Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362012-08-06T20:33:00ZEcoinformatics Redmine
Redmine Bug #5646 (New): Switching some of the add-on modules to corehttps://projects.ecoinformatics.org/ecoinfo/issues/56462012-08-06T20:33:00ZIlkay Altintasaltintas@sdsc.edu
<p>Before 2.5, we need a discussion on switching some of the key modules, e.g., modules in the reporting suite, to the core suite and release process.</p> Bug #5036 (New): All workflows that do not work should be moved.https://projects.ecoinformatics.org/ecoinfo/issues/50362010-05-28T18:30:08ZDavid Welkerwelker4kepler@gmail.com
<p>I am moving all workflows that do not work to an unsupported directory so that people are not surprised when they try out such a workflow and find it doesn't work.</p> Bug #5027 (New): Users should be able to build installers for the Kepler-2.0 branchhttps://projects.ecoinformatics.org/ecoinfo/issues/50272010-05-24T17:32:46ZChristopher Brookscxh@eecs.berkeley.edu
<p>Kepler users should be able to build installers so that they may deploy<br />a shrinkwrapped installation to other users. Currently, "ant installer" <br />works in the Kepler devel trunk, but fails in the 2.0 branch.</p>
<p>[installer] Writing installer file to /Users/cxh/src/kepler-2.0/build-area/installer/install.xml<br /> [izpack] ERROR: 'The content of elements must consist of well-formed character data or markup.'<br /> [izpack] ERROR: 'com.sun.org.apache.xml.internal.utils.WrappedRuntimeException: The content of elements must consist of well-formed character data or markup.'<br /> [izpack] javax.xml.transform.TransformerException: javax.xml.transform.TransformerException: com.sun.org.apache.xml.internal.utils.WrappedRuntimeException: The content of elements must consist of well-formed character data or markup.<br /> [izpack] at com.sun.org.apache.xalan.internal.xsltc.trax.TransformerImpl.transform(TransformerImpl.java:673)<br /> [izpack] at com.sun.org.apache.xalan.internal.xsltc.trax.TransformerImpl.transform(TransformerImpl.java:300)<br /> [izpack] at com.izforge.izpack.adaptator.impl.XMLParser.parseLineNrFromInputSource(Unknown Source)</p>
<p>We are not currently exposing the "ant installer" command to users, so<br />this is an RFE, not a bug.</p>
<p>See bug 4994 at<br /><a class="external" href="http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4994">http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4994</a></p> Bug #4003 (New): Support for non-GUI Kepler installer.https://projects.ecoinformatics.org/ecoinfo/issues/40032009-04-21T16:12:59Zjianwu jianwujianwu@sdsc.edu
<p>Many users need to install Kepler on a cluster or other distributed environments where they do not have a GUI. So it would be nice if we support Kepler no-GUI installation. An ideal way is to provide a Kepler rpm package.</p> Bug #3973 (New): Additional information for 64-bit users installing 1.0.0https://projects.ecoinformatics.org/ecoinfo/issues/39732009-04-10T23:12:04ZOliver Soongsoong@nceas.ucsb.edu
<p>Kepler 1.0.0 on 64-bit Windows systems seems to require a 32-bit java install, which is not the default provided by java.com. The error claims Java 1.5.0 could not be found, even if 1.5.0 is installed and even though it works with Java 1.6.0. At the very least, a note indicating such at kepler-project.org would help, and this seems to affect both XP and Vista.</p> Bug #3785 (New): Unclear Java requirements for Kepler installer on Vista 64-bithttps://projects.ecoinformatics.org/ecoinfo/issues/37852009-01-29T18:09:45ZJim Regetzregetz@nceas.ucsb.edu
<p>On a Vista 64-bit machine, the Kepler 1.0.0 installer for Windows failed with 64-bit JRE 5.0 (Update 16) installed, reporting the error "Cannot find Java 1.5.0". Adding the correct Java bin directory to the path variable didn't make a difference, nor did running the installer as administrator, nor did running it in compatibility mode for XP.</p>
<p>After I closed the installer error window, a web browser window automatically opened at the Sun download page for (32-bit) Java 6 -- not 1.5.x, as the Kepler documentation suggests. Nevertheless, after I installed this, Kepler installation proceeded normally, and Kepler itself seemed to work (superficially at least). Subsequent experimentation indicated that installing 32-bit Java 1.5 also works, as documented.</p>
<p>Is the Kepler installer simply having problems finding the 64-bit Java binaries, or is 32-bit Java actually required? In either case, it would be helpful if the Kepler documentation provided more clarity on the matter, ideally with a note included on (or directly linked to) the downloads page. It is also confusing that the installer error complains about missing Java 1.5.0, but the user is prompted to install Java 6 (in conflict with the documentation).</p> Bug #3694 (In Progress): Sharing installation among users fails, users must have write permissionhttps://projects.ecoinformatics.org/ecoinfo/issues/36942008-12-05T19:33:37ZChristopher Brookscxh@eecs.berkeley.edu
<p>Jianwu Wang writes:</p>
<blockquote>
<p>Hi all,</p>
<p>One of our partner has the following requirements, which I think it is >quite common.<br />They want to install Kepler on one machine only once and it can be shared >by multiple users. So Kepler was installed by root user and it was started >through kepler.sh command by other users. But we got the following exception:</p>
<p>regArray: >org.ecoinformatics.ecogrid.registry.stub.RegistryEntryArrayType@312ae32c<br />ERROR >(org.ecoinformatics.seek.ecogrid.SearchRegistryAction:queryRegistryRewriteConfig:246) >Problem writing new services to config file<br />Unable to process kar file: /home/invite/SANDIEGO/kepler/./kar/actors/ImageJ.kar</p>
<p>The exception is because that the user do not the right to write the config >file.</p>
<p>To make Kepler sharable by multiple users, can we divide the config file<br />into public part and private part so that each user can read the public part<br />from the $Kepler directory and write the private part into private file, such<br />as in $HOME/.kepler directory?</p>
</blockquote>
<blockquote>
<p>To go future and make actors sharable, can we also divide the config file of >actors into public part and private part so that each user can use the public >actors from the $Kepler directory and private actors from private file, such >as in $HOME/.kepler directory? In this way, each user can make/import his/her >own kar files and use the actors.</p>
</blockquote>
<p>I noticed this yesterday . . .</p>
<p>Under Windows 2003 Server, I installed Kepler 1.0.0 as adminstrator<br />and then ran Kepler by clicking on the icon as non-administrator and <br />the following appeared in a console window that was brought up by Kepler:</p>
<p>log4j:ERROR setFile(null,true) call failed.<br />java.io.FileNotFoundException: keplerLog4J.log (Access is denied)<br /> at java.io.FileOutputStream.openAppend(Native Method)<br /> at java.io.FileOutputStream.<init>(Unknown Source)<br /> at java.io.FileOutputStream.<init>(Unknown Source)<br /> at org.apache.log4j.FileAppender.setFile(FileAppender.java:272)<br /> at org.apache.log4j.RollingFileAppender.setFile(RollingFileAppender.java<br />:156)<br /> at org.apache.log4j.FileAppender.activateOptions(FileAppender.java:151)<br /> at org.apache.log4j.config.PropertySetter.activate(PropertySetter.java:2<br />47)<br /> at org.apache.log4j.config.PropertySetter.setProperties(PropertySetter.j<br />ava:123)<br /> at org.apache.log4j.config.PropertySetter.setProperties(PropertySetter.j<br />ava:87)<br /> at org.apache.log4j.PropertyConfigurator.parseAppender(PropertyConfigura<br />tor.java:645)<br /> at org.apache.log4j.PropertyConfigurator.parseCategory(PropertyConfigura<br />tor.java:603)<br /> at org.apache.log4j.PropertyConfigurator.configureRootCategory(PropertyC<br />onfigurator.java:500)<br /> at org.apache.log4j.PropertyConfigurator.doConfigure(PropertyConfigurato<br />r.java:406)<br /> at org.apache.log4j.PropertyConfigurator.doConfigure(PropertyConfigurato<br />r.java:432)<br /> at org.apache.log4j.helpers.OptionConverter.selectAndConfigure(OptionCon<br />verter.java:460)<br /> at org.apache.log4j.LogManager.<clinit>(LogManager.java:113)<br /> at org.apache.log4j.Logger.getLogger(Logger.java:85)<br /> at org.apache.commons.logging.impl.Log4JLogger.<init>(Log4JLogger.java:1<br />02)<br /> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)</p>
<pre><code>at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)</code></pre>
<pre><code>at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Sou<br />rce)<br /> at java.lang.reflect.Constructor.newInstance(Unknown Source)<br /> at org.apache.commons.logging.impl.LogFactoryImpl.newInstance(LogFactory<br />Impl.java:525)<br /> at org.apache.commons.logging.impl.LogFactoryImpl.getInstance(LogFactory<br />Impl.java:272)<br /> at org.apache.commons.logging.LogFactory.getLog(LogFactory.java:414)<br /> at org.ecoinformatics.util.Config.&lt;clinit&gt;(Config.java:90)<br /> at org.kepler.gui.KeplerApplication.main(KeplerApplication.java:63)<br /> at org.kepler.loader.Kepler.main(Kepler.java:100)<br />KAR Library directories: [C:\Program Files\Kepler\kar\actors, C:\Program Files\K<br />epler\kar\directors]<br />regArray: org.ecoinformatics.ecogrid.registry.stub.RegistryEntryArrayType@312ae3<br />2c<br />ERROR (org.ecoinformatics.seek.ecogrid.EcoGridServicesController:mergeServicesLi<br />st:392) could not add service:The service type is invalid or null: KeplerSlaveNo<br />de. Couldn't be added to list<br />ERROR (org.ecoinformatics.seek.ecogrid.EcoGridServicesController:mergeServicesLi<br />st:392) could not add service:The service type is invalid or null: KeplerSlaveNo<br />de. Couldn't be added to list<br />ERROR (org.ecoinformatics.seek.ecogrid.EcoGridServicesController:mergeServicesLi<br />st:392) could not add service:The service type is invalid or null: KeplerSlaveNo<br />de. Couldn't be added to list<br />ERROR (org.ecoinformatics.seek.ecogrid.EcoGridServicesController:mergeServicesLi<br />st:392) could not add service:The service type is invalid or null: KeplerSlaveNo<br />de. Couldn't be added to list<br />ERROR (org.ecoinformatics.seek.ecogrid.EcoGridServicesController:mergeServicesLi<br />st:392) could not add service:The service type is invalid or null: KeplerSlaveNo<br />de. Couldn't be added to list<br />ERROR (org.ecoinformatics.seek.ecogrid.EcoGridServicesController:mergeServicesLi<br />st:392) could not add service:The service type is invalid or null: KeplerSlaveNo<br />de. Couldn't be added to list<br />ERROR (org.ecoinformatics.seek.ecogrid.EcoGridServicesController:mergeServicesLi<br />st:392) could not add service:The service type is invalid or null: KeplerSlaveNo<br />de. Couldn't be added to list<br />ERROR (org.ecoinformatics.seek.ecogrid.EcoGridServicesController:mergeServicesLi<br />st:392) could not add service:The service type is invalid or null: KeplerSlaveNo<br />de. Couldn't be added to list<br />ERROR (org.ecoinformatics.seek.ecogrid.EcoGridServicesController:mergeServicesLi<br />st:392) could not add service:The service type is invalid or null: KeplerSlaveNo<br />de. Couldn't be added to list<br />ERROR (org.ecoinformatics.seek.ecogrid.EcoGridServicesController:mergeServicesLi<br />st:392) could not add service:The service type is invalid or null: KeplerSlaveNo<br />de. Couldn't be added to list<br />ERROR (org.ecoinformatics.seek.ecogrid.EcoGridServicesController:mergeServicesLi<br />st:392) could not add service:The service type is invalid or null: KeplerSlaveNo<br />de. Couldn't be added to list<br />ERROR (org.ecoinformatics.seek.ecogrid.EcoGridServicesController:mergeServicesLi<br />st:392) could not add service:The service type is invalid or null: KeplerSlaveNo<br />de. Couldn't be added to list<br />ERROR (org.ecoinformatics.seek.ecogrid.EcoGridServicesController:mergeServicesLi<br />st:392) could not add service:The service type is invalid or null: KeplerSlaveNo<br />de. Couldn't be added to list<br />ERROR (org.ecoinformatics.seek.ecogrid.EcoGridServicesController:mergeServicesLi<br />st:392) could not add service:The service type is invalid or null: KeplerSlaveNo<br />de. Couldn't be added to list<br />ERROR (org.ecoinformatics.seek.ecogrid.EcoGridServicesController:mergeServicesLi<br />st:392) could not add service:The service type is invalid or null: KeplerSlaveNo<br />de. Couldn't be added to list<br />ERROR (org.ecoinformatics.seek.ecogrid.SearchRegistryAction:queryRegistryRewrite<br />Config:246) Problem writing new services to config file</code></pre>
<p>And this stack trace occurred in a stack trace window:<br />java.io.FileNotFoundException: C:\Program Files\Kepler\lib\config.xml (Access is denied)<br /> at java.io.FileOutputStream.open(Native Method)<br /> at java.io.FileOutputStream.<init>(Unknown Source)<br /> at java.io.FileOutputStream.<init>(Unknown Source)<br /> at java.io.FileWriter.<init>(Unknown Source)<br /> at edu.ucsb.nceas.configxml.ConfigXML.saveDOM(ConfigXML.java:648)<br /> at edu.ucsb.nceas.configxml.ConfigXML.save(ConfigXML.java:622)<br /> at org.ecoinformatics.util.Config.save(Config.java:392)<br /> at org.ecoinformatics.seek.ecogrid.EcoGridServicesController.writeServicesToConfig(EcoGridServicesController.java:937)<br /> at org.ecoinformatics.seek.ecogrid.SearchRegistryAction.queryRegistryRewriteConfig(SearchRegistryAction.java:241)<br /> at org.kepler.gui.KeplerInitializer$1.run(KeplerInitializer.java:215)<br /> at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)<br /> at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)<br /> at java.util.concurrent.FutureTask.run(Unknown Source)<br /> at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(Unknown Source)<br /> at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(Unknown Source)<br /> at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source)<br /> at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)<br /> at java.lang.Thread.run(Unknown Source)</p>
<p>_Christopher</p> Bug #2921 (New): Way to temporarily comment out actors or connectionshttps://projects.ecoinformatics.org/ecoinfo/issues/29212007-08-31T21:49:39ZBruce Charcharbw@drexel.edu
<p>The development canvas should allow developers to temporarily "comment out" an actor or connection. As it has been explained to me, the alternatives are either deleting the actor (making it cumbersome to restore it if there's no copy of the actor handy), or to delete the connection to the actor and hoping that the director running the workflow doesn't get too confused. Deleting connections also requires the developer to remember what the connections were like which may be burdensome if multiple items are being removed.</p> Bug #2494 (In Progress): Problem with Microsoft zip extractor and Kepler ziphttps://projects.ecoinformatics.org/ecoinfo/issues/24942006-07-19T21:30:16ZDan Higginshiggins@nceas.ucsb.edu
<p>The nightly build of Kepler creates a nightly zip file that contains all the code needed to run kepler from a shell/batch file. The zip file is quite large (~100MB). WinZip handles extraction of the zipped files nicely, but if one uses Microsoft's built in zip extractor, IT TAKES FOREVER (if it works at all!). The Microsoft zip extractor does seem to work OK for smaller zip files.</p>
<p>Note: This is not a bug in Kepler, but in MS unzip. Mentioned here primarily as a recond of this known problem.</p>