[Go-essp-tech] unable to unpublish and publish the datasets @ NCI gateway
Muhammad Atif
muhammad.atif at anu.edu.au
Mon Jan 2 21:30:29 MST 2012
Hi,
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 :(
There are two distinct issues, I am starting one email thread for each.
While trying to publish new version of the dataset, we decided to remove
the previous version from the gateway completely.
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".
Following is an example of one such case. The same happens if we try to
unpublish output2 part of it.
*cmip5.output1.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAnt.mon.atmos.Amon.r1i1p1
*
/[root at esgnode1 tmp]# esgunpublish --skip-thredds
cmip5.output1.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAnt.mon.atmos.Amon.r1i1p1
/
INFO 2012-01-03 13:58:09,122 Deleting
cmip5.output1.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAnt.mon.atmos.Amon.r1i1p1
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)
INFO 2012-01-03 13:58:09,443 Result: UNSUCCESSFUL
/[root at esgnode1 tmp]# esgunpublish --skip-thredds
cmip5.output1.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAnt.mon.atmos.Amon.r1i1p1
/
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
INFO 2012-01-03 14:05:29,663 Writing THREDDS ESG master catalog
/data/esg-node/tds-content/thredds/esgcet/catalog.xml
INFO 2012-01-03 14:05:31,133 Reinitializing THREDDS server
Traceback (most recent call last):
File "/usr/local/cdat/bin/esgunpublish", line 5, in <module>
pkg_resources.run_script('esgcet==2.8.4', 'esgunpublish')
File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 489, in
run_script
File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 1207, in
run_script
File
"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/EGG-INFO/scripts/esgunpublish",
line 221, in <module>
main(sys.argv[1:])
File
"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/EGG-INFO/scripts/esgunpublish",
line 184, in main
result = deleteDatasetList(datasetNames, Session, gatewayOp, thredds,
las, deleteDset, deleteAll=deleteAll, republish=republish)
File
"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/esgcet/publish/unpublish.py",
line 272, in deleteDatasetList
result = reinitializeThredds()
File
"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/esgcet/publish/thredds.py",
line 1041, in reinitializeThredds
raise ESGPublishError("Error reinitializing the THREDDS Data Server:
Fatal error: %s\n%s"%(errorMessage, str(result)))
esgcet.exceptions.ESGPublishError: Error reinitializing the THREDDS Data
Server: Fatal error: **Fatal: InvCatalogFactory.readXML failed
Catalog init catalog.xml
[2012-01-03T03:05:33GMT]
/[root at esgnode1 tmp]# esgunpublish --database-delete
cmip5.output1.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAnt.mon.atmos.Amon.r1i1p1
/
INFO 2012-01-03 14:19:12,597 Deleting
cmip5.output1.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAnt.mon.atmos.Amon.r1i1p1
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)
INFO 2012-01-03 14:19:12,822 Result: UNSUCCESSFUL
INFO 2012-01-03 14:19:12,864 Writing THREDDS ESG master catalog
/data/esg-node/tds-content/thredds/esgcet/catalog.xml
INFO 2012-01-03 14:19:13,395 Reinitializing THREDDS server
Traceback (most recent call last):
File "/usr/local/cdat/bin/esgunpublish", line 5, in <module>
pkg_resources.run_script('esgcet==2.8.4', 'esgunpublish')
File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 489, in
run_script
File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 1207, in
run_script
File
"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/EGG-INFO/scripts/esgunpublish",
line 221, in <module>
main(sys.argv[1:])
File
"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/EGG-INFO/scripts/esgunpublish",
line 184, in main
result = deleteDatasetList(datasetNames, Session, gatewayOp,
thredds, las, deleteDset, deleteAll=deleteAll, republish=republish)
File
"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/esgcet/publish/unpublish.py",
line 272, in deleteDatasetList
result = reinitializeThredds()
File
"/usr/local/cdat/lib/python2.6/site-packages/esgcet-2.8.4-py2.6.egg/esgcet/publish/thredds.py",
line 1041, in reinitializeThredds
raise ESGPublishError("Error reinitializing the THREDDS Data
Server: Fatal error: %s\n%s"%(errorMessage, str(result)))
esgcet.exceptions.ESGPublishError: Error reinitializing the THREDDS Data
Server: Fatal error: **Fatal: InvCatalogFactory.readXML failed
Catalog init catalog.xml
[2012-01-03T04:19:34GMT]
In short, if I delete output1 and output2 of the dataset, they are not
completely removed from the database; e.g.
[root at esgnode1 esgcet]# esglist_datasets cmip5 | grep
".historicalAnt.mon.atmos.Amon.r1i1p1"
| 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 |
| 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 |
*If we try to publish the data, we get the following error:*
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
INFO 2011-12-29 22:56:49,738 Result: PROCESSING
INFO 2011-12-29 22:56:52,817 Result: UNSUCCESSFUL
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:
http://esgnode1.nci.org.au/thredds/esgcet/8/cmip5.output1.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAnt.mon.atmos.Amon.r1i1p1.v20111221.xml
Overwrite mode: ALWAYS_UPDATE
Completed.
Publishing task description. THREDDS catalog:
http://esgnode1.nci.org.au/thredds/esgcet/8/cmip5.output1.CSIRO-QCCCE.CSIRO-Mk3-6-0.historicalAnt.mon.atmos.Amon.r1i1p1.v20111221.xml
Parent: CSIRO-Mk3-6-0 model CMIP5 output1 data
Overwrite mode: ALWAYS_UPDATE
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
at
org.springframework.orm.hibernate3.SessionFactoryUtils.convertHibernateAccessException(SessionFactoryUtils.java:637)
at
org.springframework.orm.hibernate3.HibernateTransactionManager.convertHibernateAccessException(HibernateTransactionManager.java:793)
at
org.springframework.orm.hibernate3.HibernateTransactionManager.doCommit(HibernateTransactionManager.java:664)
at
org.springframework.transaction.support.AbstractPlatformTransactionManager.processCommit(AbstractPlatformTransactionManager.java:754)
at
org.springframework.transaction.support.AbstractPlatformTransactionManager.commit(AbstractPlatformTransactionManager.java:723)
at
org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:147)
at
sgf.gateway.metadata.ingestor.impl.TransactionalMetadataIngestorImpl.ingest(TransactionalMetadataIngestorImpl.java:66)
at
sgf.gateway.metadata.complete.thredds.PublishingTaskImpl.handleExecuteInternal(PublishingTaskImpl.java:137)
at
sgf.gateway.metadata.complete.AbstractPublishingTask.execute(AbstractPublishingTask.java:60)
at
sgf.gateway.metadata.complete.service.impl.PublishingOperationExectionServiceImpl$CallableTaskWrapper.call(PublishingOperationExectionServiceImpl.java:75)
at
sgf.gateway.metadata.complete.service.impl.PublishingOperationExectionServiceImpl$CallableTaskWrapper.call(PublishingOperationExectionServiceImpl.java:54)
at
java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
at java.lang.Thread.run(Thread.java:636)
Caused by: org.hibernate.exception.ConstraintViolationException: Could
not execute JDBC batch update
at
org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:94)
at
org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:66)
at
org.hibernate.jdbc.AbstractBatcher.executeBatch(AbstractBatcher.java:275)
at
org.hibernate.jdbc.AbstractBatcher.prepareStatement(AbstractBatcher.java:114)
at
org.hibernate.jdbc.AbstractBatcher.prepareStatement(AbstractBatcher.java:109)
at
org.hibernate.jdbc.AbstractBatcher.prepareBatchStatement(AbstractBatcher.java:244)
at
org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2252)
at
org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2688)
at
org.hibernate.action.EntityInsertAction.execute(EntityInsertAction.java:79)
at org.hibernate.engine.ActionQueue.execute(ActionQueue.java:279)
at
org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:263)
at
org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:167)
at
org.hibernate.event.def.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:321)
at
org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:50)
at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1027)
at
org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java:365)
at
org.hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java:137)
at
org.springframework.orm.hibernate3.HibernateTransactionManager.doCommit(HibernateTransactionManager.java:656)
... 13 more
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.
at
org.postgresql.jdbc2.AbstractJdbc2Statement$BatchResultHandler.handleError(AbstractJdbc2Statement.java:2537)
at
org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1328)
at
org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:351)
at
org.postgresql.jdbc2.AbstractJdbc2Statement.executeBatch(AbstractJdbc2Statement.java:2674)
at
org.apache.commons.dbcp.DelegatingStatement.executeBatch(DelegatingStatement.java:297)
at
org.apache.commons.dbcp.DelegatingStatement.executeBatch(DelegatingStatement.java:297)
at
org.hibernate.jdbc.BatchingBatcher.doExecuteBatch(BatchingBatcher.java:70)
at
org.hibernate.jdbc.AbstractBatcher.executeBatch(AbstractBatcher.java:268)
... 28 more
Any pointers/help is welcome. I can provide the logs if these are cryptic.
Regards,
--
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 http://anusf.anu.edu.au
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