Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362008-05-02T21:21:33ZEcoinformatics Redmine
Redmine Bug #3270 (Resolved): disable DIGIR Data Source by defaulthttps://projects.ecoinformatics.org/ecoinfo/issues/32702008-05-02T21:21:33ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>chatting on irc, chad jing and i think we should disable DIGIR in the Services List panel by default, since it's still severely slowing down search.</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 #3216 (Resolved): Demo workflows do not runhttps://projects.ecoinformatics.org/ecoinfo/issues/32162008-04-09T18:32:31ZSean Riddleswriddle@gmail.com
<p>I have run into a couple of demo workflows that don't run while checking the replacement of the embedded documentation. I will append this with more if I find them.</p>
<p>demos/ENM/GARP_MultipleSpecies-*<br />Exception - "Actor is not ready to fire. in [workflowname].SDF Director and [workflowname].Get Species/Location information.Line Reader"</p> Bug #3209 (Resolved): ecogrid SearchRegistryAction error when disconnected from networkhttps://projects.ecoinformatics.org/ecoinfo/issues/32092008-04-04T17:00:35ZDaniel Crawldanielcrawl@gmail.com
<p>About 30 seconds after starting kepler with no network connection, a long error<br />message is displayed, starting with:</p>
<pre><code>[java] ERROR (org.ecoinformatics.seek.ecogrid.SearchRegistryAction:queryRegistryRewriteConfig:210) problem looking up registry entries using endpoint: <a class="external" href="http://knb.ecoinformatics.org/registry/services/RegistryService">http://knb.ecoinformatics.org/registry/services/RegistryService</a></code></pre>
<p>Most likely caused by the fix for 3124.<br /><a class="external" href="http://bugzilla.ecoinformatics.org/show_bug.cgi?id=3124">http://bugzilla.ecoinformatics.org/show_bug.cgi?id=3124</a></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 #3206 (Resolved): ecogrid error message occurs when running disconnected from networkhttps://projects.ecoinformatics.org/ecoinfo/issues/32062008-04-03T23:30:24ZDaniel Crawldanielcrawl@gmail.com
<p>[java] ERROR (org.ecoinformatics.seek.datasource.EcogridDataCacheItem:cleanUpCache:373) Couldn't close the output stream to cache file null<br /> [java] *** EcogridUtils readXMLFile2DOM - file /Users/crawl/.kepler/cache//cachedata/urn.lsid.localhost.cb8a2275.0.0 does not exist or is zero length!<br /> [java] getEndpoint - ENDPOINT attr is null.</p>
<p>To reproduce:</p>
<p>1. remove kepler cache<br />2. disconnect from network<br />3. start kepler</p> Bug #3179 (Resolved): Distinguish "download" and "information" attribute values in eml distributl...https://projects.ecoinformatics.org/ecoinfo/issues/31792008-03-18T22:40:02ZJing Taotao@nceas.ucsb.edu
<p>I agree, I don't think it does handle this, but this is a bug in my opinion. It should distinguish these URL types. The intention of the "function" attribute in EML was to handle exactly what Wade is trying to do, so Kepler should look for it and only really try to parse and download data from 'download' URLs. If a "function" attribute has not been provided on the URL, then maybe it should try to download it as well, but that is open to discussion. I've been looking for the query specification in Kepler -- but to no avail.</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 #3154 (Resolved): Documentation missing for DarwinCoreDataSourcehttps://projects.ecoinformatics.org/ecoinfo/issues/31542008-02-21T19:47:38ZDan Higginshiggins@nceas.ucsb.edu
<p>When a DarwinCoreDataSource is dragged to the work area from the actor list, there is no documentation available. The same problem occurs when the actor is the result of a search.</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 #2853 (Resolved): Documentation (where to save it; customization)https://projects.ecoinformatics.org/ecoinfo/issues/28532007-05-24T20:15:20ZDan Higginshiggins@nceas.ucsb.edu
<p>Kepler actors now have documentation stored in the kar files under a 'KeplerDocumentation' parameter. However, when you right click on the background of a workflow and select "Documentation/Customize', the documentation for a workflow get stored in the workflow moml under the property "DocAttribute" rather than the 'KeplerDocumentation'. This works fine for workflows but we have documentation in two different places.</p>
<p>Also, with actor documentation stored as a 'KeplerDocumentation' parameter, customizing the documentation (with the menu 'Documentation/Customize' no longer works! This is particularly a problem with customizing RExpression actors.</p>
<p>There is also the issue of what documentation is used in the repository.</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>