[InterMine Dev] precompute templates error

Julie Sullivan julie at flymine.org
Tue Jul 7 08:40:18 BST 2015


Hi Kalpana,

On the outer join, a trailing AND is added to the generated SQL with no 
clause after it. We haven't figured out why yet:

	https://github.com/intermine/intermine/issues/725

Your template will still run, it just won't be as fast as if it had the 
precomputed table.

Julie

On 06/07/15 22:26, Kalpana Karra wrote:
> Hello,
>
> I used to have precompute-templates step as part of the weekly build. Not sure at what point precompute-templates step started to fail, but, in trying to understand what the problem is..I am seeing SQL cannot be parsed error on most templates (I tried to identify the problem one by adding the offending templates to -Dignore=xx,yy list, but, that kept growing) and it seems to be a systemic problem.
>
> It seems like it might have something to do with ‘Lists’ in looking at SQL, but, am not sure why that would be part of this process.
>
> Any pointers will be appreciated.
>
> Thanks,
> -Kalpana
>
>
> BUILD FAILED
> /data/tools/intermine/prod/intermine/imbuild/application.xml:231: Exception creating objectstore/profile manager
> 	at org.intermine.web.task.PrecomputeTemplatesTask.execute(PrecomputeTemplatesTask.java:152)
> 	at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
> 	at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
> 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> 	at java.lang.reflect.Method.invoke(Method.java:597)
> 	at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
> 	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:1399)
> 	at org.apache.tools.ant.Project.executeTarget(Project.java:1368)
> 	at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
> 	at org.apache.tools.ant.Project.executeTargets(Project.java:1251)
> 	at org.apache.tools.ant.Main.runBuild(Main.java:809)
> 	at org.apache.tools.ant.Main.startAnt(Main.java:217)
> 	at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
> 	at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
> Caused by: org.intermine.objectstore.ObjectStoreException: Query SQL cannot be parsed, so cannot be precomputed: SELECT intermine_default.subjectId AS "bagId", intermine_default.id AS intermine_defaultid, a1_.id AS a1_id FROM CrossReference AS intermine_default, DataSource AS a1_ WHERE intermine_default.sourceId = a1_.id AND  ORDER BY intermine_default.subjectId, intermine_default.id, a1_.id, IQL: SELECT bag.id AS bagId, default, a1_ FROM !::org.intermine.model.bio.Gene AS bag, org.intermine.model.bio.CrossReference AS default, org.intermine.model.bio.DataSource AS a1_ WHERE (default.source CONTAINS a1_ AND bag.crossReferences CONTAINS default)
> 	at org.intermine.web.task.PrecomputeTemplatesTask.precomputeTemplates(PrecomputeTemplatesTask.java:218)
> 	at org.intermine.web.task.PrecomputeTemplatesTask.execute(PrecomputeTemplatesTask.java:150)
> 	... 16 more
> Caused by: org.intermine.objectstore.ObjectStoreException: Query SQL cannot be parsed, so cannot be precomputed: SELECT intermine_default.subjectId AS "bagId", intermine_default.id AS intermine_defaultid, a1_.id AS a1_id FROM CrossReference AS intermine_default, DataSource AS a1_ WHERE intermine_default.sourceId = a1_.id AND  ORDER BY intermine_default.subjectId, intermine_default.id, a1_.id, IQL: SELECT bag.id AS bagId, default, a1_ FROM !::org.intermine.model.bio.Gene AS bag, org.intermine.model.bio.CrossReference AS default, org.intermine.model.bio.DataSource AS a1_ WHERE (default.source CONTAINS a1_ AND bag.crossReferences CONTAINS default)
> 	at org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.precomputeWithConnection(ObjectStoreInterMineImpl.java:2047)
> 	at org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.precomputeWithConnection(ObjectStoreInterMineImpl.java:2028)
> 	at org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.precompute(ObjectStoreInterMineImpl.java:1877)
> 	at org.intermine.objectstore.intermine.ParallelPrecomputer.precomputeQuery(ParallelPrecomputer.java:297)
> 	at org.intermine.objectstore.intermine.ParallelPrecomputer$Job.execute(ParallelPrecomputer.java:202)
> 	at org.intermine.objectstore.intermine.ParallelPrecomputer$Job.access$500(ParallelPrecomputer.java:144)
> 	at org.intermine.objectstore.intermine.ParallelPrecomputer.executeJob(ParallelPrecomputer.java:276)
> 	at org.intermine.objectstore.intermine.ParallelPrecomputer.precompute(ParallelPrecomputer.java:109)
> 	at org.intermine.web.task.PrecomputeTemplatesTask.precomputeTemplates(PrecomputeTemplatesTask.java:216)
> 	... 17 more
> Caused by: java.lang.IllegalArgumentException: [81, SELECT], [35, intermine_default], [96, .], [35, subjectId], [92, AS], [34, "bagId"], [83, ,], [35, intermine_default], [96, .], [35, id], [92, AS], [35, intermine_defaultid], [83, ,], [35, a1_], [96, .], [35, id], [92, AS], [35, a1_id], [84, FROM], [35, CrossReference], [92, AS], [35, intermine_default], [83, ,], [35, DataSource], [92, AS], [35, a1_], [85, WHERE], [35, intermine_default], [96, .], [35, sourceId], [76, =], [35, a1_], [96, .], [35, id], [101, AND], [89, ORDER], [87, BY], [35, intermine_default], [96, .], [35, subjectId], [83, ,], [35, intermine_default], [96, .], [35, id], [83, ,], [35, a1_], [96, .], [35, id]
> 	at org.intermine.sql.query.Query.<init>(Query.java:210)
> 	at org.intermine.sql.query.Query.<init>(Query.java:127)
> 	at org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.precomputeWithConnection(ObjectStoreInterMineImpl.java:1918)
> 	... 25 more
> Caused by: line 1:211: unexpected token: AND
> 	at org.intermine.sql.query.SqlParser.select_command(SqlParser.java:346)
> 	at org.intermine.sql.query.SqlParser.sql_statement(SqlParser.java:166)
> 	at org.intermine.sql.query.SqlParser.sql(SqlParser.java:121)
> 	at org.intermine.sql.query.SqlParser.start_rule(SqlParser.java:73)
> 	at org.intermine.sql.query.Query.<init>(Query.java:170)
> 	... 27 more
>
> Total time: 49 seconds
>
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