@Override @Transactional public Institution convertFromString(String str) { if (str == null) return null; return IntactContext.getCurrentInstance().getDaoFactory().getInstitutionDao().getByShortLabel(str); }
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> 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; }
/** * Checks if the object is managed. * @param io the IntactObject * @return true is the object is found to be managed, otherwise false. */ public static boolean isManaged( IntactObject io ) { return IntactContext.getCurrentInstance().getDaoFactory().getEntityManager().contains( io ); }
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; }
/** * Checks if the object is managed. * @param io the IntactObject * @return true is the object is found to be managed, otherwise false. */ public static boolean isManaged( IntactObject io ) { return IntactContext.getCurrentInstance().getDaoFactory().getEntityManager().contains( io ); }
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 static Institution getInstitution(IntactContext intactContext, User user) { Preference preference = user.getPreference(Preference.KEY_INSTITUTION_AC); if (preference != null) { String institutionAc = preference.getValue(); return intactContext.getDaoFactory().getInstitutionDao().getByAc(institutionAc); } return null; }
protected void changeStatus(Publication publication, String cvPublicationStatusIdentifier) { IntactContext intactContext = IntactContext.getCurrentInstance(); final CvObjectDao<CvPublicationStatus> cvObjectDao = intactContext.getDaoFactory().getCvObjectDao( CvPublicationStatus.class ); CvPublicationStatus publicationStatus = cvObjectDao.getByIdentifier( cvPublicationStatusIdentifier ); publication.setStatus(publicationStatus); }
public static Institution getInstitution(IntactContext intactContext, User user) { Preference preference = user.getPreference(Preference.KEY_INSTITUTION_AC); if (preference != null) { String institutionAc = preference.getValue(); return intactContext.getDaoFactory().getInstitutionDao().getByAc(institutionAc); } return null; }
protected void changeStatus(Publication publication, String cvPublicationStatusIdentifier) { IntactContext intactContext = IntactContext.getCurrentInstance(); final CvObjectDao<CvPublicationStatus> cvObjectDao = intactContext.getDaoFactory().getCvObjectDao( CvPublicationStatus.class ); CvPublicationStatus publicationStatus = cvObjectDao.getByIdentifier( cvPublicationStatusIdentifier ); publication.setStatus(publicationStatus); }
public static User getMentorReviewer(IntactContext intactContext, User user) { if (user != null) { Preference preference = user.getPreference(Preference.KEY_MENTOR_REVIEWER); if (preference != null) { String mentorAc = preference.getValue(); return intactContext.getDaoFactory().getUserDao().getByAc(mentorAc); } } return null; }
public static User getMentorReviewer(IntactContext intactContext, User user) { if (user != null) { Preference preference = user.getPreference(Preference.KEY_MENTOR_REVIEWER); if (preference != null) { String mentorAc = preference.getValue(); return intactContext.getDaoFactory().getUserDao().getByAc(mentorAc); } } return null; }
private SelectionRandomizer<User> createSelectionRandomizer() { SelectionRandomizer<User> selectionRandomizer = new SelectionRandomizer<User>(); List<User> reviewers = IntactContext.getCurrentInstance().getDaoFactory().getUserDao().getByRole(Role.ROLE_REVIEWER); for (User reviewer : reviewers) { Integer availability = UserUtils.getReviewerAvailability(reviewer); selectionRandomizer.addObject(reviewer, availability); } return selectionRandomizer; }
private SelectionRandomizer<User> createSelectionRandomizer() { SelectionRandomizer<User> selectionRandomizer = new SelectionRandomizer<User>(); List<User> reviewers = IntactContext.getCurrentInstance().getDaoFactory().getUserDao().getByRole(Role.ROLE_REVIEWER); for (User reviewer : reviewers) { Integer availability = UserUtils.getReviewerAvailability(reviewer); selectionRandomizer.addObject(reviewer, availability); } return selectionRandomizer; }
private static Collection<Annotation> fetchAnnotations(Interaction interaction) { Collection<Annotation> annotations; if (IntactCore.isInitialized(interaction.getAnnotations())) { annotations = interaction.getAnnotations(); } else { annotations = IntactContext.getCurrentInstance().getDaoFactory().getAnnotationDao().getByParentAc(InteractionImpl.class, interaction.getAc()); } return annotations; }
private static Collection<Annotation> fetchAnnotations(Interaction interaction) { Collection<Annotation> annotations; if (IntactCore.isInitialized(interaction.getAnnotations())) { annotations = interaction.getAnnotations(); } else { annotations = IntactContext.getCurrentInstance().getDaoFactory().getAnnotationDao().getByParentAc(InteractionImpl.class, interaction.getAc()); } return annotations; }
protected void addLifecycleEvent(Publication publication, String cvLifecycleEventIdentifier, String comment) { IntactContext intactContext = IntactContext.getCurrentInstance(); final CvObjectDao<CvLifecycleEvent> cvObjectDao = intactContext.getDaoFactory().getCvObjectDao( CvLifecycleEvent.class ); CvLifecycleEvent lifecycleEvent = cvObjectDao.getByIdentifier( cvLifecycleEventIdentifier ); publication.addLifecycleEvent(new LifecycleEvent(lifecycleEvent, intactContext.getUserContext().getUser(), comment)); }
protected void addLifecycleEvent(Publication publication, String cvLifecycleEventIdentifier, String comment) { IntactContext intactContext = IntactContext.getCurrentInstance(); final CvObjectDao<CvLifecycleEvent> cvObjectDao = intactContext.getDaoFactory().getCvObjectDao( CvLifecycleEvent.class ); CvLifecycleEvent lifecycleEvent = cvObjectDao.getByIdentifier( cvLifecycleEventIdentifier ); publication.addLifecycleEvent(new LifecycleEvent(lifecycleEvent, intactContext.getUserContext().getUser(), comment)); }