How to use

getDaoFactory

method

in

uk.ac.ebi.intact.core.context.IntactContext

@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));
}