[InterMine Dev] Failing to release webapp

Vallejos, Andrew avallejos at mcw.edu
Thu Mar 24 16:45:33 GMT 2011


You should look in
your_mine/dbmodel/resources/objectstoresummary.config.properties.

You should be able to comment out the offending relation.

-----Original Message-----
From: James Blackshaw [mailto:jab250 at mrc-mbu.cam.ac.uk] 
Sent: Thursday, March 24, 2011 10:29 AM
To: Vallejos, Andrew
Subject: Re: [InterMine Dev] Failing to release webapp

I am, and I tried running it separately. It was more informative running

it under verbose, but I am now unsure what the missing relation is, and 
where I need to define it. The build reports 'relation 
"proteinspublication" does not exist'.

-James

BUILD FAILED
/home/jab250/intermine_09_03_edit/imbuild/application.xml:29: failed to 
get the object store summary
     at 
org.intermine.task.SummariseObjectStoreTask.execute(SummariseObjectStore
Task.java:114)
     at
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
     at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
     at 
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
Impl.java:43)
     at java.lang.reflect.Method.invoke(Method.java:616)
     at 
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
06)
     at org.apache.tools.ant.Task.perform(Task.java:348)
     at org.apache.tools.ant.Target.execute(Target.java:390)
     at org.apache.tools.ant.Target.performTasks(Target.java:411)
     at
org.apache.tools.ant.Project.executeSortedTargets(Project.java:1360)
     at org.apache.tools.ant.Project.executeTarget(Project.java:1329)
     at 
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecut
or.java:41)
     at org.apache.tools.ant.Project.executeTargets(Project.java:1212)
     at org.apache.tools.ant.Main.runBuild(Main.java:801)
     at org.apache.tools.ant.Main.startAnt(Main.java:218)
     at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
     at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
Caused by: java.lang.RuntimeException: ObjectStore error has occurred 
(in get)
     at org.intermine.objectstore.query.Results.get(Results.java:250)
     at 
org.intermine.objectstore.query.Results$Iter.hasNext(Results.java:395)
     at 
org.intermine.objectstore.ObjectStoreSummary.lookForEmptyThings(ObjectSt
oreSummary.java:356)
     at 
org.intermine.objectstore.ObjectStoreSummary.lookForEmptyThings(ObjectSt
oreSummary.java:291)
     at 
org.intermine.objectstore.ObjectStoreSummary.<init>(ObjectStoreSummary.j
ava:120)
     at 
org.intermine.task.SummariseObjectStoreTask.execute(SummariseObjectStore
Task.java:92)
     ... 16 more
Caused by: org.intermine.objectstore.ObjectStoreException: Problem 
running SQL statement "SELECT 1 AS a1_ WHERE EXISTS(SELECT a2_.id FROM 
Publication AS a1_, Protein AS a2_, ProteinsPublication AS indirect0 
WHERE a1_.id = indirect0.Publication AND indirect0.Proteins = a2_.id) 
LIMIT 1" while executing query "SELECT 1 AS a1_ WHERE (EXISTS (SELECT 
a2_ FROM org.intermine.model.bio.Publication AS a1_, 
org.intermine.model.bio.Protein AS a2_ WHERE (a1_.proteins CONTAINS
a2_)))"
     at 
org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.executeWith
Connection(ObjectStoreInterMineImpl.java:1262)
     at 
org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.executeWith
Connection(ObjectStoreInterMineImpl.java:1059)
     at 
org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.execute(Obj
ectStoreInterMineImpl.java:958)
     at 
org.intermine.objectstore.query.ResultsBatches.fetchBatchFromObjectStore
(ResultsBatches.java:192)
     at 
org.intermine.objectstore.query.PrefetchManager.doRequest(PrefetchManage
r.java:240)
     at 
org.intermine.objectstore.query.PrefetchManager.doRequest(PrefetchManage
r.java:145)
     at 
org.intermine.objectstore.query.ResultsBatches.getBatch(ResultsBatches.j
ava:164)
     at 
org.intermine.objectstore.query.ResultsBatches.getRowsFromBatch(ResultsB
atches.java:139)
     at org.intermine.objectstore.query.Results.range(Results.java:196)
     at org.intermine.objectstore.query.Results.get(Results.java:242)
     ... 21 more
Caused by: org.postgresql.util.PSQLException: ERROR: relation 
"proteinspublication" does not exist
   Position: 85
     at 
org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecu
torImpl.java:2079)
     at 
org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImp
l.java:1812)
     at 
org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:
257)
     at 
org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Stateme
nt.java:500)
     at 
org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdb
c2Statement.java:374)
     at 
org.postgresql.jdbc2.AbstractJdbc2Statement.executeQuery(AbstractJdbc2St
atement.java:254)
     at sun.reflect.GeneratedMethodAccessor47.invoke(Unknown Source)
     at 
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
Impl.java:43)
     at java.lang.reflect.Method.invoke(Method.java:616)
     at 
org.postgresql.ds.jdbc23.AbstractJdbc23PooledConnection$StatementHandler
.invoke(AbstractJdbc23PooledConnection.java:455)
     at $Proxy3.executeQuery(Unknown Source)
     at 
org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.executeWith
Connection(ObjectStoreInterMineImpl.java:1158)
     ... 30 more

Total time: 46 seconds


On 24/03/2011 14:55, Vallejos, Andrew wrote:
> Are you running the summarise-objectstore post-process before
releasing
> the webapp?
>
> -Andrew
>
> -----Original Message-----
> From: dev-bounces at intermine.org [mailto:dev-bounces at intermine.org] On
> Behalf Of James Blackshaw
> Sent: Thursday, March 24, 2011 9:29 AM
> To: Intermine
> Subject: [InterMine Dev] Failing to release webapp
>
> Hi,
> I can release the webapp when I only load one organism's data in from
> Uniprot, but if I load any more organisms in, the webapp release
fails.
> The build and integration beforehand both work fine, and I can see the
> data in MySQL. I just can't get the webapp released.
>
> -James
>
>
> The error:
>
> -init-summarise-objectstore:
>
> retrieve-objectstore-summary:
>        [echo] Retrieving object store summary from os.production...
> [summarise-objectstore] summarising objectstore...
>
> BUILD FAILED
> /home/jab250/intermine_09_03_edit/imbuild/application.xml:29: failed
to
> get the object store summary
>
>
> _______________________________________________
> dev mailing list
> dev at intermine.org
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev




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