Ticket #1108 (closed defect: fixed)

Opened 18 months ago

Last modified 10 months ago

promoted a note to a formal correction and the body was eaten

Reported by: russ Owned by: dragisak
Priority: critical Milestone: 0.9.5_rc1
Component: ambra Version: 0.9.1_rc1
Keywords: annotation correction Cc:

Description

susanne created a note on pone.0004369

later (more than 24h later) she flagged the note.

she then went in adminTop.action and converted the note into a formal correction

after converting the note, the note no longer had a body. it shows up as "null".

i confirmed that there is no body triple in mulgara for the note.

from the mulgara.tx.log, it's clear that when the note was deleted and recreated as part of the conversion process, the body triple was deleted and then not inserted.

there are no errors in ambra.log.

the same bug occurred on another formal correction.

i've been unable to reproduce this on a single box install - maybe it requires a multi-server?

Attachments

createElevate.jmx (37.3 KB) - added by russ 10 months ago.
jMeter script to programatically create, flag, and elevate notes

Change History

  Changed 18 months ago by russ

mulgara.tx.log:

c921dfce-9702-4632-abbe-f13d62fdfde0 is the formal correction. i assume that 8cd302fb-c7bd-4dd0-b83c-89fbe15b7e3c is the flag. 

2009-02-10/mulgara.tx.log.1:1578:delete <info:doi/10.1371/annotation/c921dfce-9702-4632-abbe-f13d62fdfde0> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2000/10/annotation-ns#Annotation> <info:doi/10.1371/annotation/c921dfce-9702-4632-abbe-f13d62fdfde0> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2000/10/annotationType#Comment> <info:doi/10.1371/annotation/c921dfce-9702-4632-abbe-f13d62fdfde0> <http://purl.org/dc/elements/1.1/creator> 'info:doi/10.1371/account/38098' <info:doi/10.1371/annotation/c921dfce-9702-4632-abbe-f13d62fdfde0> <http://purl.org/dc/elements/1.1/title> 'Correction to Article Title and Citation' <info:doi/10.1371/annotation/c921dfce-9702-4632-abbe-f13d62fdfde0> <http://purl.org/dc/terms/mediator> 'topaz-ambra' <info:doi/10.1371/annotation/c921dfce-9702-4632-abbe-f13d62fdfde0> <http://rdf.topazproject.org/RDF/state> '0'^^<http://www.w3.org/2001/XMLSchema#int> <info:doi/10.1371/annotation/c921dfce-9702-4632-abbe-f13d62fdfde0> <http://www.w3.org/2000/10/annotation-ns#annotates> <info:doi/10.1371/journal.pone.0004369> <info:doi/10.1371/annotation/c921dfce-9702-4632-abbe-f13d62fdfde0> <http://www.w3.org/2000/10/annotation-ns#body> <info:fedora/PLoS:4983> <info:doi/10.1371/annotation/c921dfce-9702-4632-abbe-f13d62fdfde0> <http://www.w3.org/2000/10/annotation-ns#context> 'info:doi/10.1371/journal.pone.0004369#xpointer(string-range%28%2Farticle%5B1%5D%2Ffront%5B1%5D%2Farticle-meta%5B1%5D%2Fabstract%5B1%5D%2Fp%5B1%5D%2C+%27%27%2C+1%2C+95%29%5B1%5D)' <info:doi/10.1371/annotation/c921dfce-9702-4632-abbe-f13d62fdfde0> <http://www.w3.org/2000/10/annotation-ns#created> '2009-02-07T00:48:14.408Z'^^<http://www.w3.org/2001/XMLSchema#dateTime> from <local:///topazproject#filter:graph=ri>;
2009-02-10/mulgara.tx.log.1:1579:delete <info:doi/10.1371/annotation/8cd302fb-c7bd-4dd0-b83c-89fbe15b7e3c> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2000/10/annotation-ns#Annotation> <info:doi/10.1371/annotation/8cd302fb-c7bd-4dd0-b83c-89fbe15b7e3c> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2000/10/annotationType#Comment> <info:doi/10.1371/annotation/8cd302fb-c7bd-4dd0-b83c-89fbe15b7e3c> <http://purl.org/dc/elements/1.1/creator> 'info:doi/10.1371/account/38098' <info:doi/10.1371/annotation/8cd302fb-c7bd-4dd0-b83c-89fbe15b7e3c> <http://purl.org/dc/terms/mediator> 'topaz-ambra' <info:doi/10.1371/annotation/8cd302fb-c7bd-4dd0-b83c-89fbe15b7e3c> <http://rdf.topazproject.org/RDF/state> '0'^^<http://www.w3.org/2001/XMLSchema#int> <info:doi/10.1371/annotation/8cd302fb-c7bd-4dd0-b83c-89fbe15b7e3c> <http://www.w3.org/2000/10/annotation-ns#annotates> <info:doi/10.1371/annotation/c921dfce-9702-4632-abbe-f13d62fdfde0> <info:doi/10.1371/annotation/8cd302fb-c7bd-4dd0-b83c-89fbe15b7e3c> <http://www.w3.org/2000/10/annotation-ns#body> <info:fedora/PLoS:4984> <info:doi/10.1371/annotation/8cd302fb-c7bd-4dd0-b83c-89fbe15b7e3c> <http://www.w3.org/2000/10/annotation-ns#created> '2009-02-07T00:48:14.662Z'^^<http://www.w3.org/2001/XMLSchema#dateTime> from <local:///topazproject#filter:graph=ri>;
2009-02-10/mulgara.tx.log.1:1580:insert <info:doi/10.1371/annotation/c921dfce-9702-4632-abbe-f13d62fdfde0> <http://rdf.topazproject.org/RDF/state> '0'^^<http://www.w3.org/2001/XMLSchema#int> <info:doi/10.1371/annotation/c921dfce-9702-4632-abbe-f13d62fdfde0> <http://purl.org/dc/terms/mediator> 'topaz-ambra' <info:doi/10.1371/annotation/c921dfce-9702-4632-abbe-f13d62fdfde0> <http://www.w3.org/2000/10/annotation-ns#created> '2009-02-07T00:48:14.408Z'^^<http://www.w3.org/2001/XMLSchema#dateTime> <info:doi/10.1371/annotation/c921dfce-9702-4632-abbe-f13d62fdfde0> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://rdf.topazproject.org/RDF/2008/01/annotationType#FormalCorrection> <info:doi/10.1371/annotation/c921dfce-9702-4632-abbe-f13d62fdfde0> <http://www.w3.org/2000/10/annotation-ns#context> 'info:doi/10.1371/journal.pone.0004369#xpointer(string-range%28%2Farticle%5B1%5D%2Ffront%5B1%5D%2Farticle-meta%5B1%5D%2Fabstract%5B1%5D%2Fp%5B1%5D%2C+%27%27%2C+1%2C+95%29%5B1%5D)' <info:doi/10.1371/annotation/c921dfce-9702-4632-abbe-f13d62fdfde0> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2000/10/annotationType#Change> <info:doi/10.1371/annotation/c921dfce-9702-4632-abbe-f13d62fdfde0> <http://purl.org/dc/elements/1.1/title> 'Correction to Article Title and Citation' <info:doi/10.1371/annotation/c921dfce-9702-4632-abbe-f13d62fdfde0> <http://www.w3.org/2000/10/annotation-ns#annotates> <info:doi/10.1371/journal.pone.0004369> <info:doi/10.1371/annotation/c921dfce-9702-4632-abbe-f13d62fdfde0> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2000/10/annotation-ns#Annotation> <info:doi/10.1371/annotation/c921dfce-9702-4632-abbe-f13d62fdfde0> <http://purl.org/dc/elements/1.1/creator> 'info:doi/10.1371/account/38098' into <local:///topazproject#filter:graph=ri>;

  Changed 18 months ago by russ

ambra.log: 

2009-02-09 14:38:19,052 INFO  LoggingInterceptor(PLoSONE)> Finishing execution stack for action /admin/processFlags [TP-Processor15 com.opensymphony.xwork2.interceptor.LoggingInterceptor]
2009-02-09 14:38:19,052 WARN  Preparer(PLoSONE)> executing transaction with 0 enlisted resource [TP-Processor15 bitronix.tm.twopc.Preparer]
2009-02-09 14:38:19,053 INFO  DenyBiasedPEP(PLoSONE)> 'permit-admin' permits 'info:doi/10.1371/account/6662' to do 'admin:Guard' on 'dummy:dummy' [TP-Processor15 org.topazproject.ambra.xacml.DenyBiasedPEP]
2009-02-09 14:38:19,053 WARN  Preparer(PLoSONE)> executing transaction with 0 enlisted resource [TP-Processor15 bitronix.tm.twopc.Preparer]
2009-02-09 14:38:19,076 INFO  DenyBiasedPEP(PLoSONE)> 'permit-admin' permits 'info:doi/10.1371/account/6662' to do 'annotations:deleteAnnotation' on 'info:doi/10.1371/annotation/8cd302fb-c7bd-4dd0-b83c-89fbe15b7e3c' [TP-Processor15 org.topazproject.ambra.xacml.DenyBiasedPEP]
2009-02-09 14:38:19,078 INFO  DenyBiasedPEP(PLoSONE)> 'permit-admin' permits 'info:doi/10.1371/account/6662' to do 'permissions:cancelPropagatePermissions' on 'info:doi/10.1371/annotation/8cd302fb-c7bd-4dd0-b83c-89fbe15b7e3c' [TP-Processor15 org.topazproject.ambra.xacml.DenyBiasedPEP]
2009-02-09 14:38:19,157 INFO  DenyBiasedPEP(PLoSONE)> 'permit-admin' permits 'info:doi/10.1371/account/6662' to do 'permissions:cancelGrants' on 'info:doi/10.1371/annotation/8cd302fb-c7bd-4dd0-b83c-89fbe15b7e3c' [TP-Processor15 org.topazproject.ambra.xacml.DenyBiasedPEP]
2009-02-09 14:38:19,161 INFO  PermissionsService(PLoSONE)> permissions:cancelGrants succeeded for resource info:doi/10.1371/annotation/8cd302fb-c7bd-4dd0-b83c-89fbe15b7e3c
permissions:
[annotations:getAnnotationInfo]
principals:
[http://rdf.topazproject.org/RDF/permissions#all] [TP-Processor15 org.topazproject.ambra.permission.service.PermissionsService]
2009-02-09 14:38:19,161 INFO  DenyBiasedPEP(PLoSONE)> 'permit-admin' permits 'info:doi/10.1371/account/6662' to do 'permissions:cancelRevokes' on 'info:doi/10.1371/annotation/8cd302fb-c7bd-4dd0-b83c-89fbe15b7e3c' [TP-Processor15 org.topazproject.ambra.xacml.DenyBiasedPEP]
2009-02-09 14:38:19,165 INFO  PermissionsService(PLoSONE)> permissions:cancelRevokes succeeded for resource info:doi/10.1371/annotation/8cd302fb-c7bd-4dd0-b83c-89fbe15b7e3c
permissions:
[annotations:deleteAnnotation, annotations:supersede]
principals:
[http://rdf.topazproject.org/RDF/permissions#all] [TP-Processor15 org.topazproject.ambra.permission.service.PermissionsService]
2009-02-09 14:38:19,180 INFO  DenyBiasedPEP(PLoSONE)> 'permit-admin' permits 'info:doi/10.1371/account/6662' to do 'annotations:deleteAnnotation' on 'info:doi/10.1371/annotation/d3071951-327b-4560-a234-6af861192567' [TP-Processor15 org.topazproject.ambra.xacml.DenyBiasedPEP]
2009-02-09 14:38:19,183 INFO  DenyBiasedPEP(PLoSONE)> 'permit-admin' permits 'info:doi/10.1371/account/6662' to do 'permissions:cancelPropagatePermissions' on 'info:doi/10.1371/annotation/d3071951-327b-4560-a234-6af861192567' [TP-Processor15 org.topazproject.ambra.xacml.DenyBiasedPEP]
2009-02-09 14:38:19,257 INFO  DenyBiasedPEP(PLoSONE)> 'permit-admin' permits 'info:doi/10.1371/account/6662' to do 'permissions:cancelGrants' on 'info:doi/10.1371/annotation/d3071951-327b-4560-a234-6af861192567' [TP-Processor15 org.topazproject.ambra.xacml.DenyBiasedPEP]
2009-02-09 14:38:19,261 INFO  PermissionsService(PLoSONE)> permissions:cancelGrants succeeded for resource info:doi/10.1371/annotation/d3071951-327b-4560-a234-6af861192567
permissions:
[annotations:getAnnotationInfo]
principals:
[http://rdf.topazproject.org/RDF/permissions#all] [TP-Processor15 org.topazproject.ambra.permission.service.PermissionsService]
2009-02-09 14:38:19,261 INFO  DenyBiasedPEP(PLoSONE)> 'permit-admin' permits 'info:doi/10.1371/account/6662' to do 'permissions:cancelRevokes' on 'info:doi/10.1371/annotation/d3071951-327b-4560-a234-6af861192567' [TP-Processor15 org.topazproject.ambra.xacml.DenyBiasedPEP]
2009-02-09 14:38:19,264 INFO  PermissionsService(PLoSONE)> permissions:cancelRevokes succeeded for resource info:doi/10.1371/annotation/d3071951-327b-4560-a234-6af861192567
permissions:
[annotations:deleteAnnotation, annotations:supersede]
principals:
[http://rdf.topazproject.org/RDF/permissions#all] [TP-Processor15 org.topazproject.ambra.permission.service.PermissionsService]
2009-02-09 14:38:19,285 INFO  DenyBiasedPEP(PLoSONE)> 'permit-admin' permits 'info:doi/10.1371/account/6662' to do 'articles:readMetaData' on 'info:doi/10.1371/journal.pone.0004360' [TP-Processor15 org.topazproject.ambra.xacml.DenyBiasedPEP]
2009-02-09 14:38:19,285 INFO  DenyBiasedPEP(PLoSONE)> 'permit-admin' permits 'info:doi/10.1371/account/6662' to do 'articles:readMetaData' on 'info:doi/10.1371/journal.pone.0004363' [TP-Processor15 org.topazproject.ambra.xacml.DenyBiasedPEP]
2009-02-09 14:38:19,285 INFO  DenyBiasedPEP(PLoSONE)> 'permit-admin' permits 'info:doi/10.1371/account/6662' to do 'articles:readMetaData' on 'info:doi/10.1371/journal.pone.0004386' [TP-Processor15 org.topazproject.ambra.xacml.DenyBiasedPEP]
2009-02-09 14:38:19,285 INFO  DenyBiasedPEP(PLoSONE)> 'permit-admin' permits 'info:doi/10.1371/account/6662' to do 'articles:readMetaData' on 'info:doi/10.1371/journal.pone.0004400' [TP-Processor15 org.topazproject.ambra.xacml.DenyBiasedPEP]
2009-02-09 14:38:19,285 INFO  DenyBiasedPEP(PLoSONE)> 'permit-admin' permits 'info:doi/10.1371/account/6662' to do 'articles:readMetaData' on 'info:doi/10.1371/journal.pone.0004402' [TP-Processor15 org.topazproject.ambra.xacml.DenyBiasedPEP]
2009-02-09 14:38:19,286 INFO  DenyBiasedPEP(PLoSONE)> 'permit-admin' permits 'info:doi/10.1371/account/6662' to do 'articles:readMetaData' on 'info:doi/10.1371/journal.pone.0004415' [TP-Processor15 org.topazproject.ambra.xacml.DenyBiasedPEP]
2009-02-09 14:38:19,286 INFO  DenyBiasedPEP(PLoSONE)> 'permit-admin' permits 'info:doi/10.1371/account/6662' to do 'articles:readMetaData' on 'info:doi/10.1371/journal.pone.0004416' [TP-Processor15 org.topazproject.ambra.xacml.DenyBiasedPEP]
2009-02-09 14:38:19,286 INFO  DenyBiasedPEP(PLoSONE)> 'permit-admin' permits 'info:doi/10.1371/account/6662' to do 'articles:readMetaData' on 'info:doi/10.1371/journal.pone.0004419' [TP-Processor15 org.topazproject.ambra.xacml.DenyBiasedPEP]
2009-02-09 14:38:19,286 INFO  DenyBiasedPEP(PLoSONE)> 'permit-admin' permits 'info:doi/10.1371/account/6662' to do 'articles:readMetaData' on 'info:doi/10.1371/journal.pone.0004420' [TP-Processor15 org.topazproject.ambra.xacml.DenyBiasedPEP]
2009-02-09 14:38:19,286 INFO  DenyBiasedPEP(PLoSONE)> 'permit-admin' permits 'info:doi/10.1371/account/6662' to do 'articles:readMetaData' on 'info:doi/10.1371/journal.pone.0004421' [TP-Processor15 org.topazproject.ambra.xacml.DenyBiasedPEP]
2009-02-09 14:38:19,286 INFO  DenyBiasedPEP(PLoSONE)> 'permit-admin' permits 'info:doi/10.1371/account/6662' to do 'articles:readMetaData' on 'info:doi/10.1371/journal.pone.0004422' [TP-Processor15 org.topazproject.ambra.xacml.DenyBiasedPEP]
2009-02-09 14:38:19,286 INFO  DenyBiasedPEP(PLoSONE)> 'permit-admin' permits 'info:doi/10.1371/account/6662' to do 'articles:readMetaData' on 'info:doi/10.1371/journal.pone.0004423' [TP-Processor15 org.topazproject.ambra.xacml.DenyBiasedPEP]
2009-02-09 14:38:19,286 INFO  DenyBiasedPEP(PLoSONE)> 'permit-admin' permits 'info:doi/10.1371/account/6662' to do 'articles:readMetaData' on 'info:doi/10.1371/journal.pone.0004424' [TP-Processor15 org.topazproject.ambra.xacml.DenyBiasedPEP]
2009-02-09 14:38:19,286 INFO  DenyBiasedPEP(PLoSONE)> 'permit-admin' permits 'info:doi/10.1371/account/6662' to do 'articles:readMetaData' on 'info:doi/10.1371/journal.pone.0004426' [TP-Processor15 org.topazproject.ambra.xacml.DenyBiasedPEP]
2009-02-09 14:38:19,286 INFO  DenyBiasedPEP(PLoSONE)> 'permit-admin' permits 'info:doi/10.1371/account/6662' to do 'articles:readMetaData' on 'info:doi/10.1371/journal.pone.0004429' [TP-Processor15 org.topazproject.ambra.xacml.DenyBiasedPEP]
2009-02-09 14:38:19,389 INFO  DenyBiasedPEP(PLoSONE)> 'permit-admin' permits 'info:doi/10.1371/account/6662' to do 'annotations:getAnnotationInfo' on 'info:doi/10.1371/annotation/e737359a-0f3c-416b-ba10-560d54035a4d' [TP-Processor15 org.topazproject.ambra.xacml.DenyBiasedPEP]
2009-02-09 14:38:19,443 INFO  DenyBiasedPEP(PLoSONE)> 'permit-admin' permits 'info:doi/10.1371/account/6662' to do 'annotations:getAnnotationInfo' on 'info:doi/10.1371/annotation/40bc45cd-46d2-41ba-a0e2-6d454af5671a' [TP-Processor15 org.topazproject.ambra.xacml.DenyBiasedPEP]
2009-02-09 14:38:19,502 INFO  DenyBiasedPEP(PLoSONE)> 'permit-admin' permits 'info:doi/10.1371/account/6662' to do 'annotations:getAnnotationInfo' on 'info:doi/10.1371/annotation/9e6e6678-1ad2-4c6f-8ce0-7cd4e7a7a741' [TP-Processor15 org.topazproject.ambra.xacml.DenyBiasedPEP]
2009-02-09 14:38:23,017 INFO  LoggingInterceptor(PLoSONE)> Starting execution stack for action /admin/processFlags [TP-Processor15 com.opensymphony.xwork2.interceptor.LoggingInterceptor]
2009-02-09 14:38:23,017 INFO  TimerInterceptor(PLoSONE)> Executed action [/admin/processFlags!execute] took 3965 ms. [TP-Processor15 com.opensymphony.xwork2.interceptor.TimerInterceptor]

  Changed 18 months ago by russ

interestingly, the missing body blob still exists in fedora. 

./0206/16/48/PLoS_4983+BODY+BODY1.0

follow-up: ↓ 5   Changed 18 months ago by russ

this happened a second time on pone.4268

in this case, the mulgara.tx.log looks like the annotation was converted to a formal correction twice. 

2009-02-10/mulgara.tx.log.1:insert <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://www.w3.org/2000/10/annotation-ns#context> 'info:doi/10.1371/journal.pone.0004268#xpointer(string-range%28%2Farticle%5B1%5D%2Fbody%5B1%5D%2Fsec%5B1%5D%2Fp%5B6%5D%2C+%27%27%2C+692%2C+8%29%5B1%5D)' <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://www.w3.org/2000/10/annotation-ns#body> <info:fedora/PLoS:4994> <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://rdf.topazproject.org/RDF/state> '0'^^<http://www.w3.org/2001/XMLSchema#int> <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://www.w3.org/2000/10/annotation-ns#created> '2009-02-09T19:51:11.065Z'^^<http://www.w3.org/2001/XMLSchema#dateTime> <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://purl.org/dc/terms/mediator> 'topaz-ambra' <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2000/10/annotationType#Comment> <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://purl.org/dc/elements/1.1/creator> 'info:doi/10.1371/account/38098' <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://www.w3.org/2000/10/annotation-ns#annotates> <info:doi/10.1371/journal.pone.0004268> <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2000/10/annotation-ns#Annotation> <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://purl.org/dc/elements/1.1/title> 'Correction to Article Data' into <local:///topazproject#filter:graph=ri>;

2009-02-10/mulgara.tx.log.1:insert <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://rdf.topazproject.org/RDF/propagate-permissions-to> <info:fedora/PLoS:4994> into <local:///topazproject#filter:graph=pp>;
2009-02-10/mulgara.tx.log.1:insert <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <annotations:getAnnotationInfo> <http://rdf.topazproject.org/RDF/permissions#all> into <local:///topazproject#filter:graph=grants>;
2009-02-10/mulgara.tx.log.1:insert <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <annotations:supersede> <http://rdf.topazproject.org/RDF/permissions#all> <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <annotations:deleteAnnotation> <http://rdf.topazproject.org/RDF/permissions#all> into <local:///topazproject#filter:graph=revokes>;
2009-02-10/mulgara.tx.log.1:insert <info:doi/10.1371/annotation/9e6e6678-1ad2-4c6f-8ce0-7cd4e7a7a741> <http://www.w3.org/2000/10/annotation-ns#created> '2009-02-09T19:51:11.443Z'^^<http://www.w3.org/2001/XMLSchema#dateTime> <info:doi/10.1371/annotation/9e6e6678-1ad2-4c6f-8ce0-7cd4e7a7a741> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2000/10/annotation-ns#Annotation> <info:doi/10.1371/annotation/9e6e6678-1ad2-4c6f-8ce0-7cd4e7a7a741> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2000/10/annotationType#Comment> <info:doi/10.1371/annotation/9e6e6678-1ad2-4c6f-8ce0-7cd4e7a7a741> <http://www.w3.org/2000/10/annotation-ns#body> <info:fedora/PLoS:4995> <info:doi/10.1371/annotation/9e6e6678-1ad2-4c6f-8ce0-7cd4e7a7a741> <http://purl.org/dc/terms/mediator> 'topaz-ambra' <info:doi/10.1371/annotation/9e6e6678-1ad2-4c6f-8ce0-7cd4e7a7a741> <http://www.w3.org/2000/10/annotation-ns#annotates> <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <info:doi/10.1371/annotation/9e6e6678-1ad2-4c6f-8ce0-7cd4e7a7a741> <http://purl.org/dc/elements/1.1/creator> 'info:doi/10.1371/account/38098' <info:doi/10.1371/annotation/9e6e6678-1ad2-4c6f-8ce0-7cd4e7a7a741> <http://rdf.topazproject.org/RDF/state> '0'^^<http://www.w3.org/2001/XMLSchema#int> into <local:///topazproject#filter:graph=ri>;

2009-02-10/mulgara.tx.log.1:delete <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2000/10/annotation-ns#Annotation> <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2000/10/annotationType#Comment> <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://purl.org/dc/elements/1.1/creator> 'info:doi/10.1371/account/38098' <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://purl.org/dc/elements/1.1/title> 'Correction to Article Data' <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://purl.org/dc/terms/mediator> 'topaz-ambra' <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://rdf.topazproject.org/RDF/state> '0'^^<http://www.w3.org/2001/XMLSchema#int> <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://www.w3.org/2000/10/annotation-ns#annotates> <info:doi/10.1371/journal.pone.0004268> <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://www.w3.org/2000/10/annotation-ns#body> <info:fedora/PLoS:4994> <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://www.w3.org/2000/10/annotation-ns#context> 'info:doi/10.1371/journal.pone.0004268#xpointer(string-range%28%2Farticle%5B1%5D%2Fbody%5B1%5D%2Fsec%5B1%5D%2Fp%5B6%5D%2C+%27%27%2C+692%2C+8%29%5B1%5D)' <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://www.w3.org/2000/10/annotation-ns#created> '2009-02-09T19:51:11.065Z'^^<http://www.w3.org/2001/XMLSchema#dateTime> from <local:///topazproject#filter:graph=ri>;

2009-02-10/mulgara.tx.log.1:delete <info:doi/10.1371/annotation/9e6e6678-1ad2-4c6f-8ce0-7cd4e7a7a741> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2000/10/annotation-ns#Annotation> <info:doi/10.1371/annotation/9e6e6678-1ad2-4c6f-8ce0-7cd4e7a7a741> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2000/10/annotationType#Comment> <info:doi/10.1371/annotation/9e6e6678-1ad2-4c6f-8ce0-7cd4e7a7a741> <http://purl.org/dc/elements/1.1/creator> 'info:doi/10.1371/account/38098' <info:doi/10.1371/annotation/9e6e6678-1ad2-4c6f-8ce0-7cd4e7a7a741> <http://purl.org/dc/terms/mediator> 'topaz-ambra' <info:doi/10.1371/annotation/9e6e6678-1ad2-4c6f-8ce0-7cd4e7a7a741> <http://rdf.topazproject.org/RDF/state> '0'^^<http://www.w3.org/2001/XMLSchema#int> <info:doi/10.1371/annotation/9e6e6678-1ad2-4c6f-8ce0-7cd4e7a7a741> <http://www.w3.org/2000/10/annotation-ns#annotates> <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <info:doi/10.1371/annotation/9e6e6678-1ad2-4c6f-8ce0-7cd4e7a7a741> <http://www.w3.org/2000/10/annotation-ns#body> <info:fedora/PLoS:4995> <info:doi/10.1371/annotation/9e6e6678-1ad2-4c6f-8ce0-7cd4e7a7a741> <http://www.w3.org/2000/10/annotation-ns#created> '2009-02-09T19:51:11.443Z'^^<http://www.w3.org/2001/XMLSchema#dateTime> from <local:///topazproject#filter:graph=ri>;

2009-02-10/mulgara.tx.log.1:insert <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://www.w3.org/2000/10/annotation-ns#context> 'info:doi/10.1371/journal.pone.0004268#xpointer(string-range%28%2Farticle%5B1%5D%2Fbody%5B1%5D%2Fsec%5B1%5D%2Fp%5B6%5D%2C+%27%27%2C+692%2C+8%29%5B1%5D)' <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://rdf.topazproject.org/RDF/2008/01/annotationType#FormalCorrection> <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://rdf.topazproject.org/RDF/state> '0'^^<http://www.w3.org/2001/XMLSchema#int> <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://www.w3.org/2000/10/annotation-ns#created> '2009-02-09T19:51:11.065Z'^^<http://www.w3.org/2001/XMLSchema#dateTime> <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://purl.org/dc/terms/mediator> 'topaz-ambra' <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://purl.org/dc/elements/1.1/creator> 'info:doi/10.1371/account/38098' <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://www.w3.org/2000/10/annotation-ns#annotates> <info:doi/10.1371/journal.pone.0004268> <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2000/10/annotation-ns#Annotation> <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2000/10/annotationType#Change> <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://purl.org/dc/elements/1.1/title> 'Correction to Article Data' into <local:///topazproject#filter:graph=ri>;
[web@ploskow01 tmp]$ grep -n 8f64f0c8-6767-4701-8ded-7f937d953cb6 2009-02-10/*

2009-02-10/mulgara.tx.log.1:1431:insert <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://www.w3.org/2000/10/annotation-ns#context> 'info:doi/10.1371/journal.pone.0004268#xpointer(string-range%28%2Farticle%5B1%5D%2Fbody%5B1%5D%2Fsec%5B1%5D%2Fp%5B6%5D%2C+%27%27%2C+692%2C+8%29%5B1%5D)' <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://www.w3.org/2000/10/annotation-ns#body> <info:fedora/PLoS:4994> <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://rdf.topazproject.org/RDF/state> '0'^^<http://www.w3.org/2001/XMLSchema#int> <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://www.w3.org/2000/10/annotation-ns#created> '2009-02-09T19:51:11.065Z'^^<http://www.w3.org/2001/XMLSchema#dateTime> <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://purl.org/dc/terms/mediator> 'topaz-ambra' <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2000/10/annotationType#Comment> <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://purl.org/dc/elements/1.1/creator> 'info:doi/10.1371/account/38098' <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://www.w3.org/2000/10/annotation-ns#annotates> <info:doi/10.1371/journal.pone.0004268> <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2000/10/annotation-ns#Annotation> <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://purl.org/dc/elements/1.1/title> 'Correction to Article Data' into <local:///topazproject#filter:graph=ri>;

2009-02-10/mulgara.tx.log.1:1432:insert <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://rdf.topazproject.org/RDF/propagate-permissions-to> <info:fedora/PLoS:4994> into <local:///topazproject#filter:graph=pp>;
2009-02-10/mulgara.tx.log.1:1433:insert <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <annotations:getAnnotationInfo> <http://rdf.topazproject.org/RDF/permissions#all> into <local:///topazproject#filter:graph=grants>;
2009-02-10/mulgara.tx.log.1:1434:insert <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <annotations:supersede> <http://rdf.topazproject.org/RDF/permissions#all> <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <annotations:deleteAnnotation> <http://rdf.topazproject.org/RDF/permissions#all> into <local:///topazproject#filter:graph=revokes>;
2009-02-10/mulgara.tx.log.1:1435:insert <info:doi/10.1371/annotation/9e6e6678-1ad2-4c6f-8ce0-7cd4e7a7a741> <http://www.w3.org/2000/10/annotation-ns#created> '2009-02-09T19:51:11.443Z'^^<http://www.w3.org/2001/XMLSchema#dateTime> <info:doi/10.1371/annotation/9e6e6678-1ad2-4c6f-8ce0-7cd4e7a7a741> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2000/10/annotation-ns#Annotation> <info:doi/10.1371/annotation/9e6e6678-1ad2-4c6f-8ce0-7cd4e7a7a741> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2000/10/annotationType#Comment> <info:doi/10.1371/annotation/9e6e6678-1ad2-4c6f-8ce0-7cd4e7a7a741> <http://www.w3.org/2000/10/annotation-ns#body> <info:fedora/PLoS:4995> <info:doi/10.1371/annotation/9e6e6678-1ad2-4c6f-8ce0-7cd4e7a7a741> <http://purl.org/dc/terms/mediator> 'topaz-ambra' <info:doi/10.1371/annotation/9e6e6678-1ad2-4c6f-8ce0-7cd4e7a7a741> <http://www.w3.org/2000/10/annotation-ns#annotates> <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <info:doi/10.1371/annotation/9e6e6678-1ad2-4c6f-8ce0-7cd4e7a7a741> <http://purl.org/dc/elements/1.1/creator> 'info:doi/10.1371/account/38098' <info:doi/10.1371/annotation/9e6e6678-1ad2-4c6f-8ce0-7cd4e7a7a741> <http://rdf.topazproject.org/RDF/state> '0'^^<http://www.w3.org/2001/XMLSchema#int> into <local:///topazproject#filter:graph=ri>;

2009-02-10/mulgara.tx.log.1:1590:delete <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2000/10/annotation-ns#Annotation> <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2000/10/annotationType#Comment> <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://purl.org/dc/elements/1.1/creator> 'info:doi/10.1371/account/38098' <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://purl.org/dc/elements/1.1/title> 'Correction to Article Data' <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://purl.org/dc/terms/mediator> 'topaz-ambra' <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://rdf.topazproject.org/RDF/state> '0'^^<http://www.w3.org/2001/XMLSchema#int> <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://www.w3.org/2000/10/annotation-ns#annotates> <info:doi/10.1371/journal.pone.0004268> <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://www.w3.org/2000/10/annotation-ns#body> <info:fedora/PLoS:4994> <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://www.w3.org/2000/10/annotation-ns#context> 'info:doi/10.1371/journal.pone.0004268#xpointer(string-range%28%2Farticle%5B1%5D%2Fbody%5B1%5D%2Fsec%5B1%5D%2Fp%5B6%5D%2C+%27%27%2C+692%2C+8%29%5B1%5D)' <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://www.w3.org/2000/10/annotation-ns#created> '2009-02-09T19:51:11.065Z'^^<http://www.w3.org/2001/XMLSchema#dateTime> from <local:///topazproject#filter:graph=ri>;

2009-02-10/mulgara.tx.log.1:1591:delete <info:doi/10.1371/annotation/9e6e6678-1ad2-4c6f-8ce0-7cd4e7a7a741> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2000/10/annotation-ns#Annotation> <info:doi/10.1371/annotation/9e6e6678-1ad2-4c6f-8ce0-7cd4e7a7a741> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2000/10/annotationType#Comment> <info:doi/10.1371/annotation/9e6e6678-1ad2-4c6f-8ce0-7cd4e7a7a741> <http://purl.org/dc/elements/1.1/creator> 'info:doi/10.1371/account/38098' <info:doi/10.1371/annotation/9e6e6678-1ad2-4c6f-8ce0-7cd4e7a7a741> <http://purl.org/dc/terms/mediator> 'topaz-ambra' <info:doi/10.1371/annotation/9e6e6678-1ad2-4c6f-8ce0-7cd4e7a7a741> <http://rdf.topazproject.org/RDF/state> '0'^^<http://www.w3.org/2001/XMLSchema#int> <info:doi/10.1371/annotation/9e6e6678-1ad2-4c6f-8ce0-7cd4e7a7a741> <http://www.w3.org/2000/10/annotation-ns#annotates> <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <info:doi/10.1371/annotation/9e6e6678-1ad2-4c6f-8ce0-7cd4e7a7a741> <http://www.w3.org/2000/10/annotation-ns#body> <info:fedora/PLoS:4995> <info:doi/10.1371/annotation/9e6e6678-1ad2-4c6f-8ce0-7cd4e7a7a741> <http://www.w3.org/2000/10/annotation-ns#created> '2009-02-09T19:51:11.443Z'^^<http://www.w3.org/2001/XMLSchema#dateTime> from <local:///topazproject#filter:graph=ri>;

2009-02-10/mulgara.tx.log.1:1592:insert <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://www.w3.org/2000/10/annotation-ns#context> 'info:doi/10.1371/journal.pone.0004268#xpointer(string-range%28%2Farticle%5B1%5D%2Fbody%5B1%5D%2Fsec%5B1%5D%2Fp%5B6%5D%2C+%27%27%2C+692%2C+8%29%5B1%5D)' <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://rdf.topazproject.org/RDF/2008/01/annotationType#FormalCorrection> <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://rdf.topazproject.org/RDF/state> '0'^^<http://www.w3.org/2001/XMLSchema#int> <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://www.w3.org/2000/10/annotation-ns#created> '2009-02-09T19:51:11.065Z'^^<http://www.w3.org/2001/XMLSchema#dateTime> <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://purl.org/dc/terms/mediator> 'topaz-ambra' <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://purl.org/dc/elements/1.1/creator> 'info:doi/10.1371/account/38098' <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://www.w3.org/2000/10/annotation-ns#annotates> <info:doi/10.1371/journal.pone.0004268> <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2000/10/annotation-ns#Annotation> <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2000/10/annotationType#Change> <info:doi/10.1371/annotation/8f64f0c8-6767-4701-8ded-7f937d953cb6> <http://purl.org/dc/elements/1.1/title> 'Correction to Article Data' into <local:///topazproject#filter:graph=ri>;
}}

in reply to: ↑ 4   Changed 18 months ago by russ

Replying to russ:

this happened a second time on pone.4268 in this case, the mulgara.tx.log looks like the annotation was converted to a formal correction twice.

argh, never mind. i've got the same log lines twice.

  Changed 18 months ago by russ

  • owner changed from dragisak to russ
  • milestone changed from 0.9.1 RC2 to 0.9.2

taking this ticket and moving to 0.9.2

we think this is fixed, and will test after 0.9.1-final release.

  Changed 17 months ago by rcave

  • priority changed from critical to medium
  • type changed from defect to clarification

  Changed 17 months ago by russ

  • priority changed from medium to high
  • owner changed from russ to dragisak

dragisa reproduced this in 0.9.1 final, so we're still bad.

  Changed 17 months ago by dragisak

(In [7301]) Allow deletion for annotations that have no body. Annotations can end up not having body as a result of a bug. See #1108

  Changed 17 months ago by dragisak

(In [7302]) Allow deletion for annotations that have no body. Annotations can end up not having body as a result of a bug. See #1108

  Changed 17 months ago by dragisak

  • status changed from new to assigned

To reproduce flag correction multiple times. On admin page you will see more than one flag for same annotation. Mark all flags as formal correction. Body disappears !

  Changed 17 months ago by dragisak

Partially addressed by r7302

  Changed 17 months ago by dragisak

(In [7315]) Prevent redundant changes of annotation type. Partially addresses #1108

  Changed 17 months ago by dragisak

  • owner changed from dragisak to rich
  • status changed from assigned to new

  Changed 17 months ago by russ

this is happening regularly in 0.9.1 final, even when there is only a single flag on the annotation.

i've confirmed this personally. at least 3 annotations have lost their body when elevated to a formal correction. i'm not sure if any have worked correctly. in all cases, there was only one flag on the annotation.

  Changed 17 months ago by rcave

  • owner changed from rich to dragisak

  Changed 17 months ago by rcave

  • type changed from clarification to defect

  Changed 17 months ago by rcave

  • owner changed from dragisak to ssterling

I can't reproduce in this problem in a single stack. We'll need to test in a multi-stack environment.

  Changed 17 months ago by npeterson

  • owner changed from ssterling to dragisak

Reassigning this to Dragisa. It appears to be related to caching issue. Next step to try and recreate on Multi-stack.

  Changed 17 months ago by npeterson

  • owner changed from dragisak to wtoconnor

  Changed 17 months ago by rcave

  • priority changed from high to low
  • type changed from defect to clarification
  • milestone changed from 0.9.2 to 0.9.3

Dragisa has not been able to reproduce this bug in 0.9.2. I am moving this bug into 0.9.3 for final check to see if the issue has been resolved.

  Changed 17 months ago by rcave

  • owner changed from wtoconnor to rich

  Changed 16 months ago by dragisak

Another example done in 0.9.2_rc1:  http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004159

  Changed 16 months ago by dragisak

  • owner changed from rich to dragisak

  Changed 16 months ago by rcave

  • priority changed from low to high
  • milestone changed from 0.9.3 to 0.9.2

  Changed 16 months ago by rcave

  • priority changed from high to critical
  • type changed from clarification to defect

  Changed 16 months ago by dragisak

  • status changed from new to assigned

This doesn't seem to be 0.9.1 to 0.9.2 compatibility problem. New annotations created on 0.9.2 behave the same. I am able to reproduce this every time. Happens only on live servers.

  Changed 16 months ago by dragisak

(In [7582]) Add checks to prevent loosing annotation body during conversion. Addresses #1108

  Changed 16 months ago by dragisak

  • owner changed from dragisak to rich
  • status changed from assigned to new
  • type changed from defect to clarification

  Changed 16 months ago by rcave

  • owner changed from rich to russ
  • milestone changed from 0.9.2 to 0.9.3_rc1

  Changed 16 months ago by russ

  • milestone changed from 0.9.3_rc1 to 0.9.3_rc2

will test after 0.9.3_rc1 is released

  Changed 14 months ago by npeterson

  • type changed from clarification to defect

We have decided to disable Cache Replication as the first step to address these intermittent cache issues.

follow-up: ↓ 34   Changed 14 months ago by rcave

See this strange(?) log statement during a failed note elevation to correction. It occurs between the "Converting to Minor Correction" log and final rollback. Need to verify that this happens during a working elevation. 

2009-06-05 14:31:19,685 DEBUG SessionImpl(PLoSONE)> delayedLoadComplete ignored for 'body' on info:doi/10.1371/annotation/ea26635b-a402-4e6d-ba89-292c7fb46f35 [TP-Processor12 org.topazproject.otm.impl.SessionImpl]

in reply to: ↑ 33   Changed 14 months ago by dragisak

Replying to rcave:

See this strange(?) log statement during a failed note elevation to correction. It occurs between the "Converting to Minor Correction" log and final rollback. Need to verify that this happens during a working elevation.

Yes. This message is seen during working elevation too.

  Changed 14 months ago by rcave

The exception returned when you try to elevate a note to a correction: 

2009-06-05 15:18:17,934 DEBUG TransactionImpl(PLoSONE)> Setting rollback-only on transaction org.topazproject.otm.impl.TransactionImpl@6cfb00c4 [TP-Processor15 org.topazproject.otm.impl.TransactionImpl]
2009-06-05 15:18:17,934 ERROR ProcessFlagsAction(PLoSONE)> Failed to convert annotation id='info:doi/10.1371/annotation/ea26635b-a402-4e6d-ba89-292c7fb46f35' to Minor Correction annotation. [TP-Processor15 org.topazproject.ambra.admin.action.ProcessFlagsAction]
org.topazproject.ambra.ApplicationException: Trying to save annotation info:doi/10.1371/annotation/ea26635b-a402-4e6d-ba89-292c7fb46f35 with NULL body
        at org.topazproject.ambra.annotation.service.AnnotationService.convertAnnotationToType(AnnotationService.java:710)
        at org.topazproject.ambra.annotation.service.AnnotationService$$FastClassByCGLIB$$273a5710.invoke(<generated>)
        at net.sf.cglib.proxy.MethodProxy.invoke(MethodProxy.java:191)
        at org.springframework.aop.framework.Cglib2AopProxy$CglibMethodInvocation.invokeJoinpoint(Cglib2AopProxy.java:695)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:144)
        at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:107)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:166)
        at org.springframework.aop.framework.Cglib2AopProxy$DynamicAdvisedInterceptor.intercept(Cglib2AopProxy.java:630)
        at org.topazproject.ambra.annotation.service.AnnotationService$$EnhancerByCGLIB$$458e9567.convertAnnotationToType(<generated>)
        at org.topazproject.ambra.admin.action.ProcessFlagsAction.execute(ProcessFlagsAction.java:180)
        at org.topazproject.ambra.admin.action.ProcessFlagsAction$$FastClassByCGLIB$$ff2a69c5.invoke(<generated>)
        at net.sf.cglib.proxy.MethodProxy.invoke(MethodProxy.java:191)
        at org.springframework.aop.framework.Cglib2AopProxy$CglibMethodInvocation.invokeJoinpoint(Cglib2AopProxy.java:695)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:144)
        at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:107)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:166)
        at org.springframework.aop.framework.Cglib2AopProxy$DynamicAdvisedInterceptor.intercept(Cglib2AopProxy.java:630)
        at org.topazproject.ambra.admin.action.ProcessFlagsAction$$EnhancerByCGLIB$$48fbca2e.execute(<generated>)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:585)
        at com.opensymphony.xwork2.DefaultActionInvocation.invokeAction(DefaultActionInvocation.java:404)
        at com.opensymphony.xwork2.DefaultActionInvocation.invokeActionOnly(DefaultActionInvocation.java:267)
        at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:229)
        at org.topazproject.ambra.user.EnsureRoleInterceptor.intercept(EnsureRoleInterceptor.java:43)
        at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224)
        at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223)
        at com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerStack.java:455)
        at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:221)
        at org.topazproject.ambra.struts2.TransactionInterceptor.intercept(TransactionInterceptor.java:61)
        at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224)
        at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223)
        at com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerStack.java:455)
        at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:221)
        at org.topazproject.ambra.user.EnsureUserAccountInterceptor.getReturnCodeDependingOnDisplayName(EnsureUserAccountInterceptor.java:101)
        at org.topazproject.ambra.user.EnsureUserAccountInterceptor.intercept(EnsureUserAccountInterceptor.java:73)
        at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224)
        at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223)
        at com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerStack.java:455)
        at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:221)
        at org.topazproject.ambra.user.UserAccountsInterceptor.intercept(UserAccountsInterceptor.java:102)
        at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224)
        at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223)
        at com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerStack.java:455)
        at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:221)
        at org.topazproject.ambra.journal.SessionFiltersInterceptor.intercept(SessionFiltersInterceptor.java:51)
        at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224)
        at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223)
        at com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerStack.java:455)
        at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:221)
        at com.opensymphony.xwork2.interceptor.DefaultWorkflowInterceptor.doIntercept(DefaultWorkflowInterceptor.java:221)
        at com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(MethodFilterInterceptor.java:86)
        at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224)
        at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223)
        at com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerStack.java:455)
        at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:221)
        at com.opensymphony.xwork2.validator.ValidationInterceptor.doIntercept(ValidationInterceptor.java:150)
        at org.apache.struts2.interceptor.validation.AnnotationValidationInterceptor.doIntercept(AnnotationValidationInterceptor.java:48)
        at com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(MethodFilterInterceptor.java:86)
        at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224)
        at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223)
        at com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerStack.java:455)
        at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:221)
        at com.opensymphony.xwork2.interceptor.ConversionErrorInterceptor.intercept(ConversionErrorInterceptor.java:123)
        at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224)
        at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223)
        at com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerStack.java:455)
        at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:221)
        at com.opensymphony.xwork2.interceptor.ParametersInterceptor.doIntercept(ParametersInterceptor.java:184)
        at com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(MethodFilterInterceptor.java:86)
        at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224)
        at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223)
        at com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerStack.java:455)
        at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:221)
        at com.opensymphony.xwork2.interceptor.StaticParametersInterceptor.intercept(StaticParametersInterceptor.java:105)
        at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224)
        at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223)
        at com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerStack.java:455)
        at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:221)
        at org.apache.struts2.interceptor.FileUploadInterceptor.intercept(FileUploadInterceptor.java:207)
        at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224)
        at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223)
        at com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerStack.java:455)
        at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:221)
        at com.opensymphony.xwork2.interceptor.ModelDrivenInterceptor.intercept(ModelDrivenInterceptor.java:74)
        at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224)
        at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223)
        at com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerStack.java:455)
        at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:221)
        at org.apache.struts2.interceptor.debugging.DebuggingInterceptor.intercept(DebuggingInterceptor.java:206)
        at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224)
        at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223)
        at com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerStack.java:455)
        at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:221)
        at com.opensymphony.xwork2.interceptor.I18nInterceptor.intercept(I18nInterceptor.java:143)
        at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224)
        at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223)
        at com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerStack.java:455)
        at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:221)
        at com.opensymphony.xwork2.interceptor.PrepareInterceptor.doIntercept(PrepareInterceptor.java:121)
        at com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(MethodFilterInterceptor.java:86)
        at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224)
        at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223)
        at com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerStack.java:455)
        at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:221)
        at org.apache.struts2.interceptor.ServletConfigInterceptor.intercept(ServletConfigInterceptor.java:170)
        at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224)
        at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223)
        at com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerStack.java:455)
        at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:221)
        at com.opensymphony.xwork2.interceptor.AliasInterceptor.intercept(AliasInterceptor.java:123)
        at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224)
        at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223)
        at com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerStack.java:455)
        at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:221)
        at com.opensymphony.xwork2.interceptor.LoggingInterceptor.intercept(LoggingInterceptor.java:52)
        at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224)
        at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223)
        at com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerStack.java:455)
        at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:221)
        at com.opensymphony.xwork2.interceptor.TimerInterceptor.invokeUnderTiming(TimerInterceptor.java:125)
        at com.opensymphony.xwork2.interceptor.TimerInterceptor.intercept(TimerInterceptor.java:112)
        at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224)
        at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223)
        at com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerStack.java:455)
        at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:221)
        at com.opensymphony.xwork2.interceptor.ExceptionMappingInterceptor.intercept(ExceptionMappingInterceptor.java:176)
        at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224)
        at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223)
        at com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerStack.java:455)
        at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:221)
        at org.apache.struts2.impl.StrutsActionProxy.execute(StrutsActionProxy.java:50)
        at org.apache.struts2.dispatcher.Dispatcher.serviceAction(Dispatcher.java:504)
        at org.apache.struts2.dispatcher.FilterDispatcher.doFilter(FilterDispatcher.java:419)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
        at org.mortbay.servlet.UserAgentFilter.doFilter(UserAgentFilter.java:81)
        at org.mortbay.servlet.GzipFilter.doFilter(GzipFilter.java:129)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
        at org.topazproject.ambra.cas.client.filter.CASFilter.doFilter(CASFilter.java:319)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
        at org.topazproject.ambra.web.DummySSOFilter.doFilter(DummySSOFilter.java:105)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
        at org.topazproject.ambra.web.VirtualJournalContextFilter.doFilter(VirtualJournalContextFilter.java:150)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
        at org.tuckey.web.filters.urlrewrite.RuleChain.handleRewrite(RuleChain.java:164)
        at org.tuckey.web.filters.urlrewrite.RuleChain.doRules(RuleChain.java:141)
        at org.tuckey.web.filters.urlrewrite.UrlRewriter.processRequest(UrlRewriter.java:90)
        at org.tuckey.web.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:406)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
        at org.topazproject.ambra.web.MultipleRequestFilter.doFilter(MultipleRequestFilter.java:95)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)
        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172)
        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117)
        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108)
        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174)
        at org.apache.jk.server.JkCoyoteHandler.invoke(JkCoyoteHandler.java:200)
        at org.apache.jk.common.HandlerRequest.invoke(HandlerRequest.java:283)
        at org.apache.jk.common.ChannelSocket.invoke(ChannelSocket.java:773)
        at org.apache.jk.common.ChannelSocket.processConnection(ChannelSocket.java:703)
        at org.apache.jk.common.ChannelSocket$SocketConnection.runIt(ChannelSocket.java:895)
        at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689)
        at java.lang.Thread.run(Thread.java:595)
2009-06-05 15:18:17,935 DEBUG OtmTransactionManager(PLoSONE)> Transactional code has requested rollback [TP-Processor15org.topazproject.otm.spring.OtmTransactionManager]

  Changed 14 months ago by dragisak

  • status changed from new to assigned
  • owner changed from russ to dragisak

  Changed 14 months ago by dragisak

Cause:

org.apache.commons.beanutils.BeanUtilsBean completely ignored setBody() and getBody() methods.

BeanUtilsBean caches class properties. At some point cache entry for our srcAnnotation class was saved without 'body' property. Subsequent calls to BeanUtilsBean.copyProperties() would get that cached entry and body would not be copied.

follow-up: ↓ 39   Changed 14 months ago by dragisak

(In [7735]) Singleton instance of BeanUtilsBean? would cache class properties. That would cause bean properties to get 'lost' in some situations. To prevent this, we create a new instance of PropertyUtilsBean? with empty cache so that bean properties are fully introspected each time.

Addresses #1108

in reply to: ↑ 38   Changed 14 months ago by dragisak

Replying to dragisak:

(In [7735]) Singleton instance of BeanUtilsBean? would cache class properties. That would cause bean properties to get 'lost' in some situations. To prevent this, we create a new instance of PropertyUtilsBean? with empty cache so that bean properties are fully introspected each time. Addresses #1108

Problem is still occuring. It happens on single-node instance.

  Changed 14 months ago by dragisak

(In [7745]) Add more logging in order to catch situations when body property is not copied.

Addresses #1108

  Changed 14 months ago by npeterson

  • milestone changed from 0.9.3_rc2 to 0.9.3_rc3

  Changed 12 months ago by rcave

  • milestone 0.9.3_rc3 deleted

  Changed 12 months ago by ssterling

This bug seems to be reliably recreated through the process described in ticket #1401, in which one repeatedly creates a "correction" on an Article and then elevates that Annotation to a Formal Correction. Repeating this cycle dozens of times over a short span of time will result in an "Annotation body is NULL" message. Thereafter, this message appears every time one tries to elevate an Annotation to a Formal Correction.

  Changed 12 months ago by dragisak

(In [7826]) Declare AnnotationBlob? serializable.

References #1108

  Changed 12 months ago by dragisak

It looks like isWritable method returns false for FormalCorrection? object.

See  PropertyUtilsBean.copyProperties(Object dest, Object orig)

  Changed 10 months ago by npeterson

  • milestone set to 0.9.5 rc1

  Changed 10 months ago by npeterson

  • owner changed from dragisak to wtoconnor

Changed 10 months ago by russ

jMeter script to programatically create, flag, and elevate notes

  Changed 10 months ago by russ

uploaded a jMeter script.

it expects a file with a list of dois, one per line, in the same directory.

you need to set the filename, as well as a working username and password, and other variables, in the user defined variables setting before running.

i'm running this continuously against demo small, but have been unable to reproduce. next step IMO should be to get a script that reproduces the error with the minimum number of actions - scott might have a clue what's missing from this script.

i'll keep running my script in hopes of getting things borken on small demo.

  Changed 10 months ago by dragisak

(In [7915]) If copying of body from source to destination fails first time with beanutils, try it once more by calling get and set methods explicitely.

Addresses #1108

  Changed 10 months ago by dragisak

  • owner changed from wtoconnor to dragisak

It looks like the problem is related to Java bug:  6528714.

In short. Java introspection does not work well with generics. It would not detect concrete implementation of get or set methods but return the generic type.

In our case, one workaround, could be to override both set and get methods in ArticleAnnotation class.

  Changed 10 months ago by dragisak

  • status changed from assigned to closed
  • resolution set to fixed

(In [7922]) Don't create new BeanUtilisbean? for each copy. We did that thinking that that would fix #1108 but, instead, it made it worst.

  Changed 10 months ago by dragisak

(In [7923]) Work around JDK bug  http://bugs.sun.com/view_bug.do?bug_id=6528714

Because introspection does not work well with generics, PropertyUtils?.copyProperties would fail for body property if only one of set or get methods is overriden.

Addresses #1108

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