Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362008-05-02T21:05:59ZEcoinformatics Redmine
Redmine Bug #3269 (Resolved): authentication system throws NPEhttps://projects.ecoinformatics.org/ecoinfo/issues/32692008-05-02T21:05:59ZChad Berkleyberkley@nceas.ucsb.edu
<p>after a fresh install, go to the data tab. remove the digir selection, search for 'datos'. click the 'login anonymously' button when prompted. you'll get a search result.</p>
<p>restart kepler</p>
<p>do the same thing. you'll get an NPE traced to AuthenticationManager.getProxy() line 124.</p> Bug #3261 (Resolved): ApplicationFramework/CredentialRetrieve workflow has problemshttps://projects.ecoinformatics.org/ecoinfo/issues/32612008-05-01T20:49:34ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>I think this needs to be fixed or removed for release.</p>
<p>To reproduce (on Ubuntu running Kepler from Chad's latest installer at least):<br />1)Open ApplicationFramework/CredentialRetrieve.xml. <br />2)Run. <br />3)Click cancel on the login dialog box.</p>
<p>Problems:<br />1) workflow continues to execute without stopping<br />2) If you try to open any other Kepler workflows, the Kepler Open dialog box appearance has changed; it now looks like the CredentialRetrieve password dialog box.</p> Bug #3207 (Resolved): consolidate command line execution actorshttps://projects.ecoinformatics.org/ecoinfo/issues/32072008-04-04T16:03:12ZDaniel Crawldanielcrawl@gmail.com
<p>Command Line Exec and External Execution have different interfaces<br />but perform the same basic functionality. They should be combined<br />into a single actor.</p> Bug #3200 (Resolved): create a 1.0.0 branch in cvshttps://projects.ecoinformatics.org/ecoinfo/issues/32002008-04-02T15:54:37ZChad Berkleyberkley@nceas.ucsb.edu
<p>We need a branch for 1.0 targeted development so that normal dev can go on in the head. Any items that need to be in 1.0 must be checked into the branch. Anything that should not be in 1.0 (i.e. anything that is not a bug targeted to 1.0) must be checked into the head.</p> Bug #3195 (Resolved): Check all documentation for 1.0 releasehttps://projects.ecoinformatics.org/ecoinfo/issues/31952008-04-02T15:41:13ZChad Berkleyberkley@nceas.ucsb.edu
<p>All of the documentation needs to be checked for accuracy and completeness before the 1.0 release, which is currently scheduled for April 25.</p> Bug #3182 (Resolved): check for consistent licensing text in all source fileshttps://projects.ecoinformatics.org/ecoinfo/issues/31822008-03-24T17:18:35ZMatt Jonesjones@nceas.ucsb.edu
<p>Kepler is licensed under the BSD. We need to check that all code is properly licensed this way throughout the release, including all source files. Fix any licensing problems that might arise.</p>
<p>We also need to be sure any included software included in the release can be redistributed under the terms of their license, and that we follow those license terms.</p> Bug #3169 (Resolved): Cannot add documentation to a new actor from within Keplerhttps://projects.ecoinformatics.org/ecoinfo/issues/31692008-02-29T19:40:04ZDan Higginshiggins@nceas.ucsb.edu
<p>If one instantiates a new actor, it can be added to the library or saved as a KAR, but there is no way to add documentation from within Kepler!</p>
<p>If there is no current documentation, the Documentation/Customize menu item does nothing. So there is no way to add documentation other than adding it directly to the actor moml.</p>
<p>Dan HIggins - 29 Feb 2008</p> Bug #3167 (Resolved): Customize documentation fails when ports addedhttps://projects.ecoinformatics.org/ecoinfo/issues/31672008-02-29T18:40:03ZDan Higginshiggins@nceas.ucsb.edu
<p>New customized documentation dialog has a 'null' error when ports have been added.</p>
<p>To see the error, customize an RExpression actor by adding 2 new input ports. Then right click to Documentation/Customize and add some text describing the new ports. When the dialog is closed a null error occurs. If no new ports are added, customized documentation seems to work OK.</p>
<p>Dan Higgins - 29 Feb 2008</p> Bug #3144 (Resolved): add link in OSX Applications folderhttps://projects.ecoinformatics.org/ecoinfo/issues/31442008-02-11T21:51:22ZChad Berkleyberkley@nceas.ucsb.edu
<p>This bug is spawned from bug 3119. We need to figure out how to put a shortcut into the Applications folder on osx.</p> Bug #3126 (Resolved): add R system installation to the Mac installerhttps://projects.ecoinformatics.org/ecoinfo/issues/31262008-02-04T17:52:47ZMatt Jonesjones@nceas.ucsb.edu
<p>The R system is installed under windows as an option, but not under MacOS X. We need to add this so that Mac users can benefit from the R actors out-of-the-box. Need to see whether IzPack can handle this directly as it can for the Windows R installer or not.</p> Bug #3124 (Resolved): Automatically refresh ecogrid sources (endpoints) once per Keplerhttps://projects.ecoinformatics.org/ecoinfo/issues/31242008-02-02T01:27:39Zben leinfelderleinfelder@nceas.ucsb.edu
<p>Now that there are two ways in which to refresh the available Ecogrid services (as registered in the registry), the refresh should only happen once per Kepler window.<br />Currently the autorefresh will happen once for each Kepler window when the user selects the Data tab.<br />Since there has been a lot of time devoted to making startup quick, the refresh should not slow down the start up of Kepler.<br />And, of course, the user can always manually refresh the sources with the "Refresh" button that is found on the sources tab.</p> Bug #3103 (Resolved): Building actor documentation from within Kepler failshttps://projects.ecoinformatics.org/ecoinfo/issues/31032008-01-25T00:49:48ZChristopher Brookscxh@eecs.berkeley.edu
<p>If the actor documentation does not exist, then when I select<br />Documentation -> Display, a window comes up that allows me to build<br />the documentation. The build continues along for awhile and then fails with.<br />BUILD FAILED<br />c:\cxh\src\kepler\build.xml:1232: The following error occurred while executing this line:<br />c:\cxh\src\kepler\build.xml:1280: The following error occurred while executing this line:<br />c:\cxh\src\kepler\build.xml:1289: Javadoc failed: java.io.IOException: CreateProcess: "c:\program files\java\jdk1.5.0_11\bin\javadoc.exe" -d c:\cxh\src\kepler-docs\dev\documentationFramework\generatedJavadocs -J-DKEPLER=c:\cxh\src\kepler -classpath c:\cxh\ptII -sourcepath c:\cxh\ptII -doclet doc.doclets.PtDoclet -docletpath c:\cxh\ptII\lib\kepler.jar;c:\cxh\src\kepler;c:\cxh\src\kepler\configs;c:\cxh\src\kepler\lib;c:\cxh\src\kepler\lib\images;c:\cxh\src\kepler\build\kepler-configs.jar;c:\cxh\src\kepler\build\kepler-icons.jar;c:\cxh\ptII\lib\diva.jar;c:\cxh\ptII\lib\jython.jar;c:\cxh\ptII\build\ptolemy-doc.jar;c:\cxh\ptII\build\classes;c:\cxh\ptII\build\src;c:\cxh\ptII\ptolemy\distributed\jini\jar\tools.jar;c:\cxh\ptII\ptolemy\distributed\jini\jar\jini-core.jar;c:\cxh\ptII\ptolemy\distributed\jini\jar\sun-util.jar;c:\cxh\ptII\ptolemy\distributed\jini\jar\reggie.jar;c:\cxh\ptII\ptolemy\distributed\jini\jar\jsk-policy.jar;c:\cxh\ptII\ptolemy\distributed\jini\jar\jsk-platform.jar;c:\cxh\ptII\ptolemy\distributed\jini\jar\start.jar;c:\cxh\ptII\ptolemy\distributed\jini\jar\reggie-dl.jâ€</p> Bug #3063 (Resolved): CommandLineExec actor does not generate Exit codehttps://projects.ecoinformatics.org/ecoinfo/issues/30632008-01-11T21:41:46ZDan Higginshiggins@nceas.ucsb.edu
<p>Supposedly, the CommandLineExec actor will generate a '1' on the exitCode output when the execution of the command line is successful. Apparently this does NOT happen under Windows; nothing appears on the output if the command does not send anything to SysOut. This makes it impossible to run a command line operation in the middle of workflow and use it to trigger further actors.</p>
<p>See the example $KEPLER/workflows/eco/maxent.xml</p>
<p>Dan Higgins - Jan 2008</p> Bug #3026 (Resolved): Actor documentation does not appear in older workflowshttps://projects.ecoinformatics.org/ecoinfo/issues/30262007-12-12T23:32:19ZDan Higginshiggins@nceas.ucsb.edu
<p>Attempting to get actor documentation does not work in several of the older workflows, especially some in the demos directory. This is apparently due the fact that documentation is now saved inside kar files. This was changed after some existing workflows were created. They need to be rebuilt so that documentation will be added to the moml file for the workflow. (The documetation does show up when a new version of the actor is dragged to the workflow.)</p> Bug #2318 (Resolved): Copyrights and licenses of subpackages need to be handledhttps://projects.ecoinformatics.org/ecoinfo/issues/23182005-12-14T02:41:42ZChristopher Brookscxh@eecs.berkeley.edu
<p>Just so we don't forget, I'm submitting the copyright issue as a bug.</p>
<p>As a proposed feature, I modified the Kepler configuration.xml and<br />added copyright.htm so that Kepler can take advantage of the Ptolemy<br />II about: facility that helps handle copyright issues.</p>
<p>The problem is that packages such as Ptolemy and Kepler include<br />copyrighted software from various sources. Each package has<br />a different copyright that usually must be displayed somewhere<br />in the release.</p>
<p>I hacked up the about:copyright facilty to help handle this. The<br />current implementation is not perfect, but it helps.</p>
<p>Here's how it works.</p>
<p>If a URL starts with "about:", then code in ptolemy.actor.gui<br />specially interprets it.</p>
<p>"about:copyright" creates a page that includes links to some base<br />copyrights, such as the Ptolemy copyright and the Aelfred copyright.<br />It also looks for particular actors and if those actors are found, it<br />includes a link to the appropriate copyright. One issue here is<br />that searching for the actors can take time, the user might notice a lag.</p>
<p>If the configuration includes a property called _applicationCopyrights<br />then that the value of that parameter is assumed to be an array of<br />records of the form
{{actor="dot.separated.actor.class.name", copyright="relative/url/to/copyright.\<br />htm"}...}</p>
<p>So, if the util.ImageJActor actor is present, then going to about:copyright<br />will include a link to the javadoc and also to imagej-copyright.htm<br />imagej-copyright.htm does not currently exist, but usually this file<br />would include the ImageJ jar file copyright.</p>
<p>One issue as that the link to the javadoc defaults to pointing to the<br />Ptolemy website if the documentation cannot be found. We could add<br />yet another parameter that would send this traffic to the Kepler website.<br />I'll do this later.</p>
<p>So, to try this out, update your Kepler tree, run "ant run-dev" <br />and then at the bottom of the intro.htm, follow the<br />"This software is protected by this license." link.</p>
<p>On the Kepler copyright page, follow the link at the bottom:<br />"Kepler is based on Ptolemy II" <br />This will bring you to the about:copyright page.</p>
<p>On other cool feature is at the bottom of the Kepler copyright page<br />is "Other information about this configuration"</p>
<p>This brings up a page that includes a link (about:configuration) to<br />expand the configuration, which is a good way to quickly test for<br />missing classes. For Kepler, this will not expand to include all the<br />actors the way it does under Ptolemy, but it still has value.</p>
<p>There are also links to expand all the .xml files listed in a file.<br />For example, "about:demos#ptolemy/configs/kepler/intro.htm" <br />will expand all the workflows listed on the Kepler splash page.<br />One can then run all the demos.</p>
<p>Also, "about:links#ptolemy/configs/kepler/intro.htm" will open<br />up all the .htm, .pdf and .xml links on the splash page, which<br />is a good way to check documentation.</p>
<p>In both cases, the expansion is only one level deep, but I use it<br />all the time to check releases.</p>
<p>I don't think this is a perfect solution but it can be used to<br />help address the copyright problem. Further refinement would help.<br />What would need to be done is that for each actor that uses a third<br />party jar file we would need to create a web page that includes<br />the copyright. This takes quite a bit of work, but helps ensure<br />that the copyright is actually shipped with the release.</p>
<p>If this utility is not of interest, then feel free to remove<br />the link at the bottom of copyright.htm.</p>