It occurred to me I didn't include some of the required information when I posted this. So see below. Still grateful for any suggestions.
Thanks,
Andrew.
Hibernate version: 3.2.5.ga
Mapping documents:
Here's Client.hbm.xml since I used this entity in the example.
<?xml version="1.0"?>
<!DOCTYPE hibernate-mapping PUBLIC
"-//Hibernate/Hibernate Mapping DTD 3.0//EN"
"http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd">
<hibernate-mapping>
<class name="info.cathdb.funcnet_0_1.sessiondb.model.Client">
<meta attribute="class-description">Represents a FuncNet user at a specific location.</meta>
<meta attribute="class-code"> public static final long serialVersionUID = 1L; // Suppress Eclipse warning</meta>
<id column="client_id" type="integer">
<meta attribute="scope-set">protected</meta>
<generator class="increment" />
</id>
<property name="emailAddress" type="string" not-null="true">
<meta attribute="use-in-tostring">true</meta>
<meta attribute="use-in-equals">true</meta>
<meta attribute="scope-set">protected</meta>
</property>
<property name="inetAddress" type="string" not-null="true">
<meta attribute="use-in-tostring">true</meta>
<meta attribute="use-in-equals">true</meta>
<meta attribute="scope-set">protected</meta>
</property>
<!--
Taken this out because we never need to do it, and it's an extra manual step
to keep it updated.
<set name="sessions" inverse="true">
<key column="client_id" not-null="true" />
<one-to-many class="info.cathdb.funcnet_0_1.sessiondb.model.Session" />
</set>
-->
</class>
</hibernate-mapping>
Code between sessionFactory.openSession() and session.close():
The method is as follows -- the session and transaction open/close logic is wrapped around it automatically by warp-persist, using AOP method interception, as per the @Transactional annotation.
@Override @Transactional
public String createNewSession( Set<String> predictors, String emailAddress, String inetAddress, boolean enableEmailNotify )
{
if( predictors == null )
throw new IllegalArgumentException( "Predictor set may not be null" );
if( predictors.size() == 0 )
throw new IllegalArgumentException( "Predictor set may not be empty" );
if( emailAddress == null )
throw new IllegalArgumentException( "Email address may not be null" );
if( inetAddress == null )
throw new IllegalArgumentException( "Internet address may not be null" );
// Build client object, or retrieve matching one that already exists
org.hibernate.Session h3 = _h3.get();
inetAddress = inetAddress.trim();
Client client = getOrMakeClientMatching( emailAddress, inetAddress, h3 );
// Build and persist session object
String sessionID = makeSessionID();
Date now = new Date();
String status = PredictorStatus.WORKING.name(); // TODO get this working properly with enums
Session session = new Session( sessionID, now, status, client );
h3.saveOrUpdate( session );
// Build predictor session objects -- one for each predictor requested
for( String predictor : predictors )
{
PredictorSession ps = new PredictorSession( predictor, PredictorStatus.WORKING.name() );
session.getPredictors().add( ps );
}
return sessionID;
}
Full stack trace of any exception that occurs:
org.hibernate.exception.SQLGrammarException: could not execute query
at org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:67)
at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43)
at org.hibernate.loader.Loader.doList(Loader.java:2223)
at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2104)
at org.hibernate.loader.Loader.list(Loader.java:2099)
at org.hibernate.loader.criteria.CriteriaLoader.list(CriteriaLoader.java:94)
at org.hibernate.impl.SessionImpl.list(SessionImpl.java:1569)
at org.hibernate.impl.CriteriaImpl.list(CriteriaImpl.java:283)
at org.hibernate.impl.CriteriaImpl.uniqueResult(CriteriaImpl.java:305)
at info.cathdb.funcnet_0_1.sessiondb.hib3impl.HibernateRepository.getOrMakeClientMatching(HibernateRepository.java:382)
at info.cathdb.funcnet_0_1.sessiondb.hib3impl.HibernateRepository.createNewSession(HibernateRepository.java:100)
at info.cathdb.funcnet_0_1.sessiondb.hib3impl.HibernateRepository$$EnhancerByGuice$$9cd4ff07.CGLIB$createNewSession$8(<generated>)
at info.cathdb.funcnet_0_1.sessiondb.hib3impl.HibernateRepository$$EnhancerByGuice$$9cd4ff07$$FastClassByGuice$$d9d3bc19.invoke(<generated>)
at com.google.inject.cglib.proxy.MethodProxy.invokeSuper(MethodProxy.java:187)
at com.google.inject.InterceptorStackCallback$InterceptedMethodInvocation.proceed(InterceptorStackCallback.java:66)
at com.wideplay.warp.hibernate.HibernateLocalTxnInterceptor.invoke(HibernateLocalTxnInterceptor.java:68)
at com.google.inject.InterceptorStackCallback$InterceptedMethodInvocation.proceed(InterceptorStackCallback.java:66)
at com.google.inject.InterceptorStackCallback.intercept(InterceptorStackCallback.java:45)
at info.cathdb.funcnet_0_1.sessiondb.hib3impl.HibernateRepository$$EnhancerByGuice$$9cd4ff07.createNewSession(<generated>)
at info.cathdb.funcnet_0_1.sessiondb.hib3impl.RepositoryTest.createStandardSession(RepositoryTest.java:215)
at info.cathdb.funcnet_0_1.sessiondb.hib3impl.RepositoryTest.testMultipleIdenticalClientsAreUnified(RepositoryTest.java:206)
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.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:44)
at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:15)
at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:41)
at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:20)
at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:28)
at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:31)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:73)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:46)
at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:180)
at org.junit.runners.ParentRunner.access$000(ParentRunner.java:41)
at org.junit.runners.ParentRunner$1.evaluate(ParentRunner.java:173)
at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:28)
at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:31)
at org.junit.runners.ParentRunner.run(ParentRunner.java:220)
at org.eclipse.jdt.internal.junit4.runner.JUnit4TestReference.run(JUnit4TestReference.java:45)
at org.eclipse.jdt.internal.junit.runner.TestExecution.run(TestExecution.java:38)
at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:460)
at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:673)
at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.run(RemoteTestRunner.java:386)
at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.main(RemoteTestRunner.java:196)
Caused by: org.postgresql.util.PSQLException: ERROR: column this_.emailaddress does not exist
at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:1592)
at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1327)
at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:192)
at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:451)
at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:350)
at org.postgresql.jdbc2.AbstractJdbc2Statement.executeQuery(AbstractJdbc2Statement.java:254)
at org.hibernate.jdbc.AbstractBatcher.getResultSet(AbstractBatcher.java:186)
at org.hibernate.loader.Loader.getResultSet(Loader.java:1787)
at org.hibernate.loader.Loader.doQuery(Loader.java:674)
at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:236)
at org.hibernate.loader.Loader.doList(Loader.java:2220)
... 42 more
Name and version of the database you are using:
PostgreSQL 8.3.3
The generated SQL (show_sql=true):
Schema creation code from hbm2ddl:
create table client (client_id int4 not null, email_address varchar(255) not null, inet_address varchar(255) not null, primary key (client_id));
create table prediction (prediction_id int4 not null, predictor_session int4, protein1 varchar(255) not null, protein2 varchar(255) not null, raw_score float8 not null, p_value float8 not null, predictor_session_id int4 not null, primary key (prediction_id), unique (predictor_session, protein1, protein2));
create table predictor_session (predictor_session_id int4 not null, predictor_name varchar(255) not null, status varchar(255) not null, status_message varchar(255), session_id int4 not null, primary key (predictor_session_id));
create table session (session_id int4 not null, funcnet_jobid varchar(255) not null, start_time timestamp not null, status varchar(255) not null, client_id int4 not null, status_message varchar(255), comments varchar(255), enable_email_notify bool, primary key (session_id));
alter table prediction add constraint FK4537088FCA9B48B0 foreign key (predictor_session_id) references predictor_session;
alter table prediction add constraint FK4537088F5ABCC77C foreign key (predictor_session) references predictor_session;
alter table predictor_session add constraint FKA5BCDDD3406E3DEB foreign key (session_id) references session;
alter table session add constraint FK76508296E6113BC9 foreign key (client_id) references client;
But the actual query code ignores the naming strategy:
select this_.client_id as client1_3_0_, this_.emailAddress as emailAdd2_3_0_, this_.inetAddress as inetAddr3_3_0_ from Client this_ where this_.emailAddress ilike ? and this_.inetAddress ilike ?
Debug level Hibernate log excerpt:
Not sure where the stuff about naming strategies should appear, so here's the whole log for a single test case:
16:13:59,891 INFO Environment:514 - Hibernate 3.2.5
16:13:59,896 INFO Environment:532 - loaded properties from resource hibernate.properties: {hibernate.connection.driver_class=org.postgresql.Driver, hibernate.current_session_context_class=thread, hibernate.dialect=org.hibernate.dialect.PostgreSQLDialect, hibernate.jdbc.batch_size=50, hibernate.connection.username=funcnet, hibernate.connection.url=jdbc:postgresql://caffdubya/FuncNet, hibernate.bytecode.use_reflection_optimizer=false, hibernate.connection.password=****, hibernate.transaction.factory_class=org.hibernate.transaction.JDBCTransactionFactory}
16:13:59,896 INFO Environment:681 - Bytecode provider name : cglib
16:13:59,899 INFO Environment:598 - using JDK 1.4 java.sql.Timestamp handling
16:13:59,942 INFO Configuration:553 - Reading mappings from resource : Session.hbm.xml
16:13:59,985 DEBUG DTDEntityResolver:38 - trying to resolve system-id [http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd]
16:13:59,986 DEBUG DTDEntityResolver:40 - recognized hibernate namespace; attempting to resolve on classpath under org/hibernate/
16:13:59,992 DEBUG DTDEntityResolver:50 - located [http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd] in classpath
16:14:00,117 INFO HbmBinder:300 - Mapping class: info.cathdb.funcnet_0_1.sessiondb.model.Session -> Session
16:14:00,127 DEBUG HbmBinder:1270 - Mapped property: funcnetJobID -> funcnetJobID
16:14:00,128 DEBUG HbmBinder:1270 - Mapped property: startTime -> startTime
16:14:00,128 DEBUG HbmBinder:1270 - Mapped property: status -> status
16:14:00,225 DEBUG HbmBinder:1270 - Mapped property: client -> client_id
16:14:00,226 DEBUG HbmBinder:1270 - Mapped property: statusMessage -> statusMessage
16:14:00,226 DEBUG HbmBinder:1270 - Mapped property: comments -> comments
16:14:00,227 DEBUG HbmBinder:1270 - Mapped property: enableEmailNotify -> enableEmailNotify
16:14:00,230 DEBUG HbmBinder:1270 - Mapped property: predictors
16:14:00,230 DEBUG HbmBinder:2571 - Named query: info.cathdb.funcnet_0_1.sessiondb.model.Session.info.cathdb.funcnet_0_1.sessiondb.model.pairwiseScores ->
select prediction.protein1,
prediction.protein2,
-2 * sum( log( prediction.pValue ) )
from info.cathdb.funcnet_0_1.sessiondb.model.Session session
inner join session.predictors predictorSession
inner join predictorSession.predictions prediction
where session.funcnetJobID = :jobID
group by prediction.protein1,
prediction.protein2
16:14:00,231 INFO Configuration:553 - Reading mappings from resource : PredictorSession.hbm.xml
16:14:00,233 DEBUG DTDEntityResolver:38 - trying to resolve system-id [http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd]
16:14:00,234 DEBUG DTDEntityResolver:40 - recognized hibernate namespace; attempting to resolve on classpath under org/hibernate/
16:14:00,235 DEBUG DTDEntityResolver:50 - located [http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd] in classpath
16:14:00,272 INFO HbmBinder:300 - Mapping class: info.cathdb.funcnet_0_1.sessiondb.model.PredictorSession -> PredictorSession
16:14:00,272 DEBUG HbmBinder:1270 - Mapped property: predictorName -> predictorName
16:14:00,273 DEBUG HbmBinder:1270 - Mapped property: status -> status
16:14:00,273 DEBUG HbmBinder:1270 - Mapped property: statusMessage -> statusMessage
16:14:00,273 DEBUG HbmBinder:1270 - Mapped property: predictions
16:14:00,274 INFO Configuration:553 - Reading mappings from resource : Prediction.hbm.xml
16:14:00,275 DEBUG DTDEntityResolver:38 - trying to resolve system-id [http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd]
16:14:00,275 DEBUG DTDEntityResolver:40 - recognized hibernate namespace; attempting to resolve on classpath under org/hibernate/
16:14:00,279 DEBUG DTDEntityResolver:50 - located [http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd] in classpath
16:14:00,317 INFO HbmBinder:300 - Mapping class: info.cathdb.funcnet_0_1.sessiondb.model.Prediction -> Prediction
16:14:00,318 DEBUG HbmBinder:1270 - Mapped property: predictorSession -> predictorSession
16:14:00,319 DEBUG HbmBinder:1270 - Mapped property: protein1 -> protein1
16:14:00,319 DEBUG HbmBinder:1270 - Mapped property: protein2 -> protein2
16:14:00,320 DEBUG HbmBinder:1270 - Mapped property: rawScore -> rawScore
16:14:00,320 DEBUG HbmBinder:1270 - Mapped property: pValue -> pValue
16:14:00,324 INFO Configuration:553 - Reading mappings from resource : Client.hbm.xml
16:14:00,325 DEBUG DTDEntityResolver:38 - trying to resolve system-id [http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd]
16:14:00,325 DEBUG DTDEntityResolver:40 - recognized hibernate namespace; attempting to resolve on classpath under org/hibernate/
16:14:00,326 DEBUG DTDEntityResolver:50 - located [http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd] in classpath
16:14:00,357 INFO HbmBinder:300 - Mapping class: info.cathdb.funcnet_0_1.sessiondb.model.Client -> Client
16:14:00,357 DEBUG HbmBinder:1270 - Mapped property: emailAddress -> emailAddress
16:14:00,358 DEBUG HbmBinder:1270 - Mapped property: inetAddress -> inetAddress
16:14:00,513 DEBUG Configuration:1285 - Preparing to build session factory with filters : {}
16:14:00,513 DEBUG Configuration:1120 - processing extends queue
16:14:00,513 DEBUG Configuration:1124 - processing collection mappings
16:14:00,514 DEBUG CollectionSecondPass:41 - Second pass for collection: info.cathdb.funcnet_0_1.sessiondb.model.Session.predictors
16:14:00,514 INFO HbmBinder:2385 - Mapping collection: info.cathdb.funcnet_0_1.sessiondb.model.Session.predictors -> PredictorSession
16:14:00,515 DEBUG CollectionSecondPass:57 - Mapped collection key: session_id, one-to-many: info.cathdb.funcnet_0_1.sessiondb.model.PredictorSession
16:14:00,516 DEBUG CollectionSecondPass:41 - Second pass for collection: info.cathdb.funcnet_0_1.sessiondb.model.PredictorSession.predictions
16:14:00,516 INFO HbmBinder:2385 - Mapping collection: info.cathdb.funcnet_0_1.sessiondb.model.PredictorSession.predictions -> Prediction
16:14:00,516 DEBUG CollectionSecondPass:57 - Mapped collection key: predictor_session_id, one-to-many: info.cathdb.funcnet_0_1.sessiondb.model.Prediction
16:14:00,517 DEBUG Configuration:1135 - processing native query and ResultSetMapping mappings
16:14:00,517 DEBUG Configuration:1143 - processing association property references
16:14:00,517 DEBUG Configuration:1165 - processing foreign key constraints
16:14:00,518 DEBUG Configuration:1248 - resolving reference to class: info.cathdb.funcnet_0_1.sessiondb.model.PredictorSession
16:14:00,518 DEBUG Configuration:1248 - resolving reference to class: info.cathdb.funcnet_0_1.sessiondb.model.PredictorSession
16:14:00,518 DEBUG Configuration:1248 - resolving reference to class: info.cathdb.funcnet_0_1.sessiondb.model.Session
16:14:00,519 DEBUG Configuration:1248 - resolving reference to class: info.cathdb.funcnet_0_1.sessiondb.model.Client
16:14:00,523 INFO DriverManagerConnectionProvider:41 - Using Hibernate built-in connection pool (not for production use!)
16:14:00,523 INFO DriverManagerConnectionProvider:42 - Hibernate connection pool size: 20
16:14:00,524 INFO DriverManagerConnectionProvider:45 - autocommit mode: false
16:14:00,544 INFO DriverManagerConnectionProvider:80 - using driver: org.postgresql.Driver at URL: jdbc:postgresql://caffdubya/FuncNet
16:14:00,545 INFO DriverManagerConnectionProvider:83 - connection properties: {user=funcnet, password=4funcnetuse}
16:14:00,545 DEBUG DriverManagerConnectionProvider:93 - total checked-out connections: 0
16:14:00,545 DEBUG DriverManagerConnectionProvider:109 - opening new JDBC connection
16:14:00,599 DEBUG DriverManagerConnectionProvider:115 - created connection to: jdbc:postgresql://caffdubya/FuncNet, Isolation Level: 2
16:14:00,607 INFO SettingsFactory:89 - RDBMS: PostgreSQL, version: 8.3.3
16:14:00,609 INFO SettingsFactory:90 - JDBC driver: PostgreSQL Native Driver, version: PostgreSQL 8.3 JDBC4 with SSL (build 603)
16:14:00,609 DEBUG DriverManagerConnectionProvider:129 - returning connection to pool, pool size: 1
16:14:00,620 INFO Dialect:152 - Using dialect: org.hibernate.dialect.PostgreSQLDialect
16:14:00,624 INFO TransactionFactoryFactory:34 - Transaction strategy: org.hibernate.transaction.JDBCTransactionFactory
16:14:00,626 INFO TransactionManagerLookupFactory:33 - No TransactionManagerLookup configured (in JTA environment, use of read-write or transactional second-level cache is not recommended)
16:14:00,626 INFO SettingsFactory:143 - Automatic flush during beforeCompletion(): disabled
16:14:00,626 INFO SettingsFactory:147 - Automatic session close at end of transaction: disabled
16:14:00,627 INFO SettingsFactory:154 - JDBC batch size: 50
16:14:00,627 INFO SettingsFactory:157 - JDBC batch updates for versioned data: disabled
16:14:00,628 INFO SettingsFactory:162 - Scrollable result sets: enabled
16:14:00,628 DEBUG SettingsFactory:166 - Wrap result sets: disabled
16:14:00,628 INFO SettingsFactory:170 - JDBC3 getGeneratedKeys(): disabled
16:14:00,629 INFO SettingsFactory:178 - Connection release mode: auto
16:14:00,630 INFO SettingsFactory:205 - Default batch fetch size: 1
16:14:00,630 INFO SettingsFactory:209 - Generate SQL with comments: disabled
16:14:00,630 INFO SettingsFactory:213 - Order SQL updates by primary key: disabled
16:14:00,631 INFO SettingsFactory:217 - Order SQL inserts for batching: disabled
16:14:00,631 INFO SettingsFactory:386 - Query translator: org.hibernate.hql.ast.ASTQueryTranslatorFactory
16:14:00,633 INFO ASTQueryTranslatorFactory:24 - Using ASTQueryTranslatorFactory
16:14:00,633 INFO SettingsFactory:225 - Query language substitutions: {}
16:14:00,633 INFO SettingsFactory:230 - JPA-QL strict compliance: disabled
16:14:00,634 INFO SettingsFactory:235 - Second-level cache: enabled
16:14:00,634 INFO SettingsFactory:239 - Query cache: disabled
16:14:00,635 INFO SettingsFactory:373 - Cache provider: org.hibernate.cache.NoCacheProvider
16:14:00,635 INFO SettingsFactory:254 - Optimize cache for minimal puts: disabled
16:14:00,635 INFO SettingsFactory:263 - Structured second-level cache entries: disabled
16:14:00,636 DEBUG SQLExceptionConverterFactory:52 - Using dialect defined converter
16:14:00,639 INFO SettingsFactory:283 - Echoing all SQL to stdout
16:14:00,639 INFO SettingsFactory:290 - Statistics: disabled
16:14:00,640 INFO SettingsFactory:294 - Deleted entity synthetic identifier rollback: disabled
16:14:00,640 INFO SettingsFactory:309 - Default entity-mode: pojo
16:14:00,640 INFO SettingsFactory:313 - Named query checking : enabled
16:14:00,658 INFO SessionFactoryImpl:161 - building session factory
16:14:00,659 DEBUG SessionFactoryImpl:173 - Session factory constructed with filter configurations : {}
16:14:00,659 DEBUG SessionFactoryImpl:177 - instantiating session factory with properties: {java.runtime.name=Java(TM) SE Runtime Environment, hibernate.connection.password=4funcnetuse, sun.boot.library.path=/export/people/clegg/Java/jdk1.6.0_10/jre/lib/i386, java.vm.version=11.0-b15, hibernate.connection.username=funcnet, java.vm.vendor=Sun Microsystems Inc., java.vendor.url=http://java.sun.com/, path.separator=:, java.vm.name=Java HotSpot(TM) Server VM, file.encoding.pkg=sun.io, user.country=US, sun.java.launcher=SUN_STANDARD, sun.os.patch.level=unknown, java.vm.specification.name=Java Virtual Machine Specification, user.dir=/export/people/clegg/data/EmbraceWorkspace/EMBRACE/FuncNet/sessionDB, java.runtime.version=1.6.0_10-rc2-b32, java.awt.graphicsenv=sun.awt.X11GraphicsEnvironment, hibernate.current_session_context_class=thread, java.endorsed.dirs=/export/people/clegg/Java/jdk1.6.0_10/jre/lib/endorsed, os.arch=i386, java.io.tmpdir=/tmp, line.separator=
, java.vm.specification.vendor=Sun Microsystems Inc., os.name=Linux, sun.jnu.encoding=UTF-8, java.library.path=/export/people/clegg/Java/jdk1.6.0_10/jre/lib/i386/server:/export/people/clegg/Java/jdk1.6.0_10/jre/lib/i386:/export/people/clegg/Java/jdk1.6.0_10/jre/../lib/i386:/export/people/clegg/Java/java_ee_sdk-5_06/jdk/jre/lib/i386/client:/export/people/clegg/Java/java_ee_sdk-5_06/jdk/jre/lib/i386:/usr/lib/firefox-1.5.0.12:/usr/lib/firefox-1.5.0.12:/usr/java/packages/lib/i386:/lib:/usr/lib, java.specification.name=Java Platform API Specification, java.class.version=50.0, sun.management.compiler=HotSpot Tiered Compilers, hibernate.transaction.factory_class=org.hibernate.transaction.JDBCTransactionFactory, os.version=2.6.18-53.1.21.el5, user.home=/home/bsm/clegg, user.timezone=Europe/London, java.awt.printerjob=sun.print.PSPrinterJob, java.specification.version=1.6, file.encoding=UTF-8, hibernate.connection.driver_class=org.postgresql.Driver, user.name=clegg, java.class.path=/export/people/clegg/data/EmbraceWorkspace/EMBRACE/FuncNet/sessionDB/target/test-classes:/export/people/clegg/data/EmbraceWorkspace/EMBRACE/FuncNet/sessionDB/target/classes:/home/bsm/clegg/.m2/repository/antlr/antlr/2.7.6/antlr-2.7.6.jar:/home/bsm/clegg/.m2/repository/asm/asm/1.5.3/asm-1.5.3.jar:/home/bsm/clegg/.m2/repository/asm/asm-attrs/1.5.3/asm-attrs-1.5.3.jar:/home/bsm/clegg/.m2/repository/cglib/cglib/2.1_3/cglib-2.1_3.jar:/home/bsm/clegg/.m2/repository/commons-collections/commons-collections/2.1.1/commons-collections-2.1.1.jar:/home/bsm/clegg/.m2/repository/commons-logging/commons-logging/1.0.4/commons-logging-1.0.4.jar:/home/bsm/clegg/.m2/repository/dom4j/dom4j/1.6.1/dom4j-1.6.1.jar:/home/bsm/clegg/.m2/repository/net/sf/ehcache/ehcache/1.2.3/ehcache-1.2.3.jar:/home/bsm/clegg/.m2/repository/com/google/code/guice/guice/1.0/guice-1.0.jar:/home/bsm/clegg/.m2/repository/org/hibernate/hibernate/3.2.5.ga/hibernate-3.2.5.ga.jar:/home/bsm/clegg/.m2/repository/hsqldb/hsqldb/1.8.0.7/hsqldb-1.8.0.7.jar:/home/bsm/clegg/.m2/repository/javax/transaction/jta/1.1/jta-1.1.jar:/home/bsm/clegg/.m2/repository/junit/junit/4.5/junit-4.5.jar:/home/bsm/clegg/.m2/repository/log4j/log4j/1.2.14/log4j-1.2.14.jar:/home/bsm/clegg/.m2/repository/postgresql/postgresql/8.3-603.jdbc4/postgresql-8.3-603.jdbc4.jar:/home/bsm/clegg/.m2/repository/com/wideplay/warp/warp-persist/1.0.1/warp-persist-1.0.1.jar:/home/bsm/clegg/.m2/repository/postgresql/postgresql/8.3-604.jdbc4/postgresql-8.3-604.jdbc4.jar:/home/bsm/clegg/.m2/repository/aopalliance/aopalliance/1.0/aopalliance-1.0.jar:/export/people/clegg/sw/eclipse/configuration/org.eclipse.osgi/bundles/306/1/.cp/:/export/people/clegg/sw/eclipse/configuration/org.eclipse.osgi/bundles/304/1/.cp/:/export/people/clegg/sw/eclipse/configuration/org.eclipse.osgi/bundles/305/1/.cp/, hibernate.bytecode.use_reflection_optimizer=false, hibernate.show_sql=true, java.vm.specification.version=1.0, sun.arch.data.model=32, java.home=/export/people/clegg/Java/jdk1.6.0_10/jre, hibernate.connection.url=jdbc:postgresql://caffdubya/FuncNet, hibernate.dialect=org.hibernate.dialect.PostgreSQLDialect, java.specification.vendor=Sun Microsystems Inc., user.language=en, java.vm.info=mixed mode, java.version=1.6.0_10-rc2, java.ext.dirs=/export/people/clegg/Java/jdk1.6.0_10/jre/lib/ext:/usr/java/packages/lib/ext, sun.boot.class.path=/export/people/clegg/Java/jdk1.6.0_10/jre/lib/resources.jar:/export/people/clegg/Java/jdk1.6.0_10/jre/lib/rt.jar:/export/people/clegg/Java/jdk1.6.0_10/jre/lib/sunrsasign.jar:/export/people/clegg/Java/jdk1.6.0_10/jre/lib/jsse.jar:/export/people/clegg/Java/jdk1.6.0_10/jre/lib/jce.jar:/export/people/clegg/Java/jdk1.6.0_10/jre/lib/charsets.jar:/export/people/clegg/Java/jdk1.6.0_10/jre/classes, java.vendor=Sun Microsystems Inc., hibernate.jdbc.batch_size=50, file.separator=/, java.vendor.url.bug=http://java.sun.com/cgi-bin/bugreport.cgi, sun.cpu.endian=little, sun.io.unicode.encoding=UnicodeLittle, sun.desktop=gnome, sun.cpu.isalist=}
16:14:00,794 DEBUG AbstractEntityPersister:2738 - Static SQL for entity: info.cathdb.funcnet_0_1.sessiondb.model.PredictorSession
16:14:00,794 DEBUG AbstractEntityPersister:2743 - Version select: select predictor_session_id from PredictorSession where predictor_session_id =?
16:14:00,794 DEBUG AbstractEntityPersister:2746 - Snapshot select: select predictors_.predictor_session_id, predictors_.predictorName as predicto2_1_, predictors_.status as status1_, predictors_.statusMessage as statusMe4_1_ from PredictorSession predictors_ where predictors_.predictor_session_id=?
16:14:00,795 DEBUG AbstractEntityPersister:2749 - Insert 0: insert into PredictorSession (predictorName, status, statusMessage, session_id, predictor_session_id) values (?, ?, ?, ?, ?)
16:14:00,795 DEBUG AbstractEntityPersister:2750 - Update 0: update PredictorSession set predictorName=?, status=?, statusMessage=? where predictor_session_id=?
16:14:00,795 DEBUG AbstractEntityPersister:2751 - Delete 0: delete from PredictorSession where predictor_session_id=?
16:14:00,812 DEBUG AbstractEntityPersister:2738 - Static SQL for entity: info.cathdb.funcnet_0_1.sessiondb.model.Client
16:14:00,812 DEBUG AbstractEntityPersister:2743 - Version select: select client_id from Client where client_id =?
16:14:00,813 DEBUG AbstractEntityPersister:2746 - Snapshot select: select client_.client_id, client_.emailAddress as emailAdd2_3_, client_.inetAddress as inetAddr3_3_ from Client client_ where client_.client_id=?
16:14:00,813 DEBUG AbstractEntityPersister:2749 - Insert 0: insert into Client (emailAddress, inetAddress, client_id) values (?, ?, ?)
16:14:00,813 DEBUG AbstractEntityPersister:2750 - Update 0: update Client set emailAddress=?, inetAddress=? where client_id=?
16:14:00,814 DEBUG AbstractEntityPersister:2751 - Delete 0: delete from Client where client_id=?
16:14:00,822 DEBUG AbstractEntityPersister:2738 - Static SQL for entity: info.cathdb.funcnet_0_1.sessiondb.model.Prediction
16:14:00,823 DEBUG AbstractEntityPersister:2743 - Version select: select prediction_id from Prediction where prediction_id =?
16:14:00,823 DEBUG AbstractEntityPersister:2746 - Snapshot select: select prediction_.prediction_id, prediction_.predictorSession as predicto2_2_, prediction_.protein1 as protein3_2_, prediction_.protein2 as protein4_2_, prediction_.rawScore as rawScore2_, prediction_.pValue as pValue2_ from Prediction prediction_ where prediction_.prediction_id=?
16:14:00,823 DEBUG AbstractEntityPersister:2749 - Insert 0: insert into Prediction (predictorSession, protein1, protein2, rawScore, pValue, predictor_session_id, prediction_id) values (?, ?, ?, ?, ?, ?, ?)
16:14:00,824 DEBUG AbstractEntityPersister:2750 - Update 0: update Prediction set predictorSession=?, protein1=?, protein2=?, rawScore=?, pValue=? where prediction_id=?
16:14:00,824 DEBUG AbstractEntityPersister:2751 - Delete 0: delete from Prediction where prediction_id=?
16:14:00,833 DEBUG AbstractEntityPersister:2738 - Static SQL for entity: info.cathdb.funcnet_0_1.sessiondb.model.Session
16:14:00,833 DEBUG AbstractEntityPersister:2743 - Version select: select session_id from Session where session_id =?
16:14:00,833 DEBUG AbstractEntityPersister:2746 - Snapshot select: select session_.session_id, session_.funcnetJobID as funcnetJ2_0_, session_.startTime as startTime0_, session_.status as status0_, session_.client_id as client5_0_, session_.statusMessage as statusMe6_0_, session_.comments as comments0_, session_.enableEmailNotify as enableEm8_0_ from Session session_ where session_.session_id=?
16:14:00,834 DEBUG AbstractEntityPersister:2749 - Insert 0: insert into Session (funcnetJobID, startTime, status, client_id, statusMessage, comments, enableEmailNotify, session_id) values (?, ?, ?, ?, ?, ?, ?, ?)
16:14:00,834 DEBUG AbstractEntityPersister:2750 - Update 0: update Session set funcnetJobID=?, startTime=?, status=?, client_id=?, statusMessage=?, comments=?, enableEmailNotify=? where session_id=?
16:14:00,834 DEBUG AbstractEntityPersister:2751 - Delete 0: delete from Session where session_id=?
16:14:00,840 DEBUG AbstractCollectionPersister:548 - Static SQL for collection: info.cathdb.funcnet_0_1.sessiondb.model.Session.predictors
16:14:00,840 DEBUG AbstractCollectionPersister:550 - Row insert: update PredictorSession set session_id=? where predictor_session_id=?
16:14:00,841 DEBUG AbstractCollectionPersister:556 - Row delete: update PredictorSession set session_id=null where session_id=? and predictor_session_id=?
16:14:00,841 DEBUG AbstractCollectionPersister:559 - One-shot delete: update PredictorSession set session_id=null where session_id=?
16:14:00,842 DEBUG AbstractCollectionPersister:548 - Static SQL for collection: info.cathdb.funcnet_0_1.sessiondb.model.PredictorSession.predictions
16:14:00,842 DEBUG AbstractCollectionPersister:550 - Row insert: update Prediction set predictor_session_id=? where prediction_id=?
16:14:00,842 DEBUG AbstractCollectionPersister:556 - Row delete: update Prediction set predictor_session_id=null where predictor_session_id=? and prediction_id=?
16:14:00,843 DEBUG AbstractCollectionPersister:559 - One-shot delete: update Prediction set predictor_session_id=null where predictor_session_id=?
16:14:00,857 DEBUG EntityLoader:79 - Static select for entity info.cathdb.funcnet_0_1.sessiondb.model.PredictorSession: select predictors0_.predictor_session_id as predictor1_1_0_, predictors0_.predictorName as predicto2_1_0_, predictors0_.status as status1_0_, predictors0_.statusMessage as statusMe4_1_0_ from PredictorSession predictors0_ where predictors0_.predictor_session_id=?
16:14:00,857 DEBUG EntityLoader:79 - Static select for entity info.cathdb.funcnet_0_1.sessiondb.model.PredictorSession: select predictors0_.predictor_session_id as predictor1_1_0_, predictors0_.predictorName as predicto2_1_0_, predictors0_.status as status1_0_, predictors0_.statusMessage as statusMe4_1_0_ from PredictorSession predictors0_ where predictors0_.predictor_session_id=?
16:14:00,858 DEBUG EntityLoader:79 - Static select for entity info.cathdb.funcnet_0_1.sessiondb.model.PredictorSession: select predictors0_.predictor_session_id as predictor1_1_0_, predictors0_.predictorName as predicto2_1_0_, predictors0_.status as status1_0_, predictors0_.statusMessage as statusMe4_1_0_ from PredictorSession predictors0_ where predictors0_.predictor_session_id=? for update
16:14:00,858 DEBUG EntityLoader:79 - Static select for entity info.cathdb.funcnet_0_1.sessiondb.model.PredictorSession: select predictors0_.predictor_session_id as predictor1_1_0_, predictors0_.predictorName as predicto2_1_0_, predictors0_.status as status1_0_, predictors0_.statusMessage as statusMe4_1_0_ from PredictorSession predictors0_ where predictors0_.predictor_session_id=? for update
16:14:00,859 DEBUG EntityLoader:79 - Static select for entity info.cathdb.funcnet_0_1.sessiondb.model.PredictorSession: select predictors0_.predictor_session_id as predictor1_1_0_, predictors0_.predictorName as predicto2_1_0_, predictors0_.status as status1_0_, predictors0_.statusMessage as statusMe4_1_0_ from PredictorSession predictors0_ where predictors0_.predictor_session_id=? for update
16:14:00,866 DEBUG EntityLoader:34 - Static select for action ACTION_MERGE on entity info.cathdb.funcnet_0_1.sessiondb.model.PredictorSession: select predictors0_.predictor_session_id as predictor1_1_1_, predictors0_.predictorName as predicto2_1_1_, predictors0_.status as status1_1_, predictors0_.statusMessage as statusMe4_1_1_, prediction1_.predictor_session_id as predictor7_3_, prediction1_.prediction_id as prediction1_3_, prediction1_.prediction_id as prediction1_2_0_, prediction1_.predictorSession as predicto2_2_0_, prediction1_.protein1 as protein3_2_0_, prediction1_.protein2 as protein4_2_0_, prediction1_.rawScore as rawScore2_0_, prediction1_.pValue as pValue2_0_ from PredictorSession predictors0_ left outer join Prediction prediction1_ on predictors0_.predictor_session_id=prediction1_.predictor_session_id where predictors0_.predictor_session_id=?
16:14:00,867 DEBUG EntityLoader:34 - Static select for action ACTION_REFRESH on entity info.cathdb.funcnet_0_1.sessiondb.model.PredictorSession: select predictors0_.predictor_session_id as predictor1_1_1_, predictors0_.predictorName as predicto2_1_1_, predictors0_.status as status1_1_, predictors0_.statusMessage as statusMe4_1_1_, prediction1_.predictor_session_id as predictor7_3_, prediction1_.prediction_id as prediction1_3_, prediction1_.prediction_id as prediction1_2_0_, prediction1_.predictorSession as predicto2_2_0_, prediction1_.protein1 as protein3_2_0_, prediction1_.protein2 as protein4_2_0_, prediction1_.rawScore as rawScore2_0_, prediction1_.pValue as pValue2_0_ from PredictorSession predictors0_ left outer join Prediction prediction1_ on predictors0_.predictor_session_id=prediction1_.predictor_session_id where predictors0_.predictor_session_id=?
16:14:00,868 DEBUG EntityLoader:79 - Static select for entity info.cathdb.funcnet_0_1.sessiondb.model.Client: select client0_.client_id as client1_3_0_, client0_.emailAddress as emailAdd2_3_0_, client0_.inetAddress as inetAddr3_3_0_ from Client client0_ where client0_.client_id=?
16:14:00,868 DEBUG EntityLoader:79 - Static select for entity info.cathdb.funcnet_0_1.sessiondb.model.Client: select client0_.client_id as client1_3_0_, client0_.emailAddress as emailAdd2_3_0_, client0_.inetAddress as inetAddr3_3_0_ from Client client0_ where client0_.client_id=?
16:14:00,869 DEBUG EntityLoader:79 - Static select for entity info.cathdb.funcnet_0_1.sessiondb.model.Client: select client0_.client_id as client1_3_0_, client0_.emailAddress as emailAdd2_3_0_, client0_.inetAddress as inetAddr3_3_0_ from Client client0_ where client0_.client_id=? for update
16:14:00,869 DEBUG EntityLoader:79 - Static select for entity info.cathdb.funcnet_0_1.sessiondb.model.Client: select client0_.client_id as client1_3_0_, client0_.emailAddress as emailAdd2_3_0_, client0_.inetAddress as inetAddr3_3_0_ from Client client0_ where client0_.client_id=? for update
16:14:00,869 DEBUG EntityLoader:79 - Static select for entity info.cathdb.funcnet_0_1.sessiondb.model.Client: select client0_.client_id as client1_3_0_, client0_.emailAddress as emailAdd2_3_0_, client0_.inetAddress as inetAddr3_3_0_ from Client client0_ where client0_.client_id=? for update
16:14:00,870 DEBUG EntityLoader:34 - Static select for action ACTION_MERGE on entity info.cathdb.funcnet_0_1.sessiondb.model.Client: select client0_.client_id as client1_3_0_, client0_.emailAddress as emailAdd2_3_0_, client0_.inetAddress as inetAddr3_3_0_ from Client client0_ where client0_.client_id=?
16:14:00,870 DEBUG EntityLoader:34 - Static select for action ACTION_REFRESH on entity info.cathdb.funcnet_0_1.sessiondb.model.Client: select client0_.client_id as client1_3_0_, client0_.emailAddress as emailAdd2_3_0_, client0_.inetAddress as inetAddr3_3_0_ from Client client0_ where client0_.client_id=?
16:14:00,871 DEBUG EntityLoader:79 - Static select for entity info.cathdb.funcnet_0_1.sessiondb.model.Prediction: select prediction0_.prediction_id as prediction1_2_0_, prediction0_.predictorSession as predicto2_2_0_, prediction0_.protein1 as protein3_2_0_, prediction0_.protein2 as protein4_2_0_, prediction0_.rawScore as rawScore2_0_, prediction0_.pValue as pValue2_0_ from Prediction prediction0_ where prediction0_.prediction_id=?
16:14:00,871 DEBUG EntityLoader:79 - Static select for entity info.cathdb.funcnet_0_1.sessiondb.model.Prediction: select prediction0_.prediction_id as prediction1_2_0_, prediction0_.predictorSession as predicto2_2_0_, prediction0_.protein1 as protein3_2_0_, prediction0_.protein2 as protein4_2_0_, prediction0_.rawScore as rawScore2_0_, prediction0_.pValue as pValue2_0_ from Prediction prediction0_ where prediction0_.prediction_id=?
16:14:00,872 DEBUG EntityLoader:79 - Static select for entity info.cathdb.funcnet_0_1.sessiondb.model.Prediction: select prediction0_.prediction_id as prediction1_2_0_, prediction0_.predictorSession as predicto2_2_0_, prediction0_.protein1 as protein3_2_0_, prediction0_.protein2 as protein4_2_0_, prediction0_.rawScore as rawScore2_0_, prediction0_.pValue as pValue2_0_ from Prediction prediction0_ where prediction0_.prediction_id=? for update
16:14:00,872 DEBUG EntityLoader:79 - Static select for entity info.cathdb.funcnet_0_1.sessiondb.model.Prediction: select prediction0_.prediction_id as prediction1_2_0_, prediction0_.predictorSession as predicto2_2_0_, prediction0_.protein1 as protein3_2_0_, prediction0_.protein2 as protein4_2_0_, prediction0_.rawScore as rawScore2_0_, prediction0_.pValue as pValue2_0_ from Prediction prediction0_ where prediction0_.prediction_id=? for update
16:14:00,873 DEBUG EntityLoader:79 - Static select for entity info.cathdb.funcnet_0_1.sessiondb.model.Prediction: select prediction0_.prediction_id as prediction1_2_0_, prediction0_.predictorSession as predicto2_2_0_, prediction0_.protein1 as protein3_2_0_, prediction0_.protein2 as protein4_2_0_, prediction0_.rawScore as rawScore2_0_, prediction0_.pValue as pValue2_0_ from Prediction prediction0_ where prediction0_.prediction_id=? for update
16:14:00,873 DEBUG EntityLoader:34 - Static select for action ACTION_MERGE on entity info.cathdb.funcnet_0_1.sessiondb.model.Prediction: select prediction0_.prediction_id as prediction1_2_0_, prediction0_.predictorSession as predicto2_2_0_, prediction0_.protein1 as protein3_2_0_, prediction0_.protein2 as protein4_2_0_, prediction0_.rawScore as rawScore2_0_, prediction0_.pValue as pValue2_0_ from Prediction prediction0_ where prediction0_.prediction_id=?
16:14:00,874 DEBUG EntityLoader:34 - Static select for action ACTION_REFRESH on entity info.cathdb.funcnet_0_1.sessiondb.model.Prediction: select prediction0_.prediction_id as prediction1_2_0_, prediction0_.predictorSession as predicto2_2_0_, prediction0_.protein1 as protein3_2_0_, prediction0_.protein2 as protein4_2_0_, prediction0_.rawScore as rawScore2_0_, prediction0_.pValue as pValue2_0_ from Prediction prediction0_ where prediction0_.prediction_id=?
16:14:00,874 DEBUG EntityLoader:79 - Static select for entity info.cathdb.funcnet_0_1.sessiondb.model.Session: select session0_.session_id as session1_0_0_, session0_.funcnetJobID as funcnetJ2_0_0_, session0_.startTime as startTime0_0_, session0_.status as status0_0_, session0_.client_id as client5_0_0_, session0_.statusMessage as statusMe6_0_0_, session0_.comments as comments0_0_, session0_.enableEmailNotify as enableEm8_0_0_ from Session session0_ where session0_.session_id=?
16:14:00,875 DEBUG EntityLoader:79 - Static select for entity info.cathdb.funcnet_0_1.sessiondb.model.Session: select session0_.session_id as session1_0_0_, session0_.funcnetJobID as funcnetJ2_0_0_, session0_.startTime as startTime0_0_, session0_.status as status0_0_, session0_.client_id as client5_0_0_, session0_.statusMessage as statusMe6_0_0_, session0_.comments as comments0_0_, session0_.enableEmailNotify as enableEm8_0_0_ from Session session0_ where session0_.session_id=?
16:14:00,875 DEBUG EntityLoader:79 - Static select for entity info.cathdb.funcnet_0_1.sessiondb.model.Session: select session0_.session_id as session1_0_0_, session0_.funcnetJobID as funcnetJ2_0_0_, session0_.startTime as startTime0_0_, session0_.status as status0_0_, session0_.client_id as client5_0_0_, session0_.statusMessage as statusMe6_0_0_, session0_.comments as comments0_0_, session0_.enableEmailNotify as enableEm8_0_0_ from Session session0_ where session0_.session_id=? for update
16:14:00,876 DEBUG EntityLoader:79 - Static select for entity info.cathdb.funcnet_0_1.sessiondb.model.Session: select session0_.session_id as session1_0_0_, session0_.funcnetJobID as funcnetJ2_0_0_, session0_.startTime as startTime0_0_, session0_.status as status0_0_, session0_.client_id as client5_0_0_, session0_.statusMessage as statusMe6_0_0_, session0_.comments as comments0_0_, session0_.enableEmailNotify as enableEm8_0_0_ from Session session0_ where session0_.session_id=? for update
16:14:00,876 DEBUG EntityLoader:79 - Static select for entity info.cathdb.funcnet_0_1.sessiondb.model.Session: select session0_.session_id as session1_0_0_, session0_.funcnetJobID as funcnetJ2_0_0_, session0_.startTime as startTime0_0_, session0_.status as status0_0_, session0_.client_id as client5_0_0_, session0_.statusMessage as statusMe6_0_0_, session0_.comments as comments0_0_, session0_.enableEmailNotify as enableEm8_0_0_ from Session session0_ where session0_.session_id=? for update
16:14:00,877 DEBUG EntityLoader:34 - Static select for action ACTION_MERGE on entity info.cathdb.funcnet_0_1.sessiondb.model.Session: select session0_.session_id as session1_0_1_, session0_.funcnetJobID as funcnetJ2_0_1_, session0_.startTime as startTime0_1_, session0_.status as status0_1_, session0_.client_id as client5_0_1_, session0_.statusMessage as statusMe6_0_1_, session0_.comments as comments0_1_, session0_.enableEmailNotify as enableEm8_0_1_, predictors1_.session_id as session5_3_, predictors1_.predictor_session_id as predictor1_3_, predictors1_.predictor_session_id as predictor1_1_0_, predictors1_.predictorName as predicto2_1_0_, predictors1_.status as status1_0_, predictors1_.statusMessage as statusMe4_1_0_ from Session session0_ left outer join PredictorSession predictors1_ on session0_.session_id=predictors1_.session_id where session0_.session_id=?
16:14:00,877 DEBUG EntityLoader:34 - Static select for action ACTION_REFRESH on entity info.cathdb.funcnet_0_1.sessiondb.model.Session: select session0_.session_id as session1_0_1_, session0_.funcnetJobID as funcnetJ2_0_1_, session0_.startTime as startTime0_1_, session0_.status as status0_1_, session0_.client_id as client5_0_1_, session0_.statusMessage as statusMe6_0_1_, session0_.comments as comments0_1_, session0_.enableEmailNotify as enableEm8_0_1_, predictors1_.session_id as session5_3_, predictors1_.predictor_session_id as predictor1_3_, predictors1_.predictor_session_id as predictor1_1_0_, predictors1_.predictorName as predicto2_1_0_, predictors1_.status as status1_0_, predictors1_.statusMessage as statusMe4_1_0_ from Session session0_ left outer join PredictorSession predictors1_ on session0_.session_id=predictors1_.session_id where session0_.session_id=?
16:14:00,883 DEBUG OneToManyLoader:64 - Static select for one-to-many info.cathdb.funcnet_0_1.sessiondb.model.Session.predictors: select predictors0_.session_id as session5_1_, predictors0_.predictor_session_id as predictor1_1_, predictors0_.predictor_session_id as predictor1_1_0_, predictors0_.predictorName as predicto2_1_0_, predictors0_.status as status1_0_, predictors0_.statusMessage as statusMe4_1_0_ from PredictorSession predictors0_ where predictors0_.session_id=?
16:14:00,884 DEBUG OneToManyLoader:64 - Static select for one-to-many info.cathdb.funcnet_0_1.sessiondb.model.PredictorSession.predictions: select prediction0_.predictor_session_id as predictor7_1_, prediction0_.prediction_id as prediction1_1_, prediction0_.prediction_id as prediction1_2_0_, prediction0_.predictorSession as predicto2_2_0_, prediction0_.protein1 as protein3_2_0_, prediction0_.protein2 as protein4_2_0_, prediction0_.rawScore as rawScore2_0_, prediction0_.pValue as pValue2_0_ from Prediction prediction0_ where prediction0_.predictor_session_id=?
16:14:00,885 DEBUG SessionFactoryObjectFactory:39 - initializing class SessionFactoryObjectFactory
16:14:00,887 DEBUG SessionFactoryObjectFactory:76 - registered: ff8080811e3b6ceb011e3b6cecb40000 (unnamed)
16:14:00,887 INFO SessionFactoryObjectFactory:82 - Not binding factory to JNDI, no JNDI name configured
16:14:00,888 DEBUG SessionFactoryImpl:308 - instantiated session factory
16:14:00,890 DEBUG SessionFactoryImpl:392 - Checking 1 named HQL queries
16:14:00,891 DEBUG SessionFactoryImpl:400 - Checking named query: info.cathdb.funcnet_0_1.sessiondb.model.Session.info.cathdb.funcnet_0_1.sessiondb.model.pairwiseScores
16:14:00,892 DEBUG QueryPlanCache:70 - unable to locate HQL query plan in cache; generating (
select prediction.protein1,
prediction.protein2,
-2 * sum( log( prediction.pValue ) )
from info.cathdb.funcnet_0_1.sessiondb.model.Session session
inner join session.predictors predictorSession
inner join predictorSession.predictions prediction
where session.funcnetJobID = :jobID
group by prediction.protein1,
prediction.protein2
)
16:14:00,928 DEBUG QueryTranslatorImpl:246 - parse() - HQL:
select prediction.protein1,
prediction.protein2,
-2 * sum( log( prediction.pValue ) )
from info.cathdb.funcnet_0_1.sessiondb.model.Session session
inner join session.predictors predictorSession
inner join predictorSession.predictions prediction
where session.funcnetJobID = :jobID
group by prediction.protein1,
prediction.protein2
16:14:00,944 DEBUG AST:266 - --- HQL AST ---
\-[QUERY] 'query'
+-[SELECT_FROM] 'SELECT_FROM'
| +-[FROM] 'from'
| | +-[RANGE] 'RANGE'
| | | +-[DOT] '.'
| | | | +-[DOT] '.'
| | | | | +-[DOT] '.'
| | | | | | +-[DOT] '.'
| | | | | | | +-[DOT] '.'
| | | | | | | | +-[IDENT] 'info'
| | | | | | | | \-[IDENT] 'cathdb'
| | | | | | | \-[IDENT] 'funcnet_0_1'
| | | | | | \-[IDENT] 'sessiondb'
| | | | | \-[IDENT] 'model'
| | | | \-[IDENT] 'Session'
| | | \-[ALIAS] 'session'
| | +-[JOIN] 'join'
| | | +-[INNER] 'inner'
| | | +-[DOT] '.'
| | | | +-[IDENT] 'session'
| | | | \-[IDENT] 'predictors'
| | | \-[ALIAS] 'predictorSession'
| | \-[JOIN] 'join'
| | +-[INNER] 'inner'
| | +-[DOT] '.'
| | | +-[IDENT] 'predictorSession'
| | | \-[IDENT] 'predictions'
| | \-[ALIAS] 'prediction'
| \-[SELECT] 'select'
| +-[DOT] '.'
| | +-[IDENT] 'prediction'
| | \-[IDENT] 'protein1'
| +-[DOT] '.'
| | +-[IDENT] 'prediction'
| | \-[IDENT] 'protein2'
| \-[STAR] '*'
| +-[UNARY_MINUS] '-'
| | \-[NUM_INT] '2'
| \-[AGGREGATE] 'sum'
| \-[METHOD_CALL] '('
| +-[IDENT] 'log'
| \-[EXPR_LIST] 'exprList'
| \-[DOT] '.'
| +-[IDENT] 'prediction'
| \-[IDENT] 'pValue'
+-[WHERE] 'where'
| \-[EQ] '='
| +-[DOT] '.'
| | +-[IDENT] 'session'
| | \-[IDENT] 'funcnetJobID'
| \-[COLON] ':'
| \-[IDENT] 'jobID'
\-[GROUP] 'group'
+-[DOT] '.'
| +-[IDENT] 'prediction'
| \-[IDENT] 'protein1'
\-[DOT] '.'
+-[IDENT] 'prediction'
\-[IDENT] 'protein2'
16:14:00,944 DEBUG ErrorCounter:68 - throwQueryException() : no errors
16:14:00,971 DEBUG HqlSqlBaseWalker:111 - select << begin [level=1, statement=select]
16:14:00,982 DEBUG FromElement:108 - FromClause{level=1} : info.cathdb.funcnet_0_1.sessiondb.model.Session (session) -> session0_
16:14:00,984 DEBUG FromReferenceNode:51 - Resolved : session -> session0_.session_id
16:14:00,985 DEBUG FromElement:525 - handling property dereference [info.cathdb.funcnet_0_1.sessiondb.model.Session (session) -> predictors (class)]
16:14:00,985 DEBUG DotNode:568 - getDataType() : predictors -> org.hibernate.type.SetType(info.cathdb.funcnet_0_1.sessiondb.model.Session.predictors)
16:14:00,986 DEBUG FromElementFactory:360 - createEntityAssociation() : One to many - path = session.predictors role = info.cathdb.funcnet_0_1.sessiondb.model.Session.predictors associatedEntityName = info.cathdb.funcnet_0_1.sessiondb.model.PredictorSession
16:14:00,988 DEBUG FromElement:108 - FromClause{level=1} : info.cathdb.funcnet_0_1.sessiondb.model.PredictorSession (predictorSession) -> predictors1_
16:14:00,988 DEBUG FromClause:233 - addJoinByPathMap() : session.predictors -> PredictorSession predictors1_
16:14:00,988 DEBUG DotNode:284 - dereferenceCollection() : Created new FROM element for session.predictors : PredictorSession predictors1_
16:14:00,989 DEBUG FromReferenceNode:51 - Resolved : session.predictors -> .
16:14:00,990 DEBUG HqlSqlWalker:320 - createFromJoinElement() : -- join tree --
\-[JOIN_FRAGMENT] FromElement: 'PredictorSession predictors1_' FromElement{explicit,not a collection join,not a fetch join,fetch non-lazy properties,classAlias=predictorSession,role=info.cathdb.funcnet_0_1.sessiondb.model.Session.predictors,tableName=PredictorSession,tableAlias=predictors1_,origin=Session session0_,colums={session0_.session_id ,className=info.cathdb.funcnet_0_1.sessiondb.model.PredictorSession}}
16:14:00,991 DEBUG FromReferenceNode:51 - Resolved : predictorSession -> predictors1_.predictor_session_id
16:14:00,991 DEBUG FromElement:525 - handling property dereference [info.cathdb.funcnet_0_1.sessiondb.model.PredictorSession (predictorSession) -> predictions (class)]
16:14:00,991 DEBUG DotNode:568 - getDataType() : predictions -> org.hibernate.type.SetType(info.cathdb.funcnet_0_1.sessiondb.model.PredictorSession.predictions)
16:14:00,992 DEBUG FromElementFactory:360 - createEntityAssociation() : One to many - path = predictorSession.predictions role = info.cathdb.funcnet_0_1.sessiondb.model.PredictorSession.predictions associatedEntityName = info.cathdb.funcnet_0_1.sessiondb.model.Prediction
16:14:00,992 DEBUG FromElement:108 - FromClause{level=1} : info.cathdb.funcnet_0_1.sessiondb.model.Prediction (prediction) -> prediction2_
16:14:00,992 DEBUG FromClause:233 - addJoinByPathMap() : predictorSession.predictions -> Prediction prediction2_
16:14:00,992 DEBUG DotNode:284 - dereferenceCollection() : Created new FROM element for predictorSession.predictions : Prediction prediction2_
16:14:00,993 DEBUG FromReferenceNode:51 - Resolved : predictorSession.predictions -> .
16:14:00,993 DEBUG HqlSqlWalker:320 - createFromJoinElement() : -- join tree --
\-[JOIN_FRAGMENT] FromElement: 'Prediction prediction2_' FromElement{explicit,not a collection join,not a fetch join,fetch non-lazy properties,classAlias=prediction,role=info.cathdb.funcnet_0_1.sessiondb.model.PredictorSession.predictions,tableName=Prediction,tableAlias=prediction2_,origin=PredictorSession predictors1_,colums={predictors1_.predictor_session_id ,className=info.cathdb.funcnet_0_1.sessiondb.model.Prediction}}
16:14:00,994 DEBUG FromReferenceNode:51 - Resolved : prediction -> prediction2_.prediction_id
16:14:00,994 DEBUG FromElement:525 - handling property dereference [info.cathdb.funcnet_0_1.sessiondb.model.Prediction (prediction) -> protein1 (class)]
16:14:00,994 DEBUG DotNode:568 - getDataType() : protein1 -> org.hibernate.type.StringType@1de0b5e
16:14:00,995 DEBUG FromReferenceNode:51 - Resolved : prediction.protein1 -> prediction2_.protein1
16:14:00,995 DEBUG FromElement:525 - handling property dereference [info.cathdb.funcnet_0_1.sessiondb.model.Prediction (prediction) -> protein1 (class)]
16:14:00,995 DEBUG FromReferenceNode:51 - Resolved : prediction -> prediction2_.prediction_id
16:14:00,996 DEBUG FromElement:525 - handling property dereference [info.cathdb.funcnet_0_1.sessiondb.model.Prediction (prediction) -> protein2 (class)]
16:14:00,996 DEBUG DotNode:568 - getDataType() : protein2 -> org.hibernate.type.StringType@1de0b5e
16:14:00,996 DEBUG FromReferenceNode:51 - Resolved : prediction.protein2 -> prediction2_.protein2
16:14:00,996 DEBUG FromElement:525 - handling property dereference [info.cathdb.funcnet_0_1.sessiondb.model.Prediction (prediction) -> protein2 (class)]
16:14:01,005 DEBUG FromReferenceNode:51 - Resolved : prediction -> prediction2_.prediction_id
16:14:01,005 DEBUG FromElement:525 - handling property dereference [info.cathdb.funcnet_0_1.sessiondb.model.Prediction (prediction) -> pValue (class)]
16:14:01,007 DEBUG DotNode:568 - getDataType() : pValue -> org.hibernate.type.DoubleType@96212a
16:14:01,007 DEBUG FromElement:525 - handling property dereference [info.cathdb.funcnet_0_1.sessiondb.model.Prediction (prediction) -> pValue (class)]
16:14:01,007 DEBUG FromReferenceNode:51 - Resolved : prediction.pValue -> prediction2_.pValue
16:14:01,012 DEBUG FromReferenceNode:51 - Resolved : session -> session0_.session_id
16:14:01,013 DEBUG FromElement:525 - handling property dereference [info.cathdb.funcnet_0_1.sessiondb.model.Session (session) -> funcnetJobID (class)]
16:14:01,013 DEBUG DotNode:568 - getDataType() : funcnetJobID -> org.hibernate.type.StringType@1de0b5e
16:14:01,013 DEBUG FromReferenceNode:51 - Resolved : session.funcnetJobID -> session0_.funcnetJobID
16:14:01,014 DEBUG FromReferenceNode:51 - Resolved : prediction -> prediction2_.prediction_id
16:14:01,015 DEBUG FromElement:525 - handling property dereference [info.cathdb.funcnet_0_1.sessiondb.model.Prediction (prediction) -> protein1 (class)]
16:14:01,015 DEBUG DotNode:568 - getDataType() : protein1 -> org.hibernate.type.StringType@1de0b5e
16:14:01,015 DEBUG FromReferenceNode:51 - Resolved : prediction.protein1 -> prediction2_.protein1
16:14:01,016 DEBUG FromReferenceNode:51 - Resolved : prediction -> prediction2_.prediction_id
16:14:01,016 DEBUG FromElement:525 - handling property dereference [info.cathdb.funcnet_0_1.sessiondb.model.Prediction (prediction) -> protein2 (class)]
16:14:01,016 DEBUG DotNode:568 - getDataType() : protein2 -> org.hibernate.type.StringType@1de0b5e
16:14:01,016 DEBUG FromReferenceNode:51 - Resolved : prediction.protein2 -> prediction2_.protein2
16:14:01,017 DEBUG HqlSqlBaseWalker:117 - select : finishing up [level=1, statement=select]
16:14:01,017 DEBUG HqlSqlWalker:509 - processQuery() : ( SELECT ( {select clause} ( prediction2_.protein1 prediction2_.prediction_id protein1 ) ( prediction2_.protein2 prediction2_.prediction_id protein2 ) ( * ( - 2 ) ( sum ( ( log ( exprList ( prediction2_.pValue prediction2_.prediction_id pValue ) ) ) ) ) ) ( FromClause{level=1} ( Session session0_ ( PredictorSession predictors1_ Prediction prediction2_ ) ) ) ( where ( = ( session0_.funcnetJobID session0_.session_id funcnetJobID ) ? ) ) ( group ( prediction2_.protein1 prediction2_.prediction_id protein1 ) ( prediction2_.protein2 prediction2_.prediction_id protein2 ) ) )
16:14:01,023 DEBUG JoinProcessor:148 - Using FROM fragment [Session session0_]
16:14:01,023 DEBUG JoinProcessor:148 - Using FROM fragment [inner join PredictorSession predictors1_ on session0_.session_id=predictors1_.session_id]
16:14:01,023 DEBUG JoinProcessor:148 - Using FROM fragment [inner join Prediction prediction2_ on predictors1_.predictor_session_id=prediction2_.predictor_session_id]
16:14:01,023 DEBUG HqlSqlBaseWalker:123 - select >> end [level=1, statement=select]
16:14:01,025 DEBUG AST:232 - --- SQL AST ---
\-[SELECT] QueryNode: 'SELECT' querySpaces (Prediction,PredictorSession,Session)
+-[SELECT_CLAUSE] SelectClause: '{select clause}'
| +-[DOT] DotNode: 'prediction2_.protein1' {propertyName=protein1,dereferenceType=4,propertyPath=protein1,path=prediction.protein1,tableAlias=prediction2_,className=info.cathdb.funcnet_0_1.sessiondb.model.Prediction,classAlias=prediction}
| | +-[ALIAS_REF] IdentNode: 'prediction2_.prediction_id' {alias=prediction, className=info.cathdb.funcnet_0_1.sessiondb.model.Prediction, tableAlias=prediction2_}
| | \-[IDENT] IdentNode: 'protein1' {originalText=protein1}
| +-[SELECT_COLUMNS] SqlNode: ' as col_0_0_'
| +-[DOT] DotNode: 'prediction2_.protein2' {propertyName=protein2,dereferenceType=4,propertyPath=protein2,path=prediction.protein2,tableAlias=prediction2_,className=info.cathdb.funcnet_0_1.sessiondb.model.Prediction,classAlias=prediction}
| | +-[ALIAS_REF] IdentNode: 'prediction2_.prediction_id' {alias=prediction, className=info.cathdb.funcnet_0_1.sessiondb.model.Prediction, tableAlias=prediction2_}
| | \-[IDENT] IdentNode: 'protein2' {originalText=protein2}
| +-[SELECT_COLUMNS] SqlNode: ' as col_1_0_'
| +-[STAR] BinaryArithmeticOperatorNode: '*' {dataType=org.hibernate.type.DoubleType@96212a}
| | +-[UNARY_MINUS] UnaryArithmeticNode: '-'
| | | \-[NUM_INT] LiteralNode: '2'
| | \-[AGGREGATE] AggregateNode: 'sum'
| | \-[METHOD_CALL] MethodNode: '('
| | +-[METHOD_NAME] IdentNode: 'log' {originalText=log}
| | \-[EXPR_LIST] SqlNode: 'exprList'
| | \-[DOT] DotNode: 'prediction2_.pValue' {propertyName=pValue,dereferenceType=4,propertyPath=pValue,path=prediction.pValue,tableAlias=prediction2_,className=info.cathdb.funcnet_0_1.sessiondb.model.Prediction,classAlias=prediction}
| | +-[ALIAS_REF] IdentNode: 'prediction2_.prediction_id' {alias=prediction, className=info.cathdb.funcnet_0_1.sessiondb.model.Prediction, tableAlias=prediction2_}
| | \-[IDENT] IdentNode: 'pValue' {originalText=pValue}
| \-[SELECT_COLUMNS] SqlNode: ' as col_2_0_'
+-[FROM] FromClause: 'from' FromClause{level=1, fromElementCounter=3, fromElements=3, fromElementByClassAlias=[predictorSession, session, prediction], fromElementByTableAlias=[prediction2_, predictors1_, session0_], fromElementsByPath=[session.predictors, predictorSession.predictions], collectionJoinFromElementsByPath=[], impliedElements=[]}
| \-[FROM_FRAGMENT] FromElement: 'Session session0_' FromElement{explicit,not a collection join,not a fetch join,fetch non-lazy properties,classAlias=session,role=null,tableName=Session,tableAlias=session0_,origin=null,colums={,className=info.cathdb.funcnet_0_1.sessiondb.model.Session}}
| \-[JOIN_FRAGMENT] FromElement: 'inner join PredictorSession predictors1_ on session0_.session_id=predictors1_.session_id' FromElement{explicit,not a collection join,not a fetch join,fetch non-lazy properties,classAlias=predictorSession,role=info.cathdb.funcnet_0_1.sessiondb.model.Session.predictors,tableName=PredictorSession,tableAlias=predictors1_,origin=Session session0_,colums={session0_.session_id ,className=info.cathdb.funcnet_0_1.sessiondb.model.PredictorSession}}
| \-[JOIN_FRAGMENT] FromElement: 'inner join Prediction prediction2_ on predictors1_.predictor_session_id=prediction2_.predictor_session_id' FromElement{explicit,not a collection join,not a fetch join,fetch non-lazy properties,classAlias=prediction,role=info.cathdb.funcnet_0_1.sessiondb.model.PredictorSession.predictions,tableName=Prediction,tableAlias=prediction2_,origin=inner join PredictorSession predictors1_ on session0_.session_id=predictors1_.session_id,colums={predictors1_.predictor_session_id ,className=info.cathdb.funcnet_0_1.sessiondb.model.Prediction}}
+-[WHERE] SqlNode: 'where'
| \-[EQ] BinaryLogicOperatorNode: '='
| +-[DOT] DotNode: 'session0_.funcnetJobID' {propertyName=funcnetJobID,dereferenceType=4,propertyPath=funcnetJobID,path=session.funcnetJobID,tableAlias=session0_,className=info.cathdb.funcnet_0_1.sessiondb.model.Session,classAlias=session}
| | +-[ALIAS_REF] IdentNode: 'session0_.session_id' {alias=session, className=info.cathdb.funcnet_0_1.sessiondb.model.Session, tableAlias=session0_}
| | \-[IDENT] IdentNode: 'funcnetJobID' {originalText=funcnetJobID}
| \-[NAMED_PARAM] ParameterNode: '?' {name=jobID, expectedType=org.hibernate.type.StringType@1de0b5e}
\-[GROUP] SqlNode: 'group'
+-[DOT] DotNode: 'prediction2_.protein1' {propertyName=protein1,dereferenceType=4,propertyPath=protein1,path=prediction.protein1,tableAlias=prediction2_,className=info.cathdb.funcnet_0_1.sessiondb.model.Prediction,classAlias=prediction}
| +-[ALIAS_REF] IdentNode: 'prediction2_.prediction_id' {alias=prediction, className=info.cathdb.funcnet_0_1.sessiondb.model.Prediction, tableAlias=prediction2_}
| \-[IDENT] IdentNode: 'protein1' {originalText=protein1}
\-[DOT] DotNode: 'prediction2_.protein2' {propertyName=protein2,dereferenceType=4,propertyPath=protein2,path=prediction.protein2,tableAlias=prediction2_,className=info.cathdb.funcnet_0_1.sessiondb.model.Prediction,classAlias=prediction}
+-[ALIAS_REF] IdentNode: 'prediction2_.prediction_id' {alias=prediction, className=info.cathdb.funcnet_0_1.sessiondb.model.Prediction, tableAlias=prediction2_}
\-[IDENT] IdentNode: 'protein2' {originalText=protein2}
16:14:01,026 DEBUG ErrorCounter:68 - throwQueryException() : no errors
16:14:01,034 DEBUG QueryTranslatorImpl:216 - HQL:
select prediction.protein1,
prediction.protein2,
-2 * sum( log( prediction.pValue ) )
from info.cathdb.funcnet_0_1.sessiondb.model.Session session
inner join session.predictors predictorSession
inner join predictorSession.predictions prediction
where session.funcnetJobID = :jobID
group by prediction.protein1,
prediction.protein2
16:14:01,034 DEBUG QueryTranslatorImpl:217 - SQL: select prediction2_.protein1 as col_0_0_, prediction2_.protein2 as col_1_0_, -2*sum(log(prediction2_.pValue)) as col_2_0_ from Session session0_ inner join PredictorSession predictors1_ on session0_.session_id=predictors1_.session_id inner join Prediction prediction2_ on predictors1_.predictor_session_id=prediction2_.predictor_session_id where session0_.funcnetJobID=? group by prediction2_.protein1 , prediction2_.protein2
16:14:01,035 DEBUG ErrorCounter:68 - throwQueryException() : no errors
16:14:01,040 DEBUG HQLQueryPlan:269 - HQL param location recognition took 1 mills (
select prediction.protein1,
prediction.protein2,
-2 * sum( log( prediction.pValue ) )
from info.cathdb.funcnet_0_1.sessiondb.model.Session session
inner join session.predictors predictorSession
inner join predictorSession.predictions prediction
where session.funcnetJobID = :jobID
group by prediction.protein1,
prediction.protein2
)
16:14:01,042 DEBUG SessionFactoryImpl:412 - Checking 0 named SQL queries
16:14:01,066 DEBUG SessionImpl:220 - opened session at timestamp: 12293576410
16:14:01,105 DEBUG ThreadLocalSessi
|