Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362008-05-07T22:26:35ZEcoinformatics Redmine
Redmine Bug #3283 (Resolved): Welcome splash screen shows up when starting windows keplerhttps://projects.ecoinformatics.org/ecoinfo/issues/32832008-05-07T22:26:35ZJing Taotao@nceas.ucsb.edu
<p>In mac and linux, the Welcome splash screen doesn't show up when user starts kepler. However, in windows version, I did see this screen during the startup when i double clicked either kepler.exe file or kepler-console.bat file.</p> Bug #3282 (Resolved): v3 installer intro says Kepler-1.0.0 1.0.0https://projects.ecoinformatics.org/ecoinfo/issues/32822008-05-07T21:30:55ZDaniel Crawldanielcrawl@gmail.com
<p>v3 installer intro says:</p>
<p>Welcome to the installation of Kepler-1.0.0 1.0.0!</p> Bug #3276 (Resolved): MatlabExpression not finding ptmatlab.dylibhttps://projects.ecoinformatics.org/ecoinfo/issues/32762008-05-05T22:15:30ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>MatlabExpression actor is not finding ptmatlab.dylib on the mac, after setting DYLD_LIBRARY_PATH=/Applications/MATLAB_R2007b/bin/maci and launching kepler with ./kepler.sh or sh kepler.sh from term or xterm.</p> Bug #3274 (Resolved): IPCC_Base_Layers.xml work-flow gets out of memeory errorhttps://projects.ecoinformatics.org/ecoinfo/issues/32742008-05-05T19:18:22ZJing Taotao@nceas.ucsb.edu
<p>When this work-flow tried to download 10 big data files, it can finish part of downloading - maybe 6 and the rest 4 will keep busy. From log message, we can find something like:<br />Exception in thread "Data ecogrid://knb/IPCC.200735416582829.1" java.lang.OutOfMemoryError: Java heap space<br />Exception in thread "Data ecogrid://knb/IPCC.200735416192871.1" java.lang.OutOfMemoryError: Java heap space<br />Exception in thread "Data ecogrid://knb/IPCC.200735417143125.1" java.lang.OutOfMemoryError: Java heap space<br />Exception in thread "Data ecogrid://knb/IPCC.200735416271261.1" java.lang.OutOfMemoryError: Java heap space</p>
<p>When I increase the heap size of Kepler to 1.2G (current value is 5M), the downloading can be done without any problem.</p>
<p>I went to through the downloading code again, it seems to me we use input and out stream, so not sure why it uses so many memory.</p>
<p>If it is possible we can remove this work-flow from this release?</p> 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 #3267 (Resolved): ENM/GARP_SingleSpecies_BestRuleSet-IV.xml problemshttps://projects.ecoinformatics.org/ecoinfo/issues/32672008-05-02T18:14:46ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>ENM/GARP_SingleSpecies_BestRuleSet-IV.xml crashes Ubuntu Kepler.<br />On mac execution completes but gives ImageJ "Unrecognized comand: ASC TextReader" messages.</p> Bug #3264 (Resolved): workflow ENM/ASC2RAWTest gives an exception under ubuntuhttps://projects.ecoinformatics.org/ecoinfo/issues/32642008-05-01T22:33:36ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>This workflow needs to be removed or fixed for release</p>
<p>Running under Ubuntu gives an exception that starts with: "For input string: [very long string of squares with some other characters at the end]"</p>
<p>If you display stack trace, it's a java.lang.NumberFormatException. The problem is likely in AscToRaw.java</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 #3257 (Resolved): Typos in html docs and demos.https://projects.ecoinformatics.org/ecoinfo/issues/32572008-04-30T21:07:35ZAaron Aaronaschultz@nceas.ucsb.edu
<p>A couple of typos in the documentation and demos.</p> Bug #3256 (Resolved): path problems on Mac with CommandLine demo workflowshttps://projects.ecoinformatics.org/ecoinfo/issues/32562008-04-30T17:52:49ZDan Higginshiggins@nceas.ucsb.edu
<p>On 1.0 release installer check, the CommandLine_1 and CommandLine_2 demo workflows (in demos/getting-started dir) fail with a path problem on the Mac.</p>
<p>This is apparently due to moving the demos directory.</p> Bug #3253 (Resolved): IzPack Windows Installer should install in a directory with the version numberhttps://projects.ecoinformatics.org/ecoinfo/issues/32532008-04-30T15:19:49ZChristopher Brookscxh@eecs.berkeley.edu
<p>The installer should install in a directory that contains the<br />version number of the release. <br />Under Windows, the default is c:\Program Files\Kepler,<br />it should be c:\Program Files\Kepler\1.0.0.</p>
<p>The reason is so that it is possible to have multiple versions<br />of Kepler without changing the default path. If the user<br />already has an installation of Kepler, then if they overwrite<br />the old version, will "good things" happen?</p>
<p>In a similar fashion, the installer should create separate<br />menus for each version.<br />What we have now is :<br />Start -> All Programs -> Kepler -> Kepler-1.0.0<br />Start -> All Programs -> Kepler -> Kepler Uninstaller<br />Instead, we should have:<br />Start -> All Programs -> Kepler -> Kepler-1.0.0 -> Kepler-1.0.0<br />Start -> All Programs -> Kepler -> Kepler-1.0.0 -> Kepler-1.0.0 Uninstaller</p>
<p>This is just my opinion, feel free to ignore.</p> Bug #3250 (Resolved): windows exe opens dos boxhttps://projects.ecoinformatics.org/ecoinfo/issues/32502008-04-30T00:15:31ZChad Berkleyberkley@nceas.ucsb.edu
<p>try to make the kepler.exe file not open a dos box with windows.</p> Bug #3237 (Resolved): Search actor in remote repository doesn't workhttps://projects.ecoinformatics.org/ecoinfo/issues/32372008-04-23T05:06:35ZJing Taotao@nceas.ucsb.edu
<p>The reason of the search not work is that kepler sets "entity" as<br />namespace when it searches actors. In query.xsd and resultset.xsd, the type<br />of namespace is anyURL. The auto-generated stub java files will <br />match anyURL to java URI class. In java URI class, if the constructor<br />taking a string without "http://" or any other "something://", it will<br />through an exception that URI schema couldn't find. "entity" is the case.<br />So the search doesn't work.</p>
<p>Last time when we had this issue, I just hacked the auto-generated code<br />to create new jar file. It is not a good solution.</p>
<p>Here is my proposal to fix the issue:</p>
<p>Change data type to xs:string for namespace in query.xsd and resultset.xsd<br />in seek/ecogrid. I don't think this change will lose lots of things.</p>
<p>I did some preliminary developement in my test machine. Here are some<br />changes we should make:</p>
<p>1) Seek project, we need to change query.xsd, resultset.xsd,<br />EcogridJavaToMetacatJavaQueryTransformer.java and<br />MetacatResultsetParser.java. They all are minor changes.</p>
<p>2) In Kepler, we need to replace<br />org.ecoinformatics.ecogrid.QueryService-stub.jar.</p>
<p>This is for code change.</p>
<p>It is amazing that the kepler with new<br />org.ecoinformatics.ecogrid.QueryService-stub.jar can search data and<br />resgistry successfully against both old and new servers. I don't<br />understand it but it does work. So it is not in rush to update knb and<br />registry in our production machine. The only server needed being updated <br />very soon is library.kepler-org.org/kepler.</p> Bug #3234 (Resolved): IJMacro does not work in several demo workflowshttps://projects.ecoinformatics.org/ecoinfo/issues/32342008-04-18T07:38:12ZSean Riddleswriddle@gmail.com
<p>Running on an installed version of Kepler on OS X.5, in several ENM workflows that try to use IJMacro to display an image, instead a dialog pops up that reports, "Unrecognized command: ASC TextReader."</p>
<p>Workflows in question:<br />ENM/GARP_*<br />ENM/garpModel*</p> Bug #3233 (Resolved): finalize ptolemy matlab actor for 1.0 releasehttps://projects.ecoinformatics.org/ecoinfo/issues/32332008-04-17T23:44:34ZDaniel Crawldanielcrawl@gmail.com
<p>For 1.0 release, we decided to use the Ptolemy matlab actor. The following needs to be done:</p>
<p>- use TextArea for expression<br />- check documentation<br />- add demo workflows <br />- compile and check-in ptmatlab lib for all platforms</p>