Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362013-10-23T01:07:20ZEcoinformatics Redmine
Redmine Bug #6167 (New): Model Context Menu should have the enableBackwardTypeInference choicehttps://projects.ecoinformatics.org/ecoinfo/issues/61672013-10-23T01:07:20ZChristopher Brookscxh@eecs.berkeley.edu
<p>Ptolemy II now supports backward type inference. The way this is enabled is that the top level container has a parameter called "enableBackwardTypeInference" that is set to true or false.</p>
<p>In Ptolemy II's Vergil, this is visible by right clicking on the background of the top level model.</p>
<p>This functionality is not present in the devel tree of Kepler.</p>
<p>The workaround is to drag in a Parameter, name it "enableBackgroundTypeInference" and set the value to true.</p> Bug #5745 (Resolved): "./kepler.sh -runwf -nogui -nocache workflow.xml" has error message after e...https://projects.ecoinformatics.org/ecoinfo/issues/57452012-11-20T21:37:50Zjianwu jianwujianwu@sdsc.edu
<p>I saw the same message at mac and linux:<br />rm -rf ~/.kepler; ./kepler.sh -runwf -nogui -nocache outreach/workflows/demos/getting-started/04-HelloWorld.xml.</p>
<p>It works without "-nocache" option or ~/.kepler is not deleted.</p>
<pre><code>[null] loading: ptolemy.moml.MoMLCommandLineApplication args: outreach/workflows/demos/getting-started/04-HelloWorld.xml <br /> [null] invoking: ptolemy.moml.MoMLCommandLineApplication.main<br /> [null] 21 ms. Memory: 125568K Free: 46142K (37%)<br /> [null] java.sql.SQLException: Table not found in statement [insert into cacheContentTable (name, lsid, date, file, type, classname) values ( ?, ?, ?, ?, ?, ? )]<br /> [null] at org.hsqldb.jdbc.Util.throwError(Unknown Source)<br /> [null] at org.hsqldb.jdbc.jdbcPreparedStatement.&lt;init&gt;(Unknown Source)<br /> [null] at org.hsqldb.jdbc.jdbcConnection.prepareStatement(Unknown Source)<br /> [null] at org.kepler.objectmanager.cache.CacheManager.&lt;init&gt;(CacheManager.java:121)<br /> [null] at org.kepler.objectmanager.cache.CacheManager.getInstance(CacheManager.java:162)<br /> [null] at org.kepler.module.core.Shutdown.shutdownModule(Shutdown.java:57)<br /> [null] at org.kepler.Kepler._initializeModules(Kepler.java:678)<br /> [null] at org.kepler.Kepler.load(Kepler.java:514)<br /> [null] at org.kepler.Kepler.load(Kepler.java:532)<br /> [null] at org.kepler.Kepler.parseArgsAndRun(Kepler.java:410)<br /> [null] at org.kepler.Kepler.main(Kepler.java:211)</code></pre> Bug #5732 (Resolved): EML 2.1.1 option should be added to metacat data sources in keplerhttps://projects.ecoinformatics.org/ecoinfo/issues/57322012-11-08T22:29:24ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>EML 2.1.1 option should be added to metacat data sources in kepler</p> Bug #5714 (Resolved): user manual documentation for 2.4.https://projects.ecoinformatics.org/ecoinfo/issues/57142012-09-19T18:34:34Zjianwu jianwujianwu@sdsc.edu
<p>This documentation has 10 sections and 385 pages. It has to be split into sub-tasks.</p> Bug #5713 (Resolved): getting-started-guide documentation for Kepler 2.4https://projects.ecoinformatics.org/ecoinfo/issues/57132012-09-19T18:31:57Zjianwu jianwujianwu@sdsc.edu
<p>This documentation has around 50 pages and 8 Sections. It might need be split into more sub-tasks.</p> Bug #5677 (Resolved): SDF Iterations now defaults to AUTOhttps://projects.ecoinformatics.org/ecoinfo/issues/56772012-08-14T18:44:49ZChristopher Brookscxh@eecs.berkeley.edu
<p>The iterations parameter of the SDFDirector defaults to AUTO.<br />See bug <a class="issue tracker-1 status-3 priority-2 priority-default closed" title="Bug: SDF director iterations parameter default of 0 is unfriendly (Resolved)" href="https://projects.ecoinformatics.org/ecoinfo/issues/5546">#5546</a>.</p>
<p>To close this bug:<br />1) Update the Kepler version of SDFDirector.xml<br />2) Update the Kepler printed documentation</p> Bug #5661 (Resolved): Remove SwingWorker and use javax.swing.SwingWorkerhttps://projects.ecoinformatics.org/ecoinfo/issues/56612012-08-06T23:51:05ZChristopher Brookscxh@eecs.berkeley.edu
<p>./util/src/util/SwingWorker.java<br />FIXME: Remove and use javax.swing.SwingWorker.</p>
<p>See <a class="external" href="http://docs.oracle.com/javase/tutorial/uiswing/concurrency/worker.html">http://docs.oracle.com/javase/tutorial/uiswing/concurrency/worker.html</a></p>
<p>"The javax.swing.SwingWorker class was added to the Java platform in<br />Java SE 6. Prior to this, another class, also called SwingWorker, was<br />widely used for some of the same purposes. The old SwingWorker was not<br />part of the Java platform specification, and was not provided as part<br />of the JDK.</p>
<p>The new javax.swing.SwingWorker is a completely new class. Its<br />functionality is not a strict superset of the old SwingWorker. Methods<br />in the two classes that have the same function do not have the same<br />names. Also, instances of the old SwingWorker class were reusable,<br />while a new instance of javax.swing.SwingWorker is needed for each new<br />background task."</p>
<p>Also, remove ptolemy/src/ptolemy/gui/SwingWorker.java</p> Bug #5655 (Resolved): sdm spa Repeat is a duplicate of a Ptolemy actorhttps://projects.ecoinformatics.org/ecoinfo/issues/56552012-08-06T23:39:23ZChristopher Brookscxh@eecs.berkeley.edu
<p>./actors/src/org/sdm/spa/Repeat.java<br />FIXME: No documentation? If possible, Deprecate and extend<br />ptolemy/src/ptolemy/domains/sdf/lib/Repeat.java</p> Bug #5648 (Resolved): FileCopier code duplicationhttps://projects.ecoinformatics.org/ecoinfo/issues/56482012-08-06T23:23:11ZChristopher Brookscxh@eecs.berkeley.edu
<p>FileCopier:</p>
<p>./core/src/org/kepler/util/FileCopier.java - Fixed. Unused code which was removed.</p>
<p>./actors/src/org/sdm/spa/actors/transport/FileCopier.java - abstract base class extended by<br />./actors/src/org/sdm/spa/actors/transport/SftpCopier.java:public class SftpCopier extends FileCopier {<br />./actors/src/org/sdm/spa/actors/transport/ScpCopier.java:public class ScpCopier extends FileCopier {<br />./actors/src/org/sdm/spa/actors/transport/LocalFileCopier.java:public class LocalFileCopier extends FileCopier {<br />./actors/src/org/sdm/spa/actors/transport/SrmliteCopier.java:public class SrmliteCopier extends FileCopier {<br />./actors/src/org/sdm/spa/actors/transport/BbcpCopier.java:public class BbcpCopier extends FileCopier {</p>
<p>Fixed - Renamed this to FileCopierBase</p>
<p>The class that use FileCopier base is<br />actors/src/org/sdm/spa/actors/transport/FileCopierFactory.java<br />The Actor is:<br />actors/src/org/sdm/spa/actors/transport/GenericFileCopier.java</p>
<p>These two actors should be modified to call GenericFileCopier.java<br />./actors/src/org/resurgence/actor/FileCopier.java<br />./actors/src/org/kepler/actor/ssh/FileCopier.java</p> Bug #5642 (Resolved): Kepler should have access to the ShowTypes attributehttps://projects.ecoinformatics.org/ecoinfo/issues/56422012-07-20T17:09:54ZChristopher Brookscxh@eecs.berkeley.edu
<p>Edward added a ShowTypes attribute, that when dragged in to a model, annotates<br />the ports with the types.</p>
<p>In vergil, go to the left hand actor pane and do Utilities -> Analysis -> ShowTypes</p>
<p>In Kepler, Tools -> Instantiate Attribute<br />ptolemy.vergil.actor.lib.ShowTypes</p>
<p>Unfortunately, a green box without a name shows up, there is another bug for this:<br />bug <a class="issue tracker-1 status-3 priority-2 priority-default closed" title="Bug: Text in attributes not rendered properly (Resolved)" href="https://projects.ecoinformatics.org/ecoinfo/issues/4903">#4903</a></p> Bug #5636 (Resolved): outreach/demos/Database/Database_example_1.xml workflow failshttps://projects.ecoinformatics.org/ecoinfo/issues/56362012-06-27T19:13:49ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>I get an error when trying to execute this workflow:</p>
<p>ptolemy.kernel.util.IllegalActionException: fire exception DB connection<br /> in .Database_example_1.Open Database Connection<br />Because:<br />java.sql.SQLException: socket creation error<br /> in .Database_example_1.Open Database Connection<br /> at org.geon.OpenDBConnection.fire(OpenDBConnection.java:269)<br /> at ptolemy.actor.AtomicActor.iterate(AtomicActor.java:466)<br /> at ptolemy.actor.sched.StaticSchedulingDirector.fire(StaticSchedulingDirector.java:192)<br /> at ptolemy.actor.CompositeActor.fire(CompositeActor.java:460)<br /> at ptolemy.actor.Manager.iterate(Manager.java:761)<br /> at ptolemy.actor.Manager.execute(Manager.java:352)<br /> at ptolemy.actor.Manager.run(Manager.java:1173)<br /> at ptolemy.actor.Manager$PtolemyRunThread.run(Manager.java:1716)<br />Caused by: ptolemy.kernel.util.IllegalActionException: java.sql.SQLException: socket creation error<br /> in .Database_example_1.Open Database Connection<br /> at org.geon.OpenDBConnection._connect(OpenDBConnection.java:367)<br /> at org.geon.OpenDBConnection.fire(OpenDBConnection.java:261)<br /> ... 7 more<br />Caused by: ptolemy.kernel.util.IllegalActionException: java.sql.SQLException: socket creation error<br /> in .Database_example_1.Open Database Connection<br /> at org.geon.OpenDBConnection._connect(OpenDBConnection.java:367)<br /> at org.geon.OpenDBConnection.fire(OpenDBConnection.java:261)<br /> at ptolemy.actor.AtomicActor.iterate(AtomicActor.java:466)<br /> at ptolemy.actor.sched.StaticSchedulingDirector.fire(StaticSchedulingDirector.java:192)<br /> at ptolemy.actor.CompositeActor.fire(CompositeActor.java:460)<br /> at ptolemy.actor.Manager.iterate(Manager.java:761)<br /> at ptolemy.actor.Manager.execute(Manager.java:352)<br /> at ptolemy.actor.Manager.run(Manager.java:1173)<br /> at ptolemy.actor.Manager$PtolemyRunThread.run(Manager.java:1716)</p> Bug #5635 (Resolved): build-area should have a licenses.txthttps://projects.ecoinformatics.org/ecoinfo/issues/56352012-06-26T17:54:53ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>To be consistent, it seems to me build-area should have a licenses.txt listing the licenses for its included libraries in the style of other modules, which keep a module-info/licenses.txt file in a particular format.</p> Bug #5629 (Resolved): Mac DMG installer should have better background and license agreementhttps://projects.ecoinformatics.org/ecoinfo/issues/56292012-06-18T14:19:38ZChristopher Brookscxh@eecs.berkeley.edu
<p>Hello Christopher,</p>
<p>recently I have installed Kepler for Mac OS directly from the DMG file instead of using SVN.</p>
<p>I know this is not that important, but it is fairly easy to make installer look "prettier".</p>
<p>Michal Owsiak made the following suggestions about improving the<br />Mac DMG installer.</p>
<p>In case you know how to build nice looking DMG files, you can disregard the rest of the e-mail</p>
<p>Basically, there are two things you could add:</p>
<p>1. Nice looking background + nice layout of icons (example can be found below). There is a Mac OS X devote book that describes the process in details: "Apple Training Series Mac OS X Deployment v10.6"</p>
<p><a class="external" href="http://www.owsiak.org/?p=683">http://www.owsiak.org/?p=683</a></p>
<p>2. You can also quite easily add the license agreement directly into Kepler DMG file (detailed steps are below)</p>
<p><a class="external" href="http://www.owsiak.org/?p=700">http://www.owsiak.org/?p=700</a></p>
<p>This way, you can provide better user experience when it comes to Mac OS X related installation from DMG file.</p>
<p>Hope this may help.</p>
<p>In case you will have any further questions, do not hesitate to ask.</p>
<p>Regards</p>
<p>Michal</p> Bug #5621 (Resolved): Need change the access order type from denyFirst to allowFirst in kepler wh...https://projects.ecoinformatics.org/ecoinfo/issues/56212012-06-07T21:15:21ZJing Taotao@nceas.ucsb.edu
<p>When kepler uploads kar xml and kar files to the metacat repository, the two files will be associated with eml files which has the access rules.</p>
<p>In the access part of those eml files, the access order type is denyFirst. However, Metacat 2.0.0 doesn't support denyFirst - it will ignore the access rules if the order is denyFirst. Even tough the kepler says those kar xml and kar files are public readable, it will ends up that they are non-public readable.</p>
<p>So i changed the order type from denyFirst to allowFirst in the two files in the svn trunk:</p>
<p>trunk/modules/repository/src/org/kepler/kar/UploadToRepository.java<br />trunk/modules/provenance/src/org/kepler/provenance/kar/UploadKarToRepositoryNoGUI.java</p>
<p>When kepler-library is upgraded to metacat-2.0.0, the kepler-2.3 can't generate any public readable kar xml and kar file.</p> Bug #4903 (Resolved): Text in attributes not rendered properlyhttps://projects.ecoinformatics.org/ecoinfo/issues/49032010-03-24T19:30:58ZChristopher Brookscxh@eecs.berkeley.edu
<p>In a version of Kepler checked out from the svn tree, I did:<br /> Tools->Instantiate Attribute<br />and entered<br /> ptolemy.vergil.actor.lib.MonitorReceiverContents<br />and that created an attribute.</p>
<p>However, the attribute does not have the text<br />MonitorReceiverContents<br />visible</p>
<p>If I instantiate a ptolemy.actor.gui.ModelRepaintController<br />in the same manner, then the same problem occurs.</p>
<p>Dragging in a Documentation attribute has the same problem<br />1. In Search Components, enter "Documentation" <br />2. In the Search Results, under Actors-2_0, drag the<br /> Documentation attribute into the graph pane<br />3. Note that the text is not visible.</p>
<p>This occurs in the Kepler-2.0.0 Beta 1 installer and in <br />the devel tree.</p>