Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362010-02-04T20:48:06ZEcoinformatics Redmine
Redmine Bug #4735 (New): Allow params to be passed to ConfigurationManager from the command linehttps://projects.ecoinformatics.org/ecoinfo/issues/47352010-02-04T20:48:06ZChad Berkleyberkley@nceas.ucsb.edu
<p>Need a mechanism for passing params to CM from the command line. This is a post 2.0 feature.</p> Bug #4328 (New): change-to command checks out across brancheshttps://projects.ecoinformatics.org/ecoinfo/issues/43282009-08-21T18:54:18ZChad Berkleyberkley@nceas.ucsb.edu
<p>If kepler is currently in a branch, the change-to command should not update from the trunk. Once a branch is selected with the -Dbranch=xxx param, the build system should keep the current workspace in the branch until the user updated to another branch or the trunk. The build system should also print a banner alerting the user that he/she is working in a branch to avoid confusion.</p>
<p>this bug arose when we added several modules to the trunk. Matt was working in a branch (unknowingly) and when he ran 'ant change-to -Dsuite=kepler' it updated the kepler/module-info/modules.txt file from the trunk, but did not update the rest of the modules to the trunk so the build failed. The build-area was also running from the branch so the excludes file was not updated and would not allow him to build ptolemy.</p> Bug #4260 (New): Add a test suite for the build systemhttps://projects.ecoinformatics.org/ecoinfo/issues/42602009-07-22T18:25:27ZChad Berkleyberkley@nceas.ucsb.edu
<p>Need to create a testing harness for the build system to ensure that all functionality remains working as new features are added. This should be run with the nightly build.</p> Bug #3921 (New): Exported KAR files do not correctly export private classeshttps://projects.ecoinformatics.org/ecoinfo/issues/39212009-03-31T16:25:48ZChad Berkleyberkley@nceas.ucsb.edu
<p>When exporting a KAR file, if the actor contains private classes, the private classes are not exported and an exception is thrown saying the PrivateClass is not visible. Need to look into the export paradigm to see if we can extract the private classes or whether we need to change the documentation to say that private classes are not available for export and possibly check to see if private classes exist at export time and give the user a warning.</p> Bug #3210 (New): add netCDF support to Keplerhttps://projects.ecoinformatics.org/ecoinfo/issues/32102008-04-04T17:05:47ZMatt Jonesjones@nceas.ucsb.edu
<p>Many scientific data sets are represented in netcdf format (<a class="external" href="http://www.unidata.ucar.edu/software/netcdf/">http://www.unidata.ucar.edu/software/netcdf/</a>). Kepler should be able to read and expose data from these formats via a DataSource actor similar in concept to the EML, DarwinCore, RBNB, and OpenDAP actors.</p>
<p>Common libraries for parsing netcdf are available, including a Java library (<a class="external" href="http://www.unidata.ucar.edu/software/netcdf-java/">http://www.unidata.ucar.edu/software/netcdf-java/</a>).</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 #2997 (In Progress): Icons stop working after using kepler for a whilehttps://projects.ecoinformatics.org/ecoinfo/issues/29972007-11-06T22:32:37ZChad Berkleyberkley@nceas.ucsb.edu
<p>After having kepler open for some uncertain amount of time, the icons just stop working right. When you drag an actor to the canvas, the error " Error getting kar file on actor drop: For input string: "11906637555"" is displayed in the console and the icon that shows on the canvas of the newly dropped actor is either a blank box or a generic green box.</p> Bug #2987 (In Progress): Kepler Library (actor repository) Issueshttps://projects.ecoinformatics.org/ecoinfo/issues/29872007-10-26T17:47:06ZChad Berkleyberkley@nceas.ucsb.edu
<p>Kirsten has found a few bugs/issues with the actor repository.</p>
<p>1) It is possible to upload an actor without a class. This is fine, but kepler is now complaining if that class can't be found in the classpath then it won't render the rest of the search results. There are two ways this should be fixed: Either no actor should be uploaded without a class, or it should just ignore errors like this and go on to the next actor. This would be much better if the dynamic class loading worked for the repository.</p>
<p>2) There is an actor in the repository that somehow has multiple KeplerDocumentation properties with the same name. I'm not even sure how it's possible that it got uploaded. When you do a search that returns this actor, you get a skipable error, which is fine, but it doesn't tell you which actor is the problem. This make it impossible to fix.</p>
<p>3) There used to be a status bar that popped up when the search was taking a long time. For some reason, that isn't working anymore, so when the search takes 10 seconds, the search button just sits there indented and unless you're watching the terminal, it looks like kepler is hung. The status bar needs to be re-added. ProgressMonitorSwingWorker is the class that should be used.</p>
<p>4) The search facility in kepler is functioning differently from the library.kepler-project.org web page. The web page is doing a title only search while kepler is searching the entire document (via the ecogrid). This is somewhat confusing when you do a search for the same search term and get different results. I'm not sure which should be changed, the web page or kepler.</p> Bug #2895 (New): Distributed Execution Tracking Bughttps://projects.ecoinformatics.org/ecoinfo/issues/28952007-07-23T17:31:03ZChad Berkleyberkley@nceas.ucsb.edu
<p>Chad and Lucas are developing the distributed execution system for kepler. The system is currently working in a very simplified way. This bug is a consolidation of bug 1891 and bug 1899.</p>
<p>The following items need to be added:</p>
<ul>
<li>Make sure that the JNI libraries can be accessed via the slave and that the ENM actors will work on the slave</li>
</ul>
<ul>
<li>we might have to solve the problem that kepler has where you can't run multiple instances of the application with the same user account. The problem is that the cache uses an embedded database which only allows one connection at a time. the db is stored in the .kepler directory so if you try to run kepler twice at the same time, you'll get an error on the 2nd one that the db is already in use. If we have a cluster where the slave is distributed via a single home directory, this will be a problem</li>
</ul>
<ul>
<li>Matt came up with the idea of using the ecogrid registry as a way of doing node discovery.</li>
</ul>
<ul>
<li>Get this to run on the NCEAS ROCKS cluster.</li>
</ul>
<ul>
<li>we need to deal with transferring support files to the slave(s). This includes doing the indirect transfers between slaves (instead of transferring results back to the master then to the next slave, the slaves should be able to transfer data between each other).</li>
</ul> Bug #2259 (In Progress): DIALOGS: Implement New Actor Dialoghttps://projects.ecoinformatics.org/ecoinfo/issues/22592005-11-10T22:21:56ZMatthew Brookebrooke@nceas.ucsb.edu
<p>Implement New Actor Dialog, per Laura's design. See:<br /><a class="external" href="http://kepler-project.org/Wiki.jsp?page=WorkflowDirectorAndActorDialogs">http://kepler-project.org/Wiki.jsp?page=WorkflowDirectorAndActorDialogs</a></p> Bug #2258 (In Progress): DIALOGS: Implement New Director Dialoghttps://projects.ecoinformatics.org/ecoinfo/issues/22582005-11-10T22:20:47ZMatthew Brookebrooke@nceas.ucsb.edu
<p>Implement New Director Dialog, per Laura's design. See:<br /><a class="external" href="http://kepler-project.org/Wiki.jsp?page=WorkflowDirectorAndActorDialogs">http://kepler-project.org/Wiki.jsp?page=WorkflowDirectorAndActorDialogs</a></p> Bug #2257 (In Progress): DIALOGS: Implement New Workflow Dialoghttps://projects.ecoinformatics.org/ecoinfo/issues/22572005-11-10T22:19:40ZMatthew Brookebrooke@nceas.ucsb.edu
<p>Implement New Workflow Dialog, per Laura's design. See:<br /><a class="external" href="http://kepler-project.org/Wiki.jsp?page=WorkflowDirectorAndActorDialogs">http://kepler-project.org/Wiki.jsp?page=WorkflowDirectorAndActorDialogs</a></p> Bug #1587 (In Progress): Define and implement EcoGrid "dataQuery" methodhttps://projects.ecoinformatics.org/ecoinfo/issues/15872004-06-07T16:46:10ZJing Taotao@nceas.ucsb.edu
<p>This ecogrid server side data query task. Bug 1586 will implement dataQuery in<br />kepler side (client side, query local data). In task, kepler will send a sql<br />query from kepler to ecogrid node. Ecogrid will excute this query and return<br />partial data object to client.<br />This bug will be done on the base of bug 1584.</p> Bug #1548 (In Progress): consolidating data access user interfaceshttps://projects.ecoinformatics.org/ecoinfo/issues/15482004-04-30T18:52:02ZMatt Jonesjones@nceas.ucsb.edu
<p>Currently Kepler contains several distinct methods for binding data sources to a<br />workflow. These include the EML200DataSource actor, the JDBC data source<br />actor(s), the incipient EcoGrid access interfaces, the GridFTP actor, and<br />probably others. Each of these exposes the data in a different way, and is<br />therefore multiply representing data in a confusing way. We need to consolidate<br />these approaches to find a single UI that can encapsualte all of the data access<br />approaches.</p>
<p>This proposal is to use and adapt the user interface described in<br />kepler/docs/dev/screenshots and related design documents to data access in<br />EcoGrid, GridFTP, JDBC, and other sources. This would allow a user to view data<br />uniformly in the workflow, regardless of which data access protocol is used to<br />get the data. This would also allow the user to specify subsetting constraints<br />(WHERE clause) uniformly, and to choose which attributes from the joined<br />relations are exposed to the workflow. Finally, it would allow us to use richer<br />metadata descriptions of underspecified data sources (like those found at the<br />other end of JDBC connections) so that the user (and ultimately the SEEK SMS<br />system) can reason about these data sources effectively.</p>