Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362010-03-09T23:53:44ZEcoinformatics Redmine
Redmine Bug #4873 (Resolved): Actors in repository library subtree are crammed togetherhttps://projects.ecoinformatics.org/ecoinfo/issues/48732010-03-09T23:53:44ZChad Berkleyberkley@nceas.ucsb.edu
<p>On Windows XP (maybe on other versions of windows) the actor icons are crammed tightly together when you open up Actors-2_0/CoreActors,kar or the other yellow repositories. They should be spaced similarly to the mac.</p> Bug #4341 (New): rearrange the actors module into smaller moduleshttps://projects.ecoinformatics.org/ecoinfo/issues/43412009-08-26T22:54:57ZChad Berkleyberkley@nceas.ucsb.edu
<p>I'll create a list of proposed modules for the actors currently all lumped together in the actors module. The new module names should have a naming convention of "actors-xxx" so that they all sort together and so that it's evident that the module is primarily an actor module. Once I'm done with this list, I'll post it to the wiki and we can have an email discussion about how others think the actors should be re-modularized.</p> Bug #4305 (Resolved): Move actor classes into the actors modulehttps://projects.ecoinformatics.org/ecoinfo/issues/43052009-08-11T22:13:17ZChad Berkleyberkley@nceas.ucsb.edu
<p>This will facilitate better modularization of kepler. Right now, the actors (and directors) are described in the actors module, but the implementing classes are stored in other modules.</p> Bug #4174 (Resolved): Actor library not building correctlyhttps://projects.ecoinformatics.org/ecoinfo/issues/41742009-06-19T04:19:15ZAaron Aaronaschultz@nceas.ucsb.edu
<p>Many of the actors are not appearing in the actor library when using the WRP suite. No visible errors are given...</p> Bug #4120 (Resolved): Bug in OpenDBConnector actorhttps://projects.ecoinformatics.org/ecoinfo/issues/41202009-06-01T08:03:00ZJamie Vleeshouwerjamie.vleeshouwer@csiro.au
<p>It also appears that the OpenDBConnector needs to be updated too. The previous version of the driver class required a connection string which was prefixed with jdbc:microsoft:sqlserver, however the new driver requires jdbc:sqlserver. The OpenDBConnector actor automatically appends this prefix when trying to connect to a SQL server database, however it still uses the old connection string which currently makes it impossible to connect to a SQL Server database.</p>
<hr />
<p>Hi Peter,</p>
<p>I have updated the actor to use the driver class<br />com.microsoft.sqlserver.jdbc.SQLServerDriver.</p>
<p>However, the MS SQL Server JDBC jars included in Kepler appear to<br />be from "MS SQL Server 2000 Driver for JDBC", which does not<br />support Java 1.5. I have removed these jars since Kepler requires<br />Java 1.5.</p>
<p>The license for "MS SQL Server 2005 JDBC Driver 1.2" (which does<br />support Java 1.5) does not permit redistribution. You will need to<br />download the jars and place them in $KEPLER/lib/jar/. The Kepler<br />loader will automatically add them to the classpath. If you are<br />using Eclipse, you might need to add them to the .classpath file.</p>
<p>Let me know if you have questions,</p>
<pre><code>--dan</code></pre>
<p>Peter.Fitch at csiro.au wrote:</p>
<blockquote>
<p>Hi Kepler users,</p>
<p>I have found a problem with using the open database connector actor with MS SQL Server. When you set the database format to MS SQL Server you get an exception class not found com.microsoft.jdbc.sqlserver.SQLServerDriver.</p>
<p>Unfortunately the class is correct for Java 1.4 but not for 1.5 which is the current recommended version. In Java 1.5 the driver class is com.microsoft.sqlserver.jdbc.SQLServerDriver.</p>
<p>Anyone else found this?</p>
<p>Cheers<br />Peter</p>
<p>_<em><i></em></i>__<em>_</em>___________________________________<br />Kepler-users mailing list<br />Kepler-users at ecoinformatics.org<br /><a class="external" href="http://mercury.nceas.ucsb.edu/ecoinformatics/mailman/listinfo/kepler-users">http://mercury.nceas.ucsb.edu/ecoinformatics/mailman/listinfo/kepler-users</a></p>
</blockquote>
<p>Cheers</p>
<p>Jamie</p> Bug #3898 (Resolved): update .kepler instead of removing it between versionshttps://projects.ecoinformatics.org/ecoinfo/issues/38982009-03-17T16:59:32ZChristopher Brookscxh@eecs.berkeley.edu
<p>Thanks to Qiao Huijie for pointing this out.<br />When switching between Kepler-1.0.0 and the Subversion development tree,<br />the ~/.kepler directory must be removed.<br />If it is not removed, then no actors are present in the actor browser pane.</p>
<p>I'm not sure why there is an incompatibility, but the code should detect<br />this incompatibility and prompt the user.</p>
<p>In addition, upon startup, the code should check to see if the actor browser<br />pane is empty and, if it is, prompt the user to delete their ~/.kepler <br />directory</p>
<p>Also, the developer instructions should be updated to mention removing<br />the ~/.kepler directory. I'll update the instructions.</p> Bug #3194 (New): add actors to support Sun Gridhttps://projects.ecoinformatics.org/ecoinfo/issues/31942008-04-01T06:58:00ZMatt Jonesjones@nceas.ucsb.edu
<p>Chirs Zhu <<a class="email" href="mailto:chris.zhu@sun.com">chris.zhu@sun.com</a>> and others at Sun have contributed actors that allow Kepler to be used as a client for the Sun Grid. They have requested that these new actors be integrated into the release. To do so, we need to:</p>
<p>1) Test the code, including development of workflow tests and unit tests as needed<br />2) Check copyright and licensing for the contribution to be sure it can be distributed under the BSD and the authors have rights to distribute<br />3) Incorporate new actor code into Kepler CVS</p>
<p>See attachments for details.</p> Bug #3189 (New): CommandLineExec needs ability to kill spawned processhttps://projects.ecoinformatics.org/ecoinfo/issues/31892008-03-26T23:01:06ZChad Berkleyberkley@nceas.ucsb.edu
<p>Many times when authoring/debugging a workflow, the process spawned by the command line actor runs infinitely. It would be good if the CLE actor kept track of the process id and could kill the process either with a special user function or when you click the stop button. Right now the only way to do this is to either kill kepler or to figure out which process is hung and kill it manually.</p> Bug #2830 (Resolved): Actor names to change/actors to remove from applicationhttps://projects.ecoinformatics.org/ecoinfo/issues/28302007-04-23T17:58:33ZKirsten Menger-Andersonkma500@hotmail.com
<p>I'm opening a bug to keep track of notes about some actors that have come up as I've gone through the actor docs.</p>
<p>Names to change:<br />GetPoint should be named GetMineralCompositionPoint <br />Get2DPoint should be named GetMineralComposition2DPoint</p>
<p>Actors to remove:<br />Interpolate: (per efrat) I think we can omit the Interpolate actor. It's not used in any used workflow and it's not fully implemented (only inverse distance is available) and very complex to use with all the parameters. I'm using other interpolation algorithms in workflows using web services. We can leave the actor in the distribution but probably omit it from the search.</p>
<p>InvokeService: (per efrat) The InvokeService actor can definitely be omitted, it's a wrapping of WorkflowExecute to use within a workflow, but Ptolemy also provides an actor to execute a whole workflow.</p>
<p>PortLineReader: this actor, util.LineReader, is being removed<br />FTPClient: This actor may not currently work. Unclear what plan for it is.</p> Bug #2304 (Resolved): RExpression accepts only limited input size.https://projects.ecoinformatics.org/ecoinfo/issues/23042005-11-30T23:13:50ZLareo Lareodieter.zucht@freenet.de
<p>The R expression actor accepts only a very limited size of input. For example,<br />a vector x <- 1:20000 with 20000 elements cannot be in the input.<br />It was mentioned that it is planed to implement a TCP/IP binding to the R platform.<br />Maybe this binding does not have such limitation.</p>
<p>The bug is severe for the bioinformatics/microarray community. Here, dataframes<br />and tables of very large dimensions are handled.</p> Bug #2044 (Resolved): R actor for means and error by grouphttps://projects.ecoinformatics.org/ecoinfo/issues/20442005-03-11T23:37:40ZMatt Jonesjones@nceas.ucsb.edu
<p>This bug is to create an actor that wraps an R script (using the generic R actor<br />described in bug <a class="issue tracker-1 status-3 priority-5 priority-highest closed" title="Bug: need R actor (Resolved)" href="https://projects.ecoinformatics.org/ecoinfo/issues/1342">#1342</a>) for calculating the mean, standard deviation, and<br />standard error of a numeric variable that is passed into the script. Optionally<br />the stats should be calculated using a grouping variable (by group), with one<br />mean/std/se for each group.</p>
<p>There are two inputs:<br /> 1) dataValue (type double)<br /> 2) group (type string)</p>
<p>The actor will accululate all data passed in as a series of {dataValue, group}<br />tuples and pass this along to R to calculate the mean, stdev, and stderr by<br />group. If group is not present then the tuples will be {dataValue}. When the R<br />script is finished, a matrix of {group, mean, stdev, stderr} will be passed back<br />to the R actor and then emitted on the output port. So for N tokens that come<br />in on the input port the actor will output on 1 token on the output port after<br />all input data has been received (this is a grouping operation).</p> Bug #1579 (Resolved): need sub-sampling actorhttps://projects.ecoinformatics.org/ecoinfo/issues/15792004-05-25T16:36:07ZMatt Jonesjones@nceas.ucsb.edu
<p>We need an actor that can perform various sub-sampling functions such as<br />jackknife and bootstrapping operations. Most ecologists use R and similar<br />systems for this type of work. We specifically need to do some<br />spatially-explicit sub-sampling for the GARP pipeline. In addition, we could<br />probably create a sub-sampling actor as a composite actor that uses the ptolemy<br />signal processing actors.</p> Bug #1343 (Resolved): need full eml2 supporthttps://projects.ecoinformatics.org/ecoinfo/issues/13432004-02-10T17:00:54ZChad Berkleyberkley@nceas.ucsb.edu
<p>need to be able to read data files that are described by the complex textFormat<br />fields in EML2. right now the ingestor only uses the simpleDelimited fields for<br />parsing. See dataTable/physical/dataFormat/textFormat/complex in eml</p> Bug #1342 (Resolved): need R actorhttps://projects.ecoinformatics.org/ecoinfo/issues/13422004-02-10T16:56:48ZChad Berkleyberkley@nceas.ucsb.edu
<p>create an actor to execute R jobs via kepler. Later, establish a GridService<br />that can handle this for us.</p> Bug #1338 (Resolved): find GIS system for inclusion in keplerhttps://projects.ecoinformatics.org/ecoinfo/issues/13382004-02-09T19:14:52ZChad Berkleyberkley@nceas.ucsb.edu
<p>need to look at the various proposed solutions for GIS integration into Kepler.<br /> The possibilities that I've heard so far are GDAL and GRASS. It has also been<br />mentioned that the more basic GIS functionality could probably be implemented in<br />java or with a ptolemy pipeline using existing actors.</p>