Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362012-11-20T21:37:50ZEcoinformatics Redmine
Redmine 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 #5715 (New): Actor Reference documentationhttps://projects.ecoinformatics.org/ecoinfo/issues/57152012-09-19T18:36:47Zjianwu jianwujianwu@sdsc.edu
<p>this doc hasn't changed since 2.0, but in 2.4, many actors are visible for the first time. So we might need to update this doc.</p>
<p>435 pages.</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 #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 #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> Feature #5626 (New): interacting with kepler.sh to know the status and other information in batch...https://projects.ecoinformatics.org/ecoinfo/issues/56262012-06-15T19:43:39Zjianwu jianwujianwu@sdsc.edu
<p>When we run kepler in batch mode, it's good to know its status and other information.</p>
<p>CAMERA has done something for it. Jianwu will check it.</p> Bug #5625 (Resolved): create kepler documentation for 2.4https://projects.ecoinformatics.org/ecoinfo/issues/56252012-06-15T19:21:39Zjianwu jianwujianwu@sdsc.edu
<p>we need new documentation for 2.4.</p> Bug #5495 (Resolved): released kepler should allow getting patches and changing suites from comma...https://projects.ecoinformatics.org/ecoinfo/issues/54952011-09-20T21:02:43ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>You should be able to get patches and change suites from the command line with a released Kepler. See user question:<br /><a class="external" href="http://lists.nceas.ucsb.edu/kepler/pipermail/kepler-users/2011-September/002583.html">http://lists.nceas.ucsb.edu/kepler/pipermail/kepler-users/2011-September/002583.html</a></p> Bug #5487 (Resolved): blank modules.txt files created for non-suite moduleshttps://projects.ecoinformatics.org/ecoinfo/issues/54872011-09-08T23:26:16ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Tomasz Zok reported a bug with invalid modules listed in the Module Manager Gui after patching a released module, and then kepler crashing after attempting to use a patched suite.<br />It's described here:<br /><a class="external" href="http://lists.nceas.ucsb.edu/kepler/pipermail/kepler-dev/2011-August/019824.html">http://lists.nceas.ucsb.edu/kepler/pipermail/kepler-dev/2011-August/019824.html</a><br /><a class="external" href="http://lists.nceas.ucsb.edu/kepler/pipermail/kepler-dev/2011-September/019836.html">http://lists.nceas.ucsb.edu/kepler/pipermail/kepler-dev/2011-September/019836.html</a></p>
<p>I commited Sean's fix for the bug to module-manager-gui at r28451.</p>
<p>We should issue a 2.2 module-manager-gui patch for this issue since people have already put work into making 2.2 add-ons.</p> Bug #5458 (Resolved): Moving between 2.2 and 2.3 and back requires deleting ~/KeplerDatahttps://projects.ecoinformatics.org/ecoinfo/issues/54582011-08-14T17:36:21ZChristopher Brookscxh@eecs.berkeley.edu
<p>With Kepler 2.3 rc1, I had to remove my ~/KeplerData directory, see<br />bug#5457</p>
<p>However, to go from Kepler 2.3 back to Kepler 2.2, I need to remove<br />~/KeplerData again?</p>
<p>Under Mac OS X, the Console application shows:</p>
<p>8/14/11 10:30:42.410 AM [0x0-0x12b12b].org.kepler.build.runner.Kepler: JVM Memory = 5m 512m<br />8/14/11 10:30:42.411 AM [0x0-0x12b12b].org.kepler.build.runner.Kepler: Error: The following modules are missing: <br />8/14/11 10:30:42.411 AM [0x0-0x12b12b].org.kepler.build.runner.Kepler: kepler-2.3.^</p> Bug #5440 (Resolved): special checkout behavior for hardcoded ptolemy module nameshttps://projects.ecoinformatics.org/ecoinfo/issues/54402011-07-12T21:22:52ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>org.kepler.build.Get.getModule(Module module) has special behavior when it comes across the modules with names: ptolemy, ptolemy-8.0, and ptolemy-kepler-2.3. This seems to allow checking out a specific revision of pII from the ptII repository. I added ptolemy-kepler-2.3, and not ptolemy-kepler-*, because for some reason ptolemy-kepler-2.2 has a "local" copy of ptII, and i don't want to change how 2.2 works.</p>
<p>We'll have to revisit this for 2.4.</p>