Ecoinformatics Redmine: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362010-03-15T20:51:05ZEcoinformatics Redmine
Redmine Kepler - Bug #4883 (New): Need more command line options for kar fileshttps://projects.ecoinformatics.org/ecoinfo/issues/48832010-03-15T20:51:05ZChad Berkleyberkley@nceas.ucsb.edu
<p>right now, we can execute a single workflow contained in a kar file with the -runwf command line switch. It would be nice to have more options for working with kar files on the command line. The minimal options I would like to see are:</p>
<p>1) allow the user to specify which workflow within a kar file to execute (if there is >1). <br />2) allow the user to specify the output location. Either a server or local directory.<br />3) allow the use of a remote kar file with an https url (i.e. for a kar file stored in a repository).</p>
<p>Please add more requirements as you see fit. We will add this to the queue of post-2.0 enhancements.</p> Kepler - Bug #4785 (New): move cache object from 1.0 to 2.0https://projects.ecoinformatics.org/ecoinfo/issues/47852010-02-10T23:13:31ZChad Berkleyberkley@nceas.ucsb.edu
<p>Cache kar objects from 1.0 that contain customized actors (i.e. not those shipped with 1.0) need to be migrated to the 2.0 installation. Any kars that include jars must be made into modules (see bug 4702).</p> Kepler - 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> Kepler - 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> Kepler - 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> Kepler - Bug #4290 (In Progress): Separate the GUI from the execution engine.https://projects.ecoinformatics.org/ecoinfo/issues/42902009-08-07T21:49:07ZDavid Welkerwelker4kepler@gmail.com
<p>The GUI needs to be separated from the execution engine so that it is easy to develop specialized GUIs for a particular domain. The path for developing a new GUI that uses the execution engine should be well defined. For example, if one wanted to develop a new GUI with a different technology (i.e. Flex) or for a very specialized domain there should be a well-defined path for proceeding.</p>
<p>This is a Kepler/CORE grant requirement.</p> Kepler - Bug #4287 (In Progress): Separate user error messages from developer error messages.https://projects.ecoinformatics.org/ecoinfo/issues/42872009-08-07T21:40:03ZDavid Welkerwelker4kepler@gmail.com
<p>An error in the GUI should never display a nonsensical stack trace to the user. All stack traces involving the GUI and other errors made to be read by the developer should be logged to file (and optionally standard out).</p> Kepler - 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> Kepler - Bug #4246 (In Progress): Reorganize code in util, core and gui moduleshttps://projects.ecoinformatics.org/ecoinfo/issues/42462009-07-14T18:33:12ZChad Berkleyberkley@nceas.ucsb.edu
<p>The code in the main modules still needs to be reorganized a bit. There is gui code in core that needs to be moved to gui or util. The util module itself should be disassembled into other modules that are more fitting of the nature of the code. Not sure if this should be done for 2.0 or post 2.0. will target to 2.0 for now.</p> Metacat - Bug #3402 (In Progress): internal dtds are not handledhttps://projects.ecoinformatics.org/ecoinfo/issues/34022008-06-19T18:52:33ZChad Berkleyberkley@nceas.ucsb.edu
<p>XML documents with internal DTDs are not handled by metacat. The internal dtd entity callback in the sax parser is blank and doesn't do anything when presented with an internal dtd.</p> SEEK - Bug #1790 (New): Add ITIS data to TOS db v1.1.0https://projects.ecoinformatics.org/ecoinfo/issues/17902004-11-29T18:35:44ZAimee Stewartastewart@ku.eduSEEK - Bug #1761 (In Progress): Update object model (v1.1.0) to more closely mirror TCShttps://projects.ecoinformatics.org/ecoinfo/issues/17612004-11-08T15:43:46ZAimee Stewartastewart@ku.edu
<p>Relationships are handled slightly differently, return values for<br />getRelatedConcept change, objects mirror TCS more closely.</p> SEEK - Bug #1677 (In Progress): Modify concept package objects to handle relationships for TOS v1...https://projects.ecoinformatics.org/ecoinfo/issues/16772004-09-13T17:34:46ZAimee Stewartastewart@ku.edu
<p>Create CRelationshipTo objects to be held within CConcept objects. Create<br />CRelationshipAssertion objects to be used for 3rd party relationships. Remove<br />CRelatedConcept.</p> SEEK - Bug #1673 (In Progress): Work with XSLT parser to convert ITIS data for input to Taxon DBhttps://projects.ecoinformatics.org/ecoinfo/issues/16732004-09-09T22:53:50ZAimee Stewartastewart@ku.edu
<p>Modify and use XSLT parser written by Dave Thau to convert existing ITIS data<br />from v0.51 into current (0.71) schema.</p> SEEK - Bug #1648 (New): Create taxon developer web site which calculates metrics of codehttps://projects.ecoinformatics.org/ecoinfo/issues/16482004-07-27T04:11:46ZAimee Stewartastewart@ku.edu