Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362007-11-09T21:25:27ZEcoinformatics Redmine
Redmine Bug #3001 (Resolved): EML Dataset actor has trouble with file:// URLs for xml,datahttps://projects.ecoinformatics.org/ecoinfo/issues/30012007-11-09T21:25:27ZDan Higginshiggins@nceas.ucsb.edu
<p>If one uses the 'Browse' button to set EML File and Data File for the EML 2 Dataset actor, a file URL is created (i.e. "file://(file path). The actor, however, does not work with the "file://" included.</p>
<p>Need to convert from file URL to a local file string?</p> Bug #2850 (Resolved): Better Error message for missing 'R'https://projects.ecoinformatics.org/ecoinfo/issues/28502007-05-22T21:02:22ZDan Higginshiggins@nceas.ucsb.edu
<p>If a workflow containing an RExpression actor is executed and R cannot be started from the command line (missing or not in PATH), a cryptic error message like 'The pipe has been ended appears'. Need to catch this error and provide a more meaningful error message (or check for R installation in some other way).</p> Bug #2809 (Resolved): Browser Display actor fails for Mac/Linuxhttps://projects.ecoinformatics.org/ecoinfo/issues/28092007-04-03T17:40:07ZDan Higginshiggins@nceas.ucsb.edu
<p>Browser Display actor does not detect MacOSX and always uses Netscape for Linux systems. Need to detect the default browser and use that.</p>
<p>see <a class="external" href="http://www.centerkey.com/java/browser/">http://www.centerkey.com/java/browser/</a> <br />for java code that detects default browser and works across multiple OSs</p> Bug #2779 (Resolved): ASC_To_Raw actor has bug in setting output directoryhttps://projects.ecoinformatics.org/ecoinfo/issues/27792007-02-21T22:17:18ZDan Higginshiggins@nceas.ucsb.edu
<p>Actor works OK if the outputRawFileName parameter is left blank (raw files are created in the same directory as the asc files). However, if set to a directory, all but first of the *.raw files are still added to the dir *.asc files are in!</p> Bug #2556 (Resolved): "Customize Name' menu missinghttps://projects.ecoinformatics.org/ecoinfo/issues/25562006-09-21T21:19:35ZDan Higginshiggins@nceas.ucsb.edu
<p>In current versions of Kepler, the 'Customize Name' popup menu is missing, although it does appear in the Beta2 release and it is in the menu customization file!<br />The problem may be related to changes in Ptolemy where 'Customize' is now a hierarchial menu.</p> Bug #2514 (Resolved): CT Director parameter list for ODESolver is incompletehttps://projects.ecoinformatics.org/ecoinfo/issues/25142006-08-15T20:09:25ZDan Higginshiggins@nceas.ucsb.edu
<p>The default value of the ODESolver parameter is "ExplicitRK45Solver" but that value does not appear in the drop down list of choices. Thus, one changed, it cannot be reset!</p> Bug #2461 (Resolved): Add MetadataSource actor to treehttps://projects.ecoinformatics.org/ecoinfo/issues/24612006-06-15T21:49:54ZDan Higginshiggins@nceas.ucsb.edu
<p>The MetadataSource actor has been around since June 2005 but apparently was never added to the actor tree when kar system was created. It is used in the 'EcogridWriterTest.xml' workflow in $KEPLER/workflows/test/ to provide metadata to the EcogridWriter. It needs to be added to the actor tree and perhaps extended to allow metadata input on ports (in additon to the parameter input) for use in saving GARP best rulesets.</p> Bug #2398 (Resolved): change R home directory that is default of RExpression actorhttps://projects.ecoinformatics.org/ecoinfo/issues/23982006-04-06T03:38:57ZDan Higginshiggins@nceas.ucsb.edu
<p>The default working dir for R in the RExpession actor is set to the users $HOME directory. This causes a buildup of many temp files. Move the default to some subdirectory of .kepler so that it is removed when .kepler is deleted.</p>
<p>Also consider removal of contents when Kepler is shut-down(?)</p>
<p>Dan Higgins (April 5, 2006)</p> Bug #2344 (Resolved): Duplicate Actors that read directorieshttps://projects.ecoinformatics.org/ecoinfo/issues/23442006-01-26T20:06:47ZChristopher Brookscxh@eecs.berkeley.edu
<p>Dan wrote:</p>
<blockquote>
<p>Does anyone out there know if there is a difference in the basic<br />functionality of the DirectoryListing actor (author Christopher<br />Hylands, Edward A. Lee) and the FileArrayPrinter actor (author Wibke<br />Sudholt). Both seem to do the same thing (extract file lists from a<br />directory); the DirectoryListing actor seems more full featured (works<br />with URLs). Does the FileArrayPrinter do anything the Directory Listing<br />actors does not?</p>
</blockquote>
<p>Ilkay then wrote:</p>
<blockquote>
<p>AFAIK, they are the same in functionality. There might be some<br />differences between the datatypes/structures they output, and it needs<br />to be consolidated.</p>
</blockquote>
<p>Christopher wrote:</p>
<blockquote>
<p>Ptolemy II uses the DirectoryListing actor as part of the run all<br />demos demo that runs in the display case.</p>
<p>This demo is ptolemy/demo/RunDemos.xml<br />The actor is used in ptolemy/demo/RunDemosInNewProcess.xml<br />It is also used in ptolemy/actor/lib/io/demo/FilePortParamter.xml<br />and ptolemy/actor/lib/test/auto/ExecRunDemos.xml<br />and ptolemy/domains/sdf/test/auto/filePortParameter.xml</p>
<p>I'm not particularly wedded to the DirectoryListing actor, we could<br />modify it to better meet Kepler's needs and then either discard<br />FileArrayPrinter or have it call DirectoryListing but not be listed in<br />Kepler's ui. I'd prefer to discard FileArrayPrinter and move on.</p>
<p>It looks like FileArrayPrinter is used in the following models:<br />/home/eecs/cxh/src/kepler/src/org/resurgence/moml/FileListSequencer.xml:<br /><entity name="File Array Printer" <br />class="org.resurgence.actor.FileArrayPrinter"><br />/home/eecs/cxh/src/kepler/src/org/resurgence/moml/MoleculeSelector.xml:<br /><entity name="File Array Printer" <br />class="org.resurgence.actor.FileArrayPrinter"></p>
<p>Perhaps the authors of these models could use DirectoryListing or<br />else tell me how DirectoryListing should change?</p>
<p>Seems like a bug should be filed for this one. I'm tempted<br />to take it, but I'm slightly over committed.</p>
</blockquote>
<p>Wibke wrote:</p>
<blockquote>
<p>Sorry for not answering earlier, since I am the author.</p>
<p>I assume DirectoryListing and FileArrayPrinter probably do similar things (I<br />think I came across their similarity earlier), though I would need to test<br />in detail. There were, however, some reasons I had for doing a "duplicate" <br />here:</p>
<ul>
<li>This was one of my very first actors in Kepler :-) and so I potentially<br />overlooked the other one (I am a domain scientist by training).</li>
</ul>
<ul>
<li>In the workflows where FileArrayPrinter is used, actually I do not need<br />the URL, but the path. The reason for this is that later there is a lot of<br />command-line calls and processing. And I did not want to always do String<br />processing before.</li>
</ul>
<ul>
<li>For the Resurgence workflows it is very important to be able to transform<br />arrays into sequences of tokens and vice-versa. If that is possible with<br />DirectoryListing, there is probably not much sense to keep FileArrayPrinter.<br />However, I remember another discussion about a Resurgence actor (it might<br />have been about file copying/writing or similar) where it actually turned<br />out that two actors do something similarly, but not identically. The reason<br />for this has been that I always have to make sure that the Resurgence actors<br />work in very particular ways with sequences of tokens.</li>
</ul>
<p>Unfortunately, I am heavily loaded by a different project at the moment, so<br />I will need a bit time to check this. But polishing the Resurgence work is<br />anyhow somewhere on my personal to-do list ...</p>
</blockquote>
<p>I propose that FileArrayPrinter not be available in the Kepler UI, but<br />that the source code remain in the tree so that these models can continue<br />to run.</p>
<p>If someone wants to modify DirectoryListing in a backward compatibile manner,<br />I'm all for it.</p> Bug #2316 (Resolved): Conflicting jars and classpath reductionhttps://projects.ecoinformatics.org/ecoinfo/issues/23162005-12-12T22:57:11ZKevin Rulandkruland@ku.edu
<p>The current collection of jars in the lib/ directory includes many jars which<br />may not be used, many duplicated jars, and probably some conflicting jars. We<br />need to perform analysis to determine the dependencies among the jars and<br />determine which jars are required by which kepler sources (actors and base code).</p> Bug #2290 (Resolved): EML2 Data Source problem with higgins.5087.3 - 'BaselineLayers'https://projects.ecoinformatics.org/ecoinfo/issues/22902005-11-28T21:09:34ZDan Higginshiggins@nceas.ucsb.edu
<p>To reproduce this bug, do a datasearch for 'BaselineLayers'. This shold give the<br />knb package 'higgins.5087.3'. The data for this package is a zip file stored on<br />the SRB; the data is treated as a single attribute table (i.e. not really a<br />table). When this datasource is dragged to the work area, a NullPointerException<br />is thrown 'at org.kepler.objectmanager.cache.DataCacheObject.getFileName'.</p> Bug #2253 (Resolved): ENM Workflows errors on newer, faster computerhttps://projects.ecoinformatics.org/ecoinfo/issues/22532005-11-07T17:32:51ZDan Higginshiggins@nceas.ucsb.edu
<p>Errors are occurring in 'SingleSpecies_BestRuleSet_Aug2005 ENM workflow on new,<br />faster computer (Optiiplex GX620 - 3GHz dual core - Win XP) that do not occur<br />when same workflow is run on older, slower machine (null pointer error most of<br />time). Error seems to occur at end of GARP run; perhaps a file is not ready?</p>
<p>Possible threading problem?</p> Bug #2243 (Resolved): bug in inverse distance interpolation in Grid Rescaling actorhttps://projects.ecoinformatics.org/ecoinfo/issues/22432005-11-04T17:22:58ZDan Higginshiggins@nceas.ucsb.edu
<p>An attempt to smooth the IDW interpolation near NO_DATA edges of a grid has<br />resulted in errors in interpolation (that are clearly visible as a 'waffle' type<br />background in images).</p>
<p>Reason for this bug is currenly unclear. Needs to be fixed for use in ENM workflow.</p> Bug #2224 (Resolved): Annotation actor not working correctly from KAR filehttps://projects.ecoinformatics.org/ecoinfo/issues/22242005-10-10T22:03:18ZDan Higginshiggins@nceas.ucsb.edu
<p>With the new .kar files for building the actor tree, the Annotation actor gives<br />a simple rectangle with dragged to the graph area rather than an editable text<br />box. Apparently, something is wrong with the configuration.</p> Bug #1912 (Resolved): cleanup ImageJ actor to avoid multiple copies of menushttps://projects.ecoinformatics.org/ecoinfo/issues/19122005-01-24T18:27:31ZDan Higginshiggins@nceas.ucsb.edu
<p>The ImageJ actor needs to be better integrated into Kepler. Currently, the<br />control/menu screen is just opened from ImageJ code and multiple copies may<br />appear if not explicitly closed. Also, closing one of multiple images sometimes<br />crash kepler.</p>