Fwd: Help understanding an Error....

[prquinlan]

Please can someone help with this error, i have changed some of the  
settings in the speedo config file and dont understand why i get this  
problem. This has only since i have been using 1.5. At the moment i  
cannot do a full restore of the data. It isnt when it tries to persist  
a Snomed object as by the stage it crashes they are in the database. It  
seems to be when it is adding a duplicate reference to the snomed  
instance. The concurrency is managed by the database, so the cache  
shouldnt really come into it?

Any ideas?

Thanks

phil

Begin forwarded message:

> From: Philip Quinlan <p.quinlan@...>
> Date: 3 October 2006 11:00:47 BST
> To: speedo@...
> Subject: Help understanding an Error....
>
> Hi,
>
> I am having a problem when restoring a large data file, after creating  
> around 700 patients i get this error:
>
> javax.jdo.JDODataStoreException: Problem while making persistent.
> at  
> org.objectweb.speedo.jdo.JDOPersonality.newDataStoreRuntimeException(JD
> OPersonality.java:156)
> at  
> org.objectweb.speedo.pm.lib.AbstractPOManager.speedoMakePersistent(Abst
> ractPOManager.java:491)
> at  
> org.objectweb.speedo.pm.jdo.lib.JDOPOManager.makePersistent(JDOPOManage
> r.java:718)
> at  
> org.objectweb.fractal.julia.generated.Cc5baff4b_0.makePersistent(INTERF
> ACE[JDOPOManagerItf])
> at tissueBank.Application.addObject(Application.java:9415)
> at tissueBank.Data.XmlReader.endElement(XmlReader.java:1063)
> at org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown  
> Source)
> at  
> org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanEndElement(Un
> known Source)
> at  
> org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDi
> spatcher.dispatch(Unknown Source)
> at  
> org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unkn
> own Source)
> at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
> at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown Source)
> at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
> at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
> at javax.xml.parsers.SAXParser.parse(Unknown Source)
> at javax.xml.parsers.SAXParser.parse(Unknown Source)
> at Servlets.TissueServ.doGet(TissueServ.java:1504)
> at javax.servlet.http.HttpServlet.service(HttpServlet.java:696)
> at javax.servlet.http.HttpServlet.service(HttpServlet.java:809)
> at  
> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applic
> ationFilterChain.java:200)
> at  
> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFil
> terChain.java:146)
> at  
> org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperVal
> ve.java:209)
> at  
> org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext.
> invokeNext(StandardPipeline.java:596)
> at  
> org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:
> 433)
> at  
> org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:948)
> at  
> org.apache.catalina.core.StandardContextValve.invoke(StandardContextVal
> ve.java:144)
> at  
> org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext.
> invokeNext(StandardPipeline.java:596)
> at  
> org.apache.catalina.valves.CertificatesValve.invoke(CertificatesValve.j
> ava:199)
> at  
> org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext.
> invokeNext(StandardPipeline.java:594)
> at  
> org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:
> 433)
> at  
> org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:948)
> at  
> org.apache.catalina.core.StandardContext.invoke(StandardContext.java:
> 2358)
> at  
> org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.jav
> a:133)
> at  
> org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext.
> invokeNext(StandardPipeline.java:596)
> at  
> org.apache.catalina.valves.ErrorDispatcherValve.invoke(ErrorDispatcherV
> alve.java:118)
> at  
> org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext.
> invokeNext(StandardPipeline.java:594)
> at  
> org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.jav
> a:116)
> at  
> org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext.
> invokeNext(StandardPipeline.java:594)
> at  
> org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:
> 433)
> at  
> org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:948)
> at  
> org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve
> .java:127)
> at  
> org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext.
> invokeNext(StandardPipeline.java:596)
> at  
> org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:
> 433)
> at  
> org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:948)
> at  
> org.apache.coyote.tomcat4.CoyoteAdapter.service(CoyoteAdapter.java:
> 152)
> at  
> org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:
> 799)
> at  
> org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process
> Connection(Http11Protocol.java:705)
> at  
> org.apache.tomcat.util.net.TcpWorkerThread.runIt(PoolTcpEndpoint.java:
> 577)
> at  
> org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPoo
> l.java:683)
> at java.lang.Thread.run(Thread.java:552)
> NestedThrowablesStackTrace:
> org.objectweb.perseus.persistence.api.RolledBackPersistenceException:  
> Another persistent object is already present into the cache  
> (identifier=org.objectweb.jorm.facility.naming.rdbsequence.RdbSequenceP
> Name@78 / pnc: tissueBank.PathSpecimen.Snomed /  
> pncRef:org.objectweb.speedo.sequence.lib.SpeedoSequenceBinder@d3e5cf /  
> value:120)
> at  
> org.objectweb.perseus.persistence.lib.TransactionalPersistenceManagerIm
> pl.checkCacheEntry(TransactionalPersistenceManagerImpl.java:256)
> at  
> org.objectweb.perseus.persistence.lib.TransactionalPersistenceManagerIm
> pl.readIntention(TransactionalPersistenceManagerImpl.java:903)
> at  
> org.objectweb.fractal.julia.generated.Cc4304444_0.readIntention(INTERFA
> CE[TransactionalPersistenceManager])
> at  
> org.objectweb.speedo.mim.lib.AbstractHomeImpl.readIntention(AbstractHom
> eImpl.java:211)
> at tissueBank.PathSpecimen.Snomed.speedoReadIntention(Snomed.java)
> at tissueBank.PathSpecimen.Snomed.jdoGetpathRef(Snomed.java)
> at  
> tissueBank.PathSpecimen.SnomedFields.speedoAdd(SnomedFields.java:572)
> at  
> tissueBank.Pathology.PathologistJobFields.speedoElementAdded(Pathologis
> tJobFields.java:312)
> at  
> tissueBank.Pathology.PathologistJob.speedoElementAdded(PathologistJob.j
> ava)
> at  
> org.objectweb.speedo.genclass.GenClass.fireSpeedoElementAdded(GenClass.
> java:177)
> at  
> org.objectweb.speedo.genclass.collection.CollectionAccessor.add(Collect
> ionAccessor.java:260)
> at  
> org.objectweb.speedo.genclass.collection.CollectionAccessor.addAll(Coll
> ectionAccessor.java:270)
> at  
> org.objectweb.speedo.genclass.collection.CollectionAccessor.setElements
> (CollectionAccessor.java:123)
> at  
> org.objectweb.speedo.genclass.GenClass.setElements(GenClass.java:380)
> at  
> tissueBank.Pathology.PathologistJobFields.makePersistent(PathologistJob
> Fields.java:479)
> at  
> org.objectweb.speedo.pm.lib.AbstractPOManager.speedoPersist(AbstractPOM
> anager.java:460)
> at  
> org.objectweb.speedo.pm.lib.AbstractPOManager.speedoMakePersistent(Abst
> ractPOManager.java:481)
> at  
> org.objectweb.fractal.julia.generated.Cc5baff4b_0.speedoMakePersistent(
> INTERFACE[JDOPOManagerItf])
> at  
> org.objectweb.speedo.genclass.AbstractGenClassHome.makePersistent(Abstr
> actGenClassHome.java:110)
> at  
> org.objectweb.speedo.genclass.collection.CollectionAccessor.speedoAdd(C
> ollectionAccessor.java:433)
> at  
> org.objectweb.speedo.genclass.collection.CollectionAccessor.add(Collect
> ionAccessor.java:251)
> at  
> org.objectweb.speedo.genclass.collection.CollectionAccessor.addAll(Coll
> ectionAccessor.java:270)
> at  
> org.objectweb.speedo.genclass.collection.CollectionAccessor.setElements
> (CollectionAccessor.java:123)
> at  
> org.objectweb.speedo.genclass.GenClass.setElements(GenClass.java:380)
> at  
> tissueBank.Patients.PatientFields.makePersistent(PatientFields.java:
> 1205)
> at  
> org.objectweb.speedo.pm.lib.AbstractPOManager.speedoPersist(AbstractPOM
> anager.java:460)
> at  
> org.objectweb.speedo.pm.lib.AbstractPOManager.speedoMakePersistent(Abst
> ractPOManager.java:481)
> at  
> org.objectweb.speedo.pm.jdo.lib.JDOPOManager.makePersistent(JDOPOManage
> r.java:718)
> at  
> org.objectweb.fractal.julia.generated.Cc5baff4b_0.makePersistent(INTERF
> ACE[JDOPOManagerItf])
> at tissueBank.Application.addObject(Application.java:9415)
> at tissueBank.Data.XmlReader.endElement(XmlReader.java:1063)
> at org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown  
> Source)
> at  
> org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanEndElement(Un
> known Source)
> at  
> org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDi
> spatcher.dispatch(Unknown Source)
> at  
> org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unkn
> own Source)
> at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
> at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown Source)
> at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
> at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
> at javax.xml.parsers.SAXParser.parse(Unknown Source)
> at javax.xml.parsers.SAXParser.parse(Unknown Source)
> at Servlets.TissueServ.doGet(TissueServ.java:1504)
> at javax.servlet.http.HttpServlet.service(HttpServlet.java:696)
> at javax.servlet.http.HttpServlet.service(HttpServlet.java:809)
> at  
> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applic
> ationFilterChain.java:200)
> at  
> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFil
> terChain.java:146)
> at  
> org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperVal
> ve.java:209)
> at  
> org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext.
> invokeNext(StandardPipeline.java:596)
> at  
> org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:
> 433)
> at  
> org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:948)
> at  
> org.apache.catalina.core.StandardContextValve.invoke(StandardContextVal
> ve.java:144)
> at  
> org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext.
> invokeNext(StandardPipeline.java:596)
> at  
> org.apache.catalina.valves.CertificatesValve.invoke(CertificatesValve.j
> ava:199)
> at  
> org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext.
> invokeNext(StandardPipeline.java:594)
> at  
> org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:
> 433)
> at  
> org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:948)
> at  
> org.apache.catalina.core.StandardContext.invoke(StandardContext.java:
> 2358)
> at  
> org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.jav
> a:133)
> at  
> org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext.
> invokeNext(StandardPipeline.java:596)
> at  
> org.apache.catalina.valves.ErrorDispatcherValve.invoke(ErrorDispatcherV
> alve.java:118)
> at  
> org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext.
> invokeNext(StandardPipeline.java:594)
> at  
> org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.jav
> a:116)
> at  
> org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext.
> invokeNext(StandardPipeline.java:594)
> at  
> org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:
> 433)
> at  
> org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:948)
> at  
> org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve
> .java:127)
> at  
> org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext.
> invokeNext(StandardPipeline.java:596)
> at  
> org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:
> 433)
> at  
> org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:948)
> at  
> org.apache.coyote.tomcat4.CoyoteAdapter.service(CoyoteAdapter.java:
> 152)
> at  
> org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:
> 799)
> at  
> org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process
> Connection(Http11Protocol.java:705)
> at  
> org.apache.tomcat.util.net.TcpWorkerThread.runIt(PoolTcpEndpoint.java:
> 577)
> at  
> org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPoo
> l.java:683)
> at java.lang.Thread.run(Thread.java:552)
>
> Its not one i am used to getting so any help understanding where the  
> problem is with my code would be appreciated.
>
> Thanks.
>
> phil

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[Sebastien Chassande-Barrioz-2]

Hi,

The problem is not simple to understand.

After taking a look to your .jdo file, I have some questions :

- Do you really have several threads working with the SAME transaction(persistence manager) ?
If no, I advice you to set the javax.jdo.option.Multithreaded option to false (default value).

- How do you do your complete restore process ? Do you have several transactions ? Several threads ?

- Could you confirm that your application is java application and not a J2EE application ?

- Why did you desactivate the prefetch on genclass ?

Regards,
Seb

Regards,
Seb

2006/10/12, Philip Quinlan <p.quinlan@...>:

Please can someone help with this error, i have changed some of the
settings in the speedo config file and dont understand why i get this
problem. This has only since i have been using 1.5. At the moment i
cannot do a full restore of the data. It isnt when it tries to persist
a Snomed object as by the stage it crashes they are in the database. It
seems to be when it is adding a duplicate reference to the snomed
instance. The concurrency is managed by the database, so the cache
shouldnt really come into it?

Any ideas?

Thanks

phil

--
Sébastien Chassande-Barrioz
GSM: (+33) 06.73.16.09.32
MSN: klaneon@...

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To unsubscribe: mailto:speedo-unsubscribe@...
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[prquinlan]

Regarding this error, i have found that if i catch this error and then  
do evictAll and flush on the PM then it will then commit this object. I  
thought that by setting the concurrency to the database the caches  
werent really used? I cant replicate the fault, except it happens  
randomly in the 1.5 release and never happened in 1.4 which suggests to  
me it is something to do with the new way speedo implements things  
rather than a coding problem my end?

Phil


On 12 Oct 2006, at 21:37, Philip Quinlan wrote:

> Please can someone help with this error, i have changed some of the  
> settings in the speedo config file and dont understand why i get this  
> problem. This has only since i have been using 1.5. At the moment i  
> cannot do a full restore of the data. It isnt when it tries to persist  
> a Snomed object as by the stage it crashes they are in the database.  
> It seems to be when it is adding a duplicate reference to the snomed  
> instance. The concurrency is managed by the database, so the cache  
> shouldnt really come into it?
>
> Any ideas?
>
> Thanks
>
> phil
>
> Begin forwarded message:
>
>> From: Philip Quinlan <p.quinlan@...>
>> Date: 3 October 2006 11:00:47 BST
>> To: speedo@...
>> Subject: Help understanding an Error....
>>
>> Hi,
>>
>> I am having a problem when restoring a large data file, after  
>> creating around 700 patients i get this error:
>>
>> javax.jdo.JDODataStoreException: Problem while making persistent.
>> at  
>> org.objectweb.speedo.jdo.JDOPersonality.newDataStoreRuntimeException(J
>> DOPersonality.java:156)
>> at  
>> org.objectweb.speedo.pm.lib.AbstractPOManager.speedoMakePersistent(Abs
>> tractPOManager.java:491)
>> at  
>> org.objectweb.speedo.pm.jdo.lib.JDOPOManager.makePersistent(JDOPOManag
>> er.java:718)
>> at  
>> org.objectweb.fractal.julia.generated.Cc5baff4b_0.makePersistent(INTER
>> FACE[JDOPOManagerItf])
>> at tissueBank.Application.addObject(Application.java:9415)
>> at tissueBank.Data.XmlReader.endElement(XmlReader.java:1063)
>> at org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown  
>> Source)
>> at  
>> org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanEndElement(U
>> nknown Source)
>> at  
>> org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentD
>> ispatcher.dispatch(Unknown Source)
>> at  
>> org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unk
>> nown Source)
>> at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
>> at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown Source)
>> at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
>> at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
>> at javax.xml.parsers.SAXParser.parse(Unknown Source)
>> at javax.xml.parsers.SAXParser.parse(Unknown Source)
>> at Servlets.TissueServ.doGet(TissueServ.java:1504)
>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:696)
>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:809)
>> at  
>> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Appli
>> cationFilterChain.java:200)
>> at  
>> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFi
>> lterChain.java:146)
>> at  
>> org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperVa
>> lve.java:209)
>> at  
>> org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext
>> .invokeNext(StandardPipeline.java:596)
>> at  
>> org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java
>> :433)
>> at  
>> org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:948)
>> at  
>> org.apache.catalina.core.StandardContextValve.invoke(StandardContextVa
>> lve.java:144)
>> at  
>> org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext
>> .invokeNext(StandardPipeline.java:596)
>> at  
>> org.apache.catalina.valves.CertificatesValve.invoke(CertificatesValve.
>> java:199)
>> at  
>> org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext
>> .invokeNext(StandardPipeline.java:594)
>> at  
>> org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java
>> :433)
>> at  
>> org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:948)
>> at  
>> org.apache.catalina.core.StandardContext.invoke(StandardContext.java:
>> 2358)
>> at  
>> org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.ja
>> va:133)
>> at  
>> org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext
>> .invokeNext(StandardPipeline.java:596)
>> at  
>> org.apache.catalina.valves.ErrorDispatcherValve.invoke(ErrorDispatcher
>> Valve.java:118)
>> at  
>> org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext
>> .invokeNext(StandardPipeline.java:594)
>> at  
>> org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.ja
>> va:116)
>> at  
>> org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext
>> .invokeNext(StandardPipeline.java:594)
>> at  
>> org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java
>> :433)
>> at  
>> org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:948)
>> at  
>> org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValv
>> e.java:127)
>> at  
>> org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext
>> .invokeNext(StandardPipeline.java:596)
>> at  
>> org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java
>> :433)
>> at  
>> org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:948)
>> at  
>> org.apache.coyote.tomcat4.CoyoteAdapter.service(CoyoteAdapter.java:
>> 152)
>> at  
>> org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:
>> 799)
>> at  
>> org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.proces
>> sConnection(Http11Protocol.java:705)
>> at  
>> org.apache.tomcat.util.net.TcpWorkerThread.runIt(PoolTcpEndpoint.java:
>> 577)
>> at  
>> org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPo
>> ol.java:683)
>> at java.lang.Thread.run(Thread.java:552)
>> NestedThrowablesStackTrace:
>> org.objectweb.perseus.persistence.api.RolledBackPersistenceException:  
>> Another persistent object is already present into the cache  
>> (identifier=org.objectweb.jorm.facility.naming.rdbsequence.RdbSequence
>> PName@78 / pnc: tissueBank.PathSpecimen.Snomed /  
>> pncRef:org.objectweb.speedo.sequence.lib.SpeedoSequenceBinder@d3e5cf  
>> / value:120)
>> at  
>> org.objectweb.perseus.persistence.lib.TransactionalPersistenceManagerI
>> mpl.checkCacheEntry(TransactionalPersistenceManagerImpl.java:256)
>> at  
>> org.objectweb.perseus.persistence.lib.TransactionalPersistenceManagerI
>> mpl.readIntention(TransactionalPersistenceManagerImpl.java:903)
>> at  
>> org.objectweb.fractal.julia.generated.Cc4304444_0.readIntention(INTERF
>> ACE[TransactionalPersistenceManager])
>> at  
>> org.objectweb.speedo.mim.lib.AbstractHomeImpl.readIntention(AbstractHo
>> meImpl.java:211)
>> at tissueBank.PathSpecimen.Snomed.speedoReadIntention(Snomed.java)
>> at tissueBank.PathSpecimen.Snomed.jdoGetpathRef(Snomed.java)
>> at  
>> tissueBank.PathSpecimen.SnomedFields.speedoAdd(SnomedFields.java:572)
>> at  
>> tissueBank.Pathology.PathologistJobFields.speedoElementAdded(Pathologi
>> stJobFields.java:312)
>> at  
>> tissueBank.Pathology.PathologistJob.speedoElementAdded(PathologistJob.
>> java)
>> at  
>> org.objectweb.speedo.genclass.GenClass.fireSpeedoElementAdded(GenClass
>> .java:177)
>> at  
>> org.objectweb.speedo.genclass.collection.CollectionAccessor.add(Collec
>> tionAccessor.java:260)
>> at  
>> org.objectweb.speedo.genclass.collection.CollectionAccessor.addAll(Col
>> lectionAccessor.java:270)
>> at  
>> org.objectweb.speedo.genclass.collection.CollectionAccessor.setElement
>> s(CollectionAccessor.java:123)
>> at  
>> org.objectweb.speedo.genclass.GenClass.setElements(GenClass.java:380)
>> at  
>> tissueBank.Pathology.PathologistJobFields.makePersistent(PathologistJo
>> bFields.java:479)
>> at  
>> org.objectweb.speedo.pm.lib.AbstractPOManager.speedoPersist(AbstractPO
>> Manager.java:460)
>> at  
>> org.objectweb.speedo.pm.lib.AbstractPOManager.speedoMakePersistent(Abs
>> tractPOManager.java:481)
>> at  
>> org.objectweb.fractal.julia.generated.Cc5baff4b_0.speedoMakePersistent
>> (INTERFACE[JDOPOManagerItf])
>> at  
>> org.objectweb.speedo.genclass.AbstractGenClassHome.makePersistent(Abst
>> ractGenClassHome.java:110)
>> at  
>> org.objectweb.speedo.genclass.collection.CollectionAccessor.speedoAdd(
>> CollectionAccessor.java:433)
>> at  
>> org.objectweb.speedo.genclass.collection.CollectionAccessor.add(Collec
>> tionAccessor.java:251)
>> at  
>> org.objectweb.speedo.genclass.collection.CollectionAccessor.addAll(Col
>> lectionAccessor.java:270)
>> at  
>> org.objectweb.speedo.genclass.collection.CollectionAccessor.setElement
>> s(CollectionAccessor.java:123)
>> at  
>> org.objectweb.speedo.genclass.GenClass.setElements(GenClass.java:380)
>> at  
>> tissueBank.Patients.PatientFields.makePersistent(PatientFields.java:
>> 1205)
>> at  
>> org.objectweb.speedo.pm.lib.AbstractPOManager.speedoPersist(AbstractPO
>> Manager.java:460)
>> at  
>> org.objectweb.speedo.pm.lib.AbstractPOManager.speedoMakePersistent(Abs
>> tractPOManager.java:481)
>> at  
>> org.objectweb.speedo.pm.jdo.lib.JDOPOManager.makePersistent(JDOPOManag
>> er.java:718)
>> at  
>> org.objectweb.fractal.julia.generated.Cc5baff4b_0.makePersistent(INTER
>> FACE[JDOPOManagerItf])
>> at tissueBank.Application.addObject(Application.java:9415)
>> at tissueBank.Data.XmlReader.endElement(XmlReader.java:1063)
>> at org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown  
>> Source)
>> at  
>> org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanEndElement(U
>> nknown Source)
>> at  
>> org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentD
>> ispatcher.dispatch(Unknown Source)
>> at  
>> org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unk
>> nown Source)
>> at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
>> at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown Source)
>> at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
>> at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
>> at javax.xml.parsers.SAXParser.parse(Unknown Source)
>> at javax.xml.parsers.SAXParser.parse(Unknown Source)
>> at Servlets.TissueServ.doGet(TissueServ.java:1504)
>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:696)
>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:809)
>> at  
>> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Appli
>> cationFilterChain.java:200)
>> at  
>> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFi
>> lterChain.java:146)
>> at  
>> org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperVa
>> lve.java:209)
>> at  
>> org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext
>> .invokeNext(StandardPipeline.java:596)
>> at  
>> org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java
>> :433)
>> at  
>> org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:948)
>> at  
>> org.apache.catalina.core.StandardContextValve.invoke(StandardContextVa
>> lve.java:144)
>> at  
>> org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext
>> .invokeNext(StandardPipeline.java:596)
>> at  
>> org.apache.catalina.valves.CertificatesValve.invoke(CertificatesValve.
>> java:199)
>> at  
>> org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext
>> .invokeNext(StandardPipeline.java:594)
>> at  
>> org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java
>> :433)
>> at  
>> org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:948)
>> at  
>> org.apache.catalina.core.StandardContext.invoke(StandardContext.java:
>> 2358)
>> at  
>> org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.ja
>> va:133)
>> at  
>> org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext
>> .invokeNext(StandardPipeline.java:596)
>> at  
>> org.apache.catalina.valves.ErrorDispatcherValve.invoke(ErrorDispatcher
>> Valve.java:118)
>> at  
>> org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext
>> .invokeNext(StandardPipeline.java:594)
>> at  
>> org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.ja
>> va:116)
>> at  
>> org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext
>> .invokeNext(StandardPipeline.java:594)
>> at  
>> org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java
>> :433)
>> at  
>> org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:948)
>> at  
>> org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValv
>> e.java:127)
>> at  
>> org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext
>> .invokeNext(StandardPipeline.java:596)
>> at  
>> org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java
>> :433)
>> at  
>> org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:948)
>> at  
>> org.apache.coyote.tomcat4.CoyoteAdapter.service(CoyoteAdapter.java:
>> 152)
>> at  
>> org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:
>> 799)
>> at  
>> org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.proces
>> sConnection(Http11Protocol.java:705)
>> at  
>> org.apache.tomcat.util.net.TcpWorkerThread.runIt(PoolTcpEndpoint.java:
>> 577)
>> at  
>> org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPo
>> ol.java:683)
>> at java.lang.Thread.run(Thread.java:552)
>>
>> Its not one i am used to getting so any help understanding where the  
>> problem is with my code would be appreciated.
>>
>> Thanks.
>>
>> phil

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