Task #9077 (closed)
Bug: bd-pathway import 2
| Reported by: | jburel | Owned by: | jamoore |
|---|---|---|---|
| Priority: | blocker | Milestone: | OMERO-4.4 |
| Component: | General | Version: | n.a. |
| Keywords: | n.a. | Cc: | ux@…, jamoore, cxallan, mlinkert |
| Resources: | n.a. | Referenced By: | n.a. |
| References: | n.a. | Remaining Time: | n.a. |
| Sprint: | 2012-06-19 (17) |
Description (last modified by cxallan)
Import the file
from_skyking/bd-pathway/bram/42_6_1_100208_BJWT_LOPAC_05_08_10nM_R1/201-02-19_000/Experiment.exp
Clean DB, nothing else imported. server howe user root.
error follow
java.lang.RuntimeException: omero.ApiUsageException
serverStackTrace = "ome.conditions.ApiUsageException: PreparedStatementCallback; bad SQL grammar [insert into temp_ids (key, id) values (?, ?)]; nested exception is org.postgresql.util.PSQLException: ERROR: relation "temp_ids" does not exist
Position: 13
at org.springframework.jdbc.support.SQLErrorCodeSQLExceptionTranslator.doTranslate(SQLErrorCodeSQLExceptionTranslator.java:233)
at org.springframework.jdbc.support.AbstractFallbackSQLExceptionTranslator.translate(AbstractFallbackSQLExceptionTranslator.java:72)
at org.springframework.jdbc.core.JdbcTemplate.execute(JdbcTemplate.java:602)
at org.springframework.jdbc.core.JdbcTemplate.execute(JdbcTemplate.java:614)
at org.springframework.jdbc.core.JdbcTemplate.batchUpdate(JdbcTemplate.java:883)
at org.springframework.jdbc.core.BatchUpdateUtils.executeBatchUpdate(BatchUpdateUtils.java:32)
at org.springframework.jdbc.core.simple.SimpleJdbcTemplate.batchUpdate(SimpleJdbcTemplate.java:257)
at org.springframework.jdbc.core.simple.SimpleJdbcTemplate.batchUpdate(SimpleJdbcTemplate.java:253)
at ome.util.SqlAction$Impl.createIdsTempTable(SqlAction.java:370)
at ome.util.SqlAction$Impl.rewriteHql(SqlAction.java:354)
at sun.reflect.GeneratedMethodAccessor263.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
at
This is part of #8587
Change History (3)
comment:1 Changed 7 years ago by cxallan
- Description modified (diff)
- Owner set to jmoore
- Sprint set to 2012-06-19 (17)
comment:2 Changed 7 years ago by jmoore
- Resolution set to fixed
- Status changed from new to closed
Problem is reproducible with:
import omero
import omero.all
ids = range(1,10000)
params = omero.sys.ParametersI()
params.addIds(ids)
c = omero.client("localhost")
s = c.createSession("root", "ome")
q = s.getQueryService()
q.findAllByQuery("select i from Image i where i.id in (:ids)", params)
A quick fix has been pushed to sprint17-bugfixes which simply disables rewriteHql for PostreSQL:
commit 5c0ea66e73304cf080afe8d76cc9d1fceceeacbe
Author: jmoore <josh@glencoesoftware.com>
Date: Wed Jun 6 21:05:14 2012
Quick fix for temp_ids failure (See #3961, Fix #9077)
temp_ids was required for Oracle support, but was never
fully implemented for PostreSQL. This hasn't shown up
previously because only queries with more than 1000 ids
triggers the issue.
I've opened a RFE to fully fix the issue (#9109)
comment:3 Changed 7 years ago by rleigh
Imported fine for me on gretsky on 7/6/12.
Note: See
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tickets.
You may also have a look at Agilo extensions to the ticket.
Confirmed. Assigning to Josh, server side stack trace with timestamps available below:
... 2012-06-06 18:45:19,661 WARN [ ome.services.util.ServiceHandler] (l.Server-1) InvalidDataAccessResourceUsageException thrown. org.springframework.jdbc.BadSqlGrammarException: PreparedStatementCallback; bad SQL grammar [insert into temp_ids (key, id) values (?, ?)]; nested exception is org.postgresql.util.PSQLException: ERROR: relation "temp_ids" does not exist Position: 13 at org.springframework.jdbc.support.SQLErrorCodeSQLExceptionTranslator.doTranslate(SQLErrorCodeSQLExceptionTranslator.java:233) at org.springframework.jdbc.support.AbstractFallbackSQLExceptionTranslator.translate(AbstractFallbackSQLExceptionTranslator.java:72) at org.springframework.jdbc.core.JdbcTemplate.execute(JdbcTemplate.java:602) at org.springframework.jdbc.core.JdbcTemplate.execute(JdbcTemplate.java:614) at org.springframework.jdbc.core.JdbcTemplate.batchUpdate(JdbcTemplate.java:883) at org.springframework.jdbc.core.BatchUpdateUtils.executeBatchUpdate(BatchUpdateUtils.java:32) at org.springframework.jdbc.core.simple.SimpleJdbcTemplate.batchUpdate(SimpleJdbcTemplate.java:257) at org.springframework.jdbc.core.simple.SimpleJdbcTemplate.batchUpdate(SimpleJdbcTemplate.java:253) at ome.util.SqlAction$Impl.createIdsTempTable(SqlAction.java:370) at ome.util.SqlAction$Impl.rewriteHql(SqlAction.java:354) at sun.reflect.GeneratedMethodAccessor249.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) at ome.util.SqlAction$LoggingSqlAction.invoke(SqlAction.java:69) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) at $Proxy0.rewriteHql(Unknown Source) at ome.services.query.StringQuery.buildQuery(StringQuery.java:75) at ome.services.query.Query.doInHibernate(Query.java:222) at org.springframework.orm.hibernate3.HibernateTemplate.doExecute(HibernateTemplate.java:406) at org.springframework.orm.hibernate3.HibernateTemplate.execute(HibernateTemplate.java:339) at ome.logic.QueryImpl.execute(QueryImpl.java:144) at ome.logic.QueryImpl.findAllByQuery(QueryImpl.java:394) at ome.services.RawPixelsBean.prepare(RawPixelsBean.java:301) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) at ome.tools.hibernate.SessionHandler.doStateful(SessionHandler.java:182) at ome.tools.hibernate.SessionHandler.invoke(SessionHandler.java:166) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:241) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) at $Proxy93.prepare(Unknown Source) 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:597) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:98) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) at $Proxy93.prepare(Unknown Source) 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:597) at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:179) at ome.services.throttling.Callback.run(Callback.java:56) at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56) at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:137) at ome.services.blitz.impl.RawPixelsStoreI.prepare_async(RawPixelsStoreI.java:205) 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:597) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) at omero.cmd.CallContext.invoke(CallContext.java:59) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) at $Proxy94.prepare_async(Unknown Source) at omero.api._RawPixelsStoreTie.prepare_async(_RawPixelsStoreTie.java:260) at omero.api._RawPixelsStoreDisp.___prepare(_RawPixelsStoreDisp.java:413) at omero.api._RawPixelsStoreDisp.__dispatch(_RawPixelsStoreDisp.java:1285) at IceInternal.Incoming.invoke(Incoming.java:159) at Ice.ConnectionI.invokeAll(ConnectionI.java:2037) at Ice.ConnectionI.message(ConnectionI.java:972) at IceInternal.ThreadPool.run(ThreadPool.java:577) at IceInternal.ThreadPool.access$100(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971) Caused by: org.postgresql.util.PSQLException: ERROR: relation "temp_ids" does not exist Position: 13 at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2103) at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1836) at org.postgresql.core.v3.QueryExecutorImpl.sendQuery(QueryExecutorImpl.java:1091) at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:398) at org.postgresql.jdbc2.AbstractJdbc2Statement.executeBatch(AbstractJdbc2Statement.java:2754) at sun.reflect.GeneratedMethodAccessor750.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at bitronix.tm.resource.jdbc.BaseProxyHandlerClass.invoke(BaseProxyHandlerClass.java:63) at $Proxy56.executeBatch(Unknown Source) at org.springframework.jdbc.core.JdbcTemplate$4.doInPreparedStatement(JdbcTemplate.java:898) at org.springframework.jdbc.core.JdbcTemplate$4.doInPreparedStatement(JdbcTemplate.java:1) at org.springframework.jdbc.core.JdbcTemplate.execute(JdbcTemplate.java:586) ... 86 more 2012-06-06 18:45:19,662 INFO [ ome.services.util.ServiceHandler] (l.Server-1) Excp: org.springframework.jdbc.BadSqlGrammarException: PreparedStatementCallback; bad SQL grammar [insert into temp_ids (key, id) values (?, ?)]; nested exception is org.postgresql.util.PSQLException: ERROR: relation "temp_ids" does not exist Position: 13 ...