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 #6594 (New): cannot download from a taghttps://projects.ecoinformatics.org/ecoinfo/issues/65942014-09-12T17:03:26ZDaniel Crawldanielcrawl@gmail.com
<p>"ant change-to" downloads either from the trunk or branches. It'd be nice to also work with tags.</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 #6587 (New): summarize missing actorshttps://projects.ecoinformatics.org/ecoinfo/issues/65872014-08-21T16:52:36ZDaniel Crawldanielcrawl@gmail.com
<p>If a workflow is opened that contains actors that are not present in the class path, an error dialog is displayed for each actor. It would be nice if a list of all the missing actors were displayed.</p>
<p>Attached is a modified MoMLParser.java (based on ptolemy-kepler-2.4 sources) from Philippe Huyhn that displays the missing actors. The list of missing actors is written to stdout. Using MessageHandler would be preferred since it displays a dialog, but MessageHandler appears to not allow copy and paste.</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 #5715 (New): Actor Reference documentationhttps://projects.ecoinformatics.org/ecoinfo/issues/57152012-09-19T18:36:47Zjianwu jianwujianwu@sdsc.edu
<p>this doc hasn't changed since 2.0, but in 2.4, many actors are visible for the first time. So we might need to update this doc.</p>
<p>435 pages.</p> Bug #5699 (New): Change the workflow scheduler server documentation link in the workflow-schedule...https://projects.ecoinformatics.org/ecoinfo/issues/56992012-08-28T00:15:15ZJing Taotao@nceas.ucsb.edu
<p>Currently the the workflow scheduler server documentation points to the svm trunk version. In the next workflow-scheduler-gui release, the documenation should be a branch or tag version.</p> Bug #5691 (New): parameter choices are not savedhttps://projects.ecoinformatics.org/ecoinfo/issues/56912012-08-20T23:27:06ZDaniel Crawldanielcrawl@gmail.com
<p>The choices for Parameter.addChoice() are not written when the model is saved.</p> Bug #5689 (New): remove configs/.../configuration.xml overridehttps://projects.ecoinformatics.org/ecoinfo/issues/56892012-08-18T02:44:23ZDaniel Crawldanielcrawl@gmail.com
<p>The Ptolemy Configuration MoML for Kepler is in:</p>
<p>common/configs/ptolemy/configs/kepler/configuration.xml</p>
<p>This is overridden in several modules:</p>
<p>ddp-common/configs/ptolemy/configs/kepler/configuration.xml<br />fault-tolerance/configs/ptolemy/configs/kepler/configuration.xml<br />map-reduce/configs/ptolemy/configs/kepler/configuration.xml</p>
<p>As with other overrides, the problem is that when the master version changes, the copies need to be updated.</p>
<p>The difference is small:</p>
<p>diff common/configs/ptolemy/configs/kepler/configuration.xml fault-tolerance/configs/ptolemy/configs/kepler/configuration.xml <br />181a182</p>
<blockquote>
<p><input source="ptolemy/configs/kepler/contingencyTableauFactory.xml"/></p>
</blockquote>
<p>diff common/configs/ptolemy/configs/kepler/configuration.xml ddp-common/configs/ptolemy/configs/kepler/configuration.xml<br />181a182</p>
<blockquote>
<p><input source="ptolemy/configs/kepler/executionChoiceTableauFactory.xml"/></p>
</blockquote> Bug #5687 (New): investigate alternatives to workflow versioninghttps://projects.ecoinformatics.org/ecoinfo/issues/56872012-08-18T01:48:54ZDaniel Crawldanielcrawl@gmail.com
<p>As described in bug <a class="issue tracker-1 status-3 priority-2 priority-default closed" title="Bug: workflow lsid changes when running from command line (Resolved)" href="https://projects.ecoinformatics.org/ecoinfo/issues/5426">#5426</a>, the same workflow can be identified differently when executed on different machines. I fixed this by adding a command-line option to stop changing the LSID. This is sufficient for 2.4, but in the last release meeting we decided for 2.5 to take a closer look at how workflow versioning is done and possibly come up with a better design.</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> Feature #5666 (New): Build system needs a target to build all common or blessed non-core moduleshttps://projects.ecoinformatics.org/ecoinfo/issues/56662012-08-07T18:07:33ZChristopher Brookscxh@eecs.berkeley.edu
<p>There should be a way to easily build all the common or "blessed" <br />non-core modules.<br />For example, "ant change-to -Dsuite=kepler" does not check out <br />reporting or tagging.</p>
<p>We should have notion of "blessed" modules, which I would say at a minumum<br />must meet two requirements:<br />1) There is someone on kepler-dev who is actively maintaining the module<br />2) There is at least one automatic test that at least does a smoke test<br />to ensure that the module works. More tests are better, but "ant test-blessed" <br />or something should do something with each module.</p>
<p>Having blessed modules would help in refactoring the tree because we<br />would have a better idea about what will break.</p> Bug #5664 (New): Check for duplicate codehttps://projects.ecoinformatics.org/ecoinfo/issues/56642012-08-07T00:01:51ZChristopher Brookscxh@eecs.berkeley.edu
<p>See bug <a class="issue tracker-1 status-3 priority-2 priority-default closed" title="Bug: Examine Kepler for duplicated Ptolemy code (Resolved)" href="https://projects.ecoinformatics.org/ecoinfo/issues/4926">#4926</a> for how to check for duplicate code.</p>
<p>This bug is targeted to 2.5.0 so that we don't forget to do it.</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 #5646 (New): Switching some of the add-on modules to corehttps://projects.ecoinformatics.org/ecoinfo/issues/56462012-08-06T20:33:00ZIlkay Altintasaltintas@sdsc.edu
<p>Before 2.5, we need a discussion on switching some of the key modules, e.g., modules in the reporting suite, to the core suite and release process.</p>