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15:31:44,025 INFO CollectionFactory:73 - JDK 1.4+ collections available
15:31:44,028 INFO CollectionFactory:76 - Commons Collections 3.x available
15:31:44,077 DEBUG PluggableSchemaResolver:95 - Loading schema mappings from [META-INF/spring.schemas]
15:31:44,081 DEBUG PluggableSchemaResolver:101 - Loaded schema mappings: {http://www.springframework.org/schema/aop/spring-aop-2.0.xsd=org/springframework/aop/config/spring-aop-2.0.xsd, http://www.springframework.org/schema/util/spring-util.xsd=org/springframework/beans/factory/xml/spring-util-2.0.xsd, http://www.springframework.org/schema/util/spring-util-2.0.xsd=org/springframework/beans/factory/xml/spring-util-2.0.xsd, http://www.springframework.org/schema/jee/spring-jee.xsd=org/springframework/ejb/config/spring-jee-2.0.xsd, http://www.springframework.org/schema/beans/spring-beans.xsd=org/springframework/beans/factory/xml/spring-beans-2.0.xsd, http://www.springframework.org/schema/lang/spring-lang-2.0.xsd=org/springframework/scripting/config/spring-lang-2.0.xsd, http://www.springframework.org/schema/tx/spring-tx-2.0.xsd=org/springframework/transaction/config/spring-tx-2.0.xsd, http://www.springframework.org/schema/lang/spring-lang.xsd=org/springframework/scripting/config/spring-lang-2.0.xsd, http://www.springframework.org/schema/tool/spring-tool.xsd=org/springframework/beans/factory/xml/spring-tool-2.0.xsd, http://www.springframework.org/schema/aop/spring-aop.xsd=org/springframework/aop/config/spring-aop-2.0.xsd, http://www.springframework.org/schema/tx/spring-tx.xsd=org/springframework/transaction/config/spring-tx-2.0.xsd, http://www.springframework.org/schema/tool/spring-tool-2.0.xsd=org/springframework/beans/factory/xml/spring-tool-2.0.xsd, http://www.springframework.org/schema/jee/spring-jee-2.0.xsd=org/springframework/ejb/config/spring-jee-2.0.xsd, http://www.springframework.org/schema/beans/spring-beans-2.0.xsd=org/springframework/beans/factory/xml/spring-beans-2.0.xsd}
15:31:44,082 DEBUG PluggableSchemaResolver:95 - Loading schema mappings from [META-INF/spring.schemas]
15:31:44,085 DEBUG PluggableSchemaResolver:101 - Loaded schema mappings: {http://www.springframework.org/schema/aop/spring-aop-2.0.xsd=org/springframework/aop/config/spring-aop-2.0.xsd, http://www.springframework.org/schema/util/spring-util.xsd=org/springframework/beans/factory/xml/spring-util-2.0.xsd, http://www.springframework.org/schema/util/spring-util-2.0.xsd=org/springframework/beans/factory/xml/spring-util-2.0.xsd, http://www.springframework.org/schema/jee/spring-jee.xsd=org/springframework/ejb/config/spring-jee-2.0.xsd, http://www.springframework.org/schema/beans/spring-beans.xsd=org/springframework/beans/factory/xml/spring-beans-2.0.xsd, http://www.springframework.org/schema/lang/spring-lang-2.0.xsd=org/springframework/scripting/config/spring-lang-2.0.xsd, http://www.springframework.org/schema/tx/spring-tx-2.0.xsd=org/springframework/transaction/config/spring-tx-2.0.xsd, http://www.springframework.org/schema/lang/spring-lang.xsd=org/springframework/scripting/config/spring-lang-2.0.xsd, http://www.springframework.org/schema/tool/spring-tool.xsd=org/springframework/beans/factory/xml/spring-tool-2.0.xsd, http://www.springframework.org/schema/aop/spring-aop.xsd=org/springframework/aop/config/spring-aop-2.0.xsd, http://www.springframework.org/schema/tx/spring-tx.xsd=org/springframework/transaction/config/spring-tx-2.0.xsd, http://www.springframework.org/schema/tool/spring-tool-2.0.xsd=org/springframework/beans/factory/xml/spring-tool-2.0.xsd, http://www.springframework.org/schema/jee/spring-jee-2.0.xsd=org/springframework/ejb/config/spring-jee-2.0.xsd, http://www.springframework.org/schema/beans/spring-beans-2.0.xsd=org/springframework/beans/factory/xml/spring-beans-2.0.xsd}
15:31:44,094 INFO XmlBeanDefinitionReader:330 - Loading XML bean definitions from class path resource [applicationContext.xml]
15:31:44,106 DEBUG DefaultDocumentLoader:73 - Using JAXP provider [com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderFactoryImpl]
15:31:44,181 DEBUG BeansDtdResolver:72 - Found beans DTD [http://www.springframework.org/dtd/spring-beans.dtd] in classpath: spring-beans.dtd
15:31:44,228 DEBUG DefaultNamespaceHandlerResolver:110 - Loaded mappings [{http://www.springframework.org/schema/p=org.springframework.beans.factory.xml.SimplePropertyNamespaceHandler, http://www.springframework.org/schema/lang=org.springframework.scripting.config.LangNamespaceHandler, http://www.springframework.org/schema/jee=org.springframework.ejb.config.JeeNamespaceHandler, http://www.springframework.org/schema/aop=org.springframework.aop.config.AopNamespaceHandler, http://www.springframework.org/schema/util=org.springframework.beans.factory.xml.UtilNamespaceHandler, http://www.springframework.org/schema/tx=org.springframework.transaction.config.TxNamespaceHandler}]
15:31:44,235 DEBUG ClassUtils:134 - Class [groovy.lang.GroovyObject] or one of its dependencies is not present: java.lang.ClassNotFoundException: groovy.lang.GroovyObject
15:31:44,236 DEBUG ClassUtils:134 - Class [org.jruby.IRuby] or one of its dependencies is not present: java.lang.ClassNotFoundException: org.jruby.IRuby
15:31:44,241 DEBUG ClassUtils:134 - Class [bsh.Interpreter] or one of its dependencies is not present: java.lang.ClassNotFoundException: bsh.Interpreter
15:31:44,295 DEBUG DefaultBeanDefinitionDocumentReader:84 - Loading bean definitions
15:31:44,373 DEBUG BeanDefinitionParserDelegate:350 - Neither XML 'id' nor 'name' specified - using generated bean name [org.springframework.orm.hibernate3.support.IdTransferringMergeEventListener#29428e]
15:31:44,378 DEBUG XmlBeanDefinitionReader:143 - Loaded 5 bean definitions from location pattern [applicationContext.xml]
15:31:44,380 INFO ClassPathXmlApplicationContext:100 - Bean factory for application context [org.springframework.context.support.ClassPathXmlApplicationContext;hashCode=26399554]: org.springframework.beans.factory.support.DefaultListableBeanFactory defining beans [dataSource,sessionFactory,transactionManager,compoundDAO,compound]; root of BeanFactory hierarchy
15:31:44,390 INFO ClassPathXmlApplicationContext:322 - 5 beans defined in application context [org.springframework.context.support.ClassPathXmlApplicationContext;hashCode=26399554]
15:31:44,428 INFO ClassPathXmlApplicationContext:473 - Unable to locate MessageSource with name 'messageSource': using default [org.springframework.context.support.DelegatingMessageSource@f7f540]
15:31:44,431 INFO ClassPathXmlApplicationContext:495 - Unable to locate ApplicationEventMulticaster with name 'applicationEventMulticaster': using default [org.springframework.context.event.SimpleApplicationEventMulticaster@19209ea]
15:31:44,433 INFO DefaultListableBeanFactory:261 - Pre-instantiating singletons in factory [org.springframework.beans.factory.support.DefaultListableBeanFactory defining beans [dataSource,sessionFactory,transactionManager,compoundDAO,compound]; root of BeanFactory hierarchy]
15:31:44,435 DEBUG DefaultListableBeanFactory:137 - Creating shared instance of singleton bean 'dataSource'
15:31:44,435 DEBUG DefaultListableBeanFactory:346 - Creating instance of bean 'dataSource' with merged definition [Root bean: class [org.springframework.jdbc.datasource.DriverManagerDataSource]; scope=singleton; abstract=false; lazyInit=false; autowireCandidate=true; autowireMode=0; dependencyCheck=0; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in class path resource [applicationContext.xml]]
15:31:44,495 DEBUG DefaultListableBeanFactory:397 - Eagerly caching bean 'dataSource' to allow for resolving potential circular references
15:31:44,523 INFO DriverManagerDataSource:155 - Loaded JDBC driver: org.hsqldb.jdbcDriver
15:31:44,525 DEBUG DefaultListableBeanFactory:137 - Creating shared instance of singleton bean 'sessionFactory'
15:31:44,528 DEBUG DefaultListableBeanFactory:346 - Creating instance of bean 'sessionFactory' with merged definition [Root bean: class [org.springframework.orm.hibernate3.LocalSessionFactoryBean]; scope=singleton; abstract=false; lazyInit=false; autowireCandidate=true; autowireMode=0; dependencyCheck=0; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in class path resource [applicationContext.xml]]
15:31:44,576 DEBUG DefaultListableBeanFactory:397 - Eagerly caching bean 'sessionFactory' to allow for resolving potential circular references
15:31:44,577 DEBUG DefaultListableBeanFactory:202 - Returning cached instance of singleton bean 'dataSource'
15:31:44,579 DEBUG DefaultListableBeanFactory:346 - Creating instance of bean 'org.springframework.orm.hibernate3.support.IdTransferringMergeEventListener#29428e' with merged definition [Root bean: class [org.springframework.orm.hibernate3.support.IdTransferringMergeEventListener]; scope=singleton; abstract=false; lazyInit=false; autowireCandidate=true; autowireMode=0; dependencyCheck=0; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in class path resource [applicationContext.xml]]
15:31:44,632 DEBUG DefaultListableBeanFactory:1116 - Invoking afterPropertiesSet() on bean with name 'sessionFactory'
15:31:44,661 INFO Environment:500 - Hibernate 3.2.1
15:31:44,668 INFO Environment:533 - hibernate.properties not found
15:31:44,676 INFO Environment:667 - Bytecode provider name : cglib
15:31:44,682 INFO Environment:584 - using JDK 1.4 java.sql.Timestamp handling
15:31:44,797 DEBUG DTDEntityResolver:38 - trying to resolve system-id [http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd]
15:31:44,798 DEBUG DTDEntityResolver:40 - recognized hibernate namespace; attempting to resolve on classpath under org/hibernate/
15:31:44,799 DEBUG DTDEntityResolver:50 - located [http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd] in classpath
15:31:44,962 INFO HbmBinder:300 - Mapping class: com.genebio.toxico.compound.CompoundImpl -> COMPOUND
15:31:44,972 DEBUG HbmBinder:1270 - Mapped property: id -> COMPOUND_ID
15:31:44,984 DEBUG HbmBinder:1270 - Mapped property: cid -> COMPOUND_CID
15:31:44,984 DEBUG HbmBinder:1270 - Mapped property: SMILE -> COMPOUND_SMILE
15:31:44,985 INFO LocalSessionFactoryBean:742 - Building new Hibernate SessionFactory
15:31:44,986 DEBUG Configuration:1282 - Preparing to build session factory with filters : {}
15:31:44,986 DEBUG Configuration:1117 - processing extends queue
15:31:44,987 DEBUG Configuration:1121 - processing collection mappings
15:31:44,987 DEBUG Configuration:1132 - processing native query and ResultSetMapping mappings
15:31:44,987 DEBUG Configuration:1140 - processing association property references
15:31:44,990 DEBUG Configuration:1162 - processing foreign key constraints
15:31:45,076 INFO ConnectionProviderFactory:72 - Initializing connection provider: org.springframework.orm.hibernate3.LocalDataSourceConnectionProvider
15:31:45,087 DEBUG DriverManagerDataSource:289 - Creating new JDBC Connection to [jdbc:hsqldb:file:data/toxico]
15:31:45,386 INFO SettingsFactory:81 - RDBMS: HSQL Database Engine, version: 1.8.0
15:31:45,387 INFO SettingsFactory:82 - JDBC driver: HSQL Database Engine Driver, version: 1.8.0
15:31:45,410 INFO Dialect:151 - Using dialect: org.hibernate.dialect.HSQLDialect
15:31:45,417 INFO TransactionFactoryFactory:31 - Using default transaction strategy (direct JDBC transactions)
15:31:45,420 INFO TransactionManagerLookupFactory:33 - No TransactionManagerLookup configured (in JTA environment, use of read-write or transactional second-level cache is not recommended)
15:31:45,421 INFO SettingsFactory:134 - Automatic flush during beforeCompletion(): disabled
15:31:45,421 INFO SettingsFactory:138 - Automatic session close at end of transaction: disabled
15:31:45,422 INFO SettingsFactory:145 - JDBC batch size: 15
15:31:45,422 INFO SettingsFactory:148 - JDBC batch updates for versioned data: disabled
15:31:45,423 INFO SettingsFactory:153 - Scrollable result sets: enabled
15:31:45,426 DEBUG SettingsFactory:157 - Wrap result sets: disabled
15:31:45,426 INFO SettingsFactory:161 - JDBC3 getGeneratedKeys(): disabled
15:31:45,427 INFO SettingsFactory:169 - Connection release mode: on_close
15:31:45,427 INFO SettingsFactory:196 - Default batch fetch size: 1
15:31:45,428 INFO SettingsFactory:200 - Generate SQL with comments: disabled
15:31:45,428 INFO SettingsFactory:204 - Order SQL updates by primary key: disabled
15:31:45,429 INFO SettingsFactory:369 - Query translator: org.hibernate.hql.ast.ASTQueryTranslatorFactory
15:31:45,432 INFO ASTQueryTranslatorFactory:24 - Using ASTQueryTranslatorFactory
15:31:45,432 INFO SettingsFactory:212 - Query language substitutions: {}
15:31:45,433 INFO SettingsFactory:217 - JPA-QL strict compliance: disabled
15:31:45,433 INFO SettingsFactory:222 - Second-level cache: enabled
15:31:45,435 INFO SettingsFactory:226 - Query cache: disabled
15:31:45,435 INFO SettingsFactory:356 - Cache provider: org.hibernate.cache.NoCacheProvider
15:31:45,436 INFO SettingsFactory:241 - Optimize cache for minimal puts: disabled
15:31:45,436 INFO SettingsFactory:250 - Structured second-level cache entries: disabled
15:31:45,443 INFO SettingsFactory:270 - Echoing all SQL to stdout
15:31:45,444 INFO SettingsFactory:277 - Statistics: disabled
15:31:45,445 INFO SettingsFactory:281 - Deleted entity synthetic identifier rollback: disabled
15:31:45,446 INFO SettingsFactory:296 - Default entity-mode: pojo
15:31:45,487 INFO SessionFactoryImpl:161 - building session factory
15:31:45,488 DEBUG SessionFactoryImpl:173 - Session factory constructed with filter configurations : {}
15:31:45,489 DEBUG SessionFactoryImpl:177 - instantiating session factory with properties: {java.runtime.name=Java(TM) SE Runtime Environment, sun.boot.library.path=/usr/java/jdk1.6.0_01/jre/lib/i386, java.vm.version=1.6.0_01-ea-b03, java.vm.vendor=Sun Microsystems Inc., java.vendor.url=http://java.sun.com/, path.separator=:, java.vm.name=Java HotSpot(TM) Client 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=/home/yannmauron/Desktop/test/ToxicoMSJava2, java.runtime.version=1.6.0_01-ea-b03, java.awt.graphicsenv=sun.awt.X11GraphicsEnvironment, java.endorsed.dirs=/usr/java/jdk1.6.0_01/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=/usr/java/jdk1.6.0_01/jre/lib/i386/client:/usr/java/jdk1.6.0_01/jre/lib/i386:/usr/java/jdk1.6.0_01/jre/../lib/i386:/usr/lib/j2se/1.4/jre/lib/i386/client:/usr/lib/j2se/1.4/jre/lib/i386:/usr/lib/j2se/1.4/jre/../lib/i386:/usr/lib/firefox/:/usr/java/packages/lib/i386:/lib:/usr/lib, java.specification.name=Java Platform API Specification, java.class.version=50.0, sun.management.compiler=HotSpot Client Compiler, os.version=2.6.17-11-generic, user.home=/home/yannmauron, user.timezone=Europe/Zurich, hibernate.connection.release_mode=on_close, java.awt.printerjob=sun.print.PSPrinterJob, file.encoding=UTF-8, java.specification.version=1.6, user.name=yannmauron, java.class.path=/home/yannmauron/Desktop/test/ToxicoMSJava2/bin:/home/yannmauron/Desktop/test/ToxicoMSJava2/lib/cdk-0.99.1.jar:/home/yannmauron/Desktop/test/ToxicoMSJava2/lib/commons-logging-1.1.jar:/home/yannmauron/Desktop/test/ToxicoMSJava2/lib/dom4j-1.6.1.jar:/home/yannmauron/Desktop/test/ToxicoMSJava2/lib/jaxen-1.1-beta-6.jar:/home/yannmauron/Desktop/test/ToxicoMSJava2/lib/junit-4.2.jar:/home/yannmauron/Desktop/test/ToxicoMSJava2/lib/log4j-1.2.14.jar:/home/yannmauron/Desktop/test/ToxicoMSJava2/lib/ProteomeCommons.org-IO.jar:/home/yannmauron/Desktop/test/ToxicoMSJava2/lib/ProteomeCommons.org-IO-T2D.jar:/home/yannmauron/java/hsqldb.jar:/home/yannmauron/java/spring-framework-2.0.2/dist/spring.jar:/home/yannmauron/java/spring-framework-2.0.2/dist/spring-aspects.jar:/home/yannmauron/java/spring-framework-2.0.2/dist/spring-mock.jar:/home/yannmauron/java/spring-framework-2.0.2/dist/spring-src.zip:/home/yannmauron/java/spring-framework-2.0.2/lib/j2ee/jta.jar:/home/yannmauron/java/spring-framework-2.0.2/lib/cglib/cglib-nodep-2.1_3.jar:/home/yannmauron/java/spring-framework-2.0.2/lib/hibernate/jboss-archive-browsing.jar:/home/yannmauron/java/spring-framework-2.0.2/lib/hibernate/hibernate3.jar:/home/yannmauron/java/spring-framework-2.0.2/lib/jakarta-commons/commons-collections.jar:/home/yannmauron/java/spring-framework-2.0.2/lib/log4j/log4j-1.2.14.jar:/home/yannmauron/Desktop/eclipse conf/eclipse/configuration/org.eclipse.osgi/bundles/228/1/.cp/:/home/yannmauron/Desktop/eclipse conf/eclipse/plugins/org.eclipse.jdt.junit_3.2.1.r321_v20060810/junitsupport.jar:/home/yannmauron/Desktop/eclipse conf/eclipse/plugins/org.eclipse.jdt.junit.runtime_3.2.1.r321_v20060721/junitruntime.jar, hibernate.bytecode.use_reflection_optimizer=false, hibernate.show_sql=true, java.vm.specification.version=1.0, sun.arch.data.model=32, java.home=/usr/java/jdk1.6.0_01/jre, hibernate.dialect=org.hibernate.dialect.HSQLDialect, java.specification.vendor=Sun Microsystems Inc., user.language=en, java.vm.info=mixed mode, sharing, java.version=1.6.0_01-ea, java.ext.dirs=/usr/java/jdk1.6.0_01/jre/lib/ext:/usr/java/packages/lib/ext, sun.boot.class.path=/usr/java/jdk1.6.0_01/jre/lib/resources.jar:/usr/java/jdk1.6.0_01/jre/lib/rt.jar:/usr/java/jdk1.6.0_01/jre/lib/sunrsasign.jar:/usr/java/jdk1.6.0_01/jre/lib/jsse.jar:/usr/java/jdk1.6.0_01/jre/lib/jce.jar:/usr/java/jdk1.6.0_01/jre/lib/charsets.jar:/usr/java/jdk1.6.0_01/jre/classes, java.vendor=Sun Microsystems Inc., file.separator=/, java.vendor.url.bug=http://java.sun.com/cgi-bin/bugreport.cgi, hibernate.connection.provider_class=org.springframework.orm.hibernate3.LocalDataSourceConnectionProvider, sun.cpu.endian=little, sun.io.unicode.encoding=UnicodeLittle, sun.desktop=gnome, sun.cpu.isalist=} |
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