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hmsiccbl / screensaver1

Screensaver Version 1 - End of life on December 1, 2018
GNU General Public License v2.0
3 stars 3 forks source link

Well deprecator does not appear to work #99

Closed dwrobel1 closed 11 years ago

dwrobel1 commented 11 years ago

Well Deprecator utility broken:

LSBATCH: User input

./run.sh edu.harvard.med.screensaver.io.libraries.WellDeprecator -f Deprecate.txt -d 2013-05-09 -c "LC/MS of this well from retired copy I showed no peaks corresponding to either the expected molecule or possible fragments. Upon visual inspection, this well appears black on multiple plates, including the active cherry pick copy, retired copy I, and a not-thawed-since-formatted copy." -H pgsql.cl.med.harvard.edu -D screensaver -U screensaverweb -A 761 -AE djw11 -aa 761

Exited with exit code 1.

Resource usage summary:

CPU time   :     21.68 sec.
Max Memory :         2 MB
Max Swap   :        35 MB

Max Processes  :         1
Max Threads    :         1

The output (if any) follows:

log4j:ERROR setFile(null,true) call failed. java.io.FileNotFoundException: /groups/screensaver/batch/logs/screensaver.log (Permission denied) at java.io.FileOutputStream.openAppend(Native Method) at java.io.FileOutputStream.(FileOutputStream.java:192) at java.io.FileOutputStream.(FileOutputStream.java:116) at org.apache.log4j.FileAppender.setFile(FileAppender.java:294) at org.apache.log4j.FileAppender.activateOptions(FileAppender.java:165) at org.apache.log4j.DailyRollingFileAppender.activateOptions(DailyRollingFileAppender.java:223) at org.apache.log4j.config.PropertySetter.activate(PropertySetter.java:307) at org.apache.log4j.config.PropertySetter.setProperties(PropertySetter.java:172) at org.apache.log4j.config.PropertySetter.setProperties(PropertySetter.java:104) at org.apache.log4j.PropertyConfigurator.parseAppender(PropertyConfigurator.java:809) at org.apache.log4j.PropertyConfigurator.parseCategory(PropertyConfigurator.java:735) at org.apache.log4j.PropertyConfigurator.configureRootCategory(PropertyConfigurator.java:615) at org.apache.log4j.PropertyConfigurator.doConfigure(PropertyConfigurator.java:502) at org.apache.log4j.PropertyConfigurator.doConfigure(PropertyConfigurator.java:547) at org.apache.log4j.helpers.OptionConverter.selectAndConfigure(OptionConverter.java:483) at org.apache.log4j.LogManager.(LogManager.java:127) at org.apache.log4j.Logger.getLogger(Logger.java:117) at edu.harvard.med.screensaver.io.libraries.WellDeprecator.(WellDeprecator.java:47) log4j:ERROR Either File or DatePattern options are not set for appender [file]. 11:19:12,373 WARN edu.harvard.med.screensaver.ScreensaverProperties:205 - unknown feature cellHTS2 org.springframework.orm.jpa.JpaSystemException: org.hibernate.PersistentObjectException: detached entity passed to persist: edu.harvard.med.screensaver.model.users.ScreensaverUser; nested exception is javax.persistence.PersistenceException: org.hibernate.PersistentObjectException: detached entity passed to persist: edu.harvard.med.screensaver.model.users.ScreensaverUser at org.springframework.orm.jpa.EntityManagerFactoryUtils.convertJpaAccessExceptionIfPossible(EntityManagerFactoryUtils.java:311) at org.springframework.orm.jpa.DefaultJpaDialect.translateExceptionIfPossible(DefaultJpaDialect.java:120) at org.springframework.orm.jpa.JpaTransactionManager.doCommit(JpaTransactionManager.java:471) at org.springframework.transaction.support.AbstractPlatformTransactionManager.processCommit(AbstractPlatformTransactionManager.java:754) at org.springframework.transaction.support.AbstractPlatformTransactionManager.commit(AbstractPlatformTransactionManager.java:723) at org.springframework.transaction.interceptor.TransactionAspectSupport.commitTransactionAfterReturning(TransactionAspectSupport.java:393) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:120) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) at org.springframework.aop.framework.Cglib2AopProxy$DynamicAdvisedInterceptor.intercept(Cglib2AopProxy.java:621) at edu.harvard.med.screensaver.db.GenericEntityDAOImpl$$EnhancerByCGLIB$$749a8adf.doInTransaction() at edu.harvard.med.screensaver.io.libraries.WellDeprecator.main(WellDeprecator.java:80) Caused by: javax.persistence.PersistenceException: org.hibernate.PersistentObjectException: detached entity passed to persist: edu.harvard.med.screensaver.model.users.ScreensaverUser at org.hibernate.ejb.AbstractEntityManagerImpl.convert(AbstractEntityManagerImpl.java:1214) at org.hibernate.ejb.AbstractEntityManagerImpl.convert(AbstractEntityManagerImpl.java:1147) at org.hibernate.ejb.TransactionImpl.commit(TransactionImpl.java:81) at org.springframework.orm.jpa.JpaTransactionManager.doCommit(JpaTransactionManager.java:467) ... 8 more Caused by: org.hibernate.PersistentObjectException: detached entity passed to persist: edu.harvard.med.screensaver.model.users.ScreensaverUser at org.hibernate.event.def.DefaultPersistEventListener.onPersist(DefaultPersistEventListener.java:127) at org.hibernate.impl.SessionImpl.firePersistOnFlush(SessionImpl.java:834) at org.hibernate.impl.SessionImpl.persistOnFlush(SessionImpl.java:826) at org.hibernate.engine.CascadingAction$9.cascade(CascadingAction.java:357) at org.hibernate.engine.Cascade.cascadeToOne(Cascade.java:392) at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:335) at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:204) at org.hibernate.engine.Cascade.cascade(Cascade.java:161) at org.hibernate.event.def.AbstractSaveEventListener.cascadeBeforeSave(AbstractSaveEventListener.java:450) at org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:282) at org.hibernate.event.def.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:203) at org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:143) at org.hibernate.ejb.event.EJB3PersistEventListener.saveWithGeneratedId(EJB3PersistEventListener.java:69) at org.hibernate.event.def.DefaultPersistEventListener.entityIsTransient(DefaultPersistEventListener.java:179) at org.hibernate.event.def.DefaultPersistEventListener.onPersist(DefaultPersistEventListener.java:135) at org.hibernate.impl.SessionImpl.firePersistOnFlush(SessionImpl.java:834) at org.hibernate.impl.SessionImpl.persistOnFlush(SessionImpl.java:826) at org.hibernate.engine.CascadingAction$9.cascade(CascadingAction.java:357) at org.hibernate.engine.Cascade.cascadeToOne(Cascade.java:392) at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:335) at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:204) at org.hibernate.engine.Cascade.cascade(Cascade.java:161) at org.hibernate.event.def.AbstractFlushingEventListener.cascadeOnFlush(AbstractFlushingEventListener.java:154) at org.hibernate.event.def.AbstractFlushingEventListener.prepareEntityFlushes(AbstractFlushingEventListener.java:145) at org.hibernate.event.def.AbstractFlushingEventListener.flushEverythingToExecutions(AbstractFlushingEventListener.java:88) at org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:50) at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1216) at org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java:383) at org.hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java:133) at org.hibernate.ejb.TransactionImpl.commit(TransactionImpl.java:76) ... 9 more 11:19:22,560 ERROR edu.harvard.med.screensaver.io.libraries.WellDeprecator:101 - org.springframework.orm.jpa.JpaSystemException: org.hibernate.PersistentObjectException: detached entity passed to persist: edu.harvard.med.screensaver.model.users.ScreensaverUser; nested exception is javax.persistence.PersistenceException: org.hibernate.PersistentObjectException: detached entity passed to persist: edu.harvard.med.screensaver.model.users.ScreensaverUser