protected DaoFactory getDaoFactory() { return IntactContext.getCurrentInstance().getDataContext().getDaoFactory(); } }
public List<String> getInteractionsDrExportNotPassed() { DataContext dataContext = IntactContext.getCurrentInstance().getDataContext(); TransactionStatus transactionStatus = dataContext.beginTransaction(); Query query = IntactContext.getCurrentInstance().getDaoFactory().getEntityManager().createQuery(interactionsDrExportNotPassed); query.setParameter("drExport", CvTopic.UNIPROT_DR_EXPORT); query.setParameter("yes", "YES"); query.setParameter("confidence", AUTHOR_SCORE_MI); List<String> interactions = query.getResultList(); dataContext.commitTransaction(transactionStatus); return interactions; }
public void commitTransaction( TransactionStatus transactionStatus ) throws IntactTransactionException { if (transactionStatus.isCompleted()) { if (log.isWarnEnabled()) log.warn("Transaction already committed. Cannot commit again"); return; } PlatformTransactionManager transactionManager = getTransactionManager(); try { if (log.isDebugEnabled()) log.debug("Committing transaction"); transactionManager.commit(transactionStatus); } catch (TransactionException e) { rollbackTransaction(transactionStatus); throw new IntactTransactionException( e ); } }
public TransactionStatus beginTransaction( int propagation ) { return beginTransaction(propagation, createTransactionName()); }
/** * Search the IntAct database and retreive a BioSource having the given taxid and no CvCellType or CvTissue. * * @param taxid a non null taxid. * @return a BioSource or null if none is found. */ private BioSource searchIntactByTaxid(String taxid) throws BioSourceServiceException { log.debug("Searching in the database for BioSource(" + taxid + ")"); DataContext dataContext = IntactContext.getCurrentInstance().getDataContext(); TransactionStatus transactionStatus = dataContext.beginTransaction(); BioSourceDao bsDao = dataContext.getDaoFactory().getBioSourceDao(); BioSource biosource = bsDao.getByTaxonIdUnique(taxid); try { dataContext.commitTransaction(transactionStatus); } catch (IntactTransactionException e) { throw new BioSourceServiceException("Problem committing", e); } if (log.isDebugEnabled()) { if (biosource == null) { log.debug("Could not find Biosource having taxid: " + taxid); } else { log.debug("Found 1 biosource: " + biosource.getShortLabel() + " [" + biosource.getAc() + "]"); } } return biosource; }
TransactionStatus transactionStatus = dataContext.beginTransaction(); dataContext.rollbackTransaction(transactionStatus);
CvXrefQualifier identity = intactContext.getDataContext().getDaoFactory() .getCvObjectDao(CvXrefQualifier.class).getByPsiMiRef(CvXrefQualifier.IDENTITY_MI_REF); DaoFactory daoFactory = IntactContext.getCurrentInstance().getDataContext().getDaoFactory(); Institution owner = daoFactory.getInstitutionDao().getByAc( IntactContext.getCurrentInstance().getInstitution().getAc() ); identity = cvBuilder.createIdentityCvXrefQualifier( owner ); identity.setFullName("identical object"); intactContext.getDataContext().getDaoFactory().getCvObjectDao(CvXrefQualifier.class).persist(identity); CvDatabase psi = intactContext.getDataContext().getDaoFactory() .getCvObjectDao(CvDatabase.class).getByPsiMiRef(CvDatabase.PSI_MI_MI_REF); psi = cvBuilder.createPsiMiCvDatabase(IntactContext.getCurrentInstance().getInstitution()); psi.setFullName("psi-mi"); intactContext.getDataContext().getDaoFactory().getCvObjectDao(CvDatabase.class).persist(psi); intactContext.getDataContext().flushSession();
public TransactionStatus beginTransaction(String transactionName) { return beginTransaction( TransactionDefinition.PROPAGATION_REQUIRES_NEW, transactionName); }
public void rollbackTransaction( TransactionStatus transactionStatus ) throws IntactTransactionException { if (transactionStatus.isCompleted()) { if (log.isWarnEnabled()) log.warn("Transaction already complete. Cannot rollback"); return; } PlatformTransactionManager transactionManager = getTransactionManager(); try { if (log.isDebugEnabled()) log.debug("Rolling back transaction"); transactionManager.rollback(transactionStatus); } catch (TransactionException e) { throw new IntactTransactionException(e); } }
final DaoFactory daoFactory = dataContext.getDaoFactory(); TransactionStatus status = dataContext.beginTransaction(); dataContext.commitTransaction(status);
public TransactionStatus beginTransaction() { return beginTransaction( TransactionDefinition.PROPAGATION_REQUIRES_NEW, createTransactionName()); }
TransactionStatus transactionStatus = dataContext.beginTransaction(); dataContext.rollbackTransaction(transactionStatus);
CvXrefQualifier identity = intactContext.getDataContext().getDaoFactory() .getCvObjectDao(CvXrefQualifier.class).getByPsiMiRef(CvXrefQualifier.IDENTITY_MI_REF); DaoFactory daoFactory = IntactContext.getCurrentInstance().getDataContext().getDaoFactory(); Institution owner = daoFactory.getInstitutionDao().getByAc( IntactContext.getCurrentInstance().getInstitution().getAc() ); identity = cvBuilder.createIdentityCvXrefQualifier( owner ); identity.setFullName("identical object"); intactContext.getDataContext().getDaoFactory().getCvObjectDao(CvXrefQualifier.class).persist(identity); CvDatabase psi = intactContext.getDataContext().getDaoFactory() .getCvObjectDao(CvDatabase.class).getByPsiMiRef(CvDatabase.PSI_MI_MI_REF); psi = cvBuilder.createPsiMiCvDatabase(IntactContext.getCurrentInstance().getInstitution()); psi.setFullName("psi-mi"); intactContext.getDataContext().getDaoFactory().getCvObjectDao(CvDatabase.class).persist(psi); intactContext.getDataContext().flushSession();
public TransactionStatus beginTransaction(String transactionName) { return beginTransaction( TransactionDefinition.PROPAGATION_REQUIRES_NEW, transactionName); }
public void rollbackTransaction( TransactionStatus transactionStatus ) throws IntactTransactionException { if (transactionStatus.isCompleted()) { if (log.isWarnEnabled()) log.warn("Transaction already complete. Cannot rollback"); return; } PlatformTransactionManager transactionManager = getTransactionManager(); try { if (log.isDebugEnabled()) log.debug("Rolling back transaction"); transactionManager.rollback(transactionStatus); } catch (TransactionException e) { throw new IntactTransactionException(e); } }
public List<String> getInteractionInvolvingNonUniprotOrNonProtein() { DataContext dataContext = IntactContext.getCurrentInstance().getDataContext(); TransactionStatus transactionStatus = dataContext.beginTransaction(); Query query = IntactContext.getCurrentInstance().getDaoFactory().getEntityManager().createQuery(interactionInvolvingNonUniprotOrNonProtein); query.setParameter("uniprot", CvDatabase.UNIPROT_MI_REF); query.setParameter("identity", CvXrefQualifier.IDENTITY_MI_REF); query.setParameter("protein", "uk.ac.ebi.intact.model.ProteinImpl"); List<String> interactions = query.getResultList(); dataContext.commitTransaction(transactionStatus); return interactions; }
DaoFactory daoFactory = dataContext.getDaoFactory(); TransactionStatus transactionStatus = dataContext.beginTransaction(); dataContext.commitTransaction(transactionStatus); } catch (IntactTransactionException e) { throw new BioSourceServiceException("Problem committing", e);
protected Map<String, Class> getMapOfExistingCvs() { Map<String, Class> existingMi2Class = new HashMap<String, Class>(); List<CvObject> allExistingCvs = IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getCvObjectDao().getAll(); for ( CvObject cvObject : allExistingCvs ) { existingMi2Class.put( CvObjectUtils.getIdentity( cvObject ), cvObject.getClass() ); } return existingMi2Class; }
public TransactionStatus beginTransaction() { return beginTransaction( TransactionDefinition.PROPAGATION_REQUIRES_NEW, createTransactionName()); }
TransactionStatus transactionStatus = dataContext.beginTransaction(); dataContext.rollbackTransaction(transactionStatus);