Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362011-09-08T16:14:50ZEcoinformatics Redmine
Redmine Bug #5483 (New): Another Kepler GUI will nuke the ~/.kepler/cache generated by the kepler in work...https://projects.ecoinformatics.org/ecoinfo/issues/54832011-09-08T16:14:50ZJing Taotao@nceas.ucsb.edu
<p>The workflow run engine embeds a kepler at workflowrunengine/kepler. Now the workflow run engine runs the kepler by calling the API of the kepler.</p>
<p>I found an issue that if we start another kepler GUI in another location, e.g. ~/project/kepler, the kepler gui will nuke the ~/.kepler/cache directory even though they are in the same suite. This may cause a problem to run the workflow run engine. However, if we start the kepler gui from workflowrunengine/kepler, the kepler gui wouldn't nuke the cache directory generated by the run engine.</p> Bug #5482 (New): Module manager should run patch checker before restarthttps://projects.ecoinformatics.org/ecoinfo/issues/54822011-09-06T17:41:54ZSean Riddleswriddle@gmail.com
<p>If the user uses the module manager to do something that would require a restart of Kepler, for example, changing to a released suite, then relative entries in the modules.txt file are only resolved in relation to locally available modules. Upon next run, the patch checker may find remote modules that may need updating. If possible, the patch checker should be run before the restart to remove the need for the additional restart.</p> Bug #5474 (New): Make the eml actor on kepler handle multiple physical representations in an entityhttps://projects.ecoinformatics.org/ecoinfo/issues/54742011-08-19T16:17:49ZJing Taotao@nceas.ucsb.edu
<p>Wade Sheldon from GCE-LTER brought an question if the eml actor can handle mutiple physical representations in an entity.</p>
<p>I took a look at code and found kepler can't handle this correctly. In org.ecoinformatics.seek.datasource.eml.eml2.Eml200Parser class, we always use</p>
<p>physical/dataFormat/textFormat/simpleDelimited/collapseDelimiters, physical/distribution/online/url/@function and et al directly. And also we only get the value from the node which index is 0.</p>
<p>This will handle entity with one physical representation correctly. But it will failed when an entity has more than one physical representation.</p>
<p>For example, a dataTable has two physicals. The first one isn't textFormat and has a downloadable url. The second one is textFormat and has a downloadable url.</p>
<p>Kepler will download the first non-text data object and ignore the second text data object. And the worst case is that kepler will mismatch the non-text data object with the text format information from the second text data object.</p> Bug #5435 (New): passing string into a parameter for headless execution doesn't workhttps://projects.ecoinformatics.org/ecoinfo/issues/54352011-06-30T23:08:54ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>If you attempt to pass in a string to a Parameter for a headless execution, the value doesn't get used. An integer works fine. Passing in a sting as the value for a String Parameter also works fine.</p>
<p>For example "foo" below isn't used:<br />./kepler.sh -runwf -nogui -x "foo" /Users/derik/KeplerData/workflows/MyWorkflows/paramx.xml</p>
<p>The paramx workflow attached to bug#5426 can be used for testing.</p> Bug #5344 (New): Kepler ships open source software and needs to include license fileshttps://projects.ecoinformatics.org/ecoinfo/issues/53442011-03-09T01:01:38ZChristopher Brookscxh@eecs.berkeley.edu
<p>How do I view the licenses of the pieces of software that <br />are shipped with Kepler?</p>
<p>I did an analysis for Ptolemy, see below:</p>
<blockquote>
<p>There was a somewhat spammy Slashdot article about Open Source licensing<br />at<br /><a class="external" href="http://mobile.slashdot.org/story/11/03/08/2041257/Android-Devices-Are-Hives-of-License-Violations">http://mobile.slashdot.org/story/11/03/08/2041257/Android-Devices-Are-Hives-of-License-Violations</a><br />that says that phone apps are not following Open Source licenses.</p>
<p>The original article at<br /><a class="external" href="http://www.linuxplanet.com/linuxplanet/newss/7315/1/">http://www.linuxplanet.com/linuxplanet/newss/7315/1/</a><br />talks about OpenLogic's license tool, which I downloaded and ran<br />on the Ptolemy II 8.0.1 release.</p>
<p>The executive summary is that we did ok, though I missed a few<br />licenses. What I did was run the tool and then compare what the tool<br />found with what is in the copyright.htm file, which can be found<br />at<br /><a class="external" href="http://ptolemy.eecs.berkeley.edu/ptolemyII/ptII8.0/ptII8.0.1/copyright.htm">http://ptolemy.eecs.berkeley.edu/ptolemyII/ptII8.0/ptII8.0.1/copyright.htm</a></p>
<p>My comments are below.</p>
<blockquote>
<p>bash-3.2$ ./discovery --path /Applications/Ptolemy/ptII8.0.1<br />OSS Discovery 2.3.3: Initializing runtime environment...........done.<br />OSS Discovery is preparing to scan your machine or specified directory.<br />If the directory or drive being scanned contains many files this will take some time.<br />You can continue to work on your machine while the scan proceeds.<br />Loading and initializing hand-written signature groups...done loading 1 in 4.789 seconds.<br />Loading and initializing generated signature groups.............................done loading 260,159 in 26.123 seconds.<br />Scanning /Applications/Ptolemy/ptII8.0.1</p>
<p>elapsed time: half a minute - scanning '/Applications/Ptolemy/ptII8.0.1/com' - walked 20 directories - scanned 0 files</p>
<p>elapsed time: 1 minute - scanning '/Applications/Ptolemy/ptII8.0.1/ptolemy' - walked 1209 directories - scanned 109 files</p>
<p>OSSDiscovery OLEX Application Scanner Report
============================================</p>
<p>client version : ossdiscovery v2.3.3<br />ip address : 192.168.1.4<br />hostname : Christopher-Brooks-MacBook-Pro.local<br />directories walked : 1712<br />files encountered : 17928<br />archives encountered : 0<br />class file archives : 166<br />source files : 0<br />symlinks found : 27<br />symlinks not followed : 27<br />bad symlinks found : 0<br />permission denied : 0<br />files examined : 191<br />start time : Tue Mar 8 15:36:35 2011<br />end time : Tue Mar 8 15:37:55 2011<br />scan time : 00:01:20<br />distro : Mac OS X: Darwin 9.8.0 RELEASE_I386 i386<br />kernel : 9.8.0 Darwin<br />anonymous machine hash : 5480e4664b1289980e05e47b1c1b9083c3<br />package instances found : 27<br />unique packages found : 25<br />throttling : disabled (total seconds paused: 0)<br />production machine : false</p>
<p>Package Name Version Location
============ ======= ========<br />antlr unknown ptolemy/actor/ptalon/antlr/antlr.jar<br />beanshell 2.0b4 lib/bsh-2.0b4.jar<br />codegen unknown ptolemy/codegen/codegen.jar<br />colt unknown ptolemy/actor/lib/colt/colt.jar<br />copernicus unknown ptolemy/copernicus/copernicus.jar<br />diva unknown lib/diva.jar<br />eclipse unknown lib/kieler.jar!/org/eclipse/emf/common/CommonPlugin$Implementation.class<br />eclipseplugin-eclipse_gmf unknown lib/kieler.jar!/org/eclipse/gmf/runtime/notation/Alignment.class</p>
</blockquote>
<p>I asked Hauke about these. We probably need to include specific<br />language for the eclipse files.</p>
<blockquote>
<p>fsm unknown ptolemy/domains/fsm/fsm.jar<br />hdf unknown ptolemy/domains/hdf/hdf.jar<br />img unknown doc/img/img.jar<br />java_cup unknown lib/java_cup.jar</p>
</blockquote>
<p>copyright.htm does not mention java_cup. The java_cup.jar file<br />is used by Caltrop. I fixed a transposition typo in<br />ptolemy.actor.gui.GenerateCopyrights that failed to identify the<br />dependency.</p>
<blockquote>
<p>jdk unknown ptolemy/backtrack/backtrack.jar!/ptolemy/backtrack/util/java/util/AbstractCollection.class<br />jdom 1.0 ptolemy/domains/ptinyos/lib/jdom.jar</p>
</blockquote>
<p>copyright.htm does not mention jdom.jar. I updated GenerateCopyrights so that if<br />ptolemy.domains.ptinyos.util.nc2moml.MoMLLib is present, then<br />we include a link to the jdom license file.</p>
<blockquote>
<p>jgoodies-forms unknown com/jgoodies/jgoodies.jar!/com/jgoodies/forms/builder/AbstractFormBuilder.class<br />jmf unknown ptolemy/actor/lib/jmf/jmf.jar<br />junit 4.8.2 lib/junit-4.8.2.jar<br />jython unknown lib/jython.jar<br />matlab unknown lib/matlab.jar<br />matlab unknown ptolemy/matlab/matlab.jar<br />mlc unknown org/mlc/mlc.jar<br />mysql-connector 5.1.6-bin ptolemy/actor/lib/database/mysql-connector-java-5.1.6-bin.jar<br />python unknown ptolemy/actor/lib/python/python.jar<br />saxon 8 lib/saxon8.jar</p>
</blockquote>
<p>copyright.htm does not mention saxon.jar. This was caused<br />by the same typo in GenerateCopyrights.</p>
<blockquote>
<p>tdl unknown ptolemy/vergil/tdl/tdl.jar<br />x10 unknown ptolemy/actor/lib/x10/x10.jar<br />x10 unknown vendors/misc/x10/tjx10p-13/lib/x10.jar</p>
</blockquote>
<p>This is probably the worst of the lot, as this file is GPL'd.<br />I'm not sure how it happened. The about:copyright feature lists it.<br />I intended to remove the X10 functionality from the release, but did<br />not do so.</p>
<p>OpenLogic's tool missed these open source tools:</p>
<p>AElfred License<br />Rxtx License (might not be included in the release)<br />Colt License<br />JNI Launcher (obscure)<br />PDFRenderer<br />Soot License (kind of obscure)<br />Copyright for mapss jar file used by PSDF (BSD license held by UMD).</p>
</blockquote>
<p>Below is a run of the OpenLogic tool on the Mac OS Kepler 2.2rc3 installation.<br />How do I view the licenses for these packages?</p>
<p>The Kepler Copyright says that Kepler is BSD licensed, but does<br />not cover all if these other packages. Some of the packages<br />are covered by the Ptolemy copyright system, but what about ant?</p>
<p>bash-3.2$ ./discovery --path /Applications/Kepler-2.2rc3/<br />OSS Discovery 2.3.3: Initializing runtime environment...........done.<br />OSS Discovery is preparing to scan your machine or specified directory.<br />If the directory or drive being scanned contains many files this will take some time.<br />You can continue to work on your machine while the scan proceeds.<br />Loading and initializing hand-written signature groups...done loading 1 in 6.877 seconds.<br />Loading and initializing generated signature groups.............................done loading 260,159 in 37.203 seconds.<br />Scanning /Applications/Kepler-2.2rc3</p>
<p>elapsed time: 1 minute - scanning '/Applications/Kepler-2.2rc3/Kepler.app' - walked 37 directories - scanned 40 files</p>
<p>elapsed time: 2 minutes - scanning '/Applications/Kepler-2.2rc3/Kepler.app' - walked 151 directories - scanned 127 files</p>
<p>OSSDiscovery OLEX Application Scanner Report
============================================</p>
<p>client version : ossdiscovery v2.3.3<br />ip address : 192.168.1.4<br />hostname : Christopher-Brooks-MacBook-Pro.local<br />directories walked : 705<br />files encountered : 3141<br />archives encountered : 31<br />class file archives : 182<br />source files : 0<br />symlinks found : 0<br />symlinks not followed : 0<br />bad symlinks found : 0<br />permission denied : 0<br />files examined : 385<br />start time : Tue Mar 8 16:49:41 2011<br />end time : Tue Mar 8 16:51:50 2011<br />scan time : 00:02:09<br />distro : Mac OS X: Darwin 9.8.0 RELEASE_I386 i386<br />kernel : 9.8.0 Darwin<br />anonymous machine hash : 5480e4664b1289980e05e47b1c1b9083c3<br />package instances found : 181<br />unique packages found : 81<br />throttling : disabled (total seconds paused: 0)<br />production machine : false</p>
<p>Package Name Version Location
============ ======= ========<br />activation 1.0.2 Kepler.app/Contents/Resources/Java/core-2.2.0/lib/jar/base-jars/activation.jar<br />activation 1.0.2 /var/folders/7f/7f-o2nyjFgewH67h0keKu++++TI/-Tmp-/core-2.2.0.zip.37215.39736/lib/jar/base-jars/activation.jar<br />activation unknown Kepler.app/Contents/Resources/Java/core-2.2.0/core-2.2.0.zip!/lib/jar/base-jars/activation.jar<br />ant 1.7.1 Kepler.app/Contents/Resources/Java/build-area/lib/ant.jar<br />ant 1.7.1 Kepler.app/Contents/Resources/Java/module-manager-2.2.0/lib/jar/ant.jar<br />ant 1.7.1 /var/folders/7f/7f-o2nyjFgewH67h0keKu++++TI/-Tmp-/module-manager-2.2.0.zip.37215.39744/lib/jar/ant.jar<br />ant unknown Kepler.app/Contents/Resources/Java/module-manager-2.2.0/module-manager-2.2.0.zip!/lib/jar/ant.jar<br />antlr unknown Kepler.app/Contents/Resources/Java/common-2.2.0/common-2.2.0.zip!/lib/jar/sms/antlr.jar<br />antlr unknown Kepler.app/Contents/Resources/Java/common-2.2.0/lib/jar/sms/antlr.jar<br />apache-soap unknown Kepler.app/Contents/Resources/Java/core-2.2.0/core-2.2.0.zip!/lib/jar/soap.jar!/org/apache/soap/AttributeHandler.class<br />apache-soap unknown Kepler.app/Contents/Resources/Java/core-2.2.0/lib/jar/soap.jar!/org/apache/soap/AttributeHandler.class<br />authentication 2.2 Kepler.app/Contents/Resources/Java/authentication-2.2.0/target/authentication-2.2.jar<br />authentication 2.2.0 Kepler.app/Contents/Resources/Java/authentication-2.2.0/authentication-2.2.0.zip<br />axis 1.1 Kepler.app/Contents/Resources/Java/core-2.2.0/lib/jar/axis-ant.jar<br />axis 1.1 /var/folders/7f/7f-o2nyjFgewH67h0keKu++++TI/-Tmp-/core-2.2.0.zip.37215.39736/lib/jar/axis-ant.jar<br />axis unknown Kepler.app/Contents/Resources/Java/common-2.2.0/common-2.2.0.zip!/lib/jar/axis.jar!/org/apache/axis/AxisEngine.class<br />axis unknown Kepler.app/Contents/Resources/Java/common-2.2.0/lib/jar/axis.jar!/org/apache/axis/AxisEngine.class<br />axis unknown Kepler.app/Contents/Resources/Java/core-2.2.0/core-2.2.0.zip!/lib/jar/axis-ant.jar<br />batik unknown Kepler.app/Contents/Resources/Java/ptolemy-8.1.0/lib/batik-all-1.6.jar!/org/apache/batik/Version.class<br />beanshell 2.0b4 Kepler.app/Contents/Resources/Java/ptolemy-8.1.0/lib/ptolemy-lib/bsh-2.0b4.jar<br />biojava 1.7.1 Kepler.app/Contents/Resources/Java/actors-2.2.0/actors-2.2.0.zip!/lib/jar/biojava-1.7.1.jar<br />biojava 1.7.1 Kepler.app/Contents/Resources/Java/actors-2.2.0/lib/jar/biojava-1.7.1.jar<br />bouncycastle 1.35.0 Kepler.app/Contents/Resources/Java/ssh-2.1.0/lib/jar/jce-jdk13-135.jar!/org/bouncycastle/LICENSE.class<br />castor 0.9.5 Kepler.app/Contents/Resources/Java/actors-2.2.0/actors-2.2.0.zip!/lib/jar/castor-0.9.5.jar<br />castor 0.9.5 Kepler.app/Contents/Resources/Java/actors-2.2.0/lib/jar/castor-0.9.5.jar<br />commons-codec 1.3 Kepler.app/Contents/Resources/Java/opendap-2.0.0/lib/jar/opendap/commons-codec-1.3.jar<br />commons-collections 3.2.1 Kepler.app/Contents/Resources/Java/configuration-manager-2.2.0/configuration-manager-2.2.0.zip!/lib/jar/commons-collections-3.2.1.jar<br />commons-collections 3.2.1 Kepler.app/Contents/Resources/Java/configuration-manager-2.2.0/lib/jar/commons-collections-3.2.1.jar<br />commons-configuration 1.6 Kepler.app/Contents/Resources/Java/configuration-manager-2.2.0/configuration-manager-2.2.0.zip!/lib/jar/commons-configuration-1.6.jar<br />commons-configuration 1.6 Kepler.app/Contents/Resources/Java/configuration-manager-2.2.0/lib/jar/commons-configuration-1.6.jar<br />commons-digester 2.0 Kepler.app/Contents/Resources/Java/configuration-manager-2.2.0/configuration-manager-2.2.0.zip!/lib/jar/commons-digester-2.0.jar<br />commons-digester 2.0 Kepler.app/Contents/Resources/Java/configuration-manager-2.2.0/lib/jar/commons-digester-2.0.jar<br />commons-discovery 0.2 Kepler.app/Contents/Resources/Java/core-2.2.0/lib/jar/base-jars/commons-discovery.jar<br />commons-discovery 0.2 /var/folders/7f/7f-o2nyjFgewH67h0keKu++++TI/-Tmp-/core-2.2.0.zip.37215.39736/lib/jar/base-jars/commons-discovery.jar<br />commons-discovery unknown Kepler.app/Contents/Resources/Java/core-2.2.0/core-2.2.0.zip!/lib/jar/base-jars/commons-discovery.jar<br />commons-httpclient 2.0-rc2 Kepler.app/Contents/Resources/Java/core-2.2.0/core-2.2.0.zip!/lib/jar/commons-httpclient-2.0-rc2.jar<br />commons-httpclient 2.0-rc2 Kepler.app/Contents/Resources/Java/core-2.2.0/lib/jar/commons-httpclient-2.0-rc2.jar<br />commons-httpclient 3.0.1 Kepler.app/Contents/Resources/Java/actors-2.2.0/actors-2.2.0.zip!/lib/jar/commons-httpclient-3.0.1.jar<br />commons-httpclient 3.0.1 Kepler.app/Contents/Resources/Java/actors-2.2.0/lib/jar/commons-httpclient-3.0.1.jar<br />commons-lang 2.0 Kepler.app/Contents/Resources/Java/core-2.2.0/core-2.2.0.zip!/lib/jar/taxon/commons-lang-2.0.jar<br />commons-lang 2.0 Kepler.app/Contents/Resources/Java/core-2.2.0/lib/jar/taxon/commons-lang-2.0.jar<br />commons-lang 2.4 Kepler.app/Contents/Resources/Java/configuration-manager-2.2.0/configuration-manager-2.2.0.zip!/lib/jar/commons-lang-2.4.jar<br />commons-lang 2.4 Kepler.app/Contents/Resources/Java/configuration-manager-2.2.0/lib/jar/commons-lang-2.4.jar<br />commons-logging 1.1 Kepler.app/Contents/Resources/Java/kepler-tasks-2.2.0/kepler-tasks-2.2.0.zip!/lib/jar/commons-logging-1.1.jar<br />commons-logging 1.1 Kepler.app/Contents/Resources/Java/kepler-tasks-2.2.0/lib/jar/commons-logging-1.1.jar<br />commons-net 1.2.1 Kepler.app/Contents/Resources/Java/common-2.2.0/common-2.2.0.zip!/lib/jar/apache/commons-net-1.2.1.jar<br />commons-net 1.2.1 Kepler.app/Contents/Resources/Java/common-2.2.0/lib/jar/apache/commons-net-1.2.1.jar<br />concurrent unknown Kepler.app/Contents/Resources/Java/common-2.2.0/common-2.2.0.zip!/lib/jar/sms/concurrent.jar<br />concurrent unknown Kepler.app/Contents/Resources/Java/common-2.2.0/lib/jar/sms/concurrent.jar<br />dataturbine 2.1 Kepler.app/Contents/Resources/Java/dataturbine-2.1.0/target/dataturbine-2.1.jar<br />dataturbine 2.1.0 Kepler.app/Contents/Resources/Java/dataturbine-2.1.0/dataturbine-2.1.0.zip<br />diva unknown Kepler.app/Contents/Resources/Java/ptolemy-8.1.0/lib/ptolemy-lib/diva.jar<br />dlese unknown Kepler.app/Contents/Resources/Java/actors-2.2.0/actors-2.2.0.zip!/lib/jar/dlese.jar<br />dlese unknown Kepler.app/Contents/Resources/Java/actors-2.2.0/lib/jar/dlese.jar<br />dnsjava 1.3.2 Kepler.app/Contents/Resources/Java/core-2.2.0/core-2.2.0.zip!/lib/jar/dnsjava-1.3.2.jar<br />dnsjava 1.3.2 Kepler.app/Contents/Resources/Java/core-2.2.0/lib/jar/dnsjava-1.3.2.jar<br />eclipse unknown Kepler.app/Contents/Resources/Java/ptolemy-8.1.0/lib/ptolemy-lib/kieler.jar!/org/eclipse/emf/common/CommonPlugin$Implementation.class<br />eclipseplugin-eclipse_gmf unknown Kepler.app/Contents/Resources/Java/ptolemy-8.1.0/lib/ptolemy-lib/kieler.jar!/org/eclipse/gmf/runtime/notation/Alignment.class<br />fi unknown Kepler.app/Contents/Resources/Java/actors-2.2.0/actors-2.2.0.zip!/lib/jar/jwsdp/FastInfoset.jar<br />fi unknown Kepler.app/Contents/Resources/Java/actors-2.2.0/lib/jar/jwsdp/FastInfoset.jar<br />filedrop unknown Kepler.app/Contents/Resources/Java/ssh-2.1.0/lib/jar/filedrop.jar<br />gdal 12 Kepler.app/Contents/Resources/Java/common-2.2.0/common-2.2.0.zip!/lib/gdal12.dll<br />gdal 12 Kepler.app/Contents/Resources/Java/common-2.2.0/lib/gdal12.dll<br />gnu-regexp 1.0.8 Kepler.app/Contents/Resources/Java/util-2.1.0/lib/jar/gnu-regexp-1.0.8.jar<br />gnu-regexp 1.0.8 Kepler.app/Contents/Resources/Java/util-2.1.0/util-2.1.0.zip!/lib/jar/gnu-regexp-1.0.8.jar<br />gui 2.2 Kepler.app/Contents/Resources/Java/gui-2.2.0/target/gui-2.2.jar<br />gui 2.2.0 Kepler.app/Contents/Resources/Java/gui-2.2.0/gui-2.2.0.zip<br />hsqldb 1.8.0.10 Kepler.app/Contents/Resources/Java/core-2.2.0/core-2.2.0.zip!/lib/jar/base-jars/hsqldb-1.8.0.10.jar<br />hsqldb 1.8.0.10 Kepler.app/Contents/Resources/Java/core-2.2.0/lib/jar/base-jars/hsqldb-1.8.0.10.jar<br />icu4j 2.6 Kepler.app/Contents/Resources/Java/common-2.2.0/lib/jar/sms/icu4j.jar<br />icu4j 2.6 /var/folders/7f/7f-o2nyjFgewH67h0keKu++++TI/-Tmp-/common-2.2.0.zip.37215.39731/lib/jar/sms/icu4j.jar<br />icu4j unknown Kepler.app/Contents/Resources/Java/common-2.2.0/common-2.2.0.zip!/lib/jar/sms/icu4j.jar<br />imagej unknown Kepler.app/Contents/Resources/Java/util-2.1.0/lib/jar/ImageJ.jar<br />imagej unknown Kepler.app/Contents/Resources/Java/util-2.1.0/util-2.1.0.zip!/lib/jar/ImageJ.jar<br />j2ee-jax-rpc unknown Kepler.app/Contents/Resources/Java/common-2.2.0/common-2.2.0.zip!/lib/jar/jaxrpc.jar<br />j2ee-jax-rpc unknown Kepler.app/Contents/Resources/Java/common-2.2.0/lib/jar/jaxrpc.jar<br />jacorb unknown Kepler.app/Contents/Resources/Java/actors-2.2.0/actors-2.2.0.zip!/lib/jar/cipres/jacorb.jar<br />jacorb unknown Kepler.app/Contents/Resources/Java/actors-2.2.0/lib/jar/cipres/jacorb.jar<br />jargon 2.0.5 Kepler.app/Contents/Resources/Java/actors-2.2.0/actors-2.2.0.zip!/lib/jar/jargon-2.0.5.jar<br />jargon 2.0.5 Kepler.app/Contents/Resources/Java/actors-2.2.0/lib/jar/jargon-2.0.5.jar<br />java_cup unknown Kepler.app/Contents/Resources/Java/ptolemy-8.1.0/lib/ptolemy-lib/java_cup.jar<br />javamail 1.3.2 Kepler.app/Contents/Resources/Java/actors-2.2.0/actors-2.2.0.zip!/lib/jar/mail.jar!/com/sun/mail/handlers/image_gif.class<br />javamail 1.3.2 Kepler.app/Contents/Resources/Java/actors-2.2.0/lib/jar/mail.jar!/com/sun/mail/handlers/image_gif.class<br />jaxb 1.0.1 Kepler.app/Contents/Resources/Java/common-2.2.0/lib/jar/jaxb-api.jar<br />jaxb 1.0.1 /var/folders/7f/7f-o2nyjFgewH67h0keKu++++TI/-Tmp-/common-2.2.0.zip.37215.39731/lib/jar/jaxb-api.jar<br />jaxb 1.0.2 Kepler.app/Contents/Resources/Java/common-2.2.0/lib/jar/jaxb-impl.jar<br />jaxb 1.0.2 /var/folders/7f/7f-o2nyjFgewH67h0keKu++++TI/-Tmp-/common-2.2.0.zip.37215.39731/lib/jar/jaxb-impl.jar<br />jaxb unknown Kepler.app/Contents/Resources/Java/common-2.2.0/common-2.2.0.zip!/lib/jar/jaxb-api.jar<br />jdom 1.0beta10 Kepler.app/Contents/Resources/Java/common-2.2.0/lib/jar/jdom.jar<br />jdom 1.0beta10 /var/folders/7f/7f-o2nyjFgewH67h0keKu++++TI/-Tmp-/common-2.2.0.zip.37215.39731/lib/jar/jdom.jar<br />jdom unknown Kepler.app/Contents/Resources/Java/common-2.2.0/common-2.2.0.zip!/lib/jar/jdom.jar<br />jena unknown Kepler.app/Contents/Resources/Java/common-2.2.0/common-2.2.0.zip!/lib/jar/sms/jena.jar<br />jena unknown Kepler.app/Contents/Resources/Java/common-2.2.0/lib/jar/sms/jena.jar<br />jgoodies-looks 1.3.2 Kepler.app/Contents/Resources/Java/core-2.2.0/core-2.2.0.zip!/lib/jar/LnF_looks-1.3.2.jar!/com/jgoodies/looks/BorderStyle.class<br />jgoodies-looks 1.3.2 Kepler.app/Contents/Resources/Java/core-2.2.0/lib/jar/LnF_looks-1.3.2.jar!/com/jgoodies/looks/BorderStyle.class<br />jmf 1.1.2 Kepler.app/Contents/Resources/Java/core-2.2.0/core-2.2.0.zip!/lib/jar/jai_core.jar!/javax/media/jai/AreaOpImage.class<br />jmf 1.1.2 Kepler.app/Contents/Resources/Java/core-2.2.0/lib/jar/jai_core.jar!/javax/media/jai/AreaOpImage.class<br />job 2.1 Kepler.app/Contents/Resources/Java/job-2.1.0/target/job-2.1.jar<br />job 2.1.0 Kepler.app/Contents/Resources/Java/job-2.1.0/job-2.1.0.zip<br />jsch 0.1.31 Kepler.app/Contents/Resources/Java/ssh-2.1.0/lib/jar/jsch-0.1.31.jar<br />jts 1.4.0 Kepler.app/Contents/Resources/Java/actors-2.2.0/actors-2.2.0.zip!/lib/jar/jts-1.4.0.jar<br />jts 1.4.0 Kepler.app/Contents/Resources/Java/actors-2.2.0/lib/jar/jts-1.4.0.jar<br />jump 1.1.1 Kepler.app/Contents/Resources/Java/actors-2.2.0/actors-2.2.0.zip!/lib/jar/jump-1.1.1.jar<br />jump 1.1.1 Kepler.app/Contents/Resources/Java/actors-2.2.0/lib/jar/jump-1.1.1.jar<br />junit 4.5 Kepler.app/Contents/Resources/Java/kepler-tasks-2.2.0/kepler-tasks-2.2.0.zip!/lib/jar/junit-4.5.jar<br />junit 4.5 Kepler.app/Contents/Resources/Java/kepler-tasks-2.2.0/lib/jar/junit-4.5.jar<br />junit 4.8.2 Kepler.app/Contents/Resources/Java/ptolemy-8.1.0/lib/ptolemy-lib/junit-4.8.2.jar<br />jython unknown Kepler.app/Contents/Resources/Java/core-2.2.0/core-2.2.0.zip!/lib/jar/jython.jar<br />jython unknown Kepler.app/Contents/Resources/Java/core-2.2.0/lib/jar/jython.jar<br />jython unknown Kepler.app/Contents/Resources/Java/ptolemy-8.1.0/lib/ptolemy-lib/jython.jar<br />kepler 2.2 Kepler.app/Contents/Resources/Java/kepler-2.2.0/target/kepler-2.2.jar<br />kepler 2.2.0 Kepler.app/Contents/Resources/Java/kepler-2.2.0/kepler-2.2.0.zip<br />kepler unknown Kepler.app/Contents/Resources/Java/kepler.jar<br />log4j 1.2.8 Kepler.app/Contents/Resources/Java/common-2.2.0/common-2.2.0.zip!/lib/jar/log4j-1.2.8.jar<br />log4j 1.2.8 Kepler.app/Contents/Resources/Java/common-2.2.0/lib/jar/log4j-1.2.8.jar<br />matlab unknown Kepler.app/Contents/Resources/Java/ptolemy-8.1.0/lib/ptolemy-lib/matlab.jar<br />mysql-connector 5.0.8-bin Kepler.app/Contents/Resources/Java/core-2.2.0/core-2.2.0.zip!/lib/jar/dbdrivers/mysql-connector-java-5.0.8-bin.jar<br />mysql-connector 5.0.8-bin Kepler.app/Contents/Resources/Java/core-2.2.0/lib/jar/dbdrivers/mysql-connector-java-5.0.8-bin.jar<br />naomi unknown Kepler.app/Contents/Resources/Java/ptolemy-8.1.0/lib/ptolemy-lib/naomi.jar<br />opendap 0.0.10 Kepler.app/Contents/Resources/Java/opendap-2.0.0/lib/jar/opendap/opendap-0.0.10.jar<br />opendap 2.0 Kepler.app/Contents/Resources/Java/opendap-2.0.0/target/opendap-2.0.jar<br />opendap 2.0.0 Kepler.app/Contents/Resources/Java/opendap-2.0.0/opendap-2.0.0.zip<br />oro 2.0.5 Kepler.app/Contents/Resources/Java/common-2.2.0/common-2.2.0.zip!/lib/jar/sms/jakarta-oro-2.0.5.jar<br />oro 2.0.5 Kepler.app/Contents/Resources/Java/common-2.2.0/lib/jar/sms/jakarta-oro-2.0.5.jar<br />pg7 4.215.jdbc3 Kepler.app/Contents/Resources/Java/core-2.2.0/core-2.2.0.zip!/lib/jar/dbdrivers/pg74.215.jdbc3.jar<br />pg7 4.215.jdbc3 Kepler.app/Contents/Resources/Java/core-2.2.0/lib/jar/dbdrivers/pg74.215.jdbc3.jar<br />postgresql 8.4-701.jdbc3 Kepler.app/Contents/Resources/Java/core-2.2.0/core-2.2.0.zip!/lib/jar/dbdrivers/postgresql-8.4-701.jdbc3.jar<br />postgresql 8.4-701.jdbc3 Kepler.app/Contents/Resources/Java/core-2.2.0/lib/jar/dbdrivers/postgresql-8.4-701.jdbc3.jar<br />ptolemy 8.1 Kepler.app/Contents/Resources/Java/ptolemy-8.1.0/target/ptolemy-8.1.jar<br />ptolemy 8.1.0 Kepler.app/Contents/Resources/Java/ptolemy-8.1.0/ptolemy-8.1.0.zip<br />repository 2.2 Kepler.app/Contents/Resources/Java/repository-2.2.0/target/repository-2.2.jar<br />repository 2.2.0 Kepler.app/Contents/Resources/Java/repository-2.2.0/repository-2.2.0.zip<br />rmijdbc unknown Kepler.app/Contents/Resources/Java/core-2.2.0/core-2.2.0.zip!/lib/jar/dbdrivers/RmiJdbc.jar<br />rmijdbc unknown Kepler.app/Contents/Resources/Java/core-2.2.0/lib/jar/dbdrivers/RmiJdbc.jar<br />saaj 1.2.1_01 Kepler.app/Contents/Resources/Java/actors-2.2.0/lib/jar/jwsdp/saaj-impl.jar<br />saaj 1.2.1_01 /var/folders/7f/7f-o2nyjFgewH67h0keKu++++TI/-Tmp-/actors-2.2.0.zip.37215.39728/lib/jar/jwsdp/saaj-impl.jar<br />saaj unknown Kepler.app/Contents/Resources/Java/actors-2.2.0/actors-2.2.0.zip!/lib/jar/jwsdp/saaj-impl.jar<br />sax unknown Kepler.app/Contents/Resources/Java/common-2.2.0/common-2.2.0.zip!/lib/jar/sms/rdf-api-2001-01-19.jar!/org/xml/sax/AttributeList.class<br />sax unknown Kepler.app/Contents/Resources/Java/common-2.2.0/lib/jar/sms/rdf-api-2001-01-19.jar!/org/xml/sax/AttributeList.class<br />saxon 8 Kepler.app/Contents/Resources/Java/ptolemy-8.1.0/lib/ptolemy-lib/saxon8.jar<br />snakeyaml 1.2 Kepler.app/Contents/Resources/Java/configuration-manager-2.2.0/configuration-manager-2.2.0.zip!/lib/jar/SnakeYAML-1.2.jar<br />snakeyaml 1.2 Kepler.app/Contents/Resources/Java/configuration-manager-2.2.0/lib/jar/SnakeYAML-1.2.jar<br />soaplab unknown Kepler.app/Contents/Resources/Java/common-2.2.0/common-2.2.0.zip!/lib/jar/soaplab/soaplab.jar<br />soaplab unknown Kepler.app/Contents/Resources/Java/common-2.2.0/lib/jar/soaplab/soaplab.jar<br />spring 1.2.3 Kepler.app/Contents/Resources/Java/core-2.2.0/lib/jar/taxon/spring.jar<br />spring 1.2.3 /var/folders/7f/7f-o2nyjFgewH67h0keKu++++TI/-Tmp-/core-2.2.0.zip.37215.39736/lib/jar/taxon/spring.jar<br />spring unknown Kepler.app/Contents/Resources/Java/core-2.2.0/core-2.2.0.zip!/lib/jar/taxon/spring.jar<br />ssh 2.1 Kepler.app/Contents/Resources/Java/ssh-2.1.0/target/ssh-2.1.jar<br />ssh 2.1.0 Kepler.app/Contents/Resources/Java/ssh-2.1.0/ssh-2.1.0.zip<br />struts 1.3.8 Kepler.app/Contents/Resources/Java/util-2.1.0/lib/jar/struts-core-1.3.8.jar!/org/apache/struts/Globals.class<br />struts 1.3.8 Kepler.app/Contents/Resources/Java/util-2.1.0/util-2.1.0.zip!/lib/jar/struts-core-1.3.8.jar!/org/apache/struts/Globals.class<br />swing-layout 1.0.3 Kepler.app/Contents/Resources/Java/module-manager-2.2.0/lib/jar/swing-layout-1.0.3.jar<br />swing-layout 1.0.3 Kepler.app/Contents/Resources/Java/module-manager-2.2.0/module-manager-2.2.0.zip!/lib/jar/swing-layout-1.0.3.jar<br />swing-worker 1.2 Kepler.app/Contents/Resources/Java/module-manager-2.2.0/lib/jar/swing-worker-1.2.jar<br />swing-worker 1.2 Kepler.app/Contents/Resources/Java/module-manager-2.2.0/module-manager-2.2.0.zip!/lib/jar/swing-worker-1.2.jar<br />swing-worker 1.2 Kepler.app/Contents/Resources/Java/ptolemy-8.1.0/lib/ptolemy-lib/swing-worker-1.2.jar<br />wsdl4j 1.5.1 Kepler.app/Contents/Resources/Java/actors-2.2.0/lib/jar/wsdl4j.jar<br />wsdl4j 1.5.1 /var/folders/7f/7f-o2nyjFgewH67h0keKu++++TI/-Tmp-/actors-2.2.0.zip.37215.39728/lib/jar/wsdl4j.jar<br />wsdl4j unknown Kepler.app/Contents/Resources/Java/actors-2.2.0/actors-2.2.0.zip!/lib/jar/wsdl4j.jar<br />wsif unknown Kepler.app/Contents/Resources/Java/core-2.2.0/core-2.2.0.zip!/lib/jar/wsif.jar<br />wsif unknown Kepler.app/Contents/Resources/Java/core-2.2.0/lib/jar/wsif.jar<br />wsif-j2c unknown Kepler.app/Contents/Resources/Java/core-2.2.0/core-2.2.0.zip!/lib/jar/wsif-j2c.jar<br />wsif-j2c unknown Kepler.app/Contents/Resources/Java/core-2.2.0/lib/jar/wsif-j2c.jar<br />xalan 2.4.0 Kepler.app/Contents/Resources/Java/common-2.2.0/lib/jar/apache/xalan.jar<br />xalan 2.4.0 /var/folders/7f/7f-o2nyjFgewH67h0keKu++++TI/-Tmp-/common-2.2.0.zip.37215.39731/lib/jar/apache/xalan.jar<br />xalan unknown Kepler.app/Contents/Resources/Java/actors-2.2.0/actors-2.2.0.zip!/lib/jar/jwsdp/xalan.jar<br />xalan unknown Kepler.app/Contents/Resources/Java/common-2.2.0/common-2.2.0.zip!/lib/jar/apache/xalan.jar<br />xalan xalan-j_2_5_2 Kepler.app/Contents/Resources/Java/actors-2.2.0/lib/jar/jwsdp/xalan.jar<br />xalan xalan-j_2_5_2 /var/folders/7f/7f-o2nyjFgewH67h0keKu++++TI/-Tmp-/actors-2.2.0.zip.37215.39728/lib/jar/jwsdp/xalan.jar<br />xdoclet 1.2.2 Kepler.app/Contents/Resources/Java/common-2.2.0/common-2.2.0.zip!/lib/jar/xdoclet-1.2.2.jar<br />xdoclet 1.2.2 Kepler.app/Contents/Resources/Java/common-2.2.0/lib/jar/xdoclet-1.2.2.jar<br />xerces 2.6.1 Kepler.app/Contents/Resources/Java/common-2.2.0/lib/jar/sms/xercesImpl.jar<br />xerces 2.6.1 /var/folders/7f/7f-o2nyjFgewH67h0keKu++++TI/-Tmp-/common-2.2.0.zip.37215.39731/lib/jar/sms/xercesImpl.jar<br />xerces unknown Kepler.app/Contents/Resources/Java/common-2.2.0/common-2.2.0.zip!/lib/jar/sms/xercesImpl.jar<br />xml-commons 1.1.2_ibm_1 Kepler.app/Contents/Resources/Java/common-2.2.0/lib/jar/apache/xml-apis.jar<br />xml-commons 1.1.2_ibm_1 /var/folders/7f/7f-o2nyjFgewH67h0keKu++++TI/-Tmp-/common-2.2.0.zip.37215.39731/lib/jar/apache/xml-apis.jar<br />xml-commons unknown Kepler.app/Contents/Resources/Java/common-2.2.0/common-2.2.0.zip!/lib/jar/apache/xml-apis.jar<br />xml-commons unknown Kepler.app/Contents/Resources/Java/common-2.2.0/common-2.2.0.zip!/lib/jar/axis.jar!/org/apache/xml/xml_soap/MapItem.class<br />xml-commons unknown Kepler.app/Contents/Resources/Java/common-2.2.0/lib/jar/axis.jar!/org/apache/xml/xml_soap/MapItem.class<br />xmlsec unknown Kepler.app/Contents/Resources/Java/actors-2.2.0/actors-2.2.0.zip!/lib/jar/jwsdp/xmlsec.jar<br />xmlsec unknown Kepler.app/Contents/Resources/Java/actors-2.2.0/lib/jar/jwsdp/xmlsec.jar</p>
<p>To show only file names of discovered files, run discovery with --no-paths<br />To show full paths to discovered files, run discovery with --show-base-dirs<br />To show OLEX web site links for discovered packages, run discovery with --olex-links</p>
<p>NOTE: OSSDiscovery with the OLEX plugin uses the fast rules by default. To do a<br />slower, but more accurate search, run discovery with --rule-types=all</p>
<p>OSS Discovery has completed the scan<br />bash-3.2$</p> Bug #5339 (New): In Database Query actor, the output port will be string type if you choose the o...https://projects.ecoinformatics.org/ecoinfo/issues/53392011-03-04T02:05:33ZJing Taotao@nceas.ucsb.edu
<p>Derik and I found that the type of the output port is string even though we chose "record" as the output type.</p> Bug #5338 (New): In Database Query actor, the output behavior will be different if there is no re...https://projects.ecoinformatics.org/ecoinfo/issues/53382011-03-04T02:02:36ZJing Taotao@nceas.ucsb.edu
<p>If there is result set found and the output type is "array":<br />no token will be sent if you select "outputEachRowSeparately" in configuration panel;<br />no token will be send but a message "no match result for query ..." will be shown if you don't select "outputEachRowSeparately".</p>
<p>If there is result set found and the output type is "no metadata".<br />no token will be sent if you select "outputEachRowSeparately" in configuration panel;<br />A token ( I guess "/n") will be sent out if you don't select "outputEachRowSeparately".</p> Bug #5336 (New): If a user chooses "no metadata" as output format in Database Query actor, the qu...https://projects.ecoinformatics.org/ecoinfo/issues/53362011-03-04T01:45:15ZJing Taotao@nceas.ucsb.edu
<p>If user chooses the output type as "no metadata" (no column name will be shown in the result), and query looks like "select id, lastTime from sensors where id='sensor0', the result only shows:</p>
<pre><code>sensor0</code></pre>
<p>The lastTime column is missed even though the sensor0 does have a value at the lastTime column</p> Bug #5314 (New): Closing last workflow window closes Kepler applicationhttps://projects.ecoinformatics.org/ecoinfo/issues/53142011-02-18T13:58:24ZMichal Owsiakmichalo@man.poznan.pl
<p>This is not compatible with Mac OS X way of closing windows.</p>
<p>After last window is closed, application should remain running unless user explicitly presses Command-Q or chooses Kepler -> Quit</p> Bug #5271 (New): No-gui mode needs a way to access private data sourcehttps://projects.ecoinformatics.org/ecoinfo/issues/52712011-01-12T22:10:46ZJing Taotao@nceas.ucsb.edu
<p>When kepler normally executes a workflow which has actors to access the private data, kepler will prompt a login dialog box. Through the login process, the workflow can access the private data successfully.</p>
<p>However, if the workflow is execute in no-gui mode, the login dialog box wouldn't be shown up. The workflow will fail to access the data and cause the workflow running fail. We need a way to fix the issue.</p> Bug #5269 (New): Selectordialog and Case actors do not work well togetherhttps://projects.ecoinformatics.org/ecoinfo/issues/52692011-01-07T00:54:25ZRobert Weberrweber221@comcast.net
<p>The Selectordialog actor in Kepler outputs a strange sort of string array that cannot be cast or converted into a string scalar. The control port of the Case actor expects a string scalar to compare against the names of the "refinements". Therefore, these two actors, which look like they should work in tandem, fail to collaborate. The attached example shows the problem. I've tried a number of fixes none works;</p>
<p>typing the output port of Selectordialog<br />typing the control port of Case<br />using the Expression actor to recast the output of Selectordialog</p> Bug #5268 (New): Dragging modified version of Sinewave actor to canvas causes gui oddityhttps://projects.ecoinformatics.org/ecoinfo/issues/52682011-01-06T01:14:23ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>While testing <a class="external" href="http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5146">http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5146</a> , I came across some gui strangeness. To replicate:<br />- drag the Sinewave actor to canvas<br />- right-click open the actor<br />- make a change, e.g. reposition an actor<br />- right-click on the canvas and select Save Archive, saving to Sinewave2<br />- search component library for sinewave, drag out to canvas the found Sinewave actor from within the Sinewave2.kar
* the green actor will not initially appear, you'll just see its ports. It will appear if you drag it a bit.</p> Bug #5267 (New): Changing a ptolemy.kernel.util.Attribute in Kepler gui doesn't workhttps://projects.ecoinformatics.org/ecoinfo/issues/52672011-01-06T01:04:29ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>While testing <a class="external" href="http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5146">http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5146</a> , I notice if I drag the Sinewave actor to canvas, right-click open actor, and then attempt to change the Attribute "Generate a sine wave.", my changes to this text will not appear.</p> Bug #5258 (New): kepler start exception when soft links are in KeplerData/workflows/MyWorkflowshttps://projects.ecoinformatics.org/ecoinfo/issues/52582010-12-17T18:09:14Zjianwu jianwujianwu@sdsc.edu
<p>in trunk version 26536, menu item 'File --> Open' can open workflow xml file or kar file and the default directory is KeplerData/workflows/MyWorkflows.</p>
<p>When I create a soft link in KeplerData/workflows/MyWorkflows and restart kepler. Kepler can not start correctly. The exception message is blow.</p>
<p>Also the old "File --> Open File" menu item can remember the last used directory and use it for the next opening. "File --> Open" only go to the 'KeplerData/workflows/MyWorkflows' directory. Its usability is not as good as before. </p>
<pre><code>[run] java.lang.Exception: /Users/jianwu/KeplerData/workflows/MyWorkflows/useful-workflows/MultiDisplay is not in a local repository<br /> [run] at org.kepler.objectmanager.library.LibIndex.assureFolder(LibIndex.java:1549)<br /> [run] at org.kepler.objectmanager.library.LibIndex.assureKar(LibIndex.java:1479)<br /> [run] at org.kepler.objectmanager.library.LibIndex.assureKarEntry(LibIndex.java:539)<br /> [run] at org.kepler.objectmanager.library.LibIndex.rebuild(LibIndex.java:268)<br /> [run] at org.kepler.objectmanager.library.LibraryManager.buildLibrary(LibraryManager.java:357)<br /> [run] at org.kepler.moml.KARLibraryBuilder.buildLibrary(KARLibraryBuilder.java:78)<br /> [run] at ptolemy.actor.gui.UserActorLibrary.openLibrary(UserActorLibrary.java:202)<br /> [run] at ptolemy.actor.gui.UserActorLibrary.openUserLibrary(UserActorLibrary.java:140)<br /> [run] at ptolemy.vergil.VergilApplication._createDefaultConfiguration(VergilApplication.java:330)<br /> [run] at ptolemy.vergil.VergilApplication._createEmptyConfiguration(VergilApplication.java:347)<br /> [run] at ptolemy.actor.gui.ConfigurationApplication._parseArgs(ConfigurationApplication.java:1115)<br /> [run] at ptolemy.vergil.VergilApplication._parseArgs(VergilApplication.java:477)<br /> [run] at ptolemy.actor.gui.ConfigurationApplication.&lt;init&gt;(ConfigurationApplication.java:226)<br /> [run] at ptolemy.actor.gui.MoMLApplication.&lt;init&gt;(MoMLApplication.java:80)<br /> [run] at ptolemy.vergil.VergilApplication.&lt;init&gt;(VergilApplication.java:110)<br /> [run] at ptolemy.vergil.VergilApplication$1.run(VergilApplication.java:219)<br /> [run] at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)<br /> [run] at java.awt.EventQueue.dispatchEvent(EventQueue.java:633)<br /> [run] at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)<br /> [run] at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)<br /> [run] at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)<br /> [run] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)<br /> [run] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)<br /> [run] at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)<br /> [run] java.lang.Exception<br /> [run] at org.kepler.objectmanager.library.LibIndex.assureKar(LibIndex.java:1482)<br /> [run] at org.kepler.objectmanager.library.LibIndex.assureKarEntry(LibIndex.java:539)<br /> [run] at org.kepler.objectmanager.library.LibIndex.rebuild(LibIndex.java:268)<br /> [run] at org.kepler.objectmanager.library.LibraryManager.buildLibrary(LibraryManager.java:357)<br /> [run] at org.kepler.moml.KARLibraryBuilder.buildLibrary(KARLibraryBuilder.java:78)<br /> [run] at ptolemy.actor.gui.UserActorLibrary.openLibrary(UserActorLibrary.java:202)<br /> [run] at ptolemy.actor.gui.UserActorLibrary.openUserLibrary(UserActorLibrary.java:140)<br /> [run] at ptolemy.vergil.VergilApplication._createDefaultConfiguration(VergilApplication.java:330)<br /> [run] at ptolemy.vergil.VergilApplication._createEmptyConfiguration(VergilApplication.java:347)<br /> [run] at ptolemy.actor.gui.ConfigurationApplication._parseArgs(ConfigurationApplication.java:1115)<br /> [run] at ptolemy.vergil.VergilApplication._parseArgs(VergilApplication.java:477)<br /> [run] at ptolemy.actor.gui.ConfigurationApplication.&lt;init&gt;(ConfigurationApplication.java:226)<br /> [run] at ptolemy.actor.gui.MoMLApplication.&lt;init&gt;(MoMLApplication.java:80)<br /> [run] at ptolemy.vergil.VergilApplication.&lt;init&gt;(VergilApplication.java:110)<br /> [run] at ptolemy.vergil.VergilApplication$1.run(VergilApplication.java:219)<br /> [run] at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)<br /> [run] at java.awt.EventQueue.dispatchEvent(EventQueue.java:633)<br /> [run] at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)<br /> [run] at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)<br /> [run] at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)<br /> [run] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)<br /> [run] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)<br /> [run] at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)<br /> [run] java.lang.NullPointerException<br /> [run] at org.kepler.objectmanager.library.LibIndex.assureKarEntry(LibIndex.java:557)<br /> [run] at org.kepler.objectmanager.library.LibIndex.rebuild(LibIndex.java:268)<br /> [run] at org.kepler.objectmanager.library.LibraryManager.buildLibrary(LibraryManager.java:357)<br /> [run] at org.kepler.moml.KARLibraryBuilder.buildLibrary(KARLibraryBuilder.java:78)<br /> [run] at ptolemy.actor.gui.UserActorLibrary.openLibrary(UserActorLibrary.java:202)<br /> [run] at ptolemy.actor.gui.UserActorLibrary.openUserLibrary(UserActorLibrary.java:140)<br /> [run] at ptolemy.vergil.VergilApplication._createDefaultConfiguration(VergilApplication.java:330)<br /> [run] at ptolemy.vergil.VergilApplication._createEmptyConfiguration(VergilApplication.java:347)<br /> [run] at ptolemy.actor.gui.ConfigurationApplication._parseArgs(ConfigurationApplication.java:1115)<br /> [run] at ptolemy.vergil.VergilApplication._parseArgs(VergilApplication.java:477)<br /> [run] at ptolemy.actor.gui.ConfigurationApplication.&lt;init&gt;(ConfigurationApplication.java:226)<br /> [run] at ptolemy.actor.gui.MoMLApplication.&lt;init&gt;(MoMLApplication.java:80)<br /> [run] at ptolemy.vergil.VergilApplication.&lt;init&gt;(VergilApplication.java:110)<br /> [run] at ptolemy.vergil.VergilApplication$1.run(VergilApplication.java:219)<br /> [run] at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)<br /> [run] at java.awt.EventQueue.dispatchEvent(EventQueue.java:633)<br /> [run] at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)<br /> [run] at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)<br /> [run] at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)<br /> [run] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)<br /> [run] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)<br /> [run] at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)<br /> [run] Filter file is null<br /> [run] error: TabPane is null. This problem can be fixed by adding a tabPaneFactory property in the configuration.xml file.<br /> [run] java.lang.NullPointerException<br /> [run] at org.kepler.gui.FilteredVisibleTreeModel.addTreeModelListener(FilteredVisibleTreeModel.java:174)<br /> [run] at javax.swing.JTree.setModel(JTree.java:855)<br /> [run] at javax.swing.JTree.&lt;init&gt;(JTree.java:650)<br /> [run] at ptolemy.vergil.tree.PTree.&lt;init&gt;(PTree.java:72)<br /> [run] at org.kepler.gui.AnnotatedPTree.&lt;init&gt;(AnnotatedPTree.java:89)<br /> [run] at org.kepler.gui.ComponentLibraryTab.initLibraryTree(ComponentLibraryTab.java:206)<br /> [run] at org.kepler.gui.ComponentLibraryTab.initializeTab(ComponentLibraryTab.java:175)<br /> [run] at org.kepler.gui.TabPaneFactory.createTabPaneTabs(TabPaneFactory.java:110)<br /> [run] at org.kepler.gui.TabManager.initializeTabs(TabManager.java:87)<br /> [run] at org.kepler.gui.KeplerGraphFrame._initBasicGraphFrame(KeplerGraphFrame.java:373)<br /> [run] at ptolemy.vergil.basic.BasicGraphFrame.&lt;init&gt;(BasicGraphFrame.java:224)<br /> [run] at ptolemy.vergil.basic.ExtendedGraphFrame.&lt;init&gt;(ExtendedGraphFrame.java:95)<br /> [run] at ptolemy.vergil.actor.ActorGraphFrame.&lt;init&gt;(ActorGraphFrame.java:135)<br /> [run] at org.kepler.gui.KeplerGraphFrame.&lt;init&gt;(KeplerGraphFrame.java:176)<br /> [run] at org.kepler.gui.frame.KeplerGraphTableau.&lt;init&gt;(KeplerGraphTableau.java:252)<br /> [run] at org.kepler.gui.frame.KeplerGraphTableau$Factory.createTableau(KeplerGraphTableau.java:315)<br /> [run] at ptolemy.actor.gui.PtolemyTableauFactory.createTableau(PtolemyTableauFactory.java:100)<br /> [run] at ptolemy.actor.gui.TableauFactory.createTableau(TableauFactory.java:127)<br /> [run] at ptolemy.actor.gui.Configuration.createPrimaryTableau(Configuration.java:569)<br /> [run] at ptolemy.vergil.VergilApplication._createEmptyConfiguration(VergilApplication.java:401)<br /> [run] at ptolemy.actor.gui.ConfigurationApplication._parseArgs(ConfigurationApplication.java:1115)<br /> [run] at ptolemy.vergil.VergilApplication._parseArgs(VergilApplication.java:477)<br /> [run] at ptolemy.actor.gui.ConfigurationApplication.&lt;init&gt;(ConfigurationApplication.java:226)<br /> [run] at ptolemy.actor.gui.MoMLApplication.&lt;init&gt;(MoMLApplication.java:80)<br /> [run] at ptolemy.vergil.VergilApplication.&lt;init&gt;(VergilApplication.java:110)<br /> [run] at ptolemy.vergil.VergilApplication$1.run(VergilApplication.java:219)<br /> [run] at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)<br /> [run] at java.awt.EventQueue.dispatchEvent(EventQueue.java:633)<br /> [run] at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)<br /> [run] at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)<br /> [run] at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)<br /> [run] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)<br /> [run] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)<br /> [run] at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)<br /> [run] Could not create tab pane.: null<br /> [run] java.lang.NullPointerException<br /> [run] at org.kepler.gui.FilteredVisibleTreeModel.addTreeModelListener(FilteredVisibleTreeModel.java:174)<br /> [run] at javax.swing.JTree.setModel(JTree.java:855)<br /> [run] at javax.swing.JTree.&lt;init&gt;(JTree.java:650)<br /> [run] at ptolemy.vergil.tree.PTree.&lt;init&gt;(PTree.java:72)<br /> [run] at org.kepler.gui.AnnotatedPTree.&lt;init&gt;(AnnotatedPTree.java:89)<br /> [run] at org.kepler.gui.ComponentLibraryTab.initLibraryTree(ComponentLibraryTab.java:206)<br /> [run] at org.kepler.gui.ComponentLibraryTab.initializeTab(ComponentLibraryTab.java:175)<br /> [run] at org.kepler.gui.TabPaneFactory.createTabPaneTabs(TabPaneFactory.java:110)<br /> [run] at org.kepler.gui.TabManager.initializeTabs(TabManager.java:87)<br /> [run] at org.kepler.gui.KeplerGraphFrame._initBasicGraphFrame(KeplerGraphFrame.java:373)<br /> [run] at ptolemy.vergil.basic.BasicGraphFrame.&lt;init&gt;(BasicGraphFrame.java:224)<br /> [run] at ptolemy.vergil.basic.ExtendedGraphFrame.&lt;init&gt;(ExtendedGraphFrame.java:95)<br /> [run] at ptolemy.vergil.actor.ActorGraphFrame.&lt;init&gt;(ActorGraphFrame.java:135)<br /> [run] at org.kepler.gui.KeplerGraphFrame.&lt;init&gt;(KeplerGraphFrame.java:176)<br /> [run] at org.kepler.gui.frame.KeplerGraphTableau.&lt;init&gt;(KeplerGraphTableau.java:252)<br /> [run] at org.kepler.gui.frame.KeplerGraphTableau$Factory.createTableau(KeplerGraphTableau.java:315)<br /> [run] at ptolemy.actor.gui.PtolemyTableauFactory.createTableau(PtolemyTableauFactory.java:100)<br /> [run] at ptolemy.actor.gui.TableauFactory.createTableau(TableauFactory.java:127)<br /> [run] at ptolemy.actor.gui.Configuration.createPrimaryTableau(Configuration.java:569)<br /> [run] at ptolemy.vergil.VergilApplication._createEmptyConfiguration(VergilApplication.java:401)<br /> [run] at ptolemy.actor.gui.ConfigurationApplication._parseArgs(ConfigurationApplication.java:1115)<br /> [run] at ptolemy.vergil.VergilApplication._parseArgs(VergilApplication.java:477)<br /> [run] at ptolemy.actor.gui.ConfigurationApplication.&lt;init&gt;(ConfigurationApplication.java:226)<br /> [run] at ptolemy.actor.gui.MoMLApplication.&lt;init&gt;(MoMLApplication.java:80)<br /> [run] at ptolemy.vergil.VergilApplication.&lt;init&gt;(VergilApplication.java:110)<br /> [run] at ptolemy.vergil.VergilApplication$1.run(VergilApplication.java:219)<br /> [run] at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)<br /> [run] at java.awt.EventQueue.dispatchEvent(EventQueue.java:633)<br /> [run] at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)<br /> [run] at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)<br /> [run] at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)<br /> [run] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)<br /> [run] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)<br /> [run] at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)<br /> [run] ERROR: no tab named Components in the view Workflow. (Perhaps the tab's getTabName() does not match the name given in configuration.xml?)<br /> [run] ERROR: no tab named Data in the view Workflow. (Perhaps the tab's getTabName() does not match the name given in configuration.xml?)<br /> [run] ERROR: no tab named Outline in the view Workflow. (Perhaps the tab's getTabName() does not match the name given in configuration.xml?)</code></pre> Bug #5123 (New): Create an ant task to display commits since last patch of a given modulehttps://projects.ecoinformatics.org/ecoinfo/issues/51232010-08-04T19:19:53ZSean Riddleswriddle@gmail.com
<p>Patches of modules are distributed as a zip containing the entire module. This means that someone can release a patch that accidentally includes someone else's work, if that someone had been committing their changes to the release branch of the same module (possibly working on a different patch). Before issuing a patch, it is handy to look at the version control log and see if there are any suspect commits that you might be inadvertently including.</p>
<p>The new ant task would execute 'svn log' for the range of revisions between that of the last patch issuance and HEAD.</p>