Ecoinformatics Redmine: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362011-10-17T18:01:41ZEcoinformatics Redmine
Redmine Kepler - Bug #5511 (New): If Kepler-2.2 is running, then opening a .kar in Kepler trunk produces ...https://projects.ecoinformatics.org/ecoinfo/issues/55112011-10-17T18:01:41ZChristopher Brookscxh@eecs.berkeley.edu
<p>Start up Kepler-2.2. I had created a Kepler-2.2 kar by doing:</p>
<p>1. I removed my ~/.kepler and ~/KeplerData directories.<br />2. When I started up Kepler-2.2, I was prompted to upgrade some modules. The Module Manager does not allow copy and paste, but IIRC, they were some 2.2.1 modules.</p>
<p>3. I opened up a Ptolemy model and saved it as a .kar:<br /> a. Help -> Kepler Documentation -> "background information on Ptolemy" -> Quick Tour<br /> b. I then clicked on any model, in this case "Noise".<br /> c. File -> Save As -> Save as Noise.kar</p>
<p>Then, while Kepler-2.2 is still running. Start up Kepler trunk and<br />open the Noise.kar file.</p>
<p>The following appears on stdout? I don't think this is mission critical, but it does not lend confidence that running Kepler-2.2 and Kepler trunk at the<br />same time will work.</p>
<p>org.kepler.objectmanager.cache.CacheException: Exception occurred while deserializing object<br /> [run] at org.kepler.objectmanager.cache.CacheManager.getObject(CacheManager.java:535)<br /> [run] at org.kepler.kar.handlers.ActorMetadataKAREntryHandler.open(ActorMetadataKAREntryHandler.java:242)<br /> [run] at org.kepler.kar.KARFile.open(KARFile.java:974)<br /> [run] at org.kepler.kar.KARFile.openKARContents(KARFile.java:742)<br /> [run] at org.kepler.gui.kar.OpenArchiveAction.openKAR(OpenArchiveAction.java:230)<br /> [run] at org.kepler.gui.kar.OpenArchiveAction.actionPerformed(OpenArchiveAction.java:196)<br /> [run] at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)<br /> [run] at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351)<br /> [run] at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)<br /> [run] at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)<br /> [run] at javax.swing.AbstractButton.doClick(AbstractButton.java:389)<br /> [run] at com.apple.laf.ScreenMenuItem.actionPerformed(ScreenMenuItem.java:95)<br /> [run] at java.awt.MenuItem.processActionEvent(MenuItem.java:627)<br /> [run] at java.awt.MenuItem.processEvent(MenuItem.java:586)<br /> [run] at java.awt.MenuComponent.dispatchEventImpl(MenuComponent.java:337)<br /> [run] at java.awt.MenuComponent.dispatchEvent(MenuComponent.java:325)<br /> [run] at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:682)<br /> [run] at java.awt.EventQueue.access$000(EventQueue.java:85)<br /> [run] at java.awt.EventQueue$1.run(EventQueue.java:638)<br /> [run] at java.awt.EventQueue$1.run(EventQueue.java:636)<br /> [run] at java.security.AccessController.doPrivileged(Native Method)<br /> [run] at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)<br /> [run] at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)<br /> [run] at java.awt.EventQueue$2.run(EventQueue.java:652)<br /> [run] at java.awt.EventQueue$2.run(EventQueue.java:650)<br /> [run] at java.security.AccessController.doPrivileged(Native Method)<br /> [run] at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)<br /> [run] at java.awt.EventQueue.dispatchEvent(EventQueue.java:649)<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] Caused by: java.io.FileNotFoundException: /Users/cxh/.kepler/cache-2.1/objects/urn.lsid.kepler-project.org.ns..8281.2.1 (No such file or directory)<br /> [run] at java.io.FileInputStream.open(Native Method)<br /> [run] at java.io.FileInputStream.<init>(FileInputStream.java:120)<br /> [run] at org.kepler.objectmanager.cache.CacheManager.getObject(CacheManager.java:520)<br /> [run] ... 33 more</p> Kepler - 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> Kepler - Bug #5195 (New): Help | Module Documentation is emptyhttps://projects.ecoinformatics.org/ecoinfo/issues/51952010-09-29T16:40:33ZChristopher Brookscxh@eecs.berkeley.edu
<p>In the 2.0.0developer trunk and the 2.1 tree,</p>
<p>Help | Module Documentation is empty.</p>
<p>The window says "Active Modules" <br />"Module Documentation available"</p>
<p>I'm putting this in the "build system" component because we don't<br />have a "module manager" component.</p> 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 #4909 (New): Actor documentation: updates ignored, duplicate info, how to refer to o...https://projects.ecoinformatics.org/ecoinfo/issues/49092010-03-29T21:15:59ZChristopher Brookscxh@eecs.berkeley.edu
<p>A few comments about the Kepler Actor Documentation system</p>
<p>1. If I update the .xml file for a Director, then preexisting models<br />do not get the updates. I think this is wrong. For example,<br />I added text to PNDirector.xml. If a user has a preexisting model<br />that uses PNDirector, then to see the new text, they would need<br />to drag in a new PNDirector.</p>
<p>2. The model files contain copies of the documentation. This is<br />related to point 1 above. This will be an issue for large systems<br />because parsing a large file with redundant info takes time and<br />possibly consumes lots of memory</p>
<p>3. In a documentation .xml file, how do I refer to another actor<br />or director? For example in<br />kepler/directors/resources/kar/CoreDirectors/PNDirector.xml<br />I want to refer to the Ramp actor so that if the user<br />clicks on the link, then they are shown the Ramp actor documentation<br />How do I do that?</p>
<p>4. In a documentation .xml file, how do I refer to a model?<br />For example, in<br />kepler/directors/resources/kar/CoreDirectors/PNDirector.xml<br />I want to refer to<br />ptolemy/domains/pn/demo/RemoveNilTokens/RemoveNilTokens.xml<br />How do I do that?</p> Kepler - Bug #4908 (New): actor/director/attribute .xml file documentation needs to be updatedhttps://projects.ecoinformatics.org/ecoinfo/issues/49082010-03-29T21:05:36ZChristopher Brookscxh@eecs.berkeley.edu
<p>The kar files include documentation for actors, directors and attributes.</p>
<p>These files need to be checked against the corresponding Ptolemy<br />actors, directors and attributes and updated accordingly.</p>
<p>For example, the directors/resources/kar/CoreDirectors/PNDirector.xml<br />file did not include information from June, 2008 about how to stop<br />a PN model.</p>
<p>To fix this bug, all of the .kar files should be reviewed and compared<br />with the original class comments in the .java files.</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 #4254 (New): wrapping up, never ending workflow! (PN inside PN)https://projects.ecoinformatics.org/ecoinfo/issues/42542009-07-21T00:47:32ZChristopher Brookscxh@eecs.berkeley.edu
<p>[I'm going through my email logs looking for bugs that have<br />not really been solved.]</p>
<p>The problem is that a trivial example of PN inside PN<br />results in a "wrapping up" message and never terminates.</p>
<p>In January, 2009, Edward responded to email from Josep Maria Campanera.</p>
<p>Edward wrote:</p>
<blockquote>
<p>In theory, PN inside PN should behave exactly as if the inside PN director<br />were not present. Why not just delete it?</p>
<p>It is arguably a bug that the PN director doesn't tolerate<br />PN opaque actors. I think I tried to fix that once, but never<br />got it fixed...</p>
<p>Edward</p>
</blockquote>
<p>Josep Maria Campanera Alsina wrote:</p>
<blockquote>
<p>Dear all,<br />I've found out that the error comes from the fact of using a PN<br />director as an opaque director inside a worflow managed by another PN<br />director! Somehow this problem is related to "Director compatibility" <br />issue.</p>
<p>So I've decided to simplify the workflow and use a model workflow just<br />in order someone can find a trick to run it succesfully. The main idea<br />is ¿How can we can continue the execution of a workflow after the<br />execution of an opaque composite actors with PN director inside when<br />the overall director is an PN one?</p>
<p>In the attached example (exampleCompositeActors.xml), I cannot get a<br />"Execution finished" but the Kepler shows the "wrapping up" signal or<br />alternatively a permament "executing" signal although apparently<br />nothing is running (only finished partly). No error message is<br />displayed!</p>
<p>Which worflow design I should adopt? What Am I doing wrong? How Can I<br />pursue my aim to execute PN composite actors sequentially?</p>
<p>All help appreciated!</p>
<p>Josep Maria Campanera,</p>
<p>PS1: I use Kepler Release 1.0.0 (May 2008) under Linux<br />PS2: Thanks Edward for your comments,</p>
<p>2009/1/14 Edward A. Lee <<a class="email" href="mailto:eal@eecs.berkeley.edu">eal@eecs.berkeley.edu</a>>:</p>
<blockquote>
<p>This is not a situation where it is refusing to terminate because of<br />unconsumed tokens. Typically, this is called by a deadlock. If you<br />are running on a Windows machine from the command line, you can get<br />a stack trace of all the executing threads by typing control-break.<br />If you forward that to this list, we can (maybe) identify<br />the culprit...</p>
<p>Edward</p>
<p>Josep Maria Campanera Alsina wrote:</p>
<blockquote>
<p>Dear all,<br />I get a "wrapping up" message from an execution of a workflow that<br />coordinates the submission of computational chemistry jobs in a<br />cluster queue system. The workflow is based on the<br />TestJobFullCycle-SGE.xml provided by kepler itself, with some<br />variations. Find attached the mentioned workflows.</p>
<p>My workflow is a composite one. I'd like to execute sequentially<br />several tasks: 1st) submit jobs to a cluster, 2nd) collect all outputs<br />and save them locally and then 3rd) convert output files to other<br />formats. Since some tasks are designed for PN director and some for<br />SDF director the overall director is a PN director.</p>
<p>However, the task under the PN director (in charge of job submission)<br />never finishes tough the task is already completed and early shows the<br />message "wrapping up", so the execution never finish step 1st and 2nd<br />so the 3rd is never executed. Why PN director doesn't finish the task?<br />How Can I stop the director and allow the workflow to continue?</p>
<p>I think the problem is related to the PN director that as said in the<br />user manual "may refuse to automatically terminate because tokens are<br />always generated and available to downstream actors"! Here it comments<br />that "One can correct the problem by changing the firingCountLimit<br />parameter of the Constant actor to some finite value". If done that<br />but it continues with the same problem.</p>
<p>How can I overcome this? all comment will be appreciated!</p>
<p>Thanks in advance,</p>
<p>Josep Maria,</p>
</blockquote></blockquote></blockquote> 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 #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> Kepler - Bug #3106 (New): Out of memory while opening all demos, is -Xss5m or SVG the problem?https://projects.ecoinformatics.org/ecoinfo/issues/31062008-01-29T04:54:18ZChristopher Brookscxh@eecs.berkeley.edu
<p>I'm marking this as having a target milestone of 1.0.0rc1 because<br />I suspect we should remove -Xss5m from build.xml because it means<br />we cannot open up very many models. Once that is addressed, the<br />milestone should be changed to something later.</p>
<p>Under Windows XP with Java 1.5.0_11, Kepler runs out of memory when opening all the demos whereas Ptolemy does not.</p>
<p>It could be that SVG is the issue, or it could be because Kepler<br />does not do lazy evaluation and thus loads in everything.</p>
<p>To replicate<br />1) Start Kepler with "ant run-dev", which uses -Xmx512m<br />2) Help -> Documentation -> Ptolemy Documentation -> Acknowledgements<br />3) Click on the copyright link at the bottom<br />4) Click on copyrights in<br />"Other copyrights about this configuration (may take a moment to run)." <br />5) Click on about in<br />"Other information about this configuration." <br />6) In the "ptolemy/configs/doc/completeDemosPtinyKepler.htm" line, click on<br /> "Open the .htm, .html, .xml and .pdf "</p>
<p>Roughly 25 windows will open and eventually, we get:</p>
<p>Caused by: java.lang.OutOfMemoryError: unable to create new native thread<br /> at java.lang.Thread.start0(Native Method)</p>
<p>Under Windows, the task manager says we are using 330Mb of memory,</p>
<p>Editing the run-dev entry in build.xml and removing:<br /><jvmarg value="-Xss5m"/><br />means we get to 580Mb in the task manager and then Kepler hangs with the<br />CPU Usage at 99%</p>
<p>java -X says that -Xss<br />-Xss<size> set java thread stack size</p>
<p>Perhaps -Xss should be removed from build.xml?</p>
<p>If I increase the Xmx from 512 to 1024, then the show all demos works,<br />At the end the amount of memory reported by the Task Manager is <br />258Mb, with a max of 608Mb<br />Running the last demo (sr/demo/TrafficLight/TrafficLight.xml) shows<br />this memory usage under Kepler:<br /> [java] 14471 ms. Memory: 968096K Free: 211261K (22%)</p>
<p>In contrast, doing the same thing with Ptolemy (no SVG), the task<br />manager reports 142Mb with a max of 142Mb. Running the same demo<br />reports:<br />6780 ms. Memory: 117172K Free: 24710K (21%)</p> Kepler - Bug #2414 (New): Opening a preexisting model should open in a blank viewerhttps://projects.ecoinformatics.org/ecoinfo/issues/24142006-04-13T21:42:32ZChristopher Brookscxh@eecs.berkeley.edu
<p>In "add welcome screen for release 1.0" at<br /><a class="external" href="http://bugzilla.ecoinformatics.org/show_bug.cgi?id=2343">http://bugzilla.ecoinformatics.org/show_bug.cgi?id=2343</a></p>
<p>Matthew wrote:</p>
<blockquote>
<p>Now this has been added, here is a very common use case, which seems incorrect<br />(reported by Kevin):</p>
<p>1) User starts kepler - gets blank graph frame, with new welcome screen in front</p>
<p>2) User dismisses welcome screen, and is left with blank graph frame</p>
<p>3) User then does "File->Open" and opens an existing workflow</p>
<p>4) The workflow then opens in a <strong>new</strong> graph frame, leaving the original, empty <br />graph frame on the screen.</p>
<p>Proposed resolution:</p>
<p>BEST: at startup, if user does the above, then the workflow gets opened in the<br /><strong>existing</strong> blank graph frame. Subsequently-opened workflows open up in <strong>new</strong><br />graph frames, as before</p>
</blockquote>
<blockquote>
<p>INTERIM: if we don't have time to implement the above for this release, then<br />check to see if we are in the above use-case, and if so, close the blank graph<br />frame after the first workflow has been opened</p>
<p>Any other thoughts/comments/ideas?</p>
</blockquote>
<p>I wrote:</p>
<blockquote>
<p>Probably File Open should be smart enough to realize that the current window<br />is mostly blank and a candidate for replacement. I'm not sure if<br />this will be very easy. For example, when one does File -> Save As, and<br />uses a new name, a new window appears. We need to handle "Unnamed" models<br />specially. I can take a look at this at some point, but probably not before<br />early March.</p>
</blockquote>
<p>I won't have time before Kepler 1.0, so I'm opening this as a separate <br />enhancement. This new bug has to do with the blank or Unnamed models,<br /><a class="external" href="http://bugzilla.ecoinformatics.org/show_bug.cgi?id=2343">http://bugzilla.ecoinformatics.org/show_bug.cgi?id=2343</a><br />has to do with the welcome window.</p>