Ticket #615 (closed defect: wontfix)

Opened 1 year ago

Last modified 6 months ago

when ingest fails due to bibtex validation (non-integer year and issue in reference), mulgara throws another error about rollback

Reported by: russ Assigned to: ronald
Priority: medium Milestone:
Component: topaz-mulgara Version: 0.8
Keywords: ingest Cc:
Blocking: Blocked By:

Description

i tried to ingest pctr.0010005.

mulgara doesn't like the references and fails accordingly 

2007-08-27 18:24:41,964 WARN  ItqlInterpreter> Failed to insert statements into local:///topazproject#filter:model=ri [http-9091-Processor25 org.mulgara.itql.ItqlInterpreter]
org.mulgara.query.QueryException: Failed to suspend transaction at end of operation
...
Caused by: java.lang.NumberFormatException: For input string: "93 (Supplement 1)"

then mulgara fails to rollback: 

2007-08-27 18:31:48,124 FATAL ItqlInterpreter> Failed to delete statements [http-9091-Processor22 org.mulgara.itql.ItqlInterpreter]
java.lang.IllegalStateException: Transaction already failed, set autocommit true to reset
2007-08-27 18:31:48,307 WARN  ItqlInterpreter> Failed to delete statements from local:///topazproject#filter:model=ri [http-9091-Processor25 org.mulgara.itql.ItqlInterpreter]
org.mulgara.query.QueryException: Cannot use variables when deleting statements

an itql query confirms that there is leftover data in mulgara 

itql> select $p $o from <local:///topazproject#ri> where <info:doi/10.1371/journal.pctr.0010005> $p $o;
p                                                 o
------------------------------------------------- ---------------------------------------------------
http://www.w3.org/1999/02/22-rdf-syntax-ns#type   http://rdf.topazproject.org/RDF/Article
http://rdf.topazproject.org/RDF/hasCategory       info:doi/10.1371/journal.pctr.0010005/category/2
http://rdf.topazproject.org/RDF/hasCategory       info:doi/10.1371/journal.pctr.0010005/category/4
http://rdf.topazproject.org/RDF/hasCategory       info:doi/10.1371/journal.pctr.0010005/category/3
http://rdf.topazproject.org/RDF/hasCategory       info:doi/10.1371/journal.pctr.0010005/category/1
http://rdf.topazproject.org/RDF/hasCategory       info:doi/10.1371/journal.pctr.0010005/category/5
http://purl.org/dc/elements/1.1/subject           Public Health and Epidemiology
http://purl.org/dc/elements/1.1/subject           Infectious Diseases
http://purl.org/dc/elements/1.1/subject           Immunology
http://purl.org/dc/elements/1.1/subject           Microbiology/Parasitology
http://purl.org/dc/elements/1.1/subject           Virology/Vaccines
http://rdf.topazproject.org/RDF/PDF-contentType   application/pdf
http://purl.org/dc/elements/1.1/description       <sec id="st1"><title>Objective</title><p>The can...
http://purl.org/dc/elements/1.1/language          en
http://rdf.topazproject.org/RDF/XML-contentType   text/xml
http://purl.org/dc/elements/1.1/creator           Joe Cohen
http://purl.org/dc/elements/1.1/creator           Pedro L Alonso
http://purl.org/dc/elements/1.1/creator           Brian Greenwood
http://purl.org/dc/elements/1.1/creator           Filip Dubovsky
http://purl.org/dc/elements/1.1/creator           Diana Quelhas
http://purl.org/dc/elements/1.1/creator           Jahit Sacarlal
http://purl.org/dc/elements/1.1/creator           W. Ripley Ballou
http://purl.org/dc/elements/1.1/creator           John J Aponte
http://purl.org/dc/elements/1.1/creator           Carlota Dobaño
http://purl.org/dc/elements/1.1/creator           Marc Lievens
http://purl.org/dc/elements/1.1/creator           Amanda Leach
http://purl.org/dc/elements/1.1/creator           Colin J Sutherland
http://purl.org/dc/elements/1.1/creator           David J Conway
http://purl.org/dc/elements/1.1/creator           Jessica Milman
http://purl.org/dc/elements/1.1/creator           Ricardo Thompson
http://purl.org/dc/elements/1.1/creator           Sonia Enosse
http://purl.org/dc/elements/1.1/type              http://purl.org/dc/dcmitype/Text
http://rdf.topazproject.org/RDF/PDF-objectSize    741592
http://rdf.topazproject.org/RDF/isPID             doi:10.1371%2Fjournal.pctr.0010005
http://rdf.topazproject.org/RDF/hasRepresentation PDF
http://rdf.topazproject.org/RDF/hasRepresentation XML
http://purl.org/dc/elements/1.1/title             RTS,S/AS02A Malaria Vaccine Does Not Induce Para...
http://purl.org/dc/elements/1.1/date              2006-05-19
http://rdf.topazproject.org/RDF/articleState      1
http://purl.org/dc/elements/1.1/publisher         Public Library of Science
http://purl.org/dc/elements/1.1/identifier        info:doi/10.1371/journal.pctr.0010005
http://purl.org/dc/terms/available                2006-05-19
http://purl.org/dc/terms/hasPart                  info:doi/10.1371/journal.pctr.0010005.t002
http://purl.org/dc/terms/hasPart                  info:doi/10.1371/journal.pctr.0010005.g004
http://purl.org/dc/terms/hasPart                  info:doi/10.1371/journal.pctr.0010005.g001
http://purl.org/dc/terms/hasPart                  info:doi/10.1371/journal.pctr.0010005.sd001
http://purl.org/dc/terms/hasPart                  info:doi/10.1371/journal.pctr.0010005.g003
http://purl.org/dc/terms/hasPart                  info:doi/10.1371/journal.pctr.0010005.sd002
http://purl.org/dc/terms/hasPart                  info:doi/10.1371/journal.pctr.0010005.t001
http://purl.org/dc/terms/hasPart                  info:doi/10.1371/journal.pctr.0010005.g002
http://purl.org/dc/terms/issued                   2006-05-19
http://purl.org/dc/terms/dateSubmitted            2005-12-20
http://purl.org/dc/elements/1.1/rights            Enosse et al. This is an open-access article dis...
http://purl.org/dc/terms/dateAccepted             2006-03-30
http://rdf.topazproject.org/RDF/XML-objectSize    91915
http://purl.org/dc/elements/1.1/format            text/xml
http://rdf.topazproject.org/RDF/nextObject        info:doi/10.1371/journal.pctr.0010005.g001

Dependency Graph

Change History

08/27/07 18:37:42 changed by russ

  • priority changed from high to medium.

hmm.

i deleted the pctr.0010005 from the itql interpreter, reingested, and - although i got the same set of errors in mulgara - there weren't leftovers in mulgara.

so perhaps these leftovers were from a previous bad ingest.

ahh, i see lots of leftovers in mulgara. i will delete them all. lowering priority.

08/27/07 21:57:36 changed by amit

  • owner changed from ronald to russ.
  • milestone set to 0.8.

Please confirm and let us know.

08/28/07 09:59:33 changed by russ

  • status changed from new to assigned.

we're still getting the 'Failed to delete statements' on bibtex related ingest failures.

however, we're not seeing leftovers in mulgara - those were due to database problems.

i'll test again after upgrading to the newest rpms. keeping for now.

08/28/07 15:13:03 changed by russ

  • owner changed from russ to ronald.
  • status changed from assigned to new.

confirmed that this error is still happening in 3575 with a clean database.

but just the errors! there are no mulgara leftovers. there are to fedora leftovers.

09/01/07 22:20:21 changed by ronald

  • status changed from new to closed.
  • resolution set to wontfix.

The rollback is actually succeeding - it's just the way we attempt to clean up that leads to the slightly alarming warnings in the mulgara log. However, these can be basically ignored for now.

I'm going to close this because when we finally switch to mulgara 1.1 things will be different due to a complete rewrite of the transaction stuff there, and since it's actually working properly now (modulo the log messages) I therefore don't think it's worth spending time on.

09/04/07 10:29:02 changed by russ

sounds good. thank you.

07/16/08 11:00:34 changed by

  • milestone deleted.

Milestone 0.8 deleted