public TransactionStatus beginTransaction(String transactionName) { return beginTransaction( TransactionDefinition.PROPAGATION_REQUIRES_NEW, transactionName); }
@Deprecated public TransactionStatus beginTransactionManualFlush() { //getDefaultDataConfig().setAutoFlush(true); return beginTransaction( TransactionDefinition.PROPAGATION_REQUIRED ); }
@Deprecated public TransactionStatus beginTransactionManualFlush() { //getDefaultDataConfig().setAutoFlush(true); return beginTransaction( TransactionDefinition.PROPAGATION_REQUIRED ); }
public TransactionStatus beginTransaction() { return beginTransaction( TransactionDefinition.PROPAGATION_REQUIRES_NEW, createTransactionName()); }
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 List<String> getInferredInteractions() { DataContext dataContext = IntactContext.getCurrentInstance().getDataContext(); TransactionStatus transactionStatus = dataContext.beginTransaction(); Query query = IntactContext.getCurrentInstance().getDaoFactory().getEntityManager().createQuery(inferredInteractions); query.setParameter("inferred_author", INFERRED_AUTHOR); query.setParameter("inferred_curator", CvInteraction.INFERRED_BY_CURATOR_MI_REF); List<String> interactions = query.getResultList(); dataContext.commitTransaction(transactionStatus); return interactions; }
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; }
public List<String> getInteractionsFromExperimentNoExport() { DataContext dataContext = IntactContext.getCurrentInstance().getDataContext(); TransactionStatus transactionStatus = dataContext.beginTransaction(); Query query = IntactContext.getCurrentInstance().getDaoFactory().getEntityManager().createQuery(interactionsFromExperimentNoExport); query.setParameter("drExport", CvTopic.UNIPROT_DR_EXPORT); query.setParameter("no", "NO"); List<String> interactions = query.getResultList(); dataContext.commitTransaction(transactionStatus); return interactions; }
public List<Object[]> getGoComponentXrefsInIntact() { DataContext dataContext = IntactContext.getCurrentInstance().getDataContext(); TransactionStatus transactionStatus = dataContext.beginTransaction(); Query query = IntactContext.getCurrentInstance().getDaoFactory().getEntityManager().createQuery(interactionsWithGoComponentXrefs); query.setParameter("go", CvDatabase.GO_MI_REF); query.setParameter("component", CvXrefQualifier.COMPONENT_MI_REF); List<Object []> xrefs = query.getResultList(); dataContext.commitTransaction(transactionStatus); return xrefs; }
public List<String> getInteractionsFromExperimentExportYes() { DataContext dataContext = IntactContext.getCurrentInstance().getDataContext(); TransactionStatus transactionStatus = dataContext.beginTransaction(); Query query = IntactContext.getCurrentInstance().getDaoFactory().getEntityManager().createQuery(interactionsFromExperimentExportYes); query.setParameter("drExport", CvTopic.UNIPROT_DR_EXPORT); query.setParameter("yes", "YES"); List<String> interactions = query.getResultList(); dataContext.commitTransaction(transactionStatus); return interactions; }
public List<String> getInteractionsFromExperimentExportConditional() { DataContext dataContext = IntactContext.getCurrentInstance().getDataContext(); TransactionStatus transactionStatus = dataContext.beginTransaction(); Query query = IntactContext.getCurrentInstance().getDaoFactory().getEntityManager().createQuery(interactionsFromExperimentExportConditional); query.setParameter("drExport", CvTopic.UNIPROT_DR_EXPORT); query.setParameter("confidence", AUTHOR_SCORE_MI); List<String> interactions = query.getResultList(); dataContext.commitTransaction(transactionStatus); return interactions; }
public List<String> getInteractorUniprotIdentity() { DataContext dataContext = IntactContext.getCurrentInstance().getDataContext(); TransactionStatus transactionStatus = dataContext.beginTransaction(); Query query = IntactContext.getCurrentInstance().getDaoFactory().getEntityManager().createQuery(interactorUniprotIdentity); query.setParameter("uniprot", CvDatabase.UNIPROT_MI_REF); query.setParameter("identity", CvXrefQualifier.IDENTITY_MI_REF); List<String> interactors = query.getResultList(); dataContext.commitTransaction(transactionStatus); return interactors; }
public List<String> getReleasedInteractions() { DataContext dataContext = IntactContext.getCurrentInstance().getDataContext(); TransactionStatus transactionStatus = dataContext.beginTransaction(); Query query = IntactContext.getCurrentInstance().getDaoFactory().getEntityManager().createQuery(releasedInteractions); query.setParameter("released", RELEASED); query.setParameter("ready_for_release", READY_FOR_RELEASE); List<String> interactions = query.getResultList(); dataContext.commitTransaction(transactionStatus); return interactions; }
public List<String> getInteractionsFromExperimentExportSpecified() { DataContext dataContext = IntactContext.getCurrentInstance().getDataContext(); TransactionStatus transactionStatus = dataContext.beginTransaction(); Query query = IntactContext.getCurrentInstance().getDaoFactory().getEntityManager().createQuery(interactionsFromExperimentExportSpecified); query.setParameter("drExport", CvTopic.UNIPROT_DR_EXPORT); List<String> interactions = query.getResultList(); dataContext.commitTransaction(transactionStatus); return interactions; }
public List<Object[]> getMethodStatusInIntact() { DataContext dataContext = IntactContext.getCurrentInstance().getDataContext(); TransactionStatus transactionStatus = dataContext.beginTransaction(); Query query = IntactContext.getCurrentInstance().getDaoFactory().getEntityManager().createQuery(methodStatus); query.setParameter("export", CvTopic.UNIPROT_DR_EXPORT); List<Object []> methods = query.getResultList(); dataContext.commitTransaction(transactionStatus); return methods; }
public List<String> getInteractionsInvolvingInteractorsNoUniprotUpdate() { DataContext dataContext = IntactContext.getCurrentInstance().getDataContext(); TransactionStatus transactionStatus = dataContext.beginTransaction(); Query query = IntactContext.getCurrentInstance().getDaoFactory().getEntityManager().createQuery(interactionsInvolvingInteractorsNoUniprotUpdate); query.setParameter("noUniprotUpdate", CvTopic.NON_UNIPROT); List<String> interactions = query.getResultList(); dataContext.commitTransaction(transactionStatus); return interactions; }
public List<String> getNegativeInteractions() { DataContext dataContext = IntactContext.getCurrentInstance().getDataContext(); TransactionStatus transactionStatus = dataContext.beginTransaction(); Query query = IntactContext.getCurrentInstance().getDaoFactory().getEntityManager().createQuery(negativeInteractions); query.setParameter("negative", CvTopic.NEGATIVE); List<String> interactions = query.getResultList(); dataContext.commitTransaction(transactionStatus); return interactions; }
public List<String> getNonProteinInteractor() { DataContext dataContext = IntactContext.getCurrentInstance().getDataContext(); TransactionStatus transactionStatus = dataContext.beginTransaction(); Query query = IntactContext.getCurrentInstance().getDaoFactory().getEntityManager().createQuery(nonProteinInteractor); query.setParameter("protein", "uk.ac.ebi.intact.model.ProteinImpl"); List<String> interactors = query.getResultList(); dataContext.commitTransaction(transactionStatus); return interactors; }
public List<String> getInteractionInvolvedInComponents() { DataContext dataContext = IntactContext.getCurrentInstance().getDataContext(); TransactionStatus transactionStatus = dataContext.beginTransaction(); Query query = IntactContext.getCurrentInstance().getDaoFactory().getEntityManager().createQuery(interactionInvolvedInComponents); List<String> interactions = query.getResultList(); dataContext.commitTransaction(transactionStatus); return interactions; }
public List<Object[]> getTranscriptsWithDifferentParents() { DataContext dataContext = IntactContext.getCurrentInstance().getDataContext(); TransactionStatus transactionStatus = dataContext.beginTransaction(); Query query = IntactContext.getCurrentInstance().getDaoFactory().getEntityManager().createNativeQuery(isoformsWithDifferentParents); List<Object []> methods = query.getResultList(); dataContext.commitTransaction(transactionStatus); return methods; }