Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362015-12-03T00:33:05ZEcoinformatics Redmine
Redmine 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 #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 #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 #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 #5667 (New): reevaluate how opening kars vs. XML should work from actor library.https://projects.ecoinformatics.org/ecoinfo/issues/56672012-08-07T23:03:26Zjianwu jianwujianwu@sdsc.edu
<p>currently, opening kar is different from opening xml from actor library (see bug 5348). One more difference is that one kar could have multiple xmls.</p>
<p>We should reevaluate how opening kars vs. XML should work from actor library.</p> Bug #5652 (New): Geon Scp and spa Ssh2Exec have duplicate code.https://projects.ecoinformatics.org/ecoinfo/issues/56522012-08-06T23:35:23ZChristopher Brookscxh@eecs.berkeley.edu
<p>Duplicate code detected with CPD. See</p>
<p>actors/src/org/geon/Scp.java line 295<br />actors/src/org/sdm/spa/Ssh2Exec.java line 361
# lines : 143</p> Bug #5627 (New): List all possible port types in actor Types drop down listhttps://projects.ecoinformatics.org/ecoinfo/issues/56272012-06-15T22:57:34ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>It would be nice if on an actor's port Type drop down list, all possible types were listed. If this list were automatically generated, then we'd be covered. Kepler has a date token, so the list would have to account for Ptolemy and Kepler types.</p> Bug #5612 (New): String index out of range in R actorhttps://projects.ecoinformatics.org/ecoinfo/issues/56122012-06-01T17:52:52ZClaas-Thido Pfaffsabsirro@arcor.de
<p>The R actor can only hand down a certain size of string array through a port. <br />I have attached a workflow which shows that. To trigger the exception only modify the first actor. The first actor also contains more description.</p>
<p>Best regards Claas</p> Bug #5611 (New): LinearModel actor doesn't handle input variables properlyhttps://projects.ecoinformatics.org/ecoinfo/issues/56112012-05-22T21:50:39ZJim Regetzregetz@nceas.ucsb.edu
<p>The R code in the RExpression-based LinearModel actor has several problems:<br />1. In a linear model, it's the <em>independent</em> (predictor) variables that can be either numeric or factor (categorical). The dependent (response) variable must be numeric. The actor code gets this reversed, and fails with an error depending on the inputs.<br />2. The conditional is.character() in the final 'if' statement always evaluates to FALSE because of the conversion-to-factor in the first 'if' statement.<br />3. The intercept and slope aren't reported out in any useful way, and the intercept isn't even printed to the console output (if displayed).</p>
<p>I'd suggest the following replacement, which doesn't conform exactly to the intended behavior of the original actor, but I think provides a nice starter template for doing a univariate linear model fit. I also changed it to emit the fitted model object itself, which could be passed to another actor for summarizing, generating an ANOVA table, extracting coefficient estimates, etc.</p>
<p>Note that I wouldn't usually explicitly store the model formula as an object, but here I think it's useful to indicate the mapping of input ports to model variables right at the top.</p>
<p>#--------------------------------------------------<br />model <- Dependent ~ Independent</p>
<p>if (is.character(Independent)) {<br /> Independent <- factor(Independent)<br />}</p>
<ol>
<li>fit model; fitted lm object is available on output port<br />results <- lm(model)<br />print(summary(results))</li>
</ol>
<ol>
<li>plot data, adding regression line if appropriate<br />plot(model)<br />if (is.numeric(Independent)) {<br /> abline(results, col="red")<br />}<br />#--------------------------------------------------</li>
</ol> Bug #5593 (New): use setDefaultWidth in actorshttps://projects.ecoinformatics.org/ecoinfo/issues/55932012-04-28T22:05:50ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Building workflows in Kepler these days I spend a lot of time changing relation widths from Auto to 1, because w/ Auto the following error message occurs:</p>
<p>--<br />ptolemy.kernel.util.IllegalActionException: Error recording workflow structure: Error getting port width: The width of relation .DataTurbineTimeSlice.relation can not be uniquely inferred.<br />--</p>
<p>The error includes a suggestion, it sounds like we should take a pass through all actors and update code to call setDefaultWidth as appropriate:</p>
<p>--<br />Please make the width inference deterministic by explicitly specifying the width of this relation. In the user interface, right click on the relation, select Configure and change the width. Note that some actors may need to have their Java code updated to call setDefaultWidth(1) on the output port.<br />---</p> Bug #5590 (New): RExpression forces pdf if 'automatically show graphics' is checkedhttps://projects.ecoinformatics.org/ecoinfo/issues/55902012-04-26T01:34:05ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Look into this forced format change side-effect which is confusing to a user. If you select e.g. png, and 'auto show..', you get a pdf.</p> Bug #5586 (New): Get newest version of local files in EML actorhttps://projects.ecoinformatics.org/ecoinfo/issues/55862012-04-16T18:54:00ZJing Taotao@nceas.ucsb.edu
<p>Here is an email from kepler user:</p>
<p>--------------------------------------------------------------<br />Running v2.3 on Mac OSX 10.7.3 Fairly new to Kepler.</p>
<p>I'm trying to use the EML 2 Dataset Actor to read in a local copy (in a folder on my laptop drive) of a sample metadata (.xml) file using the EML 2.1.0 schema and a simple 4-column data (.txt) file. I have checked the files using the <a class="external" href="http://knb.ecoinformatics.org/emlparser/">http://knb.ecoinformatics.org/emlparser/</a> site, and both were validated.</p>
<p>Two problems:<br />i) If I change either file the Actor doesn't keep up with the changes. It seems to revert to a cached version of the file as it was when I first specified it to the Actor (via the EML File: and Data File: fields in Configure Actor).<br />ii) I wondered about checking the "Check for latest version" checkbox. However doing this generates an error dialog with the message "null Please enter a new value:" I have to uncheck to stop the error.<br />----------------------------------------------------------------</p>
<p>So we may need a feature:<br />When the "Check for latest version" box is checked, Kepler will check local files as well.</p> Bug #5585 (New): Add date format E MMM d HH:mm:ss zzz yyyy to DateToStringhttps://projects.ecoinformatics.org/ecoinfo/issues/55852012-04-11T22:55:18ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>E MMM d HH:mm:ss zzz yyyy is the format used when a date token is shown in a Display, so it seems a good example format to include in the drop down list of DateToString.</p>