Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362014-11-02T20:02:55ZEcoinformatics Redmine
Redmine 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> Feature #6434 (New): add workflow execution time and other metadata to report designerhttps://projects.ecoinformatics.org/ecoinfo/issues/64342014-02-28T21:11:23ZDaniel Crawldanielcrawl@gmail.com
<p>It would be nice if the report designer had drag and drop items for metadata stored in provenance such as the execution timestamp, who ran the workflow, etc.</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 #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 #5724 (New): Display actor's suppressBlankLines parameter not workinghttps://projects.ecoinformatics.org/ecoinfo/issues/57242012-10-23T00:24:41ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>This happens in vergil too.</p>
<p>If I create and run an SDF workflow w/ String Constant => Display, w/ Display's suppressBlankLines option turned on, and String Constant's value set to:<br />--------<br />line1</p>
<p>line3 after blank line2<br />--------<br />the resulting display includes the blank line.</p> Bug #5721 (New): Add ModelRepaintController to the Kepler libraryhttps://projects.ecoinformatics.org/ecoinfo/issues/57212012-10-01T22:48:19ZSean Riddleswriddle@gmail.com
<p>This is a bug split off of 4903. ModelRepaintController is not in the Kepler actor library and should be added.</p> Bug #5697 (New): Workflow Run Manager can fail to Force Open a run kar that Kepler canhttps://projects.ecoinformatics.org/ecoinfo/issues/56972012-08-24T19:41:25ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>After connecting the Workflow Run Manager (2.3.0) to the kepler library and using it to download the attached run kar, it will fail to Force Open it. Nothing seems to happen (I can't see the logs on Mtn Lion-- need to check for errors). Yet if you manually download the run kar from the web, and open it from Kepler's File-> Open, the workflow opens, though the run does not get imported into the WRM as it should.</p>
<p>Note we should delete kars like this from the non-dev 'official' library (so things are 'clean' for users), since it was made with an unreleased, unversioned module in the mix:</p>
<p>reporting-2.3;keplerio;ssh-2.1;workflow-run-manager-2.3;provenance-2.3;tagging-2.3;workflow-scheduler-gui-1.0;kepler-2.3;outreach-2.2;r-2.3;loader-2.2;actors-2.3;directors-2.0;opendap-2.0;dataturbine-2.2;ecogrid-2.3;authentication-gui-2.2;gui-2.3;module-manager-gui-2.3;authentication-2.3;repository-2.3;job-2.1;io-2.0;data-handling-2.1;sms-2.2;component-library-2.2;util-2.1;event-state-2.1;core-2.3;common-2.3;module-manager-2.3;configuration-manager-2.3;kepler-tasks-2.3;ptolemy-kepler-2.3</p> Bug #5695 (New): more automatic module update process.https://projects.ecoinformatics.org/ecoinfo/issues/56952012-08-24T17:18:27Zjianwu jianwujianwu@sdsc.edu
<p>As discussed for bug 5398, We should discuss the usability perspective of module upgrade management. Some of the process can be automated.</p>
<p>Close 5398 for 2.4 and open this one for future release.</p> Bug #5692 (New): Values not committed to actorshttps://projects.ecoinformatics.org/ecoinfo/issues/56922012-08-22T00:41:36ZIan Ianian.szarka@anu.edu.au
<p>Values not committed to actors</p>
<p>Open new Kepler workflow<br />Drag RExpression from Components tree<br />double click RExpression icon<br />Change test in "R function or script:" field<br />Press commit button <br />Double click on the same RExpression icon from above<br />- Any changes have been lost</p>
<p>This occurs on other actors and is not limited to the RExpression.</p> Bug #5686 (New): datasets produced by archiveDataturbineDataToMetacat workflow show samples 'slid...https://projects.ecoinformatics.org/ecoinfo/issues/56862012-08-17T23:39:07ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Data sample times slowly increase, e.g. second by second, over time, instead of staying on expected markers. This makes for irregular, messy datasets. I would guess the problem lies with SPAN.</p>
<p>A dataset available here shows examples of this:<br /><a class="external" href="http://dev2.nceas.ucsb.edu/knb/metacat?action=read&qformat=default&sessionid=&docid=doc.1345243176506661893.1&displaymodule=entity&entitytype=dataTable&entityindex=1">http://dev2.nceas.ucsb.edu/knb/metacat?action=read&qformat=default&sessionid=&docid=doc.1345243176506661893.1&displaymodule=entity&entitytype=dataTable&entityindex=1</a></p>
<p>Some example problematic changes found within:</p>
<p>timestamps data<br />2012-08-16 00:10:09 13.302116394<br />2012-08-16 00:10:39 13.302242279<br />[SNIP]<br />2012-08-16 02:46:09 13.295635223<br />2012-08-16 02:46:39 13.295513153<br />2012-08-16 02:47:10 13.295863152 # <== slip<br />2012-08-16 02:47:40 13.296142578<br />[SNIP]<br />2012-08-16 08:09:10 13.290791512<br />2012-08-16 08:09:40 13.290988922<br />2012-08-16 08:10:11 13.290698051 # <== slip<br />2012-08-16 08:10:41 13.290913582<br />...</p> Bug #5685 (New): data isn't always chunked properlyhttps://projects.ecoinformatics.org/ecoinfo/issues/56852012-08-17T23:29:49ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Jing ran the workflow in Windows XP today, and it produced at least one datapackage with data from different sampling rates. See:<br /><a class="external" href="http://dev2.nceas.ucsb.edu/knb/metacat?action=read&qformat=default&sessionid=&docid=doc.1345243176506661893.1&displaymodule=entity&entitytype=dataTable&entityindex=1">http://dev2.nceas.ucsb.edu/knb/metacat?action=read&qformat=default&sessionid=&docid=doc.1345243176506661893.1&displaymodule=entity&entitytype=dataTable&entityindex=1</a></p>
<p>Example change section from data from above link:</p>
<p>2012-08-16 22:18:14 13.28463459<br />2012-08-16 22:18:44 13.284519196<br />2012-08-16 22:19:14 13.284427643<br />2012-08-16 22:19:44 13.284352303<br />2012-08-16 22:20:19 13.284294128<br />2012-08-16 22:38:14 13.28584671<br />2012-08-16 22:38:15 13.28584671<br />2012-08-16 22:38:16 13.291329384</p>
<p>These were the results Jing got from the workflow for this particular sensor:</p>
<p>Sensor Name: gpp-data/CR800_Batt_Volt<br />Document URL: <a class="external" href="http://dev2.nceas.ucsb.edu/knb/metacat?action=read&qformat=default&docid=doc.1345243176506661893.1">http://dev2.nceas.ucsb.edu/knb/metacat?action=read&qformat=default&docid=doc.1345243176506661893.1</a><br />Time Range: 2012-08-16 00:10:09 ~ 2012-08-16 22:38:32<br />Number of Records: 2680<br />Sensor Name: gpp-data/CR800_Batt_Volt<br />Document URL: <a class="external" href="http://dev2.nceas.ucsb.edu/knb/metacat?action=read&qformat=default&docid=doc.1345243308947314582.1">http://dev2.nceas.ucsb.edu/knb/metacat?action=read&qformat=default&docid=doc.1345243308947314582.1</a><br />Time Range: 2012-08-16 22:38:34 ~ 2012-08-16 22:39:54<br />Number of Records: 75<br />Sensor Name: gpp-data/CR800_Batt_Volt<br />Document URL: <a class="external" href="http://dev2.nceas.ucsb.edu/knb/metacat?action=read&qformat=default&docid=doc.1345243447776683166.1">http://dev2.nceas.ucsb.edu/knb/metacat?action=read&qformat=default&docid=doc.1345243447776683166.1</a><br />Time Range: 2012-08-16 22:39:55 ~ 2012-08-17 22:37:21<br />Number of Records: 8186</p> Bug #5682 (New): ontology classes require unique labelhttps://projects.ecoinformatics.org/ecoinfo/issues/56822012-08-17T18:35:31ZDaniel Crawldanielcrawl@gmail.com
<p>The ontology classes have both an ID and label. If the ID is unique, but the label is not, then the class does not appear in the actor tree.</p> Bug #5678 (New): growingDegreeDays workflow at kepler repository has type resolve errorhttps://projects.ecoinformatics.org/ecoinfo/issues/56782012-08-15T23:27:54Zjianwu jianwujianwu@sdsc.edu
<p>After talking to Derik, reconfiguring the DT actor to use nibbler.nceas.ucsb.edu works for me. Derik said maybe more workflows in kepler repository need to be updated.</p> Bug #5675 (New): new ProgressMeter demo workflows give errors when opening in sensor-view-0.9.0https://projects.ecoinformatics.org/ecoinfo/issues/56752012-08-11T02:03:33ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>There are a few errors when opening these xml workflows beneath sensor-view-0.9.0, despite working in trunk, e.g.:</p>
<p>ptolemy.kernel.util.NameDuplicationException: Attempt to insert object named "init" into a container that already contains an object with that name.</p>
<p>Even though the workflow only contains one "init" PortParameter.</p>
<p>After a kepler restart, I was able to save a copy of this workflow from beneath sensor-view-0.9.0, and can then re-open this copy without error.</p>
<p>I don't know the cause. Maybe these momls will have to be resaved using sensor-view-0.9.0, and the outreach test-patch release recreated.</p> Bug #5674 (New): The patch downloader dialog can fail to automatically restart Keplerhttps://projects.ecoinformatics.org/ecoinfo/issues/56742012-08-10T23:48:09ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>In pre-release sensor-view-0.9 testing on os X 10.8, I found Kepler-2.3's patch downloader gui can fail to automatically restart kepler. It quits, the kepler icon bounces and then disappears. Subsequent start of Kepler from the Kepler icon works.<br />I think we've had this problem in the past, search for related bugs.</p>