Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362017-05-11T23:38:59ZEcoinformatics Redmine
Redmine Bug #7189 (New): memory leak in Managerhttps://projects.ecoinformatics.org/ecoinfo/issues/71892017-05-11T23:38:59ZDaniel Crawldanielcrawl@gmail.com
<p>The Manager registers a shutdown thread with the JVM, but does not unregister it after execute() is finished, which prevents the Manager from being garbage collected. run() does unregister it.</p>
<p>It also seems odd that the thread is registered only once (in the constructors), but never registered again after it is unregistered. The purpose of the thread is to "gracefully stop the execution of a model if the JVM is shut down (by control-C, the user logging out, etc.)", so I would expect the thread to be registered every time execution takes place.</p> Bug #6893 (New): DateToken value inconsistenthttps://projects.ecoinformatics.org/ecoinfo/issues/68932015-12-03T00:33:05ZDaniel Crawldanielcrawl@gmail.com
<p>DateToken stores the date internally in _value and _calendar, but these fields are not kept consistent. For example, if you use ModifyDate to add 2 seconds, _value is not updated. See the attached test workflow.</p>
<p>Also, ModifyDate changes the state of the input token instead of creating a new one - I thought this was not allowed in actors.</p> Bug #6795 (New): parameters in composite actor not configured properlyhttps://projects.ecoinformatics.org/ecoinfo/issues/67952015-07-08T11:40:04ZVincenzo Forchivforchi@eso.org
<p>If I:<br />- add a StringParameter to a composite actor<br />- configure the composite actor<br />- change the value to something<br />- press enter<br />The value is surrounded with double quotes</p>
<p>If I click on commit everything behaves as expected.</p> Bug #6794 (New): Cannot run two instances at the same time with two different usershttps://projects.ecoinformatics.org/ecoinfo/issues/67942015-07-07T16:09:35ZVincenzo Forchivforchi@eso.org
<p>If I try to run Kepler at the same time with two different users the second instance fails with the following error:</p>
<pre><code>[run] Kepler Initializing...<br /> [run] Command failed<br /> [run] Arguments: -kepler<br /> [run] <br /> [run] java.lang.Exception: Failed to parse "-kepler" <br /> [run] at ptolemy.actor.gui.ConfigurationApplication.throwArgsException(ConfigurationApplication.java:845)<br /> [run] at ptolemy.actor.gui.ConfigurationApplication.&lt;init&gt;(ConfigurationApplication.java:320)<br /> [run] at ptolemy.actor.gui.MoMLApplication.&lt;init&gt;(MoMLApplication.java:80)<br /> [run] at ptolemy.vergil.VergilApplication.&lt;init&gt;(VergilApplication.java:112)<br /> [run] at ptolemy.vergil.VergilApplication$1.run(VergilApplication.java:243)<br /> [run] at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:312)<br /> [run] at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:733)<br /> [run] at java.awt.EventQueue.access$200(EventQueue.java:103)<br /> [run] at java.awt.EventQueue$3.run(EventQueue.java:694)<br /> [run] at java.awt.EventQueue$3.run(EventQueue.java:692)<br /> [run] at java.security.AccessController.doPrivileged(Native Method)<br /> [run] at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)<br /> [run] at java.awt.EventQueue.dispatchEvent(EventQueue.java:703)<br /> [run] at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242)<br /> [run] at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161)<br /> [run] at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150)<br /> [run] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146)<br /> [run] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138)<br /> [run] at java.awt.EventDispatchThread.run(EventDispatchThread.java:91)<br /> [run] Caused by: java.lang.Exception: Failed to read configuration 'file:/diskb/scratch/vforchi/sw/reflex/common-2.4/configs/ptolemy/configs/kepler/configuration.xml'<br /> [run] at ptolemy.vergil.VergilApplication._createDefaultConfiguration(VergilApplication.java:335)<br /> [run] at ptolemy.vergil.VergilApplication._createEmptyConfiguration(VergilApplication.java:371)<br /> [run] at ptolemy.actor.gui.ConfigurationApplication._parseArgs(ConfigurationApplication.java:1327)<br /> [run] at ptolemy.vergil.VergilApplication._parseArgs(VergilApplication.java:501)<br /> [run] at ptolemy.actor.gui.ConfigurationApplication.&lt;init&gt;(ConfigurationApplication.java:244)<br /> [run] ... 17 more<br /> [run] Caused by: java.lang.Exception: Failed to call application initializer class "org.kepler.gui.KeplerInitializer". Perhaps the configuration file "file:/diskb/scratch/vforchi/sw/reflex/common-2.4/configs/ptolemy/configs/kepler/configuration.xml" has a problem?<br /> [run] at ptolemy.actor.gui.ConfigurationApplication.readConfiguration(ConfigurationApplication.java:686)<br /> [run] at ptolemy.vergil.VergilApplication._createDefaultConfiguration(VergilApplication.java:333)<br /> [run] ... 21 more<br /> [run] Caused by: java.sql.SQLException: Access is denied<br /> [run] at org.hsqldb.jdbc.Util.sqlException(Unknown Source)<br /> [run] at org.hsqldb.jdbc.jdbcConnection.&lt;init&gt;(Unknown Source)<br /> [run] at org.hsqldb.jdbcDriver.getConnection(Unknown Source)<br /> [run] at org.hsqldb.jdbcDriver.connect(Unknown Source)<br /> [run] at java.sql.DriverManager.getConnection(DriverManager.java:571)<br /> [run] at java.sql.DriverManager.getConnection(DriverManager.java:215)<br /> [run] at org.kepler.util.sql.HSQL._getConnection(HSQL.java:489)<br /> [run] at org.kepler.util.sql.DatabaseFactory.getDBConnection(DatabaseFactory.java:141)<br /> [run] at org.kepler.gui.KeplerInitializer.initializeSystem(KeplerInitializer.java:171)<br /> [run] at org.kepler.gui.KeplerInitializer.&lt;init&gt;(KeplerInitializer.java:98)<br /> [run] at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)<br /> [run] at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)<br /> [run] at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)<br /> [run] at java.lang.reflect.Constructor.newInstance(Constructor.java:526)<br /> [run] at java.lang.Class.newInstance(Class.java:374)<br /> [run] at ptolemy.actor.gui.ConfigurationApplication.readConfiguration(ConfigurationApplication.java:684)<br /> [run] ... 22 more<br /> [run] Checking for patches...</code></pre>
<p>And the attached window pops up.<br />Are there any plans to fix this or is it there a workaround?</p> Bug #6614 (New): parameter editor background color different on Linuxhttps://projects.ecoinformatics.org/ecoinfo/issues/66142014-11-02T20:02:55ZDaniel Crawldanielcrawl@gmail.com
<p>In the actor parameter editor dialog, the background color is blue for values if the string mode is true. If the parameter has choices and string mode is true, the background should also be blue, but on Linux it is white. An example is the Array Peak Search actor's scale parameter. The color is white on Linux in Kepler and Vergil, but blue on Mac in Kepler and Vergil. I also confirmed this behavior has changed since Kepler 2.0.</p> Bug #6588 (New): R actor does not have error for missing outputhttps://projects.ecoinformatics.org/ecoinfo/issues/65882014-08-21T20:27:56ZDaniel Crawldanielcrawl@gmail.com
<p>If the R actor has an output port "x", but the script does not assign a value to a variable "x", then the actor should report an error. Currently, the actor successfully runs but does not write a token to the output port.</p> Bug #6571 (New): Kepler command line execution won't exit if the parameter to be set in command l...https://projects.ecoinformatics.org/ecoinfo/issues/65712014-06-16T19:04:05Zjianwu jianwujianwu@sdsc.edu
<p>I got the same behavior for both -nocache and -cache option. I have to use Ctrl + C to kill the process.</p>
<p>Para111 in the following example is not defined in the workflow.</p>
<p>If the parameters exist in the workflow but the workflow execution goes wrong, the whole command can still exit.</p>
<p>---Console output for command line execution---<br />./kepler.sh -runwf -nogui -nocache -Para111 d /Users/jianwu/Dropbox/Hackathon-June2014/E3-Read-Text-File/solution.xml<br />The base dir is /Users/jianwu/Kepler/repository/kepler-trunk-svn<br />...<br /> [null] start of workflow-scheduler-gui module initializing<br /> [null] common tabpane configuration overridden by workflow-run-manager<br /> [null] INFO (org.kepler.util.sql.HSQL:_getConnection:654) started HSQL server at jdbc:hsqldb:hsql://localhost:56060/provenanceDB;filepath=hsqldb:file:/Users/jianwu/KeplerData/modules/provenance/provenanceDB<br /> [null] common tabpane configuration overridden by reporting<br /> [null] Unable to start application.<br /> [null] java.lang.Exception: Failed to parse "ptolemy/configs/kepler/ConfigNoGUINoCache.xml -runThenExit -Para111 d /Users/jianwu/Dropbox/Hackathon-June2014/E3-Read-Text-File/solution.xml" <br /> [null] at ptolemy.actor.gui.ConfigurationApplication.throwArgsException(ConfigurationApplication.java:845)<br /> [null] at org.kepler.KeplerConfigurationApplication.<init>(KeplerConfigurationApplication.java:388)<br /> [null] at org.kepler.Kepler.load(Kepler.java:527)<br /> [null] at org.kepler.Kepler.load(Kepler.java:571)<br /> [null] at org.kepler.Kepler.runApplication(Kepler.java:451)<br /> [null] at org.kepler.Kepler.main(Kepler.java:242)<br /> [null] Caused by: ptolemy.kernel.util.IllegalActionException: Unrecognized option: No parameter exists with name Para111<br /> [null] at org.kepler.KeplerConfigurationApplication._setParameters(KeplerConfigurationApplication.java:712)<br /> [null] at org.kepler.KeplerConfigurationApplication.<init>(KeplerConfigurationApplication.java:336)<br /> [null] ... 4 more</p>
<p>---JVM stacktrace using Ctrl + \ ---<br />^\2014-06-16 11:56:42<br />Full thread dump Java HotSpot(TM) 64-Bit Server VM (20.65-b04-462 mixed mode):</p>
<p>"Thread-4" daemon prio=5 tid=101aaa000 nid=0x10accb000 runnable [10acca000]<br /> java.lang.Thread.State: RUNNABLE<br /> at java.io.FileInputStream.readBytes(Native Method)<br /> at java.io.FileInputStream.read(FileInputStream.java:198)<br /> at java.lang.UNIXProcess$DeferredCloseInputStream.read(UNIXProcess.java:218)<br /> at org.apache.tools.ant.taskdefs.StreamPumper.run(StreamPumper.java:92)<br /> at java.lang.Thread.run(Thread.java:695)</p>
<p>"Thread-3" daemon prio=5 tid=101a7e800 nid=0x10abc8000 runnable [10abc7000]<br /> java.lang.Thread.State: RUNNABLE<br /> at java.io.FileInputStream.readBytes(Native Method)<br /> at java.io.FileInputStream.read(FileInputStream.java:220)<br /> at java.lang.UNIXProcess$DeferredCloseInputStream.read(UNIXProcess.java:227)<br /> at java.io.BufferedInputStream.fill(BufferedInputStream.java:218)<br /> at java.io.BufferedInputStream.read1(BufferedInputStream.java:258)<br /> at java.io.BufferedInputStream.read(BufferedInputStream.java:317)<br /> - locked <7f40a2160> (a java.io.BufferedInputStream)<br /> at java.io.FilterInputStream.read(FilterInputStream.java:90)<br /> at org.apache.tools.ant.taskdefs.StreamPumper.run(StreamPumper.java:92)<br /> at java.lang.Thread.run(Thread.java:695)</p>
<p>"process reaper" daemon prio=5 tid=101bbc000 nid=0x10a81a000 runnable [10a819000]<br /> java.lang.Thread.State: RUNNABLE<br /> at java.lang.UNIXProcess.waitForProcessExit(Native Method)<br /> at java.lang.UNIXProcess.access$900(UNIXProcess.java:17)<br /> at java.lang.UNIXProcess$2$1.run(UNIXProcess.java:86)</p>
<p>"Low Memory Detector" daemon prio=5 tid=1030a8800 nid=0x10a20d000 runnable [00000000]<br /> java.lang.Thread.State: RUNNABLE</p>
<p>"C2 CompilerThread1" daemon prio=9 tid=1030a8000 nid=0x10a10a000 waiting on condition [00000000]<br /> java.lang.Thread.State: RUNNABLE</p>
<p>"C2 CompilerThread0" daemon prio=9 tid=1030a7000 nid=0x10a007000 waiting on condition [00000000]<br /> java.lang.Thread.State: RUNNABLE</p>
<p>"Signal Dispatcher" daemon prio=9 tid=1030a6800 nid=0x109f04000 waiting on condition [00000000]<br /> java.lang.Thread.State: RUNNABLE</p>
<p>"Surrogate Locker Thread (Concurrent GC)" daemon prio=5 tid=1030a5800 nid=0x109e01000 waiting on condition [00000000]<br /> java.lang.Thread.State: RUNNABLE</p>
<p>"Finalizer" daemon prio=8 tid=101801800 nid=0x1098ec000 in Object.wait() [1098eb000]<br /> java.lang.Thread.State: WAITING (on object monitor)<br /> at java.lang.Object.wait(Native Method)<br /> - waiting on <7f44e2ee0> (a java.lang.ref.ReferenceQueue$Lock)<br /> at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118)<br /> - locked <7f44e2ee0> (a java.lang.ref.ReferenceQueue$Lock)<br /> at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:134)<br /> at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:171)</p>
<p>"Reference Handler" daemon prio=10 tid=10309b000 nid=0x1097e9000 in Object.wait() [1097e8000]<br /> java.lang.Thread.State: WAITING (on object monitor)<br /> at java.lang.Object.wait(Native Method)<br /> - waiting on <7f44e0848> (a java.lang.ref.Reference$Lock)<br /> at java.lang.Object.wait(Object.java:485)<br /> at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:116)<br /> - locked <7f44e0848> (a java.lang.ref.Reference$Lock)</p>
<p>"main" prio=5 tid=103000800 nid=0x100501000 in Object.wait() [100500000]<br /> java.lang.Thread.State: WAITING (on object monitor)<br /> at java.lang.Object.wait(Native Method)<br /> - waiting on <7f40cedc8> (a java.lang.UNIXProcess)<br /> at java.lang.Object.wait(Object.java:485)<br /> at java.lang.UNIXProcess.waitFor(UNIXProcess.java:115)<br /> - locked <7f40cedc8> (a java.lang.UNIXProcess)<br /> at org.apache.tools.ant.taskdefs.Execute.waitFor(Execute.java:551)<br /> at org.apache.tools.ant.taskdefs.Execute.execute(Execute.java:482)<br /> at org.apache.tools.ant.taskdefs.Java.fork(Java.java:784)<br /> at org.apache.tools.ant.taskdefs.Java.executeJava(Java.java:211)<br /> at org.apache.tools.ant.taskdefs.Java.executeJava(Java.java:132)<br /> at org.apache.tools.ant.taskdefs.Java.execute(Java.java:105)<br /> at org.kepler.build.Run.runSuite(Run.java:364)<br /> at org.kepler.build.Run.run(Run.java:235)<br /> at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:102)<br /> at org.kepler.build.runner.Kepler.run(Kepler.java:266)<br /> at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:102)<br /> at org.kepler.build.runner.Kepler.main(Kepler.java:109)</p>
<p>"VM Thread" prio=9 tid=103096000 nid=0x1096e6000 runnable</p>
<p>"Gang worker#0 (Parallel GC Threads)" prio=9 tid=103002000 nid=0x102201000 runnable</p>
<p>"Gang worker#1 (Parallel GC Threads)" prio=9 tid=103002800 nid=0x102304000 runnable</p>
<p>"Concurrent Mark-Sweep GC Thread" prio=9 tid=10304d000 nid=0x1093f0000 runnable <br />"VM Periodic Task Thread" prio=10 tid=1030ba800 nid=0x10a310000 waiting on condition</p>
<p>"Exception Catcher Thread" prio=10 tid=103001800 nid=0x1017fe000 runnable <br />JNI global references: 1341</p>
<p>Heap<br /> par new generation total 19136K, used 2087K [7f3000000, 7f44c0000, 7f44c0000)<br /> eden space 17024K, 8% used [7f3000000, 7f317d228, 7f40a0000)<br /> from space 2112K, 26% used [7f40a0000, 7f412ca40, 7f42b0000)<br /> to space 2112K, 0% used [7f42b0000, 7f42b0000, 7f44c0000)<br /> concurrent mark-sweep generation total 63872K, used 1148K [7f44c0000, 7f8320000, 7fae00000)<br /> concurrent-mark-sweep perm gen total 21248K, used 7839K [7fae00000, 7fc2c0000, 800000000)</p>
<pre><code>[null] 2014-06-16 11:56:42<br /> [null] Full thread dump Java HotSpot(TM) 64-Bit Server VM (20.65-b04-462 mixed mode):<br /> [null] <br /> [null] "DestroyJavaVM" prio=5 tid=101801000 nid=0x100501000 waiting on condition [00000000]<br /> [null] java.lang.Thread.State: RUNNABLE<br /> [null] <br /> [null] "HSQLDB Connection @690bc995" prio=5 tid=10aff7000 nid=0x10d70f000 runnable [10d70e000]<br /> [null] java.lang.Thread.State: RUNNABLE<br /> [null] at java.net.SocketInputStream.socketRead0(Native Method)<br /> [null] at java.net.SocketInputStream.read(SocketInputStream.java:129)<br /> [null] at java.io.BufferedInputStream.fill(BufferedInputStream.java:218)<br /> [null] at java.io.BufferedInputStream.read(BufferedInputStream.java:237)<br /> [null] - locked &lt;7cd8c9b48&gt; (a java.io.BufferedInputStream)<br /> [null] at java.io.DataInputStream.readInt(DataInputStream.java:370)<br /> [null] at org.hsqldb.Result.read(Unknown Source)<br /> [null] at org.hsqldb.ServerConnection.run(Unknown Source)<br />....</code></pre> Bug #6481 (New): strange issue with MultipleTabDisplay actor and with Display like actors in gene...https://projects.ecoinformatics.org/ecoinfo/issues/64812014-03-25T08:02:42ZOwsiak Michalmichal.owsiak@man.poznan.pl
<p>Hi there,</p>
<p>I will paste here description that already went to Jianwu via e-mail, but I think it describes the issue in details:</p>
<p>Some time ago we have published our patches to MultipleTabDisplay actor so it is consistent with new way of redirecting output.</p>
<p>The issue here is, that we have problem with running Kepler workflows in non-gui mode.</p>
<p>The issue lays in missing "output" port inside Multiple Tab Display actor.</p>
<p>The problem is that in GUI mode, everything works just fine (see the screen shoot).</p>
<p>In non-gui mode, we are getting an exception (see the attachment - exception.txt).</p>
<p>Command line used for starting workflow is:</p>
<p>./kepler.sh -runwf -nogui -nocache ~/Desktop/testMTD.xml</p>
<p>Problematic workflow was reduced, and now, we have smallest case that triggers exception.</p>
<p>The workflow is inside: testMTD.xml.</p>
<p>The problem occurs in case Multiple Tab Display actor is inside Composite actor. If the MTD is placed on main workflow, everything is just fine.</p>
<p>If we start testMTD workflow in GUI mode - everything is OK.<br />If we start it following way:</p>
<p>./kepler.sh -runwf -nogui -nocache testMTD.xml</p>
<p>We are getting exception.</p>
<p>I have done some initial debugging, and it looks like issue lies in reading output port from the actor. It is not reported in the code.</p>
<p>Entity.java class has method: getPort. In this method, if I take a look at the code, I can see that variable "_portList" doesn't contain "output" port.</p>
<p>This is what I can see while running Kepler in Eclipse (non-gui mode of Kepler)</p>
<p>[<br /> ptolemy.actor.TypedIOPort
{.testMTD.CompositeActor.MultipleTabDisplay.input},<br /> ptolemy.actor.TypedIOPort
{.testMTD.CompositeActor.MultipleTabDisplay.trigger}<br />]</p>
<p>This is the code, that should return "output" port.</p>
<pre><code>public Port getPort(String name) {<br /> try {<br /> _workspace.getReadAccess();<br /> return (Port) _portList.get(name);<br /> } finally {<br /> _workspace.doneReading();<br /> }<br /> }</code></pre>
<p>"_portList" doesn't contain output port, even though, this port is visible in GUI mode, and - in fact - works fine (take a look at screen shot).</p>
<p>The question here is. Where should we look for the bug? Do you have any suggestions?</p> Bug #6453 (New): Dock icon changes to coffee cuphttps://projects.ecoinformatics.org/ecoinfo/issues/64532014-03-11T21:29:03ZRich Morinrdm@cfcl.com
<p>As Kepler starts up, the normal (Mac OS X) Dock icon is replaced by a (Java) coffee cup. This is unexpected, unhelpful, and possibly confusing.</p> Bug #6413 (New): error when switching to DDF inside Case refinementhttps://projects.ecoinformatics.org/ecoinfo/issues/64132014-02-07T21:14:52ZDaniel Crawldanielcrawl@gmail.com
<p>I get an exception when switching from SDF to DDF inside a Case Refinement. It seems to be caused by having an unconnected input port.</p>
<p>To reproduce:</p>
<p>1. open $PTII/ptolemy/actor/lib/hoc/test/auto/Case1.xml<br />2. add a new input port to Case<br />3. run the model<br />4. open the Case actor and replace SDF in each Refinement with DDF<br />5. run the model</p>
<p>The error is:</p>
<p>java.lang.IllegalArgumentException: hasToken() requires a positive argument.<br /> at ptolemy.actor.Mailbox.hasToken(Mailbox.java:149)<br /> at ptolemy.actor.IOPort.hasToken(IOPort.java:2061)<br /> at ptolemy.domains.ddf.kernel.DDFDirector.prefire(DDFDirector.java:649)<br /> at ptolemy.actor.CompositeActor.prefire(CompositeActor.java:1665)<br /> at ptolemy.actor.lib.hoc.CaseDirector.prefire(CaseDirector.java:267)<br /> at ptolemy.actor.CompositeActor.prefire(CompositeActor.java:1665)<br /> at ptolemy.actor.CompositeActor.iterate(CompositeActor.java:1082)<br /> at ptolemy.actor.sched.StaticSchedulingDirector.fire(StaticSchedulingDirector.java:211)<br /> at ptolemy.domains.sdf.kernel.SDFDirector.fire(SDFDirector.java:492)<br /> at ptolemy.actor.CompositeActor.fire(CompositeActor.java:450)<br /> at ptolemy.actor.Manager.iterate(Manager.java:787)<br /> at ptolemy.actor.Manager.execute(Manager.java:352)<br /> at ptolemy.actor.Manager.run(Manager.java:1202)<br /> at ptolemy.actor.Manager$PtolemyRunThread.run(Manager.java:1760)</p> Bug #6175 (New): GenericJobSubmission actor sometimes runs job without completing data transfer.https://projects.ecoinformatics.org/ecoinfo/issues/61752013-10-26T00:03:51Zjianwu jianwujianwu@sdsc.edu
<p>A Kepler user at UCSD found that the GenericJobSubmission actor in her workflow started job submission when only partial file is copied. It looks the actor mistakenly thinks the file is ssh-copied completely when file transferred in the cluster is still about 1 MB less than the file on the local machine. The scheduler of the cluster is SGE.</p>
<p>When we use 'SSH File Copier' actor, the file is copied completely.</p> Bug #6167 (New): Model Context Menu should have the enableBackwardTypeInference choicehttps://projects.ecoinformatics.org/ecoinfo/issues/61672013-10-23T01:07:20ZChristopher Brookscxh@eecs.berkeley.edu
<p>Ptolemy II now supports backward type inference. The way this is enabled is that the top level container has a parameter called "enableBackwardTypeInference" that is set to true or false.</p>
<p>In Ptolemy II's Vergil, this is visible by right clicking on the background of the top level model.</p>
<p>This functionality is not present in the devel tree of Kepler.</p>
<p>The workaround is to drag in a Parameter, name it "enableBackgroundTypeInference" and set the value to true.</p> Bug #6102 (New): actor classes not saved properly in KAR fileshttps://projects.ecoinformatics.org/ecoinfo/issues/61022013-09-25T19:57:20ZMatt Jonesjones@nceas.ucsb.edu
<p>Kenneth Jones <a class="email" href="mailto:kennethjone@gmail.com">kennethjone@gmail.com</a> reported:<br />In Ptolemy II it is possible to use Vergil to convert a component into a class, save the class, and use it (instantiate or subclass it) in other workflows in the future. The Kepler GUI seems to have the ability to convert a component to a class and, in the workflow in which you created the class, create instances or subclasses of it, but I don't see a way to save the class, so it can be used in other workflows in the future (In Vergil there is a "save submodel only" checkbox in the File/Save dialog). Can classes be saved and reused in Kepler? If so, how?<br />------------</p>
<p>I verified this by creating a class and then attempting to save that class in a KAR file. The KAR file gets created, but does not contain the class. Attempting to open the saved KAR file produces an error in Kepler saying it can not me opened. The contents of the KAR file show it clearly is missing the class file, as all it contains is the manifest file:</p>
<p><code>$ jar tvf MyRampTestClass.kar <br /> 714 Wed Sep 25 11:41:54 AKDT 2013 META-INF/MANIFEST.MF<br /></code></p>
<p>To fix, once you have created a class in a workflow, you should be able to right click on it and select 'Save Archive (KAR)...', which allows you to save in a kar file of your choice in your 'My Workflows' directory. That should then show up in the tree on the left, and be able to be dragged to workflows for use.</p> Bug #5834 (New): Fix Kepler Javadoc warningshttps://projects.ecoinformatics.org/ecoinfo/issues/58342013-01-30T16:12:23ZChristopher Brookscxh@eecs.berkeley.edu
<p>Running "ant javadoc" produces warnings about javadoc problems.<br />The Kepler nightly build at Berkeley now reports these warnings, see<br /><a class="external" href="http://sisyphus:8079/hudson/job/kepler/warnings31">http://sisyphus:8079/hudson/job/kepler/warnings31</a></p>
<p>It would be good to fix these warnings.</p> Bug #5760 (In Progress): saving xml to existing file asks twice on machttps://projects.ecoinformatics.org/ecoinfo/issues/57602012-12-05T23:30:58ZDaniel Crawldanielcrawl@gmail.com
<p>On Mac, when saving a workflow as XML to an existing file, there are two dialogs that ask to overwrite the existing file. This occurs in Vergil, too.</p>