Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362011-11-23T22:50:58ZEcoinformatics Redmine
Redmine Bug #5552 (Resolved): Workflow Scheduler GUI needs a licenses.txt filehttps://projects.ecoinformatics.org/ecoinfo/issues/55522011-11-23T22:50:58ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>We need a licenses.txt for this suite before release.<br />See reporting's module-info/licenses.txt for example.</p> Bug #5486 (Resolved): Need a mechanism to tell the user the information about setup the scheduler...https://projects.ecoinformatics.org/ecoinfo/issues/54862011-09-08T23:22:53ZJing Taotao@nceas.ucsb.edu
<p>Since we decided not to provide a default scheduler and workflow run engine for the kepler release, we should have some information panel to let user know how to install them and how to configure them in kepler when he/she click the scheduler menu if the setup hasn't been done.</p> Bug #5456 (Resolved): Documentation for Reporting 2.3.0https://projects.ecoinformatics.org/ecoinfo/issues/54562011-08-12T02:15:08ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Documentation needs to be done for the Reporting Suite.</p>
<ul>
<li>reporting-2.3.0 - done</li>
<li>workflow-run-manager-2.3.0 - done</li>
<li>provenance-2.3.0 - partially done. TODO: schema updates, director support change(?), PR config dialog updates, ...</li>
<li>tagging-2.3.0 - done</li>
<li>workflow-scheduler-gui-1.0.0 - partially done. TODO: finish with more screenshots using official runengine.</li>
</ul>
<p>Afaik no one's reviewed the docs I list as 'done', as always feedback appreciated.</p> Bug #5434 (Resolved): run-kar result from headless kepler.sh execution doesn't contain report art...https://projects.ecoinformatics.org/ecoinfo/issues/54342011-06-30T02:03:01ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>This thread:<br /><a class="external" href="http://lists.nceas.ucsb.edu/kepler/pipermail/kepler-users/2011-June/002541.html">http://lists.nceas.ucsb.edu/kepler/pipermail/kepler-users/2011-June/002541.html</a><br /> prompted me to look into headless usage, esp wrt passing in workflow parameters. It's unclear to me if passing in parameters is supported by ant tasks like ant run-workflow-no-gui-server. So I began focusing on usage like:<br />./kepler.sh -runwf -nogui -myparam 7 /Users/derik/KeplerData/workflows/MyWorkflows/testwf.kar</p>
<p>If this testwf.kar contains a reportlayout (ROML), the reporting artifacts do not end up in the run-kar (or in provenance associated w/ the run) after execution if you specify parameters on the command line. If you don't pass in parameters, the run-kar contains everything it should.</p>
<p>I tracked this down to the WorkflowManager changeListener not hearing the change events on the model when it's changed for the parameter passed in. This is because the NamedObj this listener gets added to is a different instance than the one used a little bit later for execution. This is because the model can't be found in the ModelDirectory at the execution point, because it's not put in until that moment.</p>
<p>A solution to this bug is to call _openModel with the url to the temporary unzipped workflow.xml file immediately after it's created in KeplerConfigurationApplication(String[] args). Then the same NamedObj is utilized, and the WorkflowManager listener doesn't get lost.</p>
<p>I want to look at this a bit more before checking in the fix, e.g. to see if there's a better spot(s?) at which to put the model into the directory...</p> Bug #5433 (Resolved): use 1024m instead of 512m for reporting suitehttps://projects.ecoinformatics.org/ecoinfo/issues/54332011-06-28T22:28:19ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Kepler has a max memory setting of 512m by default. Increasing this to 1024m when using the reporting suite enables us to increase the hsqldb.cache_scale setting to 18 (which greatly improves workflow execution time performance when provenance is on by using more memory). Without making this change kepler will lock up with heap space errors after a few executions of data intensive workflows.</p> Bug #5422 (Resolved): Tools=>Tag Manager... menu option is missinghttps://projects.ecoinformatics.org/ecoinfo/issues/54222011-06-08T23:56:47ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>The Tools=>Tag Manager... menu option has gone missing. Maybe one of the other new Tools menu options (JVM Memory Settings... and Workflow Scheduler) has caused this?</p> Bug #5410 (Resolved): provenance data is not flushed to HSQL database before Kepler quit.https://projects.ecoinformatics.org/ecoinfo/issues/54102011-05-24T18:09:40Zjianwu jianwujianwu@sdsc.edu
<p>Currently, provenance data writing to HSQL database has write delay (100 ms by default). It causes some data is not update or written because the data is not flushed before Kepler quit.</p>
<p>To reproduce it,</p>
<p>1) Run workflow in Kepler GUI or non-GUI mode.<br />2) Quit Kepler if Kepler is run in GUI mode right after workflow is executed.<br />3) Use HSQL client to connect hsql provenance database.<br />4) Check 'workflow_exec' table: the record the execution might not be written in the database or the execution status might be always 'running'.</p>
<p>It should work for both GUI mode or non-GUI mode. Not sure whether it works for other databases, such as Oracle and mySQL.</p> Bug #5409 (Resolved): reporting 2.1 can not start when setting "JDBC URL" in provenance.https://projects.ecoinformatics.org/ecoinfo/issues/54092011-05-24T18:00:14Zjianwu jianwujianwu@sdsc.edu
<p>After I set "JDBC URL" in provenance configuration file, Kepler can not start. The exception is the same with GUI or without GUI.</p>
<p>provenance configuration file:<br /> <pair><br /> <name>JDBC URL</name><br /> <value>jdbc:hsqldb:file:/Users/jianwu/KeplerData/modules/provenance/db-2.1/provenanceDB</value><br /> </pair></p>
<p>kepler:Kepler jianwu$ rm -rf ~/KeplerData/modules/<br />kepler:Kepler jianwu$ ./kepler.sh <br />setting dock icon to -Xdock:icon=/Applications/Kepler-2.0/Kepler.app/Kepler/common-2.1.0/resources/icons/kepler-dock-icon.png<br />Set environment variable: PATH = /opt/subversion/bin:/Applications/MATLAB64/MATLAB_R2010a/MATLAB_R2010a.app/bin:/Users/jianwu/Projects/hadoop/hadoop-0.20.2-cdh3u0/bin:/System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/bin:/Users/jianwu/tools/netCDF/bin:/Users/jianwu/tools/netCDF/include:/usr/local/mysql/bin:/Users/jianwu/Projects/FUSE:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/local/git/bin:/usr/X11/bin:/sw/bin:/sw/sbin:/opt/subversion/bin:/Applications/MATLAB64/MATLAB_R2010a/MATLAB_R2010a.app/bin:/Users/jianwu/tools/netCDF/bin:/Users/jianwu/tools/netCDF/include:/usr/local/mysql/bin:/Users/jianwu/Projects/FUSE:/opt/local/bin:/Users/jianwu/Projects/EC2-Client/ec2-api-tools-1.3-62308/bin:/usr/X11R6/bin:/Users/jianwu/Projects/EC2-Client/ec2-api-tools-1.3-62308/bin:/Applications/Kepler-2.0/Kepler.app/Kepler/reporting-2.1.0/lib:/Applications/Kepler-2.0/Kepler.app/Kepler/workflow-run-manager-2.1.0/lib:/Applications/Kepler-2.0/Kepler.app/Kepler/provenance-2.1.0/lib:/Applications/Kepler-2.0/Kepler.app/Kepler/tagging-2.1.0/lib:/Applications/Kepler-2.0/Kepler.app/Kepler/kepler-2.1.0/lib:/Applications/Kepler-2.0/Kepler.app/Kepler/outreach-2.1.0/lib:/Applications/Kepler-2.0/Kepler.app/Kepler/apple-extensions-2.0.0/lib:/Applications/Kepler-2.0/Kepler.app/Kepler/r-2.1.0/lib:/Applications/Kepler-2.0/Kepler.app/Kepler/loader-2.0.0/lib:/Applications/Kepler-2.0/Kepler.app/Kepler/actors-2.1.0/lib:/Applications/Kepler-2.0/Kepler.app/Kepler/directors-2.0.0/lib:/Applications/Kepler-2.0/Kepler.app/Kepler/opendap-2.0.0/lib:/Applications/Kepler-2.0/Kepler.app/Kepler/dataturbine-2.0.0/lib:/Applications/Kepler-2.0/Kepler.app/Kepler/ecogrid-2.1.0/lib:/Applications/Kepler-2.0/Kepler.app/Kepler/authentication-gui-2.0.0/lib:/Applications/Kepler-2.0/Kepler.app/Kepler/module-manager-gui-2.1.0/lib:/Applications/Kepler-2.0/Kepler.app/Kepler/gui-2.1.0/lib:/Applications/Kepler-2.0/Kepler.app/Kepler/authentication-2.1.0/lib:/Applications/Kepler-2.0/Kepler.app/Kepler/repository-2.1.0/lib:/Applications/Kepler-2.0/Kepler.app/Kepler/job-2.0.0/lib:/Applications/Kepler-2.0/Kepler.app/Kepler/io-2.0.0/lib:/Applications/Kepler-2.0/Kepler.app/Kepler/ssh-2.0.0/lib:/Applications/Kepler-2.0/Kepler.app/Kepler/data-handling-2.0.0/lib:/Applications/Kepler-2.0/Kepler.app/Kepler/sms-2.1.0/lib:/Applications/Kepler-2.0/Kepler.app/Kepler/component-library-2.0.0/lib:/Applications/Kepler-2.0/Kepler.app/Kepler/util-2.0.0/lib:/Applications/Kepler-2.0/Kepler.app/Kepler/event-state-2.0.0/lib:/Applications/Kepler-2.0/Kepler.app/Kepler/core-2.1.0/lib:/Applications/Kepler-2.0/Kepler.app/Kepler/common-2.1.0/lib:/Applications/Kepler-2.0/Kepler.app/Kepler/module-manager-2.1.0/lib:/Applications/Kepler-2.0/Kepler.app/Kepler/configuration-manager-2.1.0/lib:/Applications/Kepler-2.0/Kepler.app/Kepler/kepler-tasks-2.1.0/lib:/Applications/Kepler-2.0/Kepler.app/Kepler/ptolemy-8.0.0/lib<br />Set environment variable: R_HOME = /Library/Frameworks/R.framework/Resources<br /> [null] /Applications/Kepler-2.0/Kepler.app/Kepler<br /> [null] Checking for patches...<br /> [null] reporting-2.1.0 workflow dir does not exist.<br /> [null] workflow-run-manager-2.1.0 workflow dir does not exist.<br /> [null] provenance-2.1.0 workflow dir already copied, no need to copy.<br /> [null] tagging-2.1.0 workflow dir does not exist.<br /> [null] kepler-2.1.0 workflow dir does not exist.<br /> [null] outreach-2.1.0 workflow dir already copied, no need to copy.<br /> [null] apple-extensions-2.0.0 workflow dir does not exist.<br /> [null] r-2.1.0 workflow dir already copied, no need to copy.<br /> [null] loader-2.0.0 workflow dir does not exist.<br /> [null] actors-2.1.0 workflow dir already copied, no need to copy.<br /> [null] directors-2.0.0 workflow dir does not exist.<br /> [null] opendap-2.0.0 workflow dir does not exist.<br /> [null] dataturbine-2.0.0 workflow dir does not exist.<br /> [null] ecogrid-2.1.0 workflow dir does not exist.<br /> [null] authentication-gui-2.0.0 workflow dir does not exist.<br /> [null] module-manager-gui-2.1.0 workflow dir does not exist.<br /> [null] gui-2.1.0 workflow dir does not exist.<br /> [null] authentication-2.1.0 workflow dir does not exist.<br /> [null] repository-2.1.0 workflow dir does not exist.<br /> [null] job-2.0.0 workflow dir does not exist.<br /> [null] io-2.0.0 workflow dir does not exist.<br /> [null] ssh-2.0.0 workflow dir does not exist.<br /> [null] data-handling-2.0.0 workflow dir does not exist.<br /> [null] sms-2.1.0 workflow dir does not exist.<br /> [null] component-library-2.0.0 workflow dir does not exist.<br /> [null] util-2.0.0 workflow dir does not exist.<br /> [null] event-state-2.0.0 workflow dir does not exist.<br /> [null] core-2.1.0 workflow dir does not exist.<br /> [null] common-2.1.0 workflow dir does not exist.<br /> [null] module-manager-2.1.0 workflow dir does not exist.<br /> [null] configuration-manager-2.1.0 workflow dir does not exist.<br /> [null] kepler-tasks-2.1.0 workflow dir does not exist.<br /> [null] ptolemy-8.0.0 workflow dir does not exist.<br /> [null] Found OS Extension file: /Applications/Kepler-2.0/Kepler.app/Kepler/apple-extensions-2.0.0/module-info/osextension.txt<br /> [null] loading OS extensions for OS Mac OS X with class org.kepler.osx.KeplerOSXExtension<br /> [null] Building Kars...<br /> [null] Ran additional initialization for module gui from class org.kepler.module.gui.Initialize<br /> [null] Ran additional initialization for module tagging from class org.kepler.module.tagging.Initialize<br /> [null] Ran additional initialization for module provenance from class org.kepler.module.provenance.Initialize<br /> [null] common tabpane configuration overridden by WRM<br /> [null] class java.lang.NullPointerException: null<br /> [null] java.lang.NullPointerException<br /> [null] at org.kepler.util.sql.DatabaseType.tableExists(DatabaseType.java:749)<br /> [null] at org.kepler.util.sql.DatabaseType._getVersion(DatabaseType.java:542)<br /> [null] at org.kepler.util.sql.DatabaseType.getMajorVersion(DatabaseType.java:491)<br /> [null] at org.kepler.provenance.sql.Schemas.checkVersion(Schemas.java:309)<br /> [null] at org.kepler.provenance.sql.SQLQueryV8._init(SQLQueryV8.java:2170)<br /> [null] at org.kepler.provenance.sql.SQLQueryV8.<init>(SQLQueryV8.java:87)<br /> [null] at org.kepler.workflowrunmanager.WorkflowRunManager.connect(WorkflowRunManager.java:116)<br /> [null] at org.kepler.module.workflowrunmanager.Initialize.initializeModule(Initialize.java:148)<br /> [null] at org.kepler.Kepler._initializeModules(Kepler.java:512)<br /> [null] at org.kepler.Kepler.initialize(Kepler.java:399)<br /> [null] at org.kepler.Kepler.parseArgsAndRun(Kepler.java:285)<br /> [null] at org.kepler.Kepler.main(Kepler.java:222)</p> Bug #5407 (Resolved): wrm/tagging have errors when starting with provenance turned offhttps://projects.ecoinformatics.org/ecoinfo/issues/54072011-05-21T00:40:25ZDaniel Crawldanielcrawl@gmail.com
<p>If I start with provenance turned off (change Recording Type to Ignore in configuration.xml), the follow error occurs:</p>
<pre><code>[run] java.lang.NullPointerException<br /> [run] at org.kepler.workflowrunmanager.gui.WorkflowRunManagerPanel.getWindowId(WorkflowRunManagerPanel.java:588)<br /> [run] at org.kepler.workflowrunmanager.gui.WorkflowRunManagerPanel.setTagContextToWorkflow(WorkflowRunManagerPanel.java:1058)<br /> [run] at org.kepler.workflowrunmanager.gui.WorkflowRunManagerPanel.toggle(WorkflowRunManagerPanel.java:1657)<br /> [run] at org.kepler.provenance.ProvenanceRecorder.addEnabledListener(ProvenanceRecorder.java:510)<br /> [run] at org.kepler.workflowrunmanager.gui.WorkflowRunManagerPanel.resetProvenanceInfo(WorkflowRunManagerPanel.java:928)<br /> [run] at org.kepler.workflowrunmanager.gui.WorkflowRunManagerPanel.initializeTab(WorkflowRunManagerPanel.java:228)<br /> [run] at org.kepler.gui.TabPaneFactory.createTabPaneTabs(TabPaneFactory.java:110)<br /> [run] at org.kepler.gui.TabManager.initializeTabs(TabManager.java:87)<br /> [run] at org.kepler.gui.KeplerGraphFrame._initBasicGraphFrame(KeplerGraphFrame.java:367)<br /> [run] at ptolemy.vergil.basic.BasicGraphFrame.&lt;init&gt;(BasicGraphFrame.java:221)</code></pre> Bug #5405 (Resolved): remove tagging's BasicGraphController overridehttps://projects.ecoinformatics.org/ecoinfo/issues/54052011-05-17T22:07:52ZDaniel Crawldanielcrawl@gmail.com
<p>The tagging module overrides ptolemy's BasicGraphController. Currently, workflows cannot be executed because the BasicGraphController in tagging is missing a method:</p>
<p>java.lang.NoSuchMethodError: ptolemy.vergil.basic.RunnableGraphController._getClearAllErrorHighlightsChangeRequest()Lptolemy/kernel/util/ChangeRequest;<br /> at ptolemy.vergil.basic.RunnableGraphController.managerStateChanged(RunnableGraphController.java:167)<br /> at ptolemy.actor.Manager._notifyListenersOfStateChange(Manager.java:1498)<br /> at ptolemy.actor.Manager._setState(Manager.java:1513)<br /> at ptolemy.actor.Manager.execute(Manager.java:408)<br /> at ptolemy.actor.Manager.run(Manager.java:1169)<br /> at ptolemy.actor.Manager$3.run(Manager.java:1222)</p>
<p>Instead of adding this method to BasicGraphController in tagging, the changes in that class should be merged into ptolemy.</p> Bug #5337 (Resolved): NPE from WorkflowManager when configuring actor within compositehttps://projects.ecoinformatics.org/ecoinfo/issues/53372011-03-04T01:59:05ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Sometimes when you right-click Configure Actor an actor within a composite, and actually make a change, you'll get an Exception Change Failed message. This is due to an NPE from WorkflowManager.changeExecuted. oldLayout is null.</p> Bug #5320 (Resolved): Get "could not find entity 1876 in parameter table" when run the dataturbin...https://projects.ecoinformatics.org/ecoinfo/issues/53202011-02-23T19:07:24ZJing Taotao@nceas.ucsb.edu
<p>This is the second time to see the error. But I didn't figure out the pattern.<br /><jing> ERROR: could not find entity 1876 in parameter table<br /><jing> at org.kepler.provenance.ProvenanceRecorder._recordWorkflowContents(ProvenanceRecorder.java:2398)<br /><jing> at org.kepler.provenance.ProvenanceRecorder.preinitialize(ProvenanceRecorder.java:535)<br /><jing> at ptolemy.actor.CompositeActor.preinitialize(CompositeActor.java:1683)<br /><jing> at ptolemy.actor.Manager.preinitializeAndResolveTypes(Manager.java:983)<br /><jing> at ptolemy.actor.Manager.initialize(Manager.java:643)<br /><jing> at ptolemy.actor.Manager.execute(Manager.java:340)<br /><jing> at ptolemy.actor.Manager.run(Manager.java:1164)<br /><jing> at ptolemy.actor.Manager$3.run(Manager.java:1217)</p>
<p>The first time was:<br /><jing> ERROR: could not find entity 514 in parameter table<br /><jing> at org.kepler.provenance.ProvenanceRecorder._recordWorkflowContents(ProvenanceRecorder.java:2398)<br /><jing> at org.kepler.provenance.ProvenanceRecorder.preinitialize(ProvenanceRecorder.java:535)<br /><jing> at ptolemy.actor.CompositeActor.preinitialize(CompositeActor.java:1683)<br /><jing> at ptolemy.actor.Manager.preinitializeAndResolveTypes(Manager.java:983)<br /><jing> at ptolemy.actor.Manager.initialize(Manager.java:643)<br /><jing> at ptolemy.actor.Manager.execute(Manager.java:340)<br /><jing> at ptolemy.actor.Manager.run(Manager.java:1164)<br /><jing> at ptolemy.actor.Manager$3.run(Manager.java:1217)</p>
<p>After delete ~/KeplerData/modules, it worked.</p> Bug #5302 (Resolved): module_dependencies column defined too shorthttps://projects.ecoinformatics.org/ecoinfo/issues/53022011-02-10T20:50:30ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>The v8 schema has the module_dependencies varchar column defined at 255 characters, but this is too small. This isn't an issue for hsql, but for other db's like mysql. One user reports needing to change it to be 1000; the module dependency list could of course technically be arbitrarily long</p> Bug #5301 (Resolved): clicking on Image item Scale Property Value sometimes gives ArrayIndexOutOf...https://projects.ecoinformatics.org/ecoinfo/issues/53012011-02-10T01:31:29ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Clicking on Image item Scale Property Value sometimes gives ArrayIndexOutOfBoundException, seems to happen after changing the scale of another report item.</p> Bug #5296 (Resolved): Workflow Run Manager - multiple window, remote store gui refresh issuehttps://projects.ecoinformatics.org/ecoinfo/issues/52962011-02-07T20:09:13ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>If you have two windows open, and in both connect the WRM to the same remote repository using the dropdowns in rapid succession, the second window WRM will eventually show the remote runs, but the first will not. The first window will show them if you do anything with the search cells, or hit the refresh button, but not initially.</p>