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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Muhammad,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">These problems are difficult to diagnose. These errors suggest an inconsistency problem with your Gateway database and/or THREDDS catalogs. I suspect you
are missing a root THREDDS catalog in the TDS contents directory or it is somehow unreadable. Check what the TDS looks like in your browser. Can you view the top-level catalog as XML? Is the XML valid?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I'm also concerned that your Gateway database may be inconsistent. Check the the tables metadata.persistent_identifier, metadata.resource and metadata.dataset
for the id </span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">"</span><tt><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">cmip5.restricted.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAntNoAA.mon.ocean.Omon.r10i1p1".
They all share the same uuid: resource_id==dataset_id.</span></tt><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Cheers,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Stephen.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas;color:#1F497D">---<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas;color:#1F497D">Stephen Pascoe +44 (0)1235 445980<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas;color:#1F497D">Centre of Environmental Data Archival<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas;color:#1F497D">STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0QX, UK<o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<div>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext"> esg-gateway-dev-bounces@mailman.earthsystemgrid.org
[mailto:esg-gateway-dev-bounces@mailman.earthsystemgrid.org] <b>On Behalf Of </b>
Muhammad Atif<br>
<b>Sent:</b> 04 January 2012 02:40<br>
<b>To:</b> Karl Taylor<br>
<b>Cc:</b> Pascoe, Stephen (STFC,RAL,RALSP); go-essp-tech@ucar.edu; esg-gateway-dev@earthsystemgrid.org<br>
<b>Subject:</b> Re: [esg-gateway-dev] [Go-essp-tech] publishing error (invalid hour)<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks for the tips; however I am now facing the problem that I stated in the previous email.
<br>
I wanted to pin point the file which was causing the issue and for that tried to publish the datasets one by one. Now I cannot even delete the said data.
<br>
<span style="font-size:10.0pt;font-family:"Courier New""><br>
<br>
<tt><b>[root@esgnode1 debug-historicalAntNoAA]# esgunpublish --skip-thredds cmip5.restricted.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAntNoAA.mon.ocean.Omon.r10i1p1</b></tt><br>
<tt>INFO 2012-01-04 13:39:49,576 Deleting cmip5.restricted.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAntNoAA.mon.ocean.Omon.r10i1p1</tt><br>
<tt>WARNING 2012-01-04 13:39:49,687 Deletion/retraction failed for dataset cmip5.restricted.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAntNoAA.mon.ocean.Omon.r10i1p1 with message: Java ServiceException: The persistent identifier=cmip5.restricted.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAntNoAA.mon.ocean.Omon.r10i1p1
does not correspond to a dataset at sgf.gateway.service.security.impl.acegi.AcegiCatalogAccessDecisionVoter.vote(AcegiCatalogAccessDecisionVoter.java:74)</tt><br>
<tt>INFO 2012-01-04 13:39:49,706 Result: UNSUCCESSFUL</tt><br>
<br>
<tt><b>[root@esgnode1 debug-historicalAntNoAA]# esgunpublish --skip-gateway cmip5.restricted.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAntNoAA.mon.ocean.Omon.r10i1p1</b></tt><br>
<tt>INFO 2012-01-04 13:40:35,331 Writing THREDDS ESG master catalog /data/esg-node/tds-content/thredds/esgcet/catalog.xml</tt><br>
<tt>INFO 2012-01-04 13:40:35,719 Reinitializing THREDDS server</tt><br>
<tt>Traceback (most recent call last):</tt><br>
<tt> File "/usr/local/cdat/bin/esgunpublish", line 5, in <module></tt><br>
<tt> pkg_resources.run_script('esgcet==2.8.4', 'esgunpublish')</tt><br>
<tt> File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 489, in run_script</tt><br>
<tt> File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 1207, in run_script</tt><br>
<tt> File "/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/EGG-INFO/scripts/esgunpublish", line 221, in <module></tt><br>
<tt> main(sys.argv[1:])</tt><br>
<tt> File "/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/EGG-INFO/scripts/esgunpublish", line 184, in main</tt><br>
<tt> result = deleteDatasetList(datasetNames, Session, gatewayOp, thredds, las, deleteDset, deleteAll=deleteAll, republish=republish)</tt><br>
<tt> File "/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/esgcet/publish/unpublish.py", line 272, in deleteDatasetList</tt><br>
<tt> result = reinitializeThredds()</tt><br>
<tt> File "/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/esgcet/publish/thredds.py", line 1041, in reinitializeThredds</tt><br>
<tt> raise ESGPublishError("Error reinitializing the THREDDS Data Server: Fatal error: %s\n%s"%(errorMessage, str(result)))</tt><br>
<tt>esgcet.exceptions.ESGPublishError: Error reinitializing the THREDDS Data Server: Fatal error: **Fatal: InvCatalogFactory.readXML failed</tt><br>
<tt>Catalog init catalog.xml</tt><br>
<tt>[2012-01-04T02:40:35GMT]</tt><br>
<br>
<tt><b>[root@esgnode1 debug-historicalAntNoAA]# esgunpublish --database-delete cmip5.restricted.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAntNoAA.mon.ocean.Omon.r10i1p1</b></tt><br>
<tt>INFO 2012-01-04 13:34:34,130 Deleting cmip5.restricted.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAntNoAA.mon.ocean.Omon.r10i1p1</tt><br>
<tt>WARNING 2012-01-04 13:34:34,257 Deletion/retraction failed for dataset cmip5.restricted.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAntNoAA.mon.ocean.Omon.r10i1p1 with message: Java ServiceException: The persistent identifier=cmip5.restricted.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAntNoAA.mon.ocean.Omon.r10i1p1
does not correspond to a dataset at sgf.gateway.service.security.impl.acegi.AcegiCatalogAccessDecisionVoter.vote(AcegiCatalogAccessDecisionVoter.java:74)</tt><br>
<tt>INFO 2012-01-04 13:34:34,274 Result: UNSUCCESSFUL</tt><br>
<tt>INFO 2012-01-04 13:34:34,286 Writing THREDDS ESG master catalog /data/esg-node/tds-content/thredds/esgcet/catalog.xml</tt><br>
<tt>INFO 2012-01-04 13:34:34,661 Reinitializing THREDDS server</tt><br>
<tt>Traceback (most recent call last):</tt><br>
<tt> File "/usr/local/cdat/bin/esgunpublish", line 5, in <module></tt><br>
<tt> pkg_resources.run_script('esgcet==2.8.4', 'esgunpublish')</tt><br>
<tt> File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 489, in run_script</tt><br>
<tt> File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 1207, in run_script</tt><br>
<tt> File "/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/EGG-INFO/scripts/esgunpublish", line 221, in <module></tt><br>
<tt> main(sys.argv[1:])</tt><br>
<tt> File "/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/EGG-INFO/scripts/esgunpublish", line 184, in main</tt><br>
<tt> result = deleteDatasetList(datasetNames, Session, gatewayOp, thredds, las, deleteDset, deleteAll=deleteAll, republish=republish)</tt><br>
<tt> File "/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/esgcet/publish/unpublish.py", line 272, in deleteDatasetList</tt><br>
<tt> result = reinitializeThredds()</tt><br>
<tt> File "/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/esgcet/publish/thredds.py", line 1041, in reinitializeThredds</tt><br>
<tt> raise ESGPublishError("Error reinitializing the THREDDS Data Server: Fatal error: %s\n%s"%(errorMessage, str(result)))</tt><br>
<tt>esgcet.exceptions.ESGPublishError: Error reinitializing the THREDDS Data Server: Fatal error: **Fatal: InvCatalogFactory.readXML failed</tt><br>
<tt>Catalog init catalog.xml</tt><br>
<tt>[2012-01-04T02:34:34GMT]</tt><br>
<tt>readCatalog(): full path=/data/esg-node/tds-content/thredds/catalog.xml; path=catalog.xml</tt><br>
<tt>readCatalog(): valid catalog -- ----Catalog Validation version 1.0.01</tt></span><br>
<br>
<tt><b><span style="font-size:10.0pt">[root@esgnode1 debug-historicalAntNoAA]# esglist_datasets cmip5 | grep CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAntNoAA.mon.ocean.Omon.r10i1p1</span></b></tt><span style="font-size:10.0pt;font-family:"Courier New""><br>
<tt>| 4422 | cmip5.restricted.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAntNoAA.mon.ocean.Omon.r10i1p1 | cmip5 | CSIRO-Mk3-6-0 | historicalAntNoAA | r10i1p1 | False | None | restricted | mon | ocean | Omon | r10i1p1 | CSIRO-QCCCE
| 2012-01-04 13:39:49 | DELETE_DATASET_FAILED | cmip5.restricted.CSIRO-QCCCE.CSIRO-Mk3-6-0 | 20120104 | cmip5.restricted.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAntNoAA.mon.ocean.Omon.r10i1p1.v20120104 | None |</tt></span><br>
<br>
<br>
Thanks for your help in advance. <br>
<br>
Regards,<br>
<br>
On 04/01/12 04:41, Karl Taylor wrote: <o:p></o:p></p>
<p class="MsoNormal">Hi Muhammad,<br>
<br>
Better yet, execute "ncdump -c". This will return both the header information and the coordinate values. It would be good to see what the time coordinate values are in the file.<br>
<br>
thanks,<br>
Karl<br>
<br>
On 1/3/12 6:34 AM, <a href="mailto:stephen.pascoe@stfc.ac.uk">stephen.pascoe@stfc.ac.uk</a> wrote:
<o:p></o:p></p>
<pre>Hi Muhammad,<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Can you send a dump of the NetCDF metadata for this file. The command is "ncdump -h". Whether a time value is valid depends on the time:units attribute and sometimes other attributes.<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Cheers,<o:p></o:p></pre>
<pre>Stephen.<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>---<o:p></o:p></pre>
<pre>Stephen Pascoe +44 (0)1235 445980<o:p></o:p></pre>
<pre>Centre of Environmental Data Archival<o:p></o:p></pre>
<pre>STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0QX, UK<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre>-----Original Message-----<o:p></o:p></pre>
<pre>From: <a href="mailto:esg-gateway-dev-bounces@mailman.earthsystemgrid.org">esg-gateway-dev-bounces@mailman.earthsystemgrid.org</a> [<a href="mailto:esg-gateway-dev-bounces@mailman.earthsystemgrid.org">mailto:esg-gateway-dev-bounces@mailman.earthsystemgrid.org</a>] On Behalf Of Muhammad Atif<o:p></o:p></pre>
<pre>Sent: 03 January 2012 04:37<o:p></o:p></pre>
<pre>To: <a href="mailto:go-essp-tech@ucar.edu">go-essp-tech@ucar.edu</a>; <a href="mailto:esg-gateway-dev@earthsystemgrid.org">esg-gateway-dev@earthsystemgrid.org</a><o:p></o:p></pre>
<pre>Subject: [esg-gateway-dev] publishing error (invalid hour)<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Dear All,<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>In an unrelated problem from the previous email, we are facing another <o:p></o:p></pre>
<pre>error that gives "CDMS error: Error on time conversion: invalid hour = <o:p></o:p></pre>
<pre>28864363504146.773438"<o:p></o:p></pre>
<pre>Please let me know what to do with it. The modelers suggest that they <o:p></o:p></pre>
<pre>were not able to find any funny stuff.<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>INFO 2011-12-28 12:24:32,436 Writing THREDDS catalog <o:p></o:p></pre>
<pre>/data/esg-node/tds-content/thredds/esgcet/9/cmip5.restricted.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAntNoAA.mon.ocean.Omon.r10i1p1.v20111228.xml<o:p></o:p></pre>
<pre>CDMS error: Error on time conversion: invalid hour = 28864363504146.773438<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Traceback (most recent call last):<o:p></o:p></pre>
<pre> File "/usr/local/cdat/bin/esgpublish", line 5, in <module><o:p></o:p></pre>
<pre> pkg_resources.run_script('esgcet==2.8.4', 'esgpublish')<o:p></o:p></pre>
<pre> File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 489, in <o:p></o:p></pre>
<pre>run_script<o:p></o:p></pre>
<pre> File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 1207, in <o:p></o:p></pre>
<pre>run_script<o:p></o:p></pre>
<pre> File <o:p></o:p></pre>
<pre>"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/EGG-INFO/scripts/esgpublish", <o:p></o:p></pre>
<pre>line 434, in <module><o:p></o:p></pre>
<pre> main(sys.argv[1:])<o:p></o:p></pre>
<pre> File <o:p></o:p></pre>
<pre>"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/EGG-INFO/scripts/esgpublish", <o:p></o:p></pre>
<pre>line 420, in main<o:p></o:p></pre>
<pre> result = publishDatasetList(datasetNames, Session, publish=publish, <o:p></o:p></pre>
<pre>thredds=thredds, las=las, parentId=parent, service=service, <o:p></o:p></pre>
<pre>perVariable=perVariable)<o:p></o:p></pre>
<pre> File <o:p></o:p></pre>
<pre>"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/esgcet/publish/publish.py", <o:p></o:p></pre>
<pre>line 244, in publishDatasetList<o:p></o:p></pre>
<pre> generateThredds(datasetName, Session, threddsOutput, handler, <o:p></o:p></pre>
<pre>service=service, perVariable=perVariable, versionNumber=versionno)<o:p></o:p></pre>
<pre> File <o:p></o:p></pre>
<pre>"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/esgcet/publish/thredds.py", <o:p></o:p></pre>
<pre>line 726, in generateThredds<o:p></o:p></pre>
<pre> _generateThreddsV2(datasetName, outputFile, handler, session, dset, <o:p></o:p></pre>
<pre>context, project, model, experiment, config, section, genRoot=genRoot, <o:p></o:p></pre>
<pre>service=service, perVariable=perVariable, versionNumber=versionNumber)<o:p></o:p></pre>
<pre> File <o:p></o:p></pre>
<pre>"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/esgcet/publish/thredds.py", <o:p></o:p></pre>
<pre>line 950, in _generateThreddsV2<o:p></o:p></pre>
<pre> _genPerVariableDatasetsV2(datasetElem, dset, datasetName, <o:p></o:p></pre>
<pre>resolution, filesRootLoc, filesRootPath, datasetRootDict, <o:p></o:p></pre>
<pre>excludeVariables, offline, serviceName, serviceDict, aggServiceName, <o:p></o:p></pre>
<pre>handler, project, model, experiment, lasConfigure, lasTimeDelta, <o:p></o:p></pre>
<pre>versionNumber, variables, variableElemDict, lasServiceSpecs, <o:p></o:p></pre>
<pre>lasServiceHash, gridftpMap=gridftpMapDatasetRoots)<o:p></o:p></pre>
<pre> File <o:p></o:p></pre>
<pre>"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/esgcet/publish/thredds.py", <o:p></o:p></pre>
<pre>line 563, in _genPerVariableDatasetsV2<o:p></o:p></pre>
<pre> timeFirst = mdhandler.genTime(variable.aggdim_first, <o:p></o:p></pre>
<pre>dataset.aggdim_units, dataset.calendar)<o:p></o:p></pre>
<pre> File <o:p></o:p></pre>
<pre>"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/esgcet/config/cf_handler.py", <o:p></o:p></pre>
<pre>line 179, in genTime<o:p></o:p></pre>
<pre> c = t.tocomp(_tagToCalendar[calendarTag])<o:p></o:p></pre>
<pre>Cdtime error: Invalid component time<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Regards,<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<p class="MsoNormal"><br>
<br>
<br>
<o:p></o:p></p>
<pre>-- <o:p></o:p></pre>
<pre>Muhammad Atif<o:p></o:p></pre>
<pre>ANU Supercomputer Facility NCI National Facility<o:p></o:p></pre>
<pre>Leonard Huxley, Mills Road Room 318, Bldg # 56<o:p></o:p></pre>
<pre>Australian National University Ph: +61 2 6125 5031<o:p></o:p></pre>
<pre>Canberra, ACT 0200, Australia M: 0430 393863<o:p></o:p></pre>
<pre>CRICOS Provider #00120C <a href="http://anusf.anu.edu.au">http://anusf.anu.edu.au</a><o:p></o:p></pre>
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