Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362010-09-29T22:23:55ZEcoinformatics Redmine
Redmine Bug #5196 (Resolved): uploading to remote server error.https://projects.ecoinformatics.org/ecoinfo/issues/51962010-09-29T22:23:55Zjianwu jianwujianwu@sdsc.edu
<p>First of all, I think the popup dialog for workflow run uploading is not quite clear. It is 'To upload to a remote repository, select one from the component search preferences.'. I think a better one is like 'To upload to a remote repository, please first select choose one remote save site at Tools->Preferences->Components.'</p>
<p>I chose library.kepler-project.org, and get exception when uploading a workflow run on my windows machine. I don't know why it tries to access this directory: /var/kepler/temporary/uploads/04-Helloworld-run2.kar</p>
<pre><code>[run] d: SEEK username: kepler password: <strong><b></strong> org: unaffiliated<br /> [run] auth with dn: uid=kepler,o=unaffiliated,dc=ecoinformatics,dc=org<br /> [run] ==============authenticating with url: <a class="external" href="http://library.kepler-project">http://library.kepler-project</a><br />.org/kepler/services/AuthenticationService<br /> [run] Authenticating with user: uid=kepler,o=unaffiliated,dc=ecoinformatic<br />s,dc=org and password: <strong></b></strong>**<br /> [run] using AuthenticationServiceClient to authenticate...<br /> [run] EcogridUtils: The time to create instance is =========== 0<br /> [run] AuthenticationServiceClient.login_action - return string: ACC3D77247<br />5F72B605218C8ABA1ADEEE<br /> [run] Done authenticating with AuthenticationServiceClient.<br /> [run] Time authenticating: 19 seconds.<br /> [run] EcogridUtils: The time to create instance is =========== 0<br /> [run] EcogridUtils: The time to create instance is =========== 0<br /> [run] org.kepler.objectmanager.repository.RepositoryException: java.rmi.Re<br />moteException: <?xml version="1.0"?><br /> [run] &lt;error&gt;<br /> [run] Error: problem reading multipart data: /var/kepler/temporary/uploads<br />/04-Helloworld-run2.kar (Permission denied)<br /> [run] &lt;/error&gt;<br /> [run]<br /> [run] at org.kepler.objectmanager.repository.EcogridRepository.put(Eco<br />gridRepository.java:214)<br /> [run] at org.kepler.kar.UploadToRepository.uploadFile(UploadToReposito<br />ry.java:212)<br /> [run] at org.kepler.gui.kar.ComponentUploader.upload(ComponentUploader<br />.java:99)<br /> [run] at org.kepler.gui.kar.ExportArchiveAction.actionPerformed(Export<br />ArchiveAction.java:476)<br /> [run] at org.kepler.workflowrunmanager.gui.kar.ExportRunsArchiveAction<br />.actionPerformed(ExportRunsArchiveAction.java:108)<br /> [run] at org.kepler.workflowrunmanager.gui.WorkflowRunManagerPanel$5.a<br />ctionPerformed(WorkflowRunManagerPanel.java:1070)<br /> [run] at javax.swing.AbstractButton.fireActionPerformed(AbstractButton<br />.java:1995)<br /> [run] at javax.swing.AbstractButton$Handler.actionPerformed(AbstractBu<br />tton.java:2318)<br /> [run] at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultBut<br />tonModel.java:387)<br /> [run] at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.<br />java:242)<br /> [run] at javax.swing.AbstractButton.doClick(AbstractButton.java:357)<br /> [run] at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemU<br />I.java:1223)<br /> [run] at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(<br />BasicMenuItemUI.java:1264)<br /> [run] at java.awt.Component.processMouseEvent(Component.java:6263)<br /> [run] at javax.swing.JComponent.processMouseEvent(JComponent.java:3267<br />)<br /> [run] at java.awt.Component.processEvent(Component.java:6028)<br /> [run] at java.awt.Container.processEvent(Container.java:2041)<br /> [run] at java.awt.Component.dispatchEventImpl(Component.java:4630)<br /> [run] at java.awt.Container.dispatchEventImpl(Container.java:2099)<br /> [run] at java.awt.Component.dispatchEvent(Component.java:4460)<br /> [run] at java.awt.LightweightDispatcher.retargetMouseEvent(Container.j<br />ava:4574)<br /> [run] at java.awt.LightweightDispatcher.processMouseEvent(Container.ja<br />va:4238)<br /> [run] at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4<br />168)<br /> [run] at java.awt.Container.dispatchEventImpl(Container.java:2085)<br /> [run] at java.awt.Window.dispatchEventImpl(Window.java:2478)<br /> [run] at java.awt.Component.dispatchEvent(Component.java:4460)<br /> [run] at java.awt.EventQueue.dispatchEvent(EventQueue.java:599)<br /> [run] at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDisp<br />atchThread.java:269)<br /> [run] at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatc<br />hThread.java:184)<br /> [run] at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDisp<br />atchThread.java:174)<br /> [run] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.j<br />ava:169)<br /> [run] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.j<br />ava:161)<br /> [run] at java.awt.EventDispatchThread.run(EventDispatchThread.java:122<br />)</code></pre> Bug #5185 (Resolved): common ontology_catalog.xml get modifiedhttps://projects.ecoinformatics.org/ecoinfo/issues/51852010-09-16T21:01:14ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Sometimes kepler modifies ontology_catalog.xml file in the common module. This shouldn't happen.</p> Bug #5184 (Resolved): sanity check(s) when attempting to open owl filehttps://projects.ecoinformatics.org/ecoinfo/issues/51842010-09-16T20:59:48ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Intermittently on startup I get an error dialog, where tagging (or something) attempts to open an ontology file from a path that doesn't make sense -- it's basically two paths stuck together.</p> Bug #5183 (Resolved): Fix 6-WebServicesAndDataTransformation.xmlhttps://projects.ecoinformatics.org/ecoinfo/issues/51832010-09-16T20:52:34ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>This work isn't working. Jianwu reports it's because a web service is down. We should fix or remove this getting-started workflow for the 2.1 release.</p> Bug #5182 (Resolved): documentation needs updating for 2.1https://projects.ecoinformatics.org/ecoinfo/issues/51822010-09-16T20:46:42ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>All the docs need reading and updating for 2.1.<br />Screenshots showing the old File menu will have to be updated when it's finished (bug#5165, bug#5180).<br />If there's discussion of KAR 2.0, that will have to be updated for KAR 2.1.</p> Bug #5181 (Resolved): welcome window shows wrong version numberhttps://projects.ecoinformatics.org/ecoinfo/issues/51812010-09-16T20:42:49ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Christopher reports the welcome window shows the wrong version number in 2.1.</p> Bug #5180 (Resolved): Add a new Export File menu option that does a Save As (model xml)https://projects.ecoinformatics.org/ecoinfo/issues/51802010-09-16T20:35:15ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>After discussion with Christopher: add a File menu Export option that does what the old Save As used to do, a save as for the model xml.</p> Bug #5179 (Resolved): determine if ptolemy 8.0.0 is the desired version for kepler 2.1.0 releasehttps://projects.ecoinformatics.org/ecoinfo/issues/51792010-09-16T20:31:44ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Christopher wants to check if there have been any critical fixes in ptolemy since kepler 2.0.0 was released, to see if we should use a newer version of ptolemy for kepler-2.1.0.</p> Bug #5178 (Resolved): Documentation links are broken in help doc-index.htmlhttps://projects.ecoinformatics.org/ecoinfo/issues/51782010-09-16T20:27:15ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Beneath Help=> Kepler Documentation<br />the documentation links in the Local Copy column are broken in the 2.1 release.</p> Bug #5165 (Resolved): implement a GUI Save action for KARshttps://projects.ecoinformatics.org/ecoinfo/issues/51652010-08-31T01:23:04ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Currently in the GUI we really only have a 'save as...' type action for saving KARs (currently called "Save Archive (KAR)...", but will soon be renamed "Save As..."). A user can't do a typical 'Save' (no dots :)) -- they're forced go through the semantic annotation dialog, and then a file chooser, and then a 'file already exists' warning. And this process is made worse by bug#5153 .</p>
<p>Once a KAR is opened, and you've got the contained workflow(s) open before you, the system no longer knows from which KAR they originated. So I think we'll need a manager that keeps a mapping of kar info (lsid, path, ...) to tableauframe(s).</p> Bug #5160 (Resolved): problem changing suites using Module Managerhttps://projects.ecoinformatics.org/ecoinfo/issues/51602010-08-24T23:44:21ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>In the test releases area, I've published all 2.1.0 modules. <br />If I launch kepler (configured to look at the test-area) and use the Module Manager to change to reporting-2.1.0, and restart, reporting comes up (good). If I then attempt to use the MM to change to workflow-run-manager-2.1.0, and restart, reporting again comes up, not wrm, and 'ant list-modules' shows it still in the list:<br />------------<br />list-modules:<br />[list-modules] reporting-2.1.0<br />[list-modules] workflow-run-manager-2.1.0<br />[list-modules] provenance-2.1.0<br />...etc...<br />------------<br />The contents of wrm's modules.txt is:<br />*provenance-2.1.^</p>
<p>If I then use the MM to change to provenance-2.1.0, wrm comes up. If I then use MM to change to provenance again, wrm still comes up.</p> Bug #5154 (Resolved): Curiously, no progress indicator shows progress during patching.https://projects.ecoinformatics.org/ecoinfo/issues/51542010-08-18T06:13:29ZDavid Welkerdavid.v.welker@gmail.com
<p>Although I seem to recall a progress indicator being existent for large patches previously, it seems to have disappeared. It is necessary for a progress indicator to show download progress so the user doesn't feel as though the patching process is lagging.</p> Bug #5147 (Resolved): Resolve issue with modules.txthttps://projects.ecoinformatics.org/ecoinfo/issues/51472010-08-12T20:40:20ZDavid Welkerdavid.v.welker@gmail.com
<p>Automatic suite resolution has some issues with regard to patching. For example, if reporting-2.1.0 contains a self-reference to reporting-2.1.^, then when reporting-2.1 is patched, this will resolve to:</p>
<p>reporting-2.1.0<br />reporting-2.1.1</p>
<p>This is clearly incorrect, especially as the patch will be overridden by the older version and both modules are clearly unnecessary.</p>
<p>This is a particularly tricky issue, as fixing this bug will affect how modules.txt is interpreted and may cause some backwards compatibility issues. I will be investigating solutions to this that are maximally backwards compatible.</p> Bug #5145 (Resolved): kepler library skin is mostly brokenhttps://projects.ecoinformatics.org/ecoinfo/issues/51452010-08-12T00:30:38ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>The kepler library skin should be reworked now that we're uploading KARs. <br /><a class="external" href="http://library.kepler-project.org/kepler/">http://library.kepler-project.org/kepler/</a><br />Maybe we can just show the kar contents on the kar pages?</p>
<p>Ben mentioned it's not very useful as it is. See an example on his test server (if it's still there):<br /><a class="external" href="http://fred.msi.ucsb.edu:8080/knb/metacat?qformat=kepler&sessionid=0&action=read&docid=2095.155.1">http://fred.msi.ucsb.edu:8080/knb/metacat?qformat=kepler&sessionid=0&action=read&docid=2095.155.1</a></p> Bug #5143 (Resolved): not getting prompted to upgrade to available patched version in test areahttps://projects.ecoinformatics.org/ecoinfo/issues/51432010-08-12T00:15:29ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>I current have published to the test area reporting-2.0.0, reporting-2.1.0, and reporting-2.1.1. If you're run reporting-2.1.0, you're not prompted on startup to get 2.1.1, like i believe is expected.</p>