Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362012-08-06T23:45:27ZEcoinformatics Redmine
Redmine Bug #5659 (Closed): Kepler CaseGraphFrame and CaseGraphTableau have duplicated Ptolemy code.https://projects.ecoinformatics.org/ecoinfo/issues/56592012-08-06T23:45:27ZChristopher Brookscxh@eecs.berkeley.edu
<p>./gui/src/org/kepler/gui/frame/CaseGraphFrame.java<br />FIXME: Refactor!<br /> Duplicate of ptolemy/src/ptolemy/vergil/modal/CaseGraphFrame.java<br /> The Kepler version extends the Kepler-specific MultiCompositeGraphFrame which extends KeplerGraphFrame</p>
<ol>
<li><br />./gui/src/org/kepler/gui/frame/CaseGraphTableau.java<br />FIXME: Refactor!<br /> Probably like CaseGraphFrame above.</li>
</ol> Bug #5447 (Resolved): Use https, not svn to check out the ptII repositoryhttps://projects.ecoinformatics.org/ecoinfo/issues/54472011-08-03T15:44:25ZChristopher Brookscxh@eecs.berkeley.edu
<p>In April, 2010, we discussed using https to check out the ptII tree instead of using the svn protocol.</p>
<p>See <br /><a class="external" href="http://lists.nceas.ucsb.edu/kepler/pipermail/kepler-dev/2010-April/018120.html">http://lists.nceas.ucsb.edu/kepler/pipermail/kepler-dev/2010-April/018120.html</a></p>
<p>See also<br /><a class="external" href="http://lists.nceas.ucsb.edu/kepler/pipermail/kepler-dev/2011-August/019712.html">http://lists.nceas.ucsb.edu/kepler/pipermail/kepler-dev/2011-August/019712.html</a></p>
<p>The primary reason to use https instead of svn is that https is more likely to<br />get through corporate firewalls.</p>
<p>One reason not do use https is because there are very few https accounts<br />with write privileges on source.eecs.berkeley.edu. Switching to https will<br />make it more difficult for Kepler developers to contribute fixes to ptII.</p> Bug #5272 (Resolved): kepler 2.1 suite can not be started using 'ant run'https://projects.ecoinformatics.org/ecoinfo/issues/52722011-01-12T23:52:49Zjianwu jianwujianwu@sdsc.edu
<p>Today, one partner tried to start Kepler 2.1 through build-area and failed.</p>
<p>We first tried the build-area at <a class="external" href="https://code.kepler-project.org/code/kepler/releases/release-branches/build-area-2.0/">https://code.kepler-project.org/code/kepler/releases/release-branches/build-area-2.0/</a>. The error message is:<br /><huynh@enea142 ~/SANDIEGOIII/kepler_2.1/build-area-2.0>ant run<br />Buildfile: build.xml</p>
<p>BUILD FAILED<br />/afs/efda-itm.eu/isip/user/huynh/SANDIEGOIII/kepler_2.1/build-area-2.0/build.xml:4: The following error occurred while executing this line:<br />/afs/efda-itm.eu/isip/user/huynh/SANDIEGOIII/kepler_2.1/build-area-2.0/settings/taskdefs.xml:114: typedef class org.kepler.build.RegisterModule cannot be found</p>
<p>Total time: 0 seconds</p>
<p>We switched to the build-area in kepler trunk, it can compile Kepler 2.1 but it get other exceptions:</p>
<p>JVM Memory = 5m 512m<br /> [run] /afs/efda-itm.eu/isip/user/huynh/SANDIEGOIII/kepler_2.1<br /> [run] java.io.FileNotFoundException: /afs/efda-itm.eu/isip/user/huynh/SANDIEGOIII/kepler_2.1/build-area/registry.txt (No such file or directory)<br /> [run] at java.io.FileInputStream.open(Native Method)<br /> [run] at java.io.FileInputStream.<init>(FileInputStream.java:106)<br /> [run] at java.io.FileReader.<init>(FileReader.java:55)<br /> [run] at org.kepler.build.project.RepositoryLocations.readModuleRegistryHelper(RepositoryLocations.java:75)<br /> [run] at org.kepler.build.project.RepositoryLocations.readModuleRegistry(RepositoryLocations.java:62)<br /> [run] at org.kepler.build.project.RepositoryLocations.getLocation(RepositoryLocations.java:96)<br /> [run] at org.kepler.build.modules.Module.<init>(Module.java:152)<br /> [run] at org.kepler.build.modules.Module.<init>(Module.java:204)<br /> [run] at org.kepler.build.modules.ModulesTxt.readHelper(ModulesTxt.java:165)<br /> [run] at org.kepler.build.modules.ModulesTxt.read(ModulesTxt.java:137)<br /> [run] at org.kepler.build.modules.ModulesTxt.init(ModulesTxt.java:58)<br /> [run] at org.kepler.build.modules.ModuleTree.init(ModuleTree.java:96)<br /> [run] at org.kepler.build.modules.ModuleTree.instance(ModuleTree.java:86)<br /> [run] at org.kepler.configuration.ConfigurationManager.loadConfiguration(ConfigurationManager.java:414)<br /> [run] at org.kepler.configuration.ConfigurationManager.<init>(ConfigurationManager.java:87)<br /> [run] at org.kepler.configuration.ConfigurationManager.getInstance(ConfigurationManager.java:116)<br /> [run] at org.kepler.configuration.ConfigurationManager.getInstance(ConfigurationManager.java:105)<br /> [run] at org.kepler.modulemanager.RepositoryLocations.initReleaseLocation(RepositoryLocations.java:24)<br /> [run] at org.kepler.modulemanager.RepositoryLocations.getReleaseLocation(RepositoryLocations.java:18)<br /> [run] at org.kepler.Kepler.main(Kepler.java:89)<br /> [run] java.lang.NullPointerException<br /> [run] at org.kepler.build.project.RepositoryLocations.getLocation(RepositoryLocations.java:98)<br /> [run] at org.kepler.build.modules.Module.<init>(Module.java:152)<br /> [run] at org.kepler.build.modules.Module.<init>(Module.java:204)<br /> [run] at org.kepler.build.modules.ModulesTxt.readHelper(ModulesTxt.java:165)<br /> [run] at org.kepler.build.modules.ModulesTxt.read(ModulesTxt.java:137)<br /> [run] at org.kepler.build.modules.ModulesTxt.init(ModulesTxt.java:58)<br /> [run] at org.kepler.build.modules.ModuleTree.init(ModuleTree.java:96)<br /> [run] at org.kepler.build.modules.ModuleTree.instance(ModuleTree.java:86)<br /> [run] at org.kepler.configuration.ConfigurationManager.loadConfiguration(ConfigurationManager.java:414)<br /> [run] at org.kepler.configuration.ConfigurationManager.<init>(ConfigurationManager.java:87)<br /> [run] at org.kepler.configuration.ConfigurationManager.getInstance(ConfigurationManager.java:116)<br /> [run] at org.kepler.configuration.ConfigurationManager.getInstance(ConfigurationManager.java:105)<br /> [run] at org.kepler.modulemanager.RepositoryLocations.initReleaseLocation(RepositoryLocations.java:24)<br /> [run] at org.kepler.modulemanager.RepositoryLocations.getReleaseLocation(RepositoryLocations.java:18)<br /> [run] at org.kepler.Kepler.main(Kepler.java:89)<br /> [run] Exception in thread "main" java.lang.RuntimeException: Could not load configuration: null<br /> [run] at org.kepler.configuration.ConfigurationManager.<init>(ConfigurationManager.java:93)<br /> [run] at org.kepler.configuration.ConfigurationManager.getInstance(ConfigurationManager.java:116)<br /> [run] at org.kepler.configuration.ConfigurationManager.getInstance(ConfigurationManager.java:105)<br /> [run] at org.kepler.modulemanager.RepositoryLocations.initReleaseLocation(RepositoryLocations.java:24)<br /> [run] at org.kepler.modulemanager.RepositoryLocations.getReleaseLocation(RepositoryLocations.java:18)<br /> [run] at org.kepler.Kepler.main(Kepler.java:89)</p>
<p>BUILD FAILED<br />/afs/efda-itm.eu/isip/user/huynh/SANDIEGOIII/kepler_2.1/build-area/build.xml:36: Java returned: 1</p> Bug #5197 (Resolved): error from provenance when opening KAR from previous versionhttps://projects.ecoinformatics.org/ecoinfo/issues/51972010-10-05T00:19:44ZMatt Jonesjones@nceas.ucsb.edu
<p>When I open a workflow from a KAR file that was produced by an earlier version of Kepler, I get an error from provenance 2.1.0 that I do not get from plain Kepler 2.1.0. The stack trace is below.</p>
<p>The KAR file is attached for reference. Once the error occurs, the workflow opens normally and will run, although provenance is disabled (red icon). Pressing the Provenance Toolbar icon to toggle it back on gives the same error message as in the stack trace below.</p>
<p>I am running Java 1.6.0_20 on a MacBookPro 2.66 Ghz Intel Core i7 with 8GB RAM.</p>
<p>ptolemy.kernel.util.NameDuplicationException: Attempt to insert object named "<Unnamed Object>" into a container that already contains an object with that name.<br /> at ptolemy.kernel.util.NamedList.append(NamedList.java:133)<br /> at ptolemy.kernel.util.NamedObj._addAttribute(NamedObj.java:2165)<br /> at ptolemy.kernel.util.Attribute.setContainer(Attribute.java:398)<br /> at org.kepler.provenance.ProvenanceRecorder.setContainer(ProvenanceRecorder.java:316)<br /> at ptolemy.kernel.util.Attribute.<init>(Attribute.java:109)<br /> at ptolemy.kernel.util.Attribute.<init>(Attribute.java:86)<br /> at org.kepler.provenance.ProvenanceRecorder.<init>(ProvenanceRecorder.java:192)<br /> at org.kepler.provenance.ProvenanceRecorder.<init>(ProvenanceRecorder.java:159)<br /> at org.kepler.provenance.gui.ProvenanceConfigureAction.addProvenanceRecorder(ProvenanceConfigureAction.java:238)<br /> at org.kepler.provenance.gui.ProvenanceConfigureAction.<init>(ProvenanceConfigureAction.java:142)<br /> at org.kepler.module.provenance.Initialize.updateFrameComponents(Initialize.java:68)<br /> at org.kepler.gui.KeplerGraphFrame._addMenus(KeplerGraphFrame.java:1315)<br /> at ptolemy.gui.Top$5.run(Top.java:375)<br /> at ptolemy.gui.Top.deferIfNecessary(Top.java:235)<br /> at ptolemy.gui.Top.pack(Top.java:398)<br /> at ptolemy.actor.gui.TableauFrame.pack(TableauFrame.java:296)<br /> at ptolemy.actor.gui.Tableau.show(Tableau.java:355)<br /> at ptolemy.actor.gui.Configuration.createPrimaryTableau(Configuration.java:582)<br /> at ptolemy.actor.gui.Effigy.showTableaux(Effigy.java:492)<br /> at ptolemy.actor.gui.Configuration._openModel(Configuration.java:1197)<br /> at ptolemy.actor.gui.Configuration.openModel(Configuration.java:941)<br /> at ptolemy.actor.gui.Configuration.openModel(Configuration.java:899)<br /> at org.kepler.gui.component.OpenCompositeAction.actionPerformed(OpenCompositeAction.java:187)<br /> at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)<br /> at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351)<br /> at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)<br /> at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)<br /> at javax.swing.AbstractButton.doClick(AbstractButton.java:389)<br /> at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1223)<br /> at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:137)<br /> at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1264)<br /> at java.awt.Component.processMouseEvent(Component.java:6348)<br /> at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)<br /> at java.awt.Component.processEvent(Component.java:6113)<br /> at java.awt.Container.processEvent(Container.java:2085)<br /> at java.awt.Component.dispatchEventImpl(Component.java:4714)<br /> at java.awt.Container.dispatchEventImpl(Container.java:2143)<br /> at java.awt.Component.dispatchEvent(Component.java:4544)<br /> at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4618)<br /> at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4282)<br /> at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4212)<br /> at java.awt.Container.dispatchEventImpl(Container.java:2129)<br /> at java.awt.Window.dispatchEventImpl(Window.java:2478)<br /> at java.awt.Component.dispatchEvent(Component.java:4544)<br /> at java.awt.EventQueue.dispatchEvent(EventQueue.java:635)<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 #5044 (Resolved): Can't insert null record using Database Writer actorhttps://projects.ecoinformatics.org/ecoinfo/issues/50442010-06-08T00:33:49ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>User reports being unable to insert null record into database using Database Writer's input port -- I don't believe there's currently a way to do this. You can send x = nil, or x = "null", or x = object(null), but none work.</p>
<p>Thread for reference:<br /><a class="external" href="http://mercury.nceas.ucsb.edu/kepler/pipermail/kepler-users/2010-June/002193.html">http://mercury.nceas.ucsb.edu/kepler/pipermail/kepler-users/2010-June/002193.html</a></p> Bug #4966 (Resolved): Make simple GUI mods for module managerhttps://projects.ecoinformatics.org/ecoinfo/issues/49662010-04-30T15:34:09Zdebi staggsstaggs@nceas.ucsb.edu
<p>Make the following modifications to the GUI of the module manager as discussed with Matt, David, and Chad.</p>
<p>1.) Hide the 'downloaded modules' tab.<br />2.) Change the 'Change to' button to read 'Apply and Restart'<br />3.) Add tooltip text to the Labels for each list of modules, suites, and selected modules.<br />4.) Remove the 'retrieve' button.</p> Bug #4849 (Resolved): ant eclipse failshttps://projects.ecoinformatics.org/ecoinfo/issues/48492010-02-26T17:10:06Zben leinfelderleinfelder@nceas.ucsb.edu
<p>[eclipse] java.io.FileNotFoundException: /Users/leinfelder/workspace_kepler/kepler/build-area/resources/eclipse/PtolemyClasspathStart (No such file or directory)</p>
<p>indeed, that file is not there. There is a PtolemyClasspath, however</p> Bug #4694 (Resolved): workflow run manager - differentiate imported runshttps://projects.ecoinformatics.org/ecoinfo/issues/46942010-01-22T23:30:34ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Eric requests a way to differentiate imported runs ("husk runs") from those you actually ran. One idea is to change the run row color. We should probably add a field to provenance to store if a run was imported.</p> Bug #4662 (Resolved): roll revision vs. new object IDhttps://projects.ecoinformatics.org/ecoinfo/issues/46622010-01-13T00:11:32ZOliver Soongsoong@nceas.ucsb.edu
<p>My current auth namespace is 3371. I have a file with an old auth namespace of 1347. If I open the XML file, view LSID, and roll revision, then generate a report and attempt to save the KAR, I get an error saying it can't be saved because the report is NULL. If I open the XML file, view LSID, new object ID, then generate a report, I can save the KAR as expected. If I open the XML file, delete an actor then undo, then generate a report, I can save the KAR as expected.</p>
<p>Thing seem to work fine if the auth namespace is the same.</p>
<p>What's the difference between roll revision and new object ID, why do we need 2, and why doesn't roll revision seem to work in this case.</p> Bug #4660 (Resolved): Clicking in a section header highlights all the text.https://projects.ecoinformatics.org/ecoinfo/issues/46602010-01-12T19:16:05ZOliver Soongsoong@nceas.ucsb.edu
<p>I have a section header with some text in it and I want to change that text. If I click on it, it highlights all of the text. If I click on it again, it highlights all of the text again. There seems to be no way to move the editing cursor to a specific location with the mouse. I can use the keyboard arrow keys, but this behavior of the section header is different from the text item and the label parts of the dynamic items.</p> Bug #4631 (Resolved): Could use some way to change the "workflow name" stored in a KARhttps://projects.ecoinformatics.org/ecoinfo/issues/46312009-12-14T22:40:37ZOliver Soongsoong@nceas.ucsb.edu
<p>Right now, if I want to change the "workflow name", I would have to export the MOML and recreate the report. It would be nice if I could just change the "workflow name" itself (without hacking the KAR).</p> Bug #4630 (Resolved): creating and changing relations don't trigger LSID bumphttps://projects.ecoinformatics.org/ecoinfo/issues/46302009-12-14T22:28:16ZOliver Soongsoong@nceas.ucsb.edu
<p>Make a workflow with at least 3 ports and only 2 connected. Check the LSID. Now move a relation from one port to another. The LSID is the same.</p> Bug #4581 (Resolved): Handle multiple revisions of components in the Component Libraryhttps://projects.ecoinformatics.org/ecoinfo/issues/45812009-11-25T05:23:19ZAaron Aaronaschultz@nceas.ucsb.edu
<p>It is possible for many different revisions of an object to contain the same semantic types. The question is how to handle this in the Component Library.</p>
<p>Imagine you have two different KARS<br />one with a component, urn:lsid:someauth:namespace:24:10<br />and the other with a component, urn:lsid:someauth:namespace:24:11<br />both of which have equivalent semantic types.</p>
<p>These two components should show up properly in the Ontology tree in the Component Library but since they would be in the same place there is a collision. For this reason, LSID cannot be used as the identifier in the Component Library. The new Library Index has a unique Library Index ID (LIID) for each item that shows up in the Component Library tree. With this LIID we can associated multiple LSIDs with any given LIID (see LIBRARY_LSIDS table in the sql).</p>
<p>This problem is not limited to LSID revisions. But also objects that have the same name and the same semantic type.</p> Bug #4570 (Resolved): dangling file handle for KARshttps://projects.ecoinformatics.org/ecoinfo/issues/45702009-11-21T01:23:46ZOliver Soongsoong@nceas.ucsb.edu
<p>I'm not a 100% certain this is the cause, but on Windows, if I open a KAR file then close it, Kepler doesn't seem to release the file handle, which prevents me from deleting the KAR. I seem to recall having problems overwriting KAR files in the past, so this is somewhat problematic. Obviously, closing Kepler releases the file handle.</p> Bug #4526 (Resolved): multi-line entries can be put into text items in reports, but they are disp...https://projects.ecoinformatics.org/ecoinfo/issues/45262009-11-04T02:59:57ZOliver Soongsoong@nceas.ucsb.edu
<p>I'm not sure if this is a bug or an enhancement request. I guess it depends on what the intention was. Are text boxes supposed to be a single "line" like <P></P> in HTML, or are they supposed to be more powerful?</p>
<p>I can live with either way, but the interface should be consistent, and it would be nice to know what I'm supposed to be doing.</p>