[InterMine Dev] precompute templates error

Kalpana Karra kkarra at stanford.edu
Mon Jul 6 22:26:21 BST 2015


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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