Ecoinformatics Redmine: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362010-09-29T15:16:30ZEcoinformatics Redmine
Redmine Kepler - Bug #5192 (New): Module Manager reacts badly to dot files in resources/configuration dir...https://projects.ecoinformatics.org/ecoinfo/issues/51922010-09-29T15:16:30ZChristopher Brookscxh@eecs.berkeley.edu
<p>I was trying to follow the 2.1 instructions at<br /><a class="external" href="https://kepler-project.org/developers/teams/build/kepler-2.1-release-roadmap/?searchterm=roadmap">https://kepler-project.org/developers/teams/build/kepler-2.1-release-roadmap/?searchterm=roadmap</a></p>
<p>and edited <br />kepler-2.1/module-manager-2.1/resources/configurations/configuration.xml<br />with Emacs, which created<br />kepler-2.1/module-manager-2.1/resources/configurations/.#configuration.xml</p>
<p>Then ant clean-all run<br />failed:</p>
<p>run:<br /> [run] setting dock icon to -Xdock:icon=/Users/cxh/src/kepler-2.1/common-2.1/resources/icons/kepler-dock-icon.png<br /> [run] Set environment variable: PATH = /Users/cxh/bin:/Users/cxh/ptII/bin:/usr/local/apache-maven/bin:/Users/cxh/bin:/Users/cxh/ptII/bin:/usr/local/apache-maven/bin:/Users/cxh/ptII/vendors/misc/dbxml-2.5.16/install/bin:/Users/cxh/bin:/Users/cxh/ptII/bin:/usr/local/apache-maven/bin:/opt/subversion/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/texbin:/usr/X11/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/texbin:/usr/local/texlive/2007/bin:/usr/local/git/bin:/Users/cxh/ptII/vendors/misc/dbxml-2.5.16/install/bin:/Users/cxh/ptII/vendors/misc/dbxml-2.5.16/install/bin:/Users/cxh/bin:/Users/cxh/ptII/bin:/usr/local/apache-maven/bin:/opt/subversion/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/texbin:/usr/X11/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/texbin:/usr/local/texlive/2007/bin:/usr/texbin:/usr/local/texlive/2007/bin:/Users/cxh/ptII/vendors/misc/dbxml-2.5.16/install/bin:/Users/cxh/src/kepler-2.1/r-2.1/lib:/Users/cxh/src/kepler-2.1/common-2.1/lib/ptolemy/matlab:/Users/cxh/src/kepler-2.1/common-2.1/lib<br /> [run] Set environment variable: R_HOME = /Library/Frameworks/R.framework/Resources<br /> [run] /Users/cxh/src/kepler-2.1<br /> [run] java.io.FileNotFoundException: /Users/cxh/src/kepler-2.1/module-manager-2.1/resources/configurations/.#configuration.xml (No such file or directory)<br /> [run] at java.io.FileInputStream.open(Native Method)<br /> [run] at java.io.FileInputStream.<init>(FileInputStream.java:106)<br /> [run] at org.kepler.configuration.CommonsConfigurationReader.loadConfiguration(CommonsConfigurationReader.java:144)<br /> [run] at org.kepler.configuration.CommonsConfigurationReader.loadConfigurations(CommonsConfigurationReader.java:92)<br /> [run] at org.kepler.configuration.CommonsConfigurationReader.loadConfigurations(CommonsConfigurationReader.java:64)<br /> [run] at org.kepler.configuration.ConfigurationManager.loadConfiguration(ConfigurationManager.java:420)<br /> [run] at org.kepler.configuration.ConfigurationManager.<init>(ConfigurationManager.java:87)<br /> [run] at org.kepler.configuration.ConfigurationManager.getInstance(ConfigurationManager.java:116)<br /> [run] at org.kepler.configuration.ConfigurationManager.getInstance(ConfigurationManager.java:105)<br /> [run] at org.kepler.modulemanager.RepositoryLocations.initReleaseLocation(RepositoryLocations.java:24)<br /> [run] at org.kepler.modulemanager.RepositoryLocations.getReleaseLocation(RepositoryLocations.java:18)<br /> [run] at org.kepler.Kepler.main(Kepler.java:89)<br /> [run] org.kepler.configuration.ConfigurationManagerException: Error loading configuration file: /Users/cxh/src/kepler-2.1/module-manager-2.1/resources/configurations/.#configuration.xml (No such file or directory)<br /> [run] at org.kepler.configuration.CommonsConfigurationReader.loadConfiguration(CommonsConfigurationReader.java:171)<br /> [run] at org.kepler.configuration.CommonsConfigurationReader.loadConfigurations(CommonsConfigurationReader.java:92)<br /> [run] at org.kepler.configuration.CommonsConfigurationReader.loadConfigurations(CommonsConfigurationReader.java:64)<br /> [run] at org.kepler.configuration.ConfigurationManager.loadConfiguration(ConfigurationManager.java:420)<br /> [run] at org.kepler.configuration.ConfigurationManager.<init>(ConfigurationManager.java:87)<br /> [run] at org.kepler.configuration.ConfigurationManager.getInstance(ConfigurationManager.java:116)<br /> [run] at org.kepler.configuration.ConfigurationManager.getInstance(ConfigurationManager.java:105)<br /> [run] at org.kepler.modulemanager.RepositoryLocations.initReleaseLocation(RepositoryLocations.java:24)<br /> [run] at org.kepler.modulemanager.RepositoryLocations.getReleaseLocation(RepositoryLocations.java:18)<br /> [run] at org.kepler.Kepler.main(Kepler.java:89)<br /> [run] org.kepler.configuration.ConfigurationManagerException: Error loading configuration: Error loading configuration file: /Users/cxh/src/kepler-2.1/module-manager-2.1/resources/configurations/.#configuration.xml (No such file or directory)<br /> [run] at org.kepler.configuration.CommonsConfigurationReader.loadConfigurations(CommonsConfigurationReader.java:105)<br /> [run] at org.kepler.configuration.CommonsConfigurationReader.loadConfigurations(CommonsConfigurationReader.java:64)<br /> [run] at org.kepler.configuration.ConfigurationManager.loadConfiguration(ConfigurationManager.java:420)<br /> [run] at org.kepler.configuration.ConfigurationManager.<init>(ConfigurationManager.java:87)<br /> [run] at org.kepler.configuration.ConfigurationManager.getInstance(ConfigurationManager.java:116)<br /> [run] at org.kepler.configuration.ConfigurationManager.getInstance(ConfigurationManager.java:105)<br /> [run] at org.kepler.modulemanager.RepositoryLocations.initReleaseLocation(RepositoryLocations.java:24)<br /> [run] at org.kepler.modulemanager.RepositoryLocations.getReleaseLocation(RepositoryLocations.java:18)<br /> [run] at org.kepler.Kepler.main(Kepler.java:89)<br /> [run] Exception in thread "main" java.lang.RuntimeException: Could not load configuration: Error loading configuration: Error loading configuration file: /Users/cxh/src/kepler-2.1/module-manager-2.1/resources/configurations/.#configuration.xml (No such file or directory)<br /> [run] at org.kepler.configuration.ConfigurationManager.<init>(ConfigurationManager.java:93)<br /> [run] at org.kepler.configuration.ConfigurationManager.getInstance(ConfigurationManager.java:116)<br /> [run] at org.kepler.configuration.ConfigurationManager.getInstance(ConfigurationManager.java:105)<br /> [run] at org.kepler.modulemanager.RepositoryLocations.initReleaseLocation(RepositoryLocations.java:24)<br /> [run] at org.kepler.modulemanager.RepositoryLocations.getReleaseLocation(RepositoryLocations.java:18)<br /> [run] at org.kepler.Kepler.main(Kepler.java:89)</p>
<p>BUILD FAILED<br />/Users/cxh/src/kepler-2.1/build-area/build.xml:36: Java returned: 1</p>
<p>Total time: 2 minutes 52 seconds<br />bash-3.2$ ls ~/src/kepler-2.1/module-manager-2.1/resources/configurations/<br />configuration.xml<br />bash-3.2$ ls -a ~/src/kepler-2.1/module-manager-2.1/resources/configurations/<br />. .. configuration.xml<br />.#configuration.xml .svn<br />bash-3.2$</p> Kepler - Bug #5155 (New): To exclude a file or directory requires updating at least four places, ...https://projects.ecoinformatics.org/ecoinfo/issues/51552010-08-18T22:53:13ZChristopher Brookscxh@eecs.berkeley.edu
<p>jianwu <<a class="email" href="mailto:jianwu@sdsc.edu">jianwu@sdsc.edu</a>> writes:</p>
<blockquote>
<p>If excluding those from building system, please make sure it's also updated for<br />eclipse building. To update it, just modify the PtolemyClasspathStart file at<br />build-area/resources/eclipse.</p>
<p>We probably also need to update corresponding files at<br />build-area/resources/netbeans and build-area/resources/idea.</p>
</blockquote>
<p>I'm mystified as to why a human has to update four locations with<br />the same data. Isn't this why we have computers?<br />I should update one master file, the Netbeans, Eclipse and Idea <br />files should be automatically updated.</p> Kepler - Bug #5081 (New): A system for adding and removing GUI menus.https://projects.ecoinformatics.org/ecoinfo/issues/50812010-07-07T17:25:27ZChristopher Brookscxh@eecs.berkeley.edu
<p>The existing system needs documentation.</p>
<p>Also, refactoring to use RCP would help here</p> Kepler - Bug #5027 (New): Users should be able to build installers for the Kepler-2.0 branchhttps://projects.ecoinformatics.org/ecoinfo/issues/50272010-05-24T17:32:46ZChristopher Brookscxh@eecs.berkeley.edu
<p>Kepler users should be able to build installers so that they may deploy<br />a shrinkwrapped installation to other users. Currently, "ant installer" <br />works in the Kepler devel trunk, but fails in the 2.0 branch.</p>
<p>[installer] Writing installer file to /Users/cxh/src/kepler-2.0/build-area/installer/install.xml<br /> [izpack] ERROR: 'The content of elements must consist of well-formed character data or markup.'<br /> [izpack] ERROR: 'com.sun.org.apache.xml.internal.utils.WrappedRuntimeException: The content of elements must consist of well-formed character data or markup.'<br /> [izpack] javax.xml.transform.TransformerException: javax.xml.transform.TransformerException: com.sun.org.apache.xml.internal.utils.WrappedRuntimeException: The content of elements must consist of well-formed character data or markup.<br /> [izpack] at com.sun.org.apache.xalan.internal.xsltc.trax.TransformerImpl.transform(TransformerImpl.java:673)<br /> [izpack] at com.sun.org.apache.xalan.internal.xsltc.trax.TransformerImpl.transform(TransformerImpl.java:300)<br /> [izpack] at com.izforge.izpack.adaptator.impl.XMLParser.parseLineNrFromInputSource(Unknown Source)</p>
<p>We are not currently exposing the "ant installer" command to users, so<br />this is an RFE, not a bug.</p>
<p>See bug 4994 at<br /><a class="external" href="http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4994">http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4994</a></p> Kepler - Bug #5022 (Resolved): 2.0-RC3 Windows installer creates Kepler 2.0-RC2 start menu choice...https://projects.ecoinformatics.org/ecoinfo/issues/50222010-05-20T19:52:20ZChristopher Brookscxh@eecs.berkeley.edu
<p>With the Kepler-2.0-RC3 Windows installer, the shortcut in Start->All Programs<br />->Kepler is Kepler 2.0-RC2, not Kepler-2.0-RC3.</p>
<p>Also, the icon for "Kepler 2.0-RC2" is missing, I get a default<br />icon, not the Kepler Icon.</p> Kepler - Bug #5020 (Resolved): 2.0-RC3 installer: R Kepler Module is not optionalhttps://projects.ecoinformatics.org/ecoinfo/issues/50202010-05-20T17:28:08ZChristopher Brookscxh@eecs.berkeley.edu
<p>When installing Kepler-2.0-RC3, I'm presented with<br />two choices:<br />Kepler<br />R Kepler Module</p>
<p>Both are required, I can't uncheck "R Kepler Module",<br />so why bother with this window?</p> Kepler - Bug #4996 (Resolved): 2.0-RC2 demos don't workhttps://projects.ecoinformatics.org/ecoinfo/issues/49962010-05-10T04:55:59ZChristopher Brookscxh@eecs.berkeley.eduKepler - Bug #4995 (In Progress): ant installer fails under Linuxhttps://projects.ecoinformatics.org/ecoinfo/issues/49952010-05-10T00:15:32ZChristopher Brookscxh@eecs.berkeley.edu
<p>In a clean Kepler 2.0 tree, "ant installer" fails under linux:</p>
<p>build-macapp:<br /> [echo] jarbunder<br /> [null] Deleting directory /home/cxh/src/kepler-2.0/Kepler.app<br />[jarbundler] Creating application bundle: /home/cxh/src/kepler-2.0/Kepler.app</p>
<p>BUILD FAILED<br />/home/cxh/src/kepler-2.0/build-area/build.xml:339: The following error occurred while executing this line:<br />/home/cxh/src/kepler-2.0/build-area/build.xml:370: The following error occurred while executing this line:<br />/home/cxh/src/kepler-2.0/build-area/build.xml:439: Cannot copy Java Application Stub: java.io.FileNotFoundException: /System/Library/Frameworks/JavaVM.framework/Versions/Current/Resources/MacOS/JavaApplicationStub (No such file or directory)</p>
<p>The problem is that the JavaApplicationStub file is not present under Linux.</p> Kepler - Bug #4994 (Resolved): ant installer fails with "Invalid directory 'dir' ... outreach-2.0...https://projects.ecoinformatics.org/ecoinfo/issues/49942010-05-08T03:14:26ZChristopher Brookscxh@eecs.berkeley.edu
<p>Working from the instructions at<br /><a class="external" href="https://kepler-project.org/developers/teams/build/building-kepler-installers">https://kepler-project.org/developers/teams/build/building-kepler-installers</a><br />and using Kepler-2.0 instead of the devel trunk, I have problems with<br />"ant install" </p>
<pre><code>mkdir kepler-2.0<br /> cd kepler-2.0<br /> svn co <a class="external" href="https://code.kepler-project.org/code/kepler/releases/release-branches/build-area-2.0/">https://code.kepler-project.org/code/kepler/releases/release-branches/build-area-2.0/</a> build-area<br /> cd build-area<br /> ant change-to -Dsuite=kepler-2.0<br /> ant clean-cache<br /> ant eclipse<br /> ant installer</code></pre>
<p>Fails with:<br />--start--<br />[installer] Appending packs from the outreach-2.0 module.<br />[installer] Appending packs from the r-2.0 module.<br />[installer] Appending packs from the ptolemy-8.0 module.<br />[installer] basedirPath: /Users/cxh/src/kepler-2.0<br />[installer] Filtering out non-used OS elements.<br />[installer] Writing installer file to /Users/cxh/src/kepler-2.0/build-area/installer/install.xml</p>
<p>BUILD FAILED<br />/Users/cxh/src/kepler-2.0/build-area/build.xml:337: The following error occurred while executing this line:<br />/Users/cxh/src/kepler-2.0/build-area/build.xml:361: com.izforge.izpack.compiler.CompilerException: installer/install.xml:252: Invalid directory 'dir': /Users/cxh/src/kepler-2.0/outreach-2.0.0/resources<br />--end--</p>
<p>build-area/installer/install.xml is generated by the build process and includes<br />a reference to outreach-2.0.0, which does not exist. outreach-2.0 does<br />exist.</p>
<p>See also<br /><a class="external" href="http://mercury.nceas.ucsb.edu/kepler/pipermail/kepler-users/2010-April/002154.html">http://mercury.nceas.ucsb.edu/kepler/pipermail/kepler-users/2010-April/002154.html</a></p>
<p>A test suite would help with this sort of problem.</p> Kepler - Bug #4993 (Resolved): Kepler-2.0 cannot be built under windows because of apple-extensionshttps://projects.ecoinformatics.org/ecoinfo/issues/49932010-05-08T01:47:46ZChristopher Brookscxh@eecs.berkeley.edu
<p>The instructions at<br /><a class="external" href="https://kepler-project.org/developers/teams/build/systems/build-system/extension-build-system">https://kepler-project.org/developers/teams/build/systems/build-system/extension-build-system</a><br />fail because of apple-extensions</p>
<p>If, under Windows Server 2003, I do:<br /> mkdir kepler-2.0<br /> cd kepler-2.0<br /> svn co <a class="external" href="https://code.kepler-project.org/code/kepler/releases/release-branches/build-area-2.0/">https://code.kepler-project.org/code/kepler/releases/release-branches/build-area-2.0/</a> build-area<br /> cd build-area<br /> ant change-to -Dsuite=kepler-2.0<br /> ant run</p>
<p>I get:</p>
<pre><code>[compile] Compiling apple-extensions-2.0...<br /> [compile] C:\tmp\cxh\src\kepler-2.0\build-area\build.xml:31: warning: 'includeantruntime' was not set, defaulting to build.syscl<br />asspath=last; set to false for repeatable builds<br /> [compile] Compiling 1 source file to C:\tmp\cxh\src\kepler-2.0\apple-extensions-2.0\target\classes<br /> [compile] C:\tmp\cxh\src\kepler-2.0\apple-extensions-2.0\src\org\kepler\osx\KeplerApplicationListener.java:50: package com.apple<br />.eawt does not exist<br /> [compile] import com.apple.eawt.ApplicationEvent;<br /> [compile] ^<br /> [compile] C:\tmp\cxh\src\kepler-2.0\apple-extensions-2.0\src\org\kepler\osx\KeplerApplicationListener.java:51: package com.apple<br />.eawt does not exist<br /> [compile] import com.apple.eawt.ApplicationListener;<br /> [compile] ^<br /> [compile] C:\tmp\cxh\src\kepler-2.0\apple-extensions-2.0\src\org\kepler\osx\KeplerApplicationListener.java:53: cannot find symbo<br />l<br /> [compile] symbol: class ApplicationListener<br /> [compile] public class KeplerApplicationListener implements ApplicationListener<br /> [compile] ^<br /> [compile] C:\tmp\cxh\src\kepler-2.0\apple-extensions-2.0\src\org\kepler\osx\KeplerApplicationListener.java:55: cannot find symbo<br />l<br /> [compile] symbol : class ApplicationEvent<br /> [compile] location: class org.kepler.osx.KeplerApplicationListener<br /> [compile] public void handleAbout(ApplicationEvent event)<br /> [compile] ^<br /> [compile] C:\tmp\cxh\src\kepler-2.0\apple-extensions-2.0\src\org\kepler\osx\KeplerApplicationListener.java:62: cannot find symbo<br />l<br /> [compile] symbol : class ApplicationEvent<br /> [compile] location: class org.kepler.osx.KeplerApplicationListener<br /> [compile] public void handleOpenApplication(ApplicationEvent event)<br /> [compile] ^<br /> [compile] C:\tmp\cxh\src\kepler-2.0\apple-extensions-2.0\src\org\kepler\osx\KeplerApplicationListener.java:67: cannot find symbo<br />l<br /> [compile] symbol : class ApplicationEvent<br /> [compile] location: class org.kepler.osx.KeplerApplicationListener<br /> [compile] public void handleOpenFile(ApplicationEvent event)<br /> [compile] ^<br /> [compile] C:\tmp\cxh\src\kepler-2.0\apple-extensions-2.0\src\org\kepler\osx\KeplerApplicationListener.java:72: cannot find symbo<br />l<br /> [compile] symbol : class ApplicationEvent<br /> [compile] location: class org.kepler.osx.KeplerApplicationListener<br /> [compile] public void handlePreferences(ApplicationEvent event)<br /> [compile] ^<br /> [compile] C:\tmp\cxh\src\kepler-2.0\apple-extensions-2.0\src\org\kepler\osx\KeplerApplicationListener.java:77: cannot find symbo<br />l<br /> [compile] symbol : class ApplicationEvent<br /> [compile] location: class org.kepler.osx.KeplerApplicationListener<br /> [compile] public void handlePrintFile(ApplicationEvent event)<br /> [compile] ^<br /> [compile] C:\tmp\cxh\src\kepler-2.0\apple-extensions-2.0\src\org\kepler\osx\KeplerApplicationListener.java:85: cannot find symbo<br />l<br /> [compile] symbol : class ApplicationEvent<br /> [compile] location: class org.kepler.osx.KeplerApplicationListener<br /> [compile] public void handleQuit(ApplicationEvent event)<br /> [compile] ^<br /> [compile] C:\tmp\cxh\src\kepler-2.0\apple-extensions-2.0\src\org\kepler\osx\KeplerApplicationListener.java:109: cannot find symb<br />ol<br /> [compile] symbol : class ApplicationEvent<br /> [compile] location: class org.kepler.osx.KeplerApplicationListener<br /> [compile] public void handleReOpenApplication(ApplicationEvent event)<br /> [compile] ^<br /> [compile] 10 errors</code></pre>
<p>BUILD FAILED<br />C:\tmp\cxh\src\kepler-2.0\build-area\build.xml:31: C:\tmp\cxh\src\kepler-2.0\build-area\build.xml:31: Compile failed; see the comp<br />iler error output for details.</p>
<p>Total time: 2 minutes 10 seconds</p>
<p>cxh@newton ~/src/kepler-2.0/build-area<br />$</p> Kepler - Bug #4887 (New): If a module is added to a configuration, the error message should inclu...https://projects.ecoinformatics.org/ecoinfo/issues/48872010-03-17T22:15:04ZChristopher Brookscxh@eecs.berkeley.edu
<p>Apparently, the dataturbine module was added to the kepler trunk.</p>
<p>After doing<br />ant update<br />ant run</p>
<p>I got:<br />run:<br /> [run] Error: The following modules are missing: <br /> [run] dataturbine</p>
<p>The fix is to do <br />ant change-to -Dsuite=kepler<br />ant run</p>
<p>It would be nice if the error message would tell the user to do an<br />ant change-to</p>
<p>Even better, it would be nice if the system would get the module.</p> Kepler - Bug #4056 (New): create developer documentation for svn configuration.https://projects.ecoinformatics.org/ecoinfo/issues/40562009-05-06T01:00:34ZChristopher Brookscxh@eecs.berkeley.edu
<p>When svn checks in files, it checks them in using a binary mode.<br />This is a problem when files are checked in using windows and checked<br />out under Linux or Mac OS X. Usually, things just work, but<br />not always. When they don't work, the failure is mysterious because<br />the file looks the same, but has the wrong end of line characters.</p>
<p>In addition, svn needs to be configured to properly set the svn keywords<br />such as Id and Version.</p>
<p>For details, see "Keyword Substition and end of line issues" <br /><a class="external" href="http://chess.eecs.berkeley.edu/ptexternal/wiki/Main/Subversion#toc22">http://chess.eecs.berkeley.edu/ptexternal/wiki/Main/Subversion#toc22</a><br />and</p>
<p><a class="external" href="http://chess.eecs.berkeley.edu/ptexternal/nightly/doc/coding/eclipse.htm#Subversive">http://chess.eecs.berkeley.edu/ptexternal/nightly/doc/coding/eclipse.htm#Subversive</a></p>
<p>One quick way to check is:</p>
<p>find . -name "*.java" | grep -v .svn > /tmp/kj<br />cat /tmp/kj | xargs ptolemy/adm/bin/svnpropcheck</p>
<p>another way is:<br />cat /tmp/kj | xargs ptolemy/util/testsuite/controlm</p>
<p>which yields:<br />./core/src/org/kepler/sms/NamedOntClass.java has controlms<br />./core/src/org/kepler/sms/NamedOntModel.java has controlms<br />./core/src/org/kepler/sms/NamedOntProperty.java has controlms<br />./core/src/org/kepler/sms/OntologyCatalog.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/luminary/domains/ptides/lib/ActuatorOutputDevice.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/luminary/domains/ptides/lib/SensorInputDevice.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/luminary/domains/ptides/lib/targets/luminary/GPOutputDeviceA.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/pret/actor/lib/gui/TimedPlotter.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Acceleration.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Const.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/CurrentTime.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Expression.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/logic/Comparator.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/MultiplyDivide.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Scale.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Source.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/data/expr/ASTPtLeafNode.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/data/expr/ASTPtProductNode.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/domains/continuous/lib/DiscreteClock.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/domains/continuous/lib/Integrator.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Lattice.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Position.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Speed.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Time.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Top.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Unitless.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Unknown.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/logicalAND/domains/continuous/lib/EventSource.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/logicalAND/domains/continuous/lib/Integrator.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/logicalAND/domains/modal/kernel/FSMActor.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/PropertyConstraintModalFSMHelper.java has controlms<br />./ptolemy/ptolemy/domains/gro/JavaDia.java has controlms<br />./ptolemy/ptolemy/domains/gro/JavaRenderer.java has controlms<br />./ptolemy/ptolemy/domains/gro/kernel/GRODirector.java has controlms<br />./ptolemy/ptolemy/domains/gro/kernel/GROScheduler.java has controlms<br />./ptolemy/ptolemy/domains/ptides/lib/targets/luminary/GPOutputDevice.java has controlms<br />./ptolemy/ptolemy/domains/ptides/lib/targets/luminary/GPOutputDeviceA.java has controlms<br />./util/src/org/camera/service/AverageGenomeSizeParserV2.java has controlms<br />./util/src/org/camera/service/CAMERARESTService.java has controlms<br />./util/src/org/camera/service/CAMERAURLProcessor.java has controlms<br />./util/src/org/camera/service/IdSizeMapForSeqFile.java has controlms<br />./util/src/org/camera/service/NameValuePair.java has controlms<br />./util/src/org/camera/service/ServiceUtils.java has controlms<br />./util/src/org/kepler/ssh/SftpExec.java has controlms<br />./util/src/org/sdm/spa/actors/transport/BbcpCopier.java has controlms<br />./util/src/org/sdm/spa/actors/transport/FileCopier.java has controlms<br />./util/src/org/sdm/spa/actors/transport/FileCopierFactory.java has controlms<br />./util/src/org/sdm/spa/actors/transport/GenericFileCopier.java has controlms<br />./util/src/org/sdm/spa/actors/transport/LocalFileCopier.java has controlms<br />./util/src/org/sdm/spa/actors/transport/ScpCopier.java has controlms<br />./util/src/org/sdm/spa/actors/transport/SftpCopier.java has controlms<br />./util/src/org/sdm/spa/actors/transport/SrmliteCopier.java has controlms<br />./util/src/org/sdm/spa/actors/transport/vo/ConnectionDetails.java has controlms<br />./util/tests/src/org/sdm/spa/actors/transport/GenericFileCopierTest.java has controlms<br />./util/tests/src/org/sdm/spa/actors/transport/RunGenericFileCopierTests.java has controlms</p>
<p>./core/src/org/kepler/sms/NamedOntClass.java has controlms<br />./core/src/org/kepler/sms/NamedOntModel.java has controlms<br />./core/src/org/kepler/sms/NamedOntProperty.java has controlms<br />./core/src/org/kepler/sms/OntologyCatalog.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/luminary/domains/ptides/lib/ActuatorOutputDevice.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/luminary/domains/ptides/lib/SensorInputDevice.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/luminary/domains/ptides/lib/targets/luminary/GPOutputDeviceA.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/pret/actor/lib/gui/TimedPlotter.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Acceleration.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Const.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/CurrentTime.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Expression.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/logic/Comparator.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/MultiplyDivide.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Scale.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Source.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/data/expr/ASTPtLeafNode.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/data/expr/ASTPtProductNode.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/domains/continuous/lib/DiscreteClock.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/domains/continuous/lib/Integrator.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Lattice.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Position.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Speed.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Time.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Top.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Unitless.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Unknown.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/logicalAND/domains/continuous/lib/EventSource.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/logicalAND/domains/continuous/lib/Integrator.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/logicalAND/domains/modal/kernel/FSMActor.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/PropertyConstraintModalFSMHelper.java has controlms<br />./ptolemy/ptolemy/domains/gro/JavaDia.java has controlms<br />./ptolemy/ptolemy/domains/gro/JavaRenderer.java has controlms<br />./ptolemy/ptolemy/domains/gro/kernel/GRODirector.java has controlms<br />./ptolemy/ptolemy/domains/gro/kernel/GROScheduler.java has controlms<br />./ptolemy/ptolemy/domains/ptides/lib/targets/luminary/GPOutputDevice.java has controlms<br />./ptolemy/ptolemy/domains/ptides/lib/targets/luminary/GPOutputDeviceA.java has controlms<br />./core/src/org/kepler/sms/NamedOntClass.java has controlms<br />./core/src/org/kepler/sms/NamedOntModel.java has controlms<br />./core/src/org/kepler/sms/NamedOntProperty.java has controlms<br />./core/src/org/kepler/sms/OntologyCatalog.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/luminary/domains/ptides/lib/ActuatorOutputDevice.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/luminary/domains/ptides/lib/SensorInputDevice.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/luminary/domains/ptides/lib/targets/luminary/GPOutputDeviceA.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/pret/actor/lib/gui/TimedPlotter.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Acceleration.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Const.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/CurrentTime.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Expression.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/logic/Comparator.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/MultiplyDivide.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Scale.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Source.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/data/expr/ASTPtLeafNode.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/data/expr/ASTPtProductNode.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/domains/continuous/lib/DiscreteClock.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/domains/continuous/lib/Integrator.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Lattice.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Position.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Speed.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Time.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Top.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Unitless.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Unknown.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/logicalAND/domains/continuous/lib/EventSource.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/logicalAND/domains/continuous/lib/Integrator.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/logicalAND/domains/modal/kernel/FSMActor.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/PropertyConstraintModalFSMHelper.java has controlms<br />./ptolemy/ptolemy/domains/gro/JavaDia.java has controlms<br />./ptolemy/ptolemy/domains/gro/JavaRenderer.java has controlms<br />./ptolemy/ptolemy/domains/gro/kernel/GRODirector.java has controlms<br />./ptolemy/ptolemy/domains/gro/kernel/GROScheduler.java has controlms<br />./ptolemy/ptolemy/domains/ptides/lib/targets/luminary/GPOutputDevice.java has controlms<br />./ptolemy/ptolemy/domains/ptides/lib/targets/luminary/GPOutputDeviceA.java has controlms<br />./core/src/org/kepler/sms/NamedOntClass.java has controlms<br />./core/src/org/kepler/sms/NamedOntModel.java has controlms<br />./core/src/org/kepler/sms/NamedOntProperty.java has controlms<br />./core/src/org/kepler/sms/OntologyCatalog.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/luminary/domains/ptides/lib/ActuatorOutputDevice.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/luminary/domains/ptides/lib/SensorInputDevice.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/luminary/domains/ptides/lib/targets/luminary/GPOutputDeviceA.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/pret/actor/lib/gui/TimedPlotter.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Acceleration.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Const.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/CurrentTime.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Expression.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/logic/Comparator.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/MultiplyDivide.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Scale.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Source.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/data/expr/ASTPtLeafNode.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/data/expr/ASTPtProductNode.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/domains/continuous/lib/DiscreteClock.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/domains/continuous/lib/Integrator.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Lattice.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Position.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Speed.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Time.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Top.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Unitless.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Unknown.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/logicalAND/domains/continuous/lib/EventSource.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/logicalAND/domains/continuous/lib/Integrator.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/logicalAND/domains/modal/kernel/FSMActor.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/PropertyConstraintModalFSMHelper.java has controlms<br />./ptolemy/ptolemy/domains/gro/JavaDia.java has controlms<br />./ptolemy/ptolemy/domains/gro/JavaRenderer.java has controlms<br />./ptolemy/ptolemy/domains/gro/kernel/GRODirector.java has controlms<br />./ptolemy/ptolemy/domains/gro/kernel/GROScheduler.java has controlms<br />./ptolemy/ptolemy/domains/ptides/lib/targets/luminary/GPOutputDevice.java has controlms<br />./ptolemy/ptolemy/domains/ptides/lib/targets/luminary/GPOutputDeviceA.java has controlms</p>
<p>I also checked the .xml files, and<br />common/etc/bundle_build.xml has control-ms<br />To fix these, run:</p>
<p>svn propset svn:eol-style native filename</p>
<p>To set the keywords on an alredy checked in file, run:</p>
<p>svn propset svn:keywords "Author Date Id Revision" filename</p>
<p>Then run:</p>
<p>svn commit</p>
<p>to commit the change.</p> Kepler - Bug #3903 (New): Use Java logging utilities instead of Apache commons logging facilityhttps://projects.ecoinformatics.org/ecoinfo/issues/39032009-03-18T19:21:30ZChristopher Brookscxh@eecs.berkeley.edu
<p>ersonally, I'd like to switch to the logging utilities that<br />now ship with Java, see<br /><a class="external" href="http://java.sun.com/j2se/1.4.2/docs/guide/util/logging/">http://java.sun.com/j2se/1.4.2/docs/guide/util/logging/</a><br />The advantage is that it would be one less jar file to ship.<br />A quick search finds 144 files that use the apache logging facility.<br />Most of these changes could be handled automatically by a script.</p>
<p>Notes about the logging system can be found at<br /><a class="external" href="https://kepler-project.org/developers/reference/using-commons-logging">https://kepler-project.org/developers/reference/using-commons-logging</a></p> Kepler - Bug #3898 (Resolved): update .kepler instead of removing it between versionshttps://projects.ecoinformatics.org/ecoinfo/issues/38982009-03-17T16:59:32ZChristopher Brookscxh@eecs.berkeley.edu
<p>Thanks to Qiao Huijie for pointing this out.<br />When switching between Kepler-1.0.0 and the Subversion development tree,<br />the ~/.kepler directory must be removed.<br />If it is not removed, then no actors are present in the actor browser pane.</p>
<p>I'm not sure why there is an incompatibility, but the code should detect<br />this incompatibility and prompt the user.</p>
<p>In addition, upon startup, the code should check to see if the actor browser<br />pane is empty and, if it is, prompt the user to delete their ~/.kepler <br />directory</p>
<p>Also, the developer instructions should be updated to mention removing<br />the ~/.kepler directory. I'll update the instructions.</p> Kepler - Bug #3204 (New): Kepler should have FSM exampleshttps://projects.ecoinformatics.org/ecoinfo/issues/32042008-04-02T21:15:37ZChristopher Brookscxh@eecs.berkeley.edu
<p>Finite State Machines are very powerful, there should<br />be a Kepler-specific scientific workflow that <br />illustrates FSMs.</p>