Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362013-01-18T02:31:18ZEcoinformatics Redmine
Redmine Bug #5790 (Resolved): Not all remote run-kars appear in Workflow Run Managerhttps://projects.ecoinformatics.org/ecoinfo/issues/57902013-01-18T02:31:18ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>I believe the Workflow Run Manager is not displaying all the remote run-kars that it should. E.g. "04-HelloWorld-execId6_20120830-204114819PDT,kar" (as seen in Component Search). My guess would be something's going wrong in the rather hideous ProvenanceStore.downloadAllWorkflowRuns method I wrote. This method avoids the very slow process of downloading all run-kars to get at their contained WorkflowRun files, and instead reassembles, in a very fragile way, WorkflowRuns from fragments returned by a query on the KarXMLs in metacat. At the time I didn't know of a way to query for/extract from results the entire WorkflowRun xmls in a cleanly delimited way, but iirc later Matt and/or Ben told me there is. Look into this...</p> Bug #5782 (Resolved): wrong behavior when trying to Export a run when module dependencies not sat...https://projects.ecoinformatics.org/ecoinfo/issues/57822013-01-15T21:09:57ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>If you attempt to Export a run from the Workflow Run Manager when its module dependencies are not satisfied, the Import Module Dependencies action is invoked. This is desirable, so the user is warned, and if relevant, offered the option to restart into the right modules. However the dialog only offers a 'Force Open' option, which doesn't make sense here -- instead it needs to offer a 'Force Export' option, with slightly different text and warning. The warning should explain that it's possible not all artifacts will make it into the KAR (inactive modules' KAR entry handlers are not present in the system to be able to place the artifacts they're responsible for into the KAR, a restriction of our KAR saving design). Also, when Force Export is used, the module dependency list in the KAR's manifest should not utilize the 'override module dependencies' functionality in our code -- e.g. if you attempt to save a run that was created within reporting, from within just the workflow-run-manager suite, the reporting artifacts will not be placed into this 'forced KAR', and it's then less desirable to include reporting in that kar's mod dep list than simply use the currently active module suite.</p>
<p>I'll commit a fix shortly.</p> Bug #5781 (Resolved): opening a workflow run leaves temp kar entry in Recent Files menu and chang...https://projects.ecoinformatics.org/ecoinfo/issues/57812013-01-15T20:57:16ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>When you open a run from the Workflow Run Manager, behind the scenes a temporary kar is created, opened, and then disposed. This leaves an entry in the new-ish Recent Files menu, and changes the user's 'last directory' setting (the directory opened by default when they next attempt to save). Both of these things are undesirable.</p>
<p>A fix will be committed shortly.</p> Bug #5778 (Resolved): Force Open doesn't (always?) currently work with Workflow Run Managerhttps://projects.ecoinformatics.org/ecoinfo/issues/57782013-01-14T20:30:34ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>There's currently at least one scenario where if a run's workflow's module dependencies are not satisfied, Force Open doesn't work (nothing appears to happen). I've started tracking it down, should be fixed soon.</p> Bug #5598 (Resolved): parameters appear as white boxes instead of dotshttps://projects.ecoinformatics.org/ecoinfo/issues/55982012-05-07T18:23:26ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Using the workflow run manager, one can download a remote workflow run kar, and then right click on the row and select Open to open the associated workflow. Under Windows 7, at least some of the time, if this workflow has parameters, they will appear as large white rectangles instead of dots. See attached screen shot.</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 #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 #5297 (Resolved): Workflow Run Manager - no indication of progress during preview runs downloadhttps://projects.ecoinformatics.org/ecoinfo/issues/52972011-02-07T20:42:57ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>There are currently about 131 run-kars on kepler-dev. Switching to kepler-dev from the workflow run manager for the first time takes (including authentication), upwards of 30s for me, and I'm on a fast university connection. A busy icon shows during the wait, but it would be better if each preview run showed up in the WRM as it was downloaded, instead of waiting until all are downloaded.<br />Also look into speeding up this process, e.g. check with Jing about caching the search results on metacat, look for bottlenecks (disk i/o with the tracker xml file?), etc.</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> Bug #5014 (Resolved): Add documentation to resources for the Workflow Run Manager modulehttps://projects.ecoinformatics.org/ecoinfo/issues/50142010-05-17T18:11:41Zdebi staggsstaggs@nceas.ucsb.edu
<p>Add resources > documentation into svn, and then place the workflow-run-manager documentation there. Documentation needs to be named the same as your module name, i.e. workflow-run-manager .pdf. This is so that the Modules Documentation for the tagging module can be found by that menu action in Kepler.</p> Bug #4976 (Resolved): Importing run archive from a different namespace is brokenhttps://projects.ecoinformatics.org/ecoinfo/issues/49762010-05-04T21:13:27ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>When you import a run, the run's execId is set to the next available execId, and we attempt to increment the run's revision. Subsequent tag events on this run also increment the revision. However, if this run comes from a different namespace, it gets an entirely new lsid. There are a few problems with this at the moment:<br />- a subsequent export of this imported run will not contain the derivedFrom lsid. This is not currently stored in provenance. We can't tell who originally created the run.<br />- opening the kar again during a subsequent kepler session will again import the run with a different lsid even though it's already been imported, because the lookup to avoid this is based on the original lsid. So you end up with two runs that are the same in all ways but run lsid. This bug doesn't happen during the same kepler session.</p>
<p>I think the solution to these issues is to make sure WorkflowRuns are getting and storing referral list, and to then store and utilize the referral list in provenance.</p> Bug #4972 (Resolved): Write documentation for workflow-run-manager modulehttps://projects.ecoinformatics.org/ecoinfo/issues/49722010-05-03T20:18:13ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Debi will try to fwd Sean and I documentation outlines to fill in.</p> Bug #4960 (Resolved): NPE from TableSorter when repeatedly executing a small workflow in WRPhttps://projects.ecoinformatics.org/ecoinfo/issues/49602010-04-27T19:16:59ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>If you're in the WRP suite and repeatedly execute a workflow, this NPE sometimes occurs with each execution. WRM does not show up in the stacktrace, but I'm fairly positive it's something to do with how WRM is using TableSorter. Afaict this bug doesn't cause any harm (let me know if you notice otherwise). Putting on 2.0 target since it's possible I may have to modify TableSorter:</p>
<p>[run] Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException<br />[run] at util.TableSorter.modelIndex(TableSorter.java:289)<br />[run] at util.TableSorter.getValueAt(TableSorter.java:326)<br />[run] at javax.swing.JTable.getValueAt(JTable.java:1903)<br />[run] at javax.swing.JTable.prepareRenderer(JTable.java:3911)<br />[run] at javax.swing.plaf.basic.BasicTableUI.paintCell(BasicTableUI.java:2069)<br />[run] at javax.swing.plaf.basic.BasicTableUI.paintCells(BasicTableUI.java:1971)<br />[run] at javax.swing.plaf.basic.BasicTableUI.paint(BasicTableUI.java:1894)<br />[run] at javax.swing.plaf.ComponentUI.update(ComponentUI.java:154)<br />[run] at javax.swing.JComponent.paintComponent(JComponent.java:737)<br />[run] at javax.swing.JComponent.paint(JComponent.java:1000)<br />[run] at javax.swing.JComponent.paintChildren(JComponent.java:837)<br />[run] at javax.swing.JComponent.paint(JComponent.java:1009)</p> Bug #4954 (Resolved): Duration value on imported runs is incorrecthttps://projects.ecoinformatics.org/ecoinfo/issues/49542010-04-21T01:06:28ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>If you export a run, then import it, the end_time for the run inserted into provenance is wrong, and hence so is the duration.</p> Bug #4927 (Resolved): Don't allow export, upload, delete of executing run in WRMhttps://projects.ecoinformatics.org/ecoinfo/issues/49272010-04-03T00:39:09ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>The workflow run manager shouldn't allow the export, upload or delete of an executing run.</p>