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 #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 #4873 (Resolved): Actors in repository library subtree are crammed togetherhttps://projects.ecoinformatics.org/ecoinfo/issues/48732010-03-09T23:53:44ZChad Berkleyberkley@nceas.ucsb.edu
<p>On Windows XP (maybe on other versions of windows) the actor icons are crammed tightly together when you open up Actors-2_0/CoreActors,kar or the other yellow repositories. They should be spaced similarly to the mac.</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 #4633 (Resolved): LSID conflictshttps://projects.ecoinformatics.org/ecoinfo/issues/46332009-12-15T01:04:31ZOliver Soongsoong@nceas.ucsb.edu
<p>Create a workflow and save a KAR (KAR1). Note the LSID. Change the workflow in some recognizable fashion and save a KAR (KAR2). The LSID bumps as expected. Close the workflow and open KAR1. Make a different change (so it's obviously not the workflow in KAR2) and save the KAR (KAR3). Notice that when the workflow reopens, it looks like KAR2 because it is KAR2 down to the MOML in KAR3.</p>
<p>I'm observing this at r22183 right now.</p> Bug #4559 (Resolved): local repositories not showing up in components treehttps://projects.ecoinformatics.org/ecoinfo/issues/45592009-11-19T22:25:52ZOliver Soongsoong@nceas.ucsb.edu
<p>Summary says it all. I'm at r21772, and the default workflows repository isn't in the components tree. Adding repositories doesn't do anything. I'm not even getting prompts to sign into KNB or DEV to cache data.</p> Bug #4515 (Resolved): Finish and Document the Save/Open KAR file functionalityhttps://projects.ecoinformatics.org/ecoinfo/issues/45152009-10-29T19:12:31ZChad Berkleyberkley@nceas.ucsb.edu
<p>We need to finish the save/open functionality as listed in the kepler roadmap. This functionality should also be documented both on the wiki and in the user manual.</p>
<p>To close this bug, test and confirm that the open/save kar functionality works in an intuitive way and document how it now works for users.</p> Bug #4514 (Resolved): Files are being saved in the Kepler installation directoryhttps://projects.ecoinformatics.org/ecoinfo/issues/45142009-10-29T19:05:50ZChad Berkleyberkley@nceas.ucsb.edu
<p>There are still files and directories being saved, at runtime, to the Kepler installation directory. These files need to be saved to the .kepler directory instead. The files/dirs that I see are:</p>
<p>configuration (dir)<br />InstanceAuthNamespace<br />InstanceAuthNamespaceTesting</p>
<p>To close this bug, change the location of these files to <user.home>/.kepler.</p> Bug #4421 (Resolved): Component Search failshttps://projects.ecoinformatics.org/ecoinfo/issues/44212009-09-28T16:26:27ZAaron Aaronaschultz@nceas.ucsb.edu
<p>Component search is throwing a ClassCastException.</p> Bug #4340 (Resolved): Resolve KAR file/module formathttps://projects.ecoinformatics.org/ecoinfo/issues/43402009-08-26T21:44:43ZChad Berkleyberkley@nceas.ucsb.edu
<p>We need to resolve the differences between the KAR file format and the module format because we have two different ways of storing very similar information. This relates to bugs 1750 and 4317. It would be nice if a kar file could include all of the same information as a module so that modules can be transported in similar ways as kars. The kar import/export system needs to know how to process actors and workflows as well as the jars/classes that they depend on.</p> Bug #4333 (Resolved): KeplerLSID AuthNamespace web servicehttps://projects.ecoinformatics.org/ecoinfo/issues/43332009-08-26T18:16:42ZAaron Aaronaschultz@nceas.ucsb.edu
<p>Currently Kepler is pinging my desktop machine to get a unique authority and namespace. We should create a more robust service and put it on a maintained server before the 2.0 release.</p>
<p>This is the current service that a new installation of Kepler connects to:<br /><a class="external" href="http://gamma.msi.ucsb.edu/OpenAuth/">http://gamma.msi.ucsb.edu/OpenAuth/</a></p>
<p>This is the code that is currently running (which does not handle collisions well). It has a description of the input and output parameters of the service:<br /><a class="external" href="http://code.kepler-project.org/code/kepler-docs/trunk/teams-and-wg/2-infr-teams/framework/AuthNamespace_WebService_Spec/">http://code.kepler-project.org/code/kepler-docs/trunk/teams-and-wg/2-infr-teams/framework/AuthNamespace_WebService_Spec/</a></p>
<p>This is the KeplerLSID spec:<br /><a class="external" href="https://kepler-project.org/developers/teams/framework/kepler-life-science-identifiers-keplerlsid/">https://kepler-project.org/developers/teams/framework/kepler-life-science-identifiers-keplerlsid/</a></p> 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> Bug #4320 (Resolved): Component Library Folders and Popup Menushttps://projects.ecoinformatics.org/ecoinfo/issues/43202009-08-17T19:09:48ZAaron Aaronaschultz@nceas.ucsb.edu
<p>The Component Library is the most used graphical component in Kepler. It is in essence the "Control Panel" for building workflows. Because of this it is important to give the user as much control over this area as possible.</p>
<p>To do this a mechanism for viewing components as they appear on disk is needed. This will allow users to organize their components however they want in folders while still providing the ability to index the components within the Kepler ontologies.</p>
<p>Popup menus allowing the user to do basic control functions like "Move, Remove (from ontology), Delete (from disk), Create New, View LSID, View Revisions, View Documentation, Open, Annotate, etc..." should be added to the components and their containers (whether the container is an ontology/concept or a folder/kar). The popup menus are displayed from AnnotatedPTree.maybeShowPopup using subclasses of the LibraryPopup class.</p> Bug #4319 (Resolved): LibraryManagerhttps://projects.ecoinformatics.org/ecoinfo/issues/43192009-08-17T18:52:48ZAaron Aaronaschultz@nceas.ucsb.edu
<p>The Component library was being built with an Index which made it difficult to dynamically add and remove components from the library. The Index does speed up Kepler startup by quite a bit though so we don't want to get rid of the Index (although it would greatly simplify the Library to not have to maintain the index). So the goal here was to split up what was previously just the LibraryIndex class into several classes that have different functions. These classes are now, SemanticTypeIndex, LibraryManager, LibraryIndex and LibraryIndexItem and it's subclasses. It may also be useful to further split up LibraryManager into two classes called LibraryIndexer and LibraryManager, where LibraryManager is responsible for dynamic changes to the library during runtime operations and the LibraryIndexer class is responsible for improving performance by syncing and building the Library on startup and shutdown of the application using the serialized LibraryIndex object.</p>