Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362014-08-21T20:27:56ZEcoinformatics Redmine
Redmine 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> Feature #6575 (New): reference parameters in R actor's scripthttps://projects.ecoinformatics.org/ecoinfo/issues/65752014-07-09T21:40:18ZDaniel Crawldanielcrawl@gmail.com
<p>It would be nice if the script in the R actor could reference parameters that were added to the R actor. Currently the R actor only converts tokens read on input ports to the R script.</p> Bug #5030 (New): RExpression2 actor will fail if the libs are not foundhttps://projects.ecoinformatics.org/ecoinfo/issues/50302010-05-26T21:20:31ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Creating a new bug from discussion originating in bug#4985, relevant sections posted below:</p>
<p>Jianwu said:<br />I also tried workflows in Kepler-2.0.0-Demos\demos\R\r-2.0.0\demos\JRI<br />directory, the whole Kepler just quit with the following message in the<br />console. It makes sense that the dll doesn't work for 64 bit machine. But just<br />quitting Kepler is too unfriendly.</p>
<pre><code>[null] Cannot find JRI native library!<br /> [null] Please make sure that the JRI native library is in a directory<br />liste<br />d in java.library.path.<br /> [null]<br /> [null] java.lang.UnsatisfiedLinkError: C:\Program<br />Files\Kepler-2.0-RC2\r-2.<br />0.0\lib\jri.dll: Can't load IA 32-bit .dll on a AMD 64-bit platform<br /> [null] at java.lang.ClassLoader$NativeLibrary.load(Native Method)<br /> [null] at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1753)<br /> [null] at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1678)<br /> [null] at java.lang.Runtime.loadLibrary0(Runtime.java:822)<br /> [null] at java.lang.System.loadLibrary(System.java:993)<br /> [null] at org.rosuda.JRI.Rengine.&lt;clinit&gt;(Rengine.java:19)<br /> [null] at<br />org.ecoinformatics.seek.R.RExpression2._initializeRengine(REx<br />pression2.java:569)<br /> [null] at<br />org.ecoinformatics.seek.R.RExpression2._fireUsingJRI(RExpress<br />ion2.java:547)<br /> [null] at<br />org.ecoinformatics.seek.R.RExpression2.fire(RExpression2.java<br />:289)<br /> [null] at ptolemy.actor.AtomicActor.iterate(AtomicActor.java:469)<br /> [null] at<br />ptolemy.actor.sched.StaticSchedulingDirector.fire(StaticSched<br />ulingDirector.java:188)<br /> [null] at ptolemy.actor.CompositeActor.fire(CompositeActor.java:458)<br /> [null] at ptolemy.actor.Manager.iterate(Manager.java:749)<br /> [null] at ptolemy.actor.Manager.execute(Manager.java:351)<br /> [null] at ptolemy.actor.Manager.run(Manager.java:1162)<br /> [null] at ptolemy.actor.Manager$3.run(Manager.java:1215)<br />Exception in thread "main" Java returned: 1<br /> at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:105)<br /> at org.kepler.build.runner.Kepler.main(Kepler.java:78)<br />Caused by: Java returned: 1<br /> at org.apache.tools.ant.taskdefs.Java.execute(Java.java:108)<br /> at org.kepler.build.Run.runSuite(Run.java:298)<br /> at org.kepler.build.Run.run(Run.java:202)<br /> at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:101)<br /> ... 1 more<br />--- Nested Exception ---<br />Java returned: 1<br /> at org.apache.tools.ant.taskdefs.Java.execute(Java.java:108)<br /> at org.kepler.build.Run.runSuite(Run.java:298)<br /> at org.kepler.build.Run.run(Run.java:202)<br /> at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:101)<br /> at org.kepler.build.runner.Kepler.main(Kepler.java:78)</code></pre>
<p>and Ben responded:<br />2. The RExpression2 (JRI-based) actor will fail if the libs are not found. This<br />is probably deep in the JRI.jar library when it cannot load the correct native<br />lib for the platform. We could probably try to detect the 32 v. 64 bitness of<br />the system and prevent the actor from attempting to use JRI if it was on a 64<br />bit machine - otherwise it will be the hard failure (system.exit)</p>
<p>and Jianwu:<br /> Matlab actors also have 32 and 64 bit issue when using JNI libraries to<br />communicate with Matlab. It will pop up an exception message when the JNI lib<br />doesn't work with the system. You can find some information at<br /><a class="external" href="https://kepler-project.org/developers/teams/build/matlab-lib-build-instructions-in-kepler-for-matlab-actor">https://kepler-project.org/developers/teams/build/matlab-lib-build-instructions-in-kepler-for-matlab-actor</a>.<br />It may help this bug.</p> Bug #4869 (In Progress): changes made to workflows during dialogs before committing (Edit Paramet...https://projects.ecoinformatics.org/ecoinfo/issues/48692010-03-04T19:04:24ZOliver Soongsoong@nceas.ucsb.edu
<p>When I make changes to an actor through the dialog, it seems like the changes are made to the workflow immediately, before the "Commit" button is clicked.</p>
<p>For example, create a workflow with an EML 2 Dataset actor. Make sure Kepler has not already authenticated with KNB. Now edit the EML 2 Dataset actor to reference a data package that requires authentication. The KNB login window will immediately pop up, even though no changes have been committed. Dismiss the window in some way. Now click the Help button and close the help window. The dialog will have disappeared. Open the actor dialog again, and the change will be there.</p>
<p>I should point out that the "Cancel" button does seem to work, but I suspect (based on debugging comments and comments in code) that this acts by reverting the changes already made.</p>
<p>I've seen this for sure on EML 2 Dataset and RExpression, since changes to one trigger visual feedback and I've mucked around in the code of the other. I suspect this is a general problem, though, and it may be a result of the underlying ptolemy design.</p> Bug #4219 (New): "Kepler Repositories" should be retrieved from the registryhttps://projects.ecoinformatics.org/ecoinfo/issues/42192009-07-06T17:37:07Zben leinfelderleinfelder@nceas.ucsb.edu
<p>Currently we use a combination of 2 .properties files to make actor/workflow/run library repositories available for users to upload to. Adding new ones requires editing configuration files - not entirely user friendly. This will probably be different with the new configuration changes.<br />We'll probably need to stick this into the EcogridServicesController stuff.</p> Bug #4002 (New): RExpression2 - handle arbitrary R data structureshttps://projects.ecoinformatics.org/ecoinfo/issues/40022009-04-21T00:06:13Zben leinfelderleinfelder@nceas.ucsb.edu
<p>Not everything in R fits into the Ptolemy types (nor the JRI types, for that matter).<br />The lm() method, for instance, returns something special.<br />It's been proposed (a few times) that there should be an RObjectToken to handle such cases so that at least R actors can communicate between each other with out loss/mutation of data.<br />The RExpression1 actor used file-based serialization to get around this limitation. We could attempt to use a hybrid approach for RExpression2 - mixing JRI with file-based serialization (best of both worlds?).</p> Bug #3931 (New): Get the R actor working with JNIhttps://projects.ecoinformatics.org/ecoinfo/issues/39312009-04-02T16:58:08ZChad Berkleyberkley@nceas.ucsb.edu
<p>We need to get the R actor working with JNI instead of having it make calls to the native executable. This will simplify many aspects of R, including file handling, installation and overall cohesiveness with the rest of the system.</p>
<p>Bug 3809 needs to get fixed first.</p> Bug #3803 (New): Cannot open a workflow through the command prompt, open with, or send to menushttps://projects.ecoinformatics.org/ecoinfo/issues/38032009-01-30T01:04:24ZOliver Soongsoong@nceas.ucsb.edu
<p>XP Pro x64 SP2, Java 1.6.0_11, Kepler 1.0.0 from kepler-project.org</p>
<p>If I right click a workflow file and select Open With->Kepler, I get an error.</p>
<p>If I add a shortcut to Kepler to my SendTo menu, then right click the workflow file and use the Send To link, I get the same error.</p>
<p>If I call Kepler from the command prompt with the workflow as the only argument, I get the same error.</p>
<p>An image of the error is at the URL.</p>
<p>I think this feature is available under linux: <br /><a class="external" href="https://dev.kepler-project.org/developers/reference/executing-kepler-from-the-command-line">https://dev.kepler-project.org/developers/reference/executing-kepler-from-the-command-line</a></p> Bug #2969 (New): Ability to join tables _across_ EML data packageshttps://projects.ecoinformatics.org/ecoinfo/issues/29692007-09-12T01:09:33Zben leinfelderleinfelder@nceas.ucsb.edu
<p>Ability to join tables <em>across</em> EML data packages or even non-EML actors.<br />Hopefully leverage some of the org.ecoinfomatics.datamanager library (eml module).</p> Bug #2968 (New): Ability to join tables within same EML data packagehttps://projects.ecoinformatics.org/ecoinfo/issues/29682007-09-12T01:06:11Zben leinfelderleinfelder@nceas.ucsb.edu
<p>Ability to join tables within same EML data package.<br />This does exist on the backend...just have UI issues with it being clear and easy-enough-to-use.</p> Bug #2964 (New): Change RExpression plotting actors to allow custom axis and title labelshttps://projects.ecoinformatics.org/ecoinfo/issues/29642007-09-12T00:53:57Zben leinfelderleinfelder@nceas.ucsb.edu
<p>If/When metadata is being passed around with workflow tokens, use the information contained within that to set the labels for chart axis, title etc...</p> Bug #2963 (New): Add data structure for tabular data and associated metadatahttps://projects.ecoinformatics.org/ecoinfo/issues/29632007-09-12T00:45:22Zben leinfelderleinfelder@nceas.ucsb.edu
<p>Essentially add support for R dataframe type to be passed around the workflow.<br />Most likely to be used for EMLDatasource -> RExpression transfer, but having the ability to transfer it among many different actors would be ideal.</p> Bug #2962 (New): Add metadata to data tokens so that it can be used downstreamhttps://projects.ecoinformatics.org/ecoinfo/issues/29622007-09-12T00:42:02Zben leinfelderleinfelder@nceas.ucsb.edu
<p>Add metadata to data tokens so that it can be used downstream (e.g., names, descriptions, units, travel with data).<br />Would be useful for plotting in the R actor (among other things) so that axis can be labeled in a meaningful way.</p> Bug #2123 (New): need a way to uniquely identify actor in a workflow and locate ithttps://projects.ecoinformatics.org/ecoinfo/issues/21232005-06-13T19:25:10ZLaura Downeyldowney@lternet.edu
<p>need a way to uniquely identify actor in a workflow that is exposed to the <br />user so that if one person says look at actor X in workflow y, they know <br />exactly which one is being referenced. There could be many of the same kind <br />of actors in a workflow and users need a way to uniquely identify a specific <br />actor.</p>
<p>This could be done by making use of and exposing the actor ID. It could be <br />exposed in the general tab on the new proposed tabbed configuration dialog for <br />an actor.</p>
<p>Searching by actor ID could be added to the advanced search.</p> Bug #2028 (In Progress): provide ability to easily visualize data at various places in workflowhttps://projects.ecoinformatics.org/ecoinfo/issues/20282005-03-11T20:48:37ZLaura Downeyldowney@lternet.edu
<p>provide the user with the capability of visualizing data and results at <br />various places in the workflow (related to bug 2027) but this adds <br />visualiation capability</p>