Ecoinformatics Redmine: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362011-01-13T17:37:32ZEcoinformatics Redmine
Redmine Metacat - Bug #5273 (Resolved): docs with inline-data allow invalid xml into metacathttps://projects.ecoinformatics.org/ecoinfo/issues/52732011-01-13T17:37:32ZChad Berkleyberkley@nceas.ucsb.edu
<p>If you insert a document with inline-data, the data is stripped out of the document before it is validated. However, when you do a GET on the document, it is read off of the disk. So if you insert a doc with inline-data that has invalid characters in it (like unescaped ampersands), metacat will not recognize that it is invalid, but when you try to get the document, you will get a parser error if you try to parse it.</p>
<p>We should be validating the document first before stripping inline-data out of it.</p> Kepler - 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> Kepler - Bug #4868 (Resolved): Update R paths in documentation and demoshttps://projects.ecoinformatics.org/ecoinfo/issues/48682010-03-04T17:11:38ZChad Berkleyberkley@nceas.ucsb.edu
<p>The demos path to the R demos should point to the R demos directory, not the outreach demos directory. Make sure this is updated in chapter 8 of the UM and in the demos themselves.</p> Kepler - 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> Kepler - 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> Kepler - 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> Kepler - Bug #4449 (Resolved): exception when dragging workflowhttps://projects.ecoinformatics.org/ecoinfo/issues/44492009-10-14T20:31:35ZChad Berkleyberkley@nceas.ucsb.edu
<p>I get the following exception when trying to drag a workflow to the canvas from the workflows folder after saving a kar.</p>
<p>com.microstar.xml.XmlException: Cannot create entity without a class name. in [external stream] at line 2 and column 31<br /> at ptolemy.moml.MoMLParser._checkForNull(MoMLParser.java:3794)<br /> at ptolemy.moml.MoMLParser._createEntity(MoMLParser.java:3975)<br /> at ptolemy.moml.MoMLParser.startElement(MoMLParser.java:2495)<br /> at com.microstar.xml.XmlParser.parseElement(XmlParser.java:921)<br /> at com.microstar.xml.XmlParser.parseContent(XmlParser.java:1104)<br /> at com.microstar.xml.XmlParser.parseElement(XmlParser.java:924)<br /> at com.microstar.xml.XmlParser.parseContent(XmlParser.java:1104)<br /> at com.microstar.xml.XmlParser.parseElement(XmlParser.java:924)<br /> at com.microstar.xml.XmlParser.parseDocument(XmlParser.java:481)<br /> at com.microstar.xml.XmlParser.doParse(XmlParser.java:159)<br /> at com.microstar.xml.XmlParser.parse(XmlParser.java:132)<br /> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1404)<br /> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1376)<br /> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1532)<br /> at ptolemy.moml.MoMLChangeRequest._execute(MoMLChangeRequest.java:270)<br /> at ptolemy.kernel.util.ChangeRequest.execute(ChangeRequest.java:171)<br /> at ptolemy.kernel.util.NamedObj.executeChangeRequests(NamedObj.java:727)<br /> at ptolemy.kernel.util.NamedObj.requestChange(NamedObj.java:1752)<br /> at ptolemy.actor.CompositeActor.requestChange(CompositeActor.java:1468)<br /> at ptolemy.vergil.basic.EditorDropTarget$DTListener.drop(EditorDropTarget.java:450)<br /> at java.awt.dnd.DropTarget.drop(DropTarget.java:430)<br /> at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:500)<br /> at sun.awt.dnd.SunDropTargetContextPeer.access$800(SunDropTargetContextPeer.java:53)<br /> at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:812)<br /> at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:736)<br /> at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:29)<br /> at java.awt.Component.dispatchEventImpl(Component.java:3926)<br /> at java.awt.Container.dispatchEventImpl(Container.java:2068)<br /> at java.awt.Component.dispatchEvent(Component.java:3903)<br /> at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4256)<br /> at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4007)<br /> at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3861)<br /> at java.awt.Container.dispatchEventImpl(Container.java:2054)<br /> at java.awt.Window.dispatchEventImpl(Window.java:1801)<br /> at java.awt.Component.dispatchEvent(Component.java:3903)<br /> at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)<br /> at java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:269)<br /> at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:190)<br /> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:184)<br /> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:176)<br /> at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)</p> Kepler - 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> Kepler - Bug #4080 (Resolved): Rework Section 11https://projects.ecoinformatics.org/ecoinfo/issues/40802009-05-18T16:47:41ZChad Berkleyberkley@nceas.ucsb.edu
<p>Rework Section 11 of the User Manual for the 2.0<br />release.</p> Kepler - Bug #4075 (Resolved): Rework Section 6https://projects.ecoinformatics.org/ecoinfo/issues/40752009-05-18T16:43:37ZChad Berkleyberkley@nceas.ucsb.edu
<p>Rework Section 6 of the User Manual for the 2.0<br />release.</p> Kepler - Bug #4019 (Resolved): Workflow View in left panehttps://projects.ecoinformatics.org/ecoinfo/issues/40192009-04-22T22:56:55ZChad Berkleyberkley@nceas.ucsb.edu
<p>A view tab in the left pane that displays workflows would be very useful. It would either allow a user to drag a workflow to the canvas, in which case it would be displayed as a composite, or allow the user to double click it in which case it would be opened in a new vergil window.</p> Kepler - Bug #4014 (Resolved): Remove "include class" checkbox in export kar dialoghttps://projects.ecoinformatics.org/ecoinfo/issues/40142009-04-22T22:32:33ZChad Berkleyberkley@nceas.ucsb.edu
<p>This check box should be removed because we do not currently support including class files in the kar.</p> Kepler - Bug #3931 (New): Get the R actor working with JNIhttps://projects.ecoinformatics.org/ecoinfo/issues/39312009-04-02T16:58:08ZChad Berkleyberkley@nceas.ucsb.edu
<p>We need to get the R actor working with JNI instead of having it make calls to the native executable. This will simplify many aspects of R, including file handling, installation and overall cohesiveness with the rest of the system.</p>
<p>Bug 3809 needs to get fixed first.</p> Metacat - Bug #3402 (In Progress): internal dtds are not handledhttps://projects.ecoinformatics.org/ecoinfo/issues/34022008-06-19T18:52:33ZChad Berkleyberkley@nceas.ucsb.edu
<p>XML documents with internal DTDs are not handled by metacat. The internal dtd entity callback in the sax parser is blank and doesn't do anything when presented with an internal dtd.</p> Morpho - Bug #1832 (In Progress): need "save as" functionality in morphohttps://projects.ecoinformatics.org/ecoinfo/issues/18322004-12-15T18:22:44ZChad Berkleyberkley@nceas.ucsb.edu
<p>users have requested a "save as" function in morpho so they can just change<br />small numbers of metadata fields for entering similar datasets. I think the<br />code already exists to do this because morpho will reassign package id's if it<br />finds a conflict. we just need to make this functionality accessible via a menu.</p>