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Hi,<br>
<br>
I am having couple of strange errors while publishing the data on
NCI gateway. Hoping someone could help me/guide me out of this mess
:(<br>
There are two distinct issues, I am starting one email thread for
each.<br>
<br>
While trying to publish new version of the dataset, we decided to
remove the previous version from the gateway completely. <br>
<br>
However, we are not able to unpublish few datasets from our gateway.
After going through the unpublish steps (logs provided towards the
end of this email), esglist_datasets has an entry in the database of
"DELETE_DATASET_FAILED". <br>
<br>
Following is an example of one such case. The same happens if we try
to unpublish output2 part of it. <br>
<br>
<style type="text/css">p { margin-bottom: 0.21cm; }</style>
<p style="margin-bottom: 0cm;"><tt><b>cmip5.output1.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAnt.mon.atmos.Amon.r1i1p1
</b></tt></p>
<p style="margin-bottom: 0cm;"><tt><font color="#000080"><i>[root@esgnode1
tmp]#
esgunpublish --skip-thredds
cmip5.output1.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAnt.mon.atmos.Amon.r1i1p1
</i></font></tt></p>
<p style="margin-bottom: 0cm;"><tt>INFO 2012-01-03 13:58:09,122
Deleting
cmip5.output1.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAnt.mon.atmos.Amon.r1i1p1<br>
WARNING 2012-01-03 13:58:09,376
Deletion/retraction failed for dataset
cmip5.output1.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAnt.mon.atmos.Amon.r1i1p1
with
message: Java ServiceException: The persistent
identifier=cmip5.output1.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAnt.mon.atmos.Amon.r1i1p1
does
not correspond to a dataset at
sgf.gateway.service.security.impl.acegi.AcegiCatalogAccessDecisionVoter.vote(AcegiCatalogAccessDecisionVoter.java:74)<br>
INFO 2012-01-03 13:58:09,443 Result: UNSUCCESSFUL
</tt></p>
<p style="margin-bottom: 0cm;"><tt><font color="#000080"><i>[root@esgnode1
tmp]#
esgunpublish --skip-thredds
cmip5.output1.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAnt.mon.atmos.Amon.r1i1p1
</i></font></tt></p>
<p style="margin-bottom: 0cm;"><tt>INFO 2012-01-03 14:05:29,441
Deleting THREDDS catalog:
/data/esg-node/tds-content/thredds/esgcet/9/cmip5.output1.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAnt.mon.atmos.Amon.r1i1p1.v20111221.xml<br>
INFO 2012-01-03 14:05:29,663
Writing THREDDS ESG master catalog
/data/esg-node/tds-content/thredds/esgcet/catalog.xml<br>
INFO 2012-01-03 14:05:31,133
Reinitializing THREDDS server<br>
Traceback (most recent call last):<br>
File
"/usr/local/cdat/bin/esgunpublish", line 5, in <module><br>
pkg_resources.run_script('esgcet==2.8.4', 'esgunpublish')<br>
File
"build/bdist.linux-x86_64/egg/pkg_resources.py", line 489,
in run_script<br>
File
"build/bdist.linux-x86_64/egg/pkg_resources.py", line 1207,
in run_script<br>
File
"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/EGG-INFO/scripts/esgunpublish",
line
221, in <module><br>
main(sys.argv[1:])<br>
File
"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/EGG-INFO/scripts/esgunpublish",
line
184, in main<br>
result =
deleteDatasetList(datasetNames, Session, gatewayOp, thredds,
las,
deleteDset, deleteAll=deleteAll, republish=republish)<br>
File
"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/esgcet/publish/unpublish.py",
line
272, in deleteDatasetList<br>
result = reinitializeThredds()
</tt></p>
<p style="margin-bottom: 0cm;"><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<br>
raise ESGPublishError("Error
reinitializing the THREDDS Data Server: Fatal error:
%s\n%s"%(errorMessage, str(result)))<br>
esgcet.exceptions.ESGPublishError:
Error reinitializing the THREDDS Data Server: Fatal error:
**Fatal: InvCatalogFactory.readXML failed<br>
Catalog init catalog.xml
</tt></p>
<p style="margin-bottom: 0cm;"><tt>[2012-01-03T03:05:33GMT]
</tt></p>
<p style="margin-bottom: 0cm;"></p>
<p style="margin-bottom: 0cm;"><tt><font color="#000080"><i>[root@esgnode1
tmp]#
esgunpublish --database-delete
cmip5.output1.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAnt.mon.atmos.Amon.r1i1p1
</i></font></tt></p>
<p style="margin-bottom: 0cm;"><tt>INFO 2012-01-03 14:19:12,597
Deleting
cmip5.output1.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAnt.mon.atmos.Amon.r1i1p1
</tt></p>
<p style="margin-bottom: 0cm;"><tt>WARNING 2012-01-03 14:19:12,778
Deletion/retraction failed for dataset
cmip5.output1.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAnt.mon.atmos.Amon.r1i1p1
with
message: Java ServiceException: The persistent
identifier=cmip5.output1.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAnt.mon.atmos.Amon.r1i1p1
does
not correspond to a dataset at
sgf.gateway.service.security.impl.acegi.AcegiCatalogAccessDecisionVoter.vote(AcegiCatalogAccessDecisionVoter.java:74)<br>
INFO 2012-01-03 14:19:12,822 Result: UNSUCCESSFUL<br>
INFO 2012-01-03 14:19:12,864
Writing THREDDS ESG master catalog
/data/esg-node/tds-content/thredds/esgcet/catalog.xml<br>
INFO 2012-01-03 14:19:13,395
Reinitializing THREDDS server
</tt></p>
<tt>Traceback (most recent call last):<br>
File "/usr/local/cdat/bin/esgunpublish", line 5, in
<module><br>
pkg_resources.run_script('esgcet==2.8.4', 'esgunpublish')<br>
File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 489,
in run_script<br>
File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 1207,
in run_script<br>
File
"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/EGG-INFO/scripts/esgunpublish",
line 221, in <module><br>
main(sys.argv[1:])<br>
File
"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/EGG-INFO/scripts/esgunpublish",
line 184, in main<br>
result = deleteDatasetList(datasetNames, Session, gatewayOp,
thredds, las, deleteDset, deleteAll=deleteAll,
republish=republish)<br>
File
"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/esgcet/publish/unpublish.py",
line 272, in deleteDatasetList<br>
result = reinitializeThredds()<br>
File
"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/esgcet/publish/thredds.py",
line 1041, in reinitializeThredds<br>
raise ESGPublishError("Error reinitializing the THREDDS Data
Server: Fatal error: %s\n%s"%(errorMessage, str(result)))<br>
esgcet.exceptions.ESGPublishError: Error reinitializing the
THREDDS Data Server: Fatal error: **Fatal:
InvCatalogFactory.readXML failed<br>
Catalog init catalog.xml<br>
[2012-01-03T04:19:34GMT]</tt><br>
<br>
<br>
In short, if I delete output1 and output2 of the dataset, they are
not completely removed from the database; e.g.<br>
<tt>[root@esgnode1 esgcet]# esglist_datasets cmip5 | grep
".historicalAnt.mon.atmos.Amon.r1i1p1"<br>
| 3296 |
cmip5.output1.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAnt.mon.atmos.Amon.r1i1p1
| cmip5 | CSIRO-Mk3-6-0 | historicalAnt | r1i1p1 | False
| None | output1 | mon | atmos |
Amon | r1i1p1 | CSIRO-QCCCE | 2012-01-03 15:23:09 |
DELETE_DATASET_FAILED | cmip5.output1.CSIRO-QCCCE.CSIRO-Mk3-6-0
| 20111221 |
cmip5.output1.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAnt.mon.atmos.Amon.r1i1p1.v20111221
| None |<br>
| 4093 |
cmip5.output2.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAnt.mon.atmos.Amon.r1i1p1
| cmip5 | CSIRO-Mk3-6-0 | historicalAnt | r1i1p1 | False
| None | output2 | mon | atmos |
Amon | r1i1p1 | CSIRO-QCCCE | 2012-01-03 15:28:35 |
DELETE_DATASET_FAILED | cmip5.output2.CSIRO-QCCCE.CSIRO-Mk3-6-0
| 20111221 |
cmip5.output2.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAnt.mon.atmos.Amon.r1i1p1.v20111221
| None |<br>
</tt><br>
<br>
<b>If we try to publish the data, we get the following error:</b><br>
<br>
<br>
<tt>INFO 2011-12-29 22:56:49,305 Publishing:
cmip5.output1.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAnt.mon.atmos.Amon.r1i1p1,
parent = cmip5.output1.CSIRO-QCCCE.CSIRO-Mk3-6-0<br>
INFO 2011-12-29 22:56:49,738 Result: PROCESSING<br>
INFO 2011-12-29 22:56:52,817 Result: UNSUCCESSFUL<br>
WARNING 2011-12-29 22:56:52,995 Publication failed for dataset
cmip5.output1.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAnt.mon.atmos.Amon.r1i1p1
with message: Publishing operation description. THREDDS catalog:
<a class="moz-txt-link-freetext" href="http://esgnode1.nci.org.au/thredds/esgcet/8/cmip5.output1.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAnt.mon.atmos.Amon.r1i1p1.v20111221.xml">http://esgnode1.nci.org.au/thredds/esgcet/8/cmip5.output1.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAnt.mon.atmos.Amon.r1i1p1.v20111221.xml</a><br>
Overwrite mode: ALWAYS_UPDATE<br>
Completed.<br>
<br>
Publishing task description. THREDDS catalog:
<a class="moz-txt-link-freetext" href="http://esgnode1.nci.org.au/thredds/esgcet/8/cmip5.output1.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAnt.mon.atmos.Amon.r1i1p1.v20111221.xml">http://esgnode1.nci.org.au/thredds/esgcet/8/cmip5.output1.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAnt.mon.atmos.Amon.r1i1p1.v20111221.xml</a><br>
Parent: CSIRO-Mk3-6-0 model CMIP5 output1 data<br>
Overwrite mode: ALWAYS_UPDATE<br>
org.springframework.dao.DataIntegrityViolationException: Could
not execute JDBC batch update; SQL [insert into
metadata.file_access_point (version, path, full_access_url,
data_access_capability_id, logical_file_id, file_name,
storage_type_id, id) values (?, ?, ?, ?, ?, ?, ?, ?)]; constraint
[null]; nested exception is
org.hibernate.exception.ConstraintViolationException: Could not
execute JDBC batch update<br>
at
org.springframework.orm.hibernate3.SessionFactoryUtils.convertHibernateAccessException(SessionFactoryUtils.java:637)<br>
at
org.springframework.orm.hibernate3.HibernateTransactionManager.convertHibernateAccessException(HibernateTransactionManager.java:793)<br>
at
org.springframework.orm.hibernate3.HibernateTransactionManager.doCommit(HibernateTransactionManager.java:664)<br>
at
org.springframework.transaction.support.AbstractPlatformTransactionManager.processCommit(AbstractPlatformTransactionManager.java:754)<br>
at
org.springframework.transaction.support.AbstractPlatformTransactionManager.commit(AbstractPlatformTransactionManager.java:723)<br>
at
org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:147)<br>
at
sgf.gateway.metadata.ingestor.impl.TransactionalMetadataIngestorImpl.ingest(TransactionalMetadataIngestorImpl.java:66)<br>
at
sgf.gateway.metadata.complete.thredds.PublishingTaskImpl.handleExecuteInternal(PublishingTaskImpl.java:137)<br>
at
sgf.gateway.metadata.complete.AbstractPublishingTask.execute(AbstractPublishingTask.java:60)<br>
at
sgf.gateway.metadata.complete.service.impl.PublishingOperationExectionServiceImpl$CallableTaskWrapper.call(PublishingOperationExectionServiceImpl.java:75)<br>
at
sgf.gateway.metadata.complete.service.impl.PublishingOperationExectionServiceImpl$CallableTaskWrapper.call(PublishingOperationExectionServiceImpl.java:54)<br>
at
java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)<br>
at
java.util.concurrent.FutureTask.run(FutureTask.java:166)<br>
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)<br>
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)<br>
at java.lang.Thread.run(Thread.java:636)<br>
Caused by: org.hibernate.exception.ConstraintViolationException:
Could not execute JDBC batch update<br>
at
org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:94)<br>
at
org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:66)<br>
at
org.hibernate.jdbc.AbstractBatcher.executeBatch(AbstractBatcher.java:275)<br>
at
org.hibernate.jdbc.AbstractBatcher.prepareStatement(AbstractBatcher.java:114)<br>
at
org.hibernate.jdbc.AbstractBatcher.prepareStatement(AbstractBatcher.java:109)<br>
at
org.hibernate.jdbc.AbstractBatcher.prepareBatchStatement(AbstractBatcher.java:244)<br>
at
org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2252)<br>
at
org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2688)<br>
at
org.hibernate.action.EntityInsertAction.execute(EntityInsertAction.java:79)<br>
at
org.hibernate.engine.ActionQueue.execute(ActionQueue.java:279)<br>
at
org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:263)<br>
at
org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:167)<br>
at
org.hibernate.event.def.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:321)<br>
at
org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:50)<br>
at
org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1027)<br>
at
org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java:365)<br>
at
org.hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java:137)<br>
at
org.springframework.orm.hibernate3.HibernateTransactionManager.doCommit(HibernateTransactionManager.java:656)<br>
... 13 more<br>
Caused by: java.sql.BatchUpdateException: Batch entry 0 insert
into metadata.file_access_point (version, path, full_access_url,
data_access_capability_id, logical_file_id, file_name,
storage_type_id, id) values (0,
/cmip5/output/CSIRO-QCCCE/CSIRO-Mk3-6-0/historicalAnt/mon/atmos/Amon/r1i1p1/v20110518/cl/,
gsiftp://esgnode1.nci.org.au:2812//cmip5/output/CSIRO-QCCCE/CSIRO-Mk3-6-0/historicalAnt/mon/atmos/Amon/r1i1p1/v20110518/cl/cl_Amon_CSIRO-Mk3-6-0_historicalAnt_r1i1p1_185001-186912.nc,
a1c5b092-59cd-11e0-8e0a-00c0f03d5b7c,
315871ae-3214-11e1-b652-00c0f03d5b7c,
cl_Amon_CSIRO-Mk3-6-0_historicalAnt_r1i1p1_185001-186912.nc, 0,
f0ccdc7c-11d9-444a-b749-76167dece157) was aborted. Call
getNextException to see the cause.<br>
at
org.postgresql.jdbc2.AbstractJdbc2Statement$BatchResultHandler.handleError(AbstractJdbc2Statement.java:2537)<br>
at
org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1328)<br>
at
org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:351)<br>
at
org.postgresql.jdbc2.AbstractJdbc2Statement.executeBatch(AbstractJdbc2Statement.java:2674)<br>
at
org.apache.commons.dbcp.DelegatingStatement.executeBatch(DelegatingStatement.java:297)<br>
at
org.apache.commons.dbcp.DelegatingStatement.executeBatch(DelegatingStatement.java:297)<br>
at
org.hibernate.jdbc.BatchingBatcher.doExecuteBatch(BatchingBatcher.java:70)<br>
at
org.hibernate.jdbc.AbstractBatcher.executeBatch(AbstractBatcher.java:268)<br>
... 28 more<br>
</tt><br>
Any pointers/help is welcome. I can provide the logs if these are
cryptic. <br>
<br>
Regards,<br>
<br>
<br>
<pre class="moz-signature" cols="72">--
Muhammad Atif
ANU Supercomputer Facility NCI National Facility
Leonard Huxley, Mills Road Room 318, Bldg # 56
Australian National University Ph: +61 2 6125 5031
Canberra, ACT 0200, Australia M: 0430 393863
CRICOS Provider #00120C <a class="moz-txt-link-freetext" href="http://anusf.anu.edu.au">http://anusf.anu.edu.au</a></pre>
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