EDIT

Andreas Kohlbecker wrote:

When creating a species a new Taxon needs to be created for this species and the new taxon needs to be related to the genus via INCLUDED_IN.

Q1:

According to #6173 6) [N1T] 2. there should always only be one taxon per name for the higher classification.

The final decision on N1T was to create multiple taxa for higher rank taxon names, 1 taxon per classification. This will also hold for taxa of rank genus. Therefore we need to create multiple INCLUDED_IN relationships depending on the number of taxa we have.

Also after import of new higher classifications we need to attache subgeneric taxa to their according taxa in bulk.

So maybe we should implement an algorithm that creates these relationships for all relevant data additionally to the algorithm which attaches a single new taxon to its parents.

Andreas Müller wrote:

Andreas Kohlbecker wrote:

When creating a species a new Taxon needs to be created for this species and the new taxon needs to be related to the genus via INCLUDED_IN.

Q1:

According to #6173 6) [N1T] 2. there should always only be one taxon per name for the higher classification.

The final decision on N1T was to create multiple taxa for higher rank taxon names, 1 taxon per classification. This will also hold for taxa of rank genus. Therefore we need to create multiple INCLUDED_IN relationships depending on the number of taxa we have.

this is a misinterpretation of the N1T schema!

There is a problem when running the test in the maven test suite. The TaxonGraphHibernateListenerTest fails when it is run after specific combinations of other tests:

AnnotationDaoTest,CdmEntityDaoBaseTest,TaxonGraphHibernateListenerTest ==> FAILS
CdmEntityDaoBaseTest,AnnotationDaoTest,TaxonGraphHibernateListenerTest ==> FAILS
AnnotationDaoTest,TaxonGraphHibernateListenerTest ==> OK
CdmEntityDaoBaseTest,TaxonGraphHibernateListenerTest ==> OK

The problem caused by the test combination is:

org.hibernate.SessionException: Session is closed!
        at org.hibernate.internal.AbstractSessionImpl.errorIfClosed(AbstractSessionImpl.java:132)
        at org.hibernate.internal.SessionImpl.clear(SessionImpl.java:384)
        at org.springframework.orm.hibernate5.SpringSessionSynchronization.afterCompletion(SpringSessionSynchronization.java:143)
        at org.springframework.transaction.support.TransactionSynchronizationUtils.invokeAfterCompletion(TransactionSynchronizationUtils.java:168)
        at org.springframework.transaction.support.AbstractPlatformTransactionManager.invokeAfterCompletion(AbstractPlatformTransactionManager.java:1001)
        at org.springframework.transaction.support.AbstractPlatformTransactionManager.triggerAfterCompletion(AbstractPlatformTransactionManager.java:976)
        at org.springframework.transaction.support.AbstractPlatformTransactionManager.processRollback(AbstractPlatformTransactionManager.java:880)
        at org.springframework.transaction.support.AbstractPlatformTransactionManager.rollback(AbstractPlatformTransactionManager.java:830)
        at eu.etaxonomy.cdm.test.integration.CdmTransactionalIntegrationTest.endTransaction(CdmTransactionalIntegrationTest.java:306)
        at eu.etaxonomy.cdm.test.integration.CdmTransactionalIntegrationTest.onTearDown(CdmTransactionalIntegrationTest.java:232)

"Session is closed!"-problem is solved now.

After moving the TaxonGraphHibernateListenerTest into cdmlib-services we are again facing problems with test being not independent.

Running

mvn  -Dtest=eu.etaxonomy.cdm.api.service.dto.TaxonRelationshipsDTOTest,eu.etaxonomy.cdm.api.service.taxonGraph.TaxonGraphHibernateListenerTest test

causes all tests in TaxonGraphHibernateListenerTest to fail due to polluted Session.

Tests in error: 
  testChangeSpecificEpithet_of_InfraSpecific(eu.etaxonomy.cdm.api.service.taxonGraph.TaxonGraphHibernateListenerTest): object references an unsaved transient instance - save the transient instance before flushing: eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType
  testChangeNomRef(eu.etaxonomy.cdm.api.service.taxonGraph.TaxonGraphHibernateListenerTest): object references an unsaved transient instance - save the transient instance before flushing: eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType
  testChangeSpecificEpithet_of_Species(eu.etaxonomy.cdm.api.service.taxonGraph.TaxonGraphHibernateListenerTest): object references an unsaved transient instance - save the transient instance before flushing: eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType
  testChangeRank(eu.etaxonomy.cdm.api.service.taxonGraph.TaxonGraphHibernateListenerTest): object references an unsaved transient instance - save the transient instance before flushing: eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType
  testNewTaxonName(eu.etaxonomy.cdm.api.service.taxonGraph.TaxonGraphHibernateListenerTest): object references an unsaved transient instance - save the transient instance before flushing: eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType
  testChangeGenus(eu.etaxonomy.cdm.api.service.taxonGraph.TaxonGraphHibernateListenerTest): object references an unsaved transient instance - save the transient instance before flushing: eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType
  testNewGenusName(eu.etaxonomy.cdm.api.service.taxonGraph.TaxonGraphHibernateListenerTest): object references an unsaved transient instance - save the transient instance before flushing: eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType

When running all test which precedeTaxonGraphHibernateListenerTest in the suite

mvn -Dtest=eu.etaxonomy.cdm.api.service.SecurityTest,eu.etaxonomy.cdm.api.service.StatisticsServiceImplTest,eu.etaxonomy.cdm.api.service.TaxonNodeDtoByNameComparatorTest,eu.etaxonomy.cdm.api.service.TaxonNodeServiceImplTest,eu.etaxonomy.cdm.api.service.TaxonServiceImplBusinessTest,eu.etaxonomy.cdm.api.service.TaxonServiceImplTest,eu.etaxonomy.cdm.api.service.TaxonServiceSearchTaxaAndNamesTest,eu.etaxonomy.cdm.api.service.TaxonServiceSearchTest,eu.etaxonomy.cdm.api.service.TermServiceImplTest,eu.etaxonomy.cdm.api.service.TransmissionEngineDistributionTest,eu.etaxonomy.cdm.api.service.TreeIndexComparatorTest,eu.etaxonomy.cdm.api.service.TypeDesignationSetManagerTest,eu.etaxonomy.cdm.api.service.UserAndGroupServiceImplTest,eu.etaxonomy.cdm.api.service.VocabularyServiceImplTest,eu.etaxonomy.cdm.api.service.dto.TaxonRelationshipsDTOTest,eu.etaxonomy.cdm.api.service.idminter.RegistrationIdentifierMinterTest,eu.etaxonomy.cdm.api.service.lsid.LSIDAuthorityServiceTest,eu.etaxonomy.cdm.api.service.lsid.LSIDDataServiceTest,eu.etaxonomy.cdm.api.service.lsid.LSIDMetadataServiceTest,eu.etaxonomy.cdm.api.service.lsid.LSIDRegistryTest,eu.etaxonomy.cdm.api.service.molecular.AmplificationServiceTest,eu.etaxonomy.cdm.api.service.molecular.PrimerServiceTest,eu.etaxonomy.cdm.api.service.molecular.SequenceServiceTest,eu.etaxonomy.cdm.api.service.pager.PagerTest,eu.etaxonomy.cdm.api.service.search.LuceneIndexToolProviderTest,eu.etaxonomy.cdm.api.service.search.QueryFactoryTest,eu.etaxonomy.cdm.api.service.taxonGraph.TaxonGraphHibernateListenerTest test

only testNewGenusName() fails

This is just like playing lotto!

Since this is not a problem with the TaxonGraphHibernateListenerTest I am creating a new issue: #7818

The problem described in #7818 was not the actual cause for the test failing in the full suite, another candidate is the RegistrationIdentifierMinterTest:

mvn -Dtest=eu.etaxonomy.cdm.api.service.idminter.RegistrationIdentifierMinterTest,eu.etaxonomy.cdm.api.service.taxonGraph.TaxonGraphHibernateListenerTest test

now the expected functionality I implemented, but we could think about refactoring the TaxonGraphHibernateListener a bit:

Andreas Müller suggested to inject the ITaxonGraphDao into TaxonGraphBeforeTransactionCompleteProcess which could be done by passing it as cunstrucor parameter of the TaxonGraphBeforeTransactionCompleteProcess. Here some example code snippets of a spring configuration class setting up the TaxonGraphHibernateListener:

@Configuration
@CdmHibernateListener // enable the configuration which activates the TaxonGraphHibernateListener bean
public class MyConfiguration {

    @Autowired
    @Qualifier("runAsAuthenticationProvider")
    private AuthenticationProvider runAsAuthenticationProvider;

    @Autowired
    private ITaxonGraphHibernateListener taxonGraphHibernateListener;


    @Autowired
    private ITaxonGraphDao taxonGraphDao;

    @Bean
    public MyBean myBean() {
     taxonGraphHibernateListener.registerProcessClass(
        TaxonGraphBeforeTransactionCompleteProcess.class, 
        new Object[]{new RunAsAdmin(runAsAuthenticationProvider), taxonGraphDao}, 
        new Class[]{IRunAs.class, ITaxonGraphDao.class});
    }

}

The constructor of the TaxonGraphBeforeTransactionCompleteProcess would need to be adapted for this to work.
The main benefit of this excercise is that we could get rid of the AbstractHibernateTaxonGraphProcessor which currently is the common base class for the dao and the TaxonGraphBeforeTransactionCompleteProcess.

And also some documentation which goes beyond linking this ticket would be nice.

Andreas Kohlbecker wrote in #note-10:

"Session is closed!"-problem is solved now.

This fix was only a workaround and the problem showed up after migration to hibernate 5.2 again. I fixed it now removing pure static handling of CdmPreferenceLookup (now ...Cache) and replacing it by a Lookup per dao. The problem is that in the test suite there are multiple application contexts created (the ordinary one and the one with authentication used by CdmEntityDaoImpl) therefore a pure static approach mixes sessions between these 2 app contexts (commit 8c6b6172722d)