Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362011-03-10T22:24:34ZEcoinformatics Redmine
Redmine Bug #5350 (Resolved): Kepler doesn't close completelyhttps://projects.ecoinformatics.org/ecoinfo/issues/53502011-03-10T22:24:34ZAaron Aaronaschultz@nceas.ucsb.edu
<p>I've noticed that when I close Kepler the process does not completely quit out. Not sure if this is due to recent memory changes or something else.</p> Bug #5146 (Resolved): modifying and saving the composite sinewave actor failshttps://projects.ecoinformatics.org/ecoinfo/issues/51462010-08-12T00:53:45ZMatt Jonesjones@nceas.ucsb.edu
<p>Trying to make changes to the Sinewave actor that ships with Kepler and then trying to save that actor as a KAR file fails with an error, and the new copy of the actor in the new KAR file is not saved correctly (the output port is missing and not connected, and there are three new boxes labeled "kepler:frequency", "kepler:phase". and "kepler:output" that were not in the original actor.</p>
<p>To reproduce:</p>
<p>1) Drag sinewave to canvas, select, and open<br />2) Modify the Annotation text to say something different.<br />3) Close the sinewave actor<br />4) An error will pop up, with the text "Save changes to jar:file:/Applications/Kepler-2.0/Kepler.app/Kepler/ptolemy-8.0.0/target/ptolemy-8.0.jar!/ptolemy/actor/lib/Sinewave.xml"</p>
<p>5) Click 'Save', which brings up the file naming dialog, choose a new name for the KAR (Sinewave2.kar), and click 'Save' (you may also get prompted to select a semantic type)<br />6) Locate the new KAR in the components panel and drag the contained actor onto the canvas<br />7a) The actor will be missing an output port<br />7b) Opening the actor will show new boxes that didn't exist before, and the missing output port</p>
<p>Expected behavior:<br />There should be no error associated with saving on top of a jar file (this is a KAR file save). The actor should have an output port connected to the same relation as before, and the square boxes should not exist. The actor copy should be identical to the original on the canvas (except maybe the LSID should have changed).</p>
<p>See attached screenshot showing the misconfigured actor.</p> Bug #5144 (Resolved): renaming an actor does not persist in saved kar fileshttps://projects.ecoinformatics.org/ecoinfo/issues/51442010-08-12T00:27:01ZMatt Jonesjones@nceas.ucsb.edu
<p>When one renames an actor on the canvas, and then selects that actor and chooses 'Save KAR...' in the context menu, a new KAR file is saved, but the actor in that KAR file contains the original name of the actor, rather than the new name.</p>
<p>To reproduce:</p>
<p>1) Drag 'Display' (or any other actor) onto the canvas<br />2) Select the actor, right click, and select 'Customize Name' from the menu<br />3) Change the name to 'MyDisplay' or another name, and click 'Commit'<br />4) Right click on the actor again and select 'Save Archive (KAR)...'<br />5) Type a name for the kar (probably 'MyDisplay.kar') and click 'Save'<br />6a) In the component tab, search for 'Display', and navigate to the newly saved kar file, click on the arrow to expand the KAR contents, which will show the original name of the actor (Display)<br />6b) Drag the new actor to the canvas, which will show the original name of the actor (Display)</p>
<p>Expected behavior:<br />For 6a, and 6b, the name shown should be the new name of the actor (e.g., 'MyDisplay')</p>
<p>This is a synopsis of an issue reported by Chris Weed on kepler-users.</p> Bug #5142 (Resolved): comma improperly inserted in kar filename rather than a period (.)https://projects.ecoinformatics.org/ecoinfo/issues/51422010-08-11T23:56:58ZMatt Jonesjones@nceas.ucsb.edu
<p>When KAR files are saved, with a name such as "foo.kar", then show up incorrectly in the kepler component pane with a comma in the name rather than the period (e.g., it becomes "foo,kar". KAR files should be saved with the normal period as the extension separator in the filename, and should display this way as well.</p> Bug #4941 (Resolved): Data search causes menus to disappear on the machttps://projects.ecoinformatics.org/ecoinfo/issues/49412010-04-16T19:09:38ZChad Berkleyberkley@nceas.ucsb.edu
<p>If you do a data search on the mac, all of the menus in the menu bar disappear and never return. To recreate, click the data tab, type in a search term, click "search". the menus will disappear.</p> Bug #4940 (Resolved): User is never notified of incorrect loginhttps://projects.ecoinformatics.org/ecoinfo/issues/49402010-04-16T18:32:00ZChad Berkleyberkley@nceas.ucsb.edu
<p>When you do a data search and login, if you put an incorrect username or password, then do a search, Kepler never tells you your username/pass is incorrect and tries to do the search anyway.</p>
<p>To recreate:<br />1) go to the data tab<br />2) search for "aphid" <br />3) input a fake username/pass<br />4) click "ok"</p>
<p>Kepler will sit there like it's searching, but if you look at the log, no search is taking place and it will never tell you that the login failed. I'm unsure if the problem is with Kepler not properly handling incorrect login results from the ecogrid or if ecogrid isn't properly notifying kepler of the failed login attempt.</p> Bug #4883 (New): Need more command line options for kar fileshttps://projects.ecoinformatics.org/ecoinfo/issues/48832010-03-15T20:51:05ZChad Berkleyberkley@nceas.ucsb.edu
<p>right now, we can execute a single workflow contained in a kar file with the -runwf command line switch. It would be nice to have more options for working with kar files on the command line. The minimal options I would like to see are:</p>
<p>1) allow the user to specify which workflow within a kar file to execute (if there is >1). <br />2) allow the user to specify the output location. Either a server or local directory.<br />3) allow the use of a remote kar file with an https url (i.e. for a kar file stored in a repository).</p>
<p>Please add more requirements as you see fit. We will add this to the queue of post-2.0 enhancements.</p> Bug #4785 (New): move cache object from 1.0 to 2.0https://projects.ecoinformatics.org/ecoinfo/issues/47852010-02-10T23:13:31ZChad Berkleyberkley@nceas.ucsb.edu
<p>Cache kar objects from 1.0 that contain customized actors (i.e. not those shipped with 1.0) need to be migrated to the 2.0 installation. Any kars that include jars must be made into modules (see bug 4702).</p> Bug #4735 (New): Allow params to be passed to ConfigurationManager from the command linehttps://projects.ecoinformatics.org/ecoinfo/issues/47352010-02-04T20:48:06ZChad Berkleyberkley@nceas.ucsb.edu
<p>Need a mechanism for passing params to CM from the command line. This is a post 2.0 feature.</p> Bug #4723 (Resolved): workflows directory should be movedhttps://projects.ecoinformatics.org/ecoinfo/issues/47232010-02-02T18:16:02ZChad Berkleyberkley@nceas.ucsb.edu
<p>There is a directory 'workflows' in the kepler installation directory where you can save kars and have them automatically show up in the library. This should be moved to ~/KeplerData/workflows. I think it should probably also be renamed, but I'm not sure what to rename it to.</p> Bug #4704 (Resolved): Generate XML for a KARFilehttps://projects.ecoinformatics.org/ecoinfo/issues/47042010-01-28T04:42:19ZAaron Aaronaschultz@nceas.ucsb.edu
<p>Create an XML string based on the Manifest and Entries of a KARFile.</p>
<p>See the example karxml file at the bottom of<br /><a class="external" href="https://kepler-project.org/developers/teams/framework/kepler-archive-kar/kar-saving-process">https://kepler-project.org/developers/teams/framework/kepler-archive-kar/kar-saving-process</a></p> Bug #4702 (Resolved): KAR to module conversion utilityhttps://projects.ecoinformatics.org/ecoinfo/issues/47022010-01-28T01:03:05ZAaron Aaronaschultz@nceas.ucsb.edu
<p>Create a utility that converts KAR files (version 1.0 and 2.0) to Kepler modules.</p>
<p>This was previously bug 1750.</p> Bug #4597 (Resolved): adding new configuration properties before/after a certain exiting configur...https://projects.ecoinformatics.org/ecoinfo/issues/45972009-12-04T00:33:06Zjianwu jianwujianwu@sdsc.edu
<p>Different modules may have their own menu items. To realize it, the module should be able to add configuration properties to files like uiMenuMappings_en_US.xml. One special requirement for menu items is that the configuration property location matters. People want to add one menu item after/before a certain exiting configuration property. So I think ConfigurationProperty class should have interface like addPropertyBefore() and addPropertyAfter().</p> Bug #4579 (Resolved): Remove all references to specific module names from the code.https://projects.ecoinformatics.org/ecoinfo/issues/45792009-11-24T22:50:30ZDavid Welkerwelker4kepler@gmail.com
<p>In certain areas of the code, there are references to specific module names. This is extremely problematic in two scenarios:</p>
<p>(1) When branching or publishing, the name of a module changes. So, module X becomes X-1.0, or X-1.0 becomes X-1.0.0</p>
<p>(2) When refactoring resources formerly in X, may end up in X, Y and Z.</p>
<p>In order to get the Kepler-1.1 branch to work, I had to refactor module names out of 7 classes across 4 different modules. This would be totally unnecessary if the new configuration system had not adopted a design where specific module names are referenced. Furthermore, when I publish the Kepler-1.1 branch, I will have to refactor all of these references once again. For every patch, these refrences will have to be refactored. And so on. At the very least, we need to solve problem (1). However, problem (2) should be solved as well, as it would be little work.</p>
<p>Finally, there is a related problem. Apparently, the name of modules is somehow referenced in setting Ptolemy names. But Ptolemy names cannot have a period. However, module names will have a period when they have a version attached.</p>
<p>The solution is to never reference a module name from the code.</p>
<p>Here is the stack trace:</p>
<p>ptolemy.kernel.util.IllegalActionException: Cannot set a name with a period: Actors-1.0<br /> [run] in .<Unnamed Object><br /> [run] at ptolemy.kernel.util.NamedObj.setName(NamedObj.java:1917)<br /> [run] at ptolemy.kernel.ComponentEntity.setName(ComponentEntity.java:603)<br /> [run] at ptolemy.kernel.util.NamedObj.<init>(NamedObj.java:246)<br /> [run] at ptolemy.kernel.util.NamedObj.<init>(NamedObj.java:215)<br /> [run] at ptolemy.kernel.InstantiableNamedObj.<init>(InstantiableNamedObj.java:119)<br /> [run] at ptolemy.kernel.Entity.<init>(Entity.java:135)<br /> [run] at ptolemy.kernel.ComponentEntity.<init>(ComponentEntity.java:105)<br /> [run] at ptolemy.kernel.CompositeEntity.<init>(CompositeEntity.java:163)<br /> [run] at ptolemy.moml.EntityLibrary.<init>(EntityLibrary.java:202)<br /> [run] at org.kepler.moml.FolderEntityLibrary.<init>(FolderEntityLibrary.java:44)<br /> [run] at org.kepler.objectmanager.library.LibraryManager.createAndAddTreeItem(LibraryManager.java:378)<br /> [run] at org.kepler.objectmanager.library.LibraryGenerator.generate(LibraryGenerator.java:83)<br /> [run] at org.kepler.objectmanager.library.LibraryManager.buildLibrary(LibraryManager.java:212)<br /> [run] at org.kepler.objectmanager.library.LibraryManager.initialize(LibraryManager.java:271)<br /> [run] at org.kepler.moml.KARLibraryBuilder.buildLibrary(KARLibraryBuilder.java:75)<br /> [run] at ptolemy.actor.gui.UserActorLibrary.openLibrary(UserActorLibrary.java:202)<br /> [run] at ptolemy.actor.gui.UserActorLibrary.openUserLibrary(UserActorLibrary.java:140)<br /> [run] at ptolemy.vergil.VergilApplication._createDefaultConfiguration(VergilApplication.java:322)<br /> [run] at ptolemy.vergil.VergilApplication._createEmptyConfiguration(VergilApplication.java:339)<br /> [run] at ptolemy.actor.gui.ConfigurationApplication._parseArgs(ConfigurationApplication.java:1116)<br /> [run] at ptolemy.vergil.VergilApplication._parseArgs(VergilApplication.java:469)<br /> [run] at ptolemy.actor.gui.ConfigurationApplication.<init>(ConfigurationApplication.java:226)<br /> [run] at ptolemy.actor.gui.MoMLApplication.<init>(MoMLApplication.java:81)<br /> [run] at ptolemy.vergil.VergilApplication.<init>(VergilApplication.java:104)<br /> [run] at ptolemy.vergil.VergilApplication$1.run(VergilApplication.java:211)<br /> [run] at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)<br /> [run] at java.awt.EventQueue.dispatchEvent(EventQueue.java:461)<br /> [run] at java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:269)<br /> [run] at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:190)<br /> [run] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:184)<br /> [run] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:176)<br /> [run] at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)<br /> [run] ptolemy.kernel.util.IllegalActionException: Cannot set a name with a period: Directors-1.0<br /> [run] in .<Unnamed Object><br /> [run] at ptolemy.kernel.util.NamedObj.setName(NamedObj.java:1917)<br /> [run] at ptolemy.kernel.ComponentEntity.setName(ComponentEntity.java:603)<br /> [run] at ptolemy.kernel.util.NamedObj.<init>(NamedObj.java:246)<br /> [run] at ptolemy.kernel.util.NamedObj.<init>(NamedObj.java:215)<br /> [run] at ptolemy.kernel.InstantiableNamedObj.<init>(InstantiableNamedObj.java:119)<br /> [run] at ptolemy.kernel.Entity.<init>(Entity.java:135)<br /> [run] at ptolemy.kernel.ComponentEntity.<init>(ComponentEntity.java:105)<br /> [run] at ptolemy.kernel.CompositeEntity.<init>(CompositeEntity.java:163)<br /> [run] at ptolemy.moml.EntityLibrary.<init>(EntityLibrary.java:202)<br /> [run] at org.kepler.moml.FolderEntityLibrary.<init>(FolderEntityLibrary.java:44)<br /> [run] at org.kepler.objectmanager.library.LibraryManager.createAndAddTreeItem(LibraryManager.java:378)<br /> [run] at org.kepler.objectmanager.library.LibraryGenerator.generate(LibraryGenerator.java:83)<br /> [run] at org.kepler.objectmanager.library.LibraryManager.buildLibrary(LibraryManager.java:212)<br /> [run] at org.kepler.objectmanager.library.LibraryManager.initialize(LibraryManager.java:271)<br /> [run] at org.kepler.moml.KARLibraryBuilder.buildLibrary(KARLibraryBuilder.java:75)<br /> [run] at ptolemy.actor.gui.UserActorLibrary.openLibrary(UserActorLibrary.java:202)<br /> [run] at ptolemy.actor.gui.UserActorLibrary.openUserLibrary(UserActorLibrary.java:140)<br /> [run] at ptolemy.vergil.VergilApplication._createDefaultConfiguration(VergilApplication.java:322)<br /> [run] at ptolemy.vergil.VergilApplication._createEmptyConfiguration(VergilApplication.java:339)<br /> [run] at ptolemy.actor.gui.ConfigurationApplication._parseArgs(ConfigurationApplication.java:1116)<br /> [run] at ptolemy.vergil.VergilApplication._parseArgs(VergilApplication.java:469)<br /> [run] at ptolemy.actor.gui.ConfigurationApplication.<init>(ConfigurationApplication.java:226)<br /> [run] at ptolemy.actor.gui.MoMLApplication.<init>(MoMLApplication.java:81)<br /> [run] at ptolemy.vergil.VergilApplication.<init>(VergilApplication.java:104)<br /> [run] at ptolemy.vergil.VergilApplication$1.run(VergilApplication.java:211)<br /> [run] at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)<br /> [run] at java.awt.EventQueue.dispatchEvent(EventQueue.java:461)<br /> [run] at java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:269)<br /> [run] at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:190)<br /> [run] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:184)<br /> [run] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:176)<br /> [run] at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)</p> Bug #4578 (Resolved): tracking bug for changes to .keplerhttps://projects.ecoinformatics.org/ecoinfo/issues/45782009-11-24T21:24:38ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Thanks everyone for your input to the "proposed changes to .kepler" email. The threads are here:<br /><a class="external" href="http://mercury.nceas.ucsb.edu/kepler/pipermail/kepler-dev/2009-November/016568.html">http://mercury.nceas.ucsb.edu/kepler/pipermail/kepler-dev/2009-November/016568.html</a><br /><a class="external" href="http://mercury.nceas.ucsb.edu/kepler/pipermail/kepler-dev/2009-November/016577.html">http://mercury.nceas.ucsb.edu/kepler/pipermail/kepler-dev/2009-November/016577.html</a></p>
<p>I don't have an exact plan yet, but this bug will track progress. I think it's clear we want to at least divide cache into temporary and persistent data areas. Things get more complicated when you ask how and when to separate by "version" of kepler.</p>