for the range of revisions between that of the last patch issuance and HEAD.</p> Kepler - 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> Kepler - Bug #4978 (In Progress): Create additional 'module' property for any menu entries that a...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> Kepler - Bug #4968 (Resolved): Could not validate generated KAR file for uploading to repositoryhttps://projects.ecoinformatics.org/ecoinfo/issues/49682010-04-30T21:05:27ZSean Riddleswriddle@gmail.com
<p>I created a KAR file by doing the following:</p>
<p>1) Instantiate:
* An SDF director (iterations=1)
* A StringConstant (value="Hello world!")
* A Display</p>
<p>2) Connect the StringConstant to the Display<br />3) Create a new report containing Display.input.<br />4) Attempt to save to a repository.</p>
<p>The following exception is produced:</p>
<p>org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'KAR-Version'. One of '{lsid}' is expected.</p> Kepler - Bug #4934 (New): Certain non-user triggered actor icon changes are not reflected immedia...https://projects.ecoinformatics.org/ecoinfo/issues/49342010-04-06T20:58:50ZSean Riddleswriddle@gmail.com
<p>If you drag an EML dataset actor onto the canvas, it will immediately start downloading data, and the icon will reflect that it is "Busy." In a few seconds, when it is finished caching data, the icon will change to the normal, non-busy one. This change will not, however, be reflected in the zoom widget in the lower left of the window. If the zoom widget is used (clicked on), it will then be updated.</p> Kepler - Bug #4932 (Resolved): Demo workflows from modules are not being copied into KeplerDatahttps://projects.ecoinformatics.org/ecoinfo/issues/49322010-04-06T19:14:39ZSean Riddleswriddle@gmail.com
<p>Specifically, the R demo ReadTable.xml is at [kepler]/r-2.0/demos/R/ReadTable.xml. I would have expected that everything in r-2.0/demos, and indeed in any module/demos, would be copied to ~/KeplerData/2.0-demos/ somewhere. This would simplify documentation (as there's one canonical demo location the user can be directed to).</p> Kepler - Bug #4798 (Resolved): Create parser for KAR XML specificationhttps://projects.ecoinformatics.org/ecoinfo/issues/47982010-02-17T00:32:30ZSean Riddleswriddle@gmail.com
<p>Create a parser for the new KAR XML format, for use especially when it is returned from a metacat query.</p> Kepler - Bug #4727 (Resolved): Cannot compile Ptolemy from IntelliJhttps://projects.ecoinformatics.org/ecoinfo/issues/47272010-02-03T00:57:25ZSean Riddleswriddle@gmail.com
<p>I can't compile the ptolemy module from within IntelliJ because the appropriate exclusions and inclusions for ptolemy have drifted, and the ptolemy module in IntelliJ does not reflect this. Ideally, the ptolemy IntelliJ module should be automatically generated from the ptolemy-includes and ptolemy-excludes files.</p> Kepler - Bug #4714 (Resolved): Adding actor documentation does not increment LSIDhttps://projects.ecoinformatics.org/ecoinfo/issues/47142010-01-29T20:25:13ZSean Riddleswriddle@gmail.com
<p>Adding documentation to an actor (through [actor context menu]->Documentation->Customize) does not increment the LSID.</p> Kepler - Bug #4322 (Resolved): Attempting to save changes to a workflow saved in a KAR file failshttps://projects.ecoinformatics.org/ecoinfo/issues/43222009-08-18T18:32:27ZSean Riddleswriddle@gmail.com
<p>The following fails:</p>
<p>1) Create new workflow<br />2) Instantiate a Constant actor<br />3) Right click on canvas and Save Archive<br />4) Create new canvas and close existing workflow<br />5) Open the workflow from the library pane by Right-clicking on Workflows->WorkflowName and select "Open Archive (KAR)" <br />6) Change the value of the Constant actor<br />7) Close canvas. Kepler will inform you it wants to save change to file [path to Kepler directory]. Of course saying 'yes' won't work.</p>
<p>Possible solutions: Either save things back correctly to the KAR file, or if this is not the desired behavior, disable the save functionality (and the save reminder, of course).</p> Kepler - Bug #3216 (Resolved): Demo workflows do not runhttps://projects.ecoinformatics.org/ecoinfo/issues/32162008-04-09T18:32:31ZSean Riddleswriddle@gmail.com
<p>I have run into a couple of demo workflows that don't run while checking the replacement of the embedded documentation. I will append this with more if I find them.</p>
<p>demos/ENM/GARP_MultipleSpecies-*<br />Exception - "Actor is not ready to fire. in [workflowname].SDF Director and [workflowname].Get Species/Location information.Line Reader"</p>