How to use

AnnotationDao

in

uk.ac.ebi.intact.core.persistence.dao

@Transactional(propagation = Propagation.REQUIRES_NEW)
/**
 * Delete hidden annotations for each cv given in the collection
 */
public void removeHiddenFrom(Collection<CvObject> cvs){
  DaoFactory factory = IntactContext.getCurrentInstance().getDaoFactory();
  AnnotationDao annDao = factory.getAnnotationDao();
  for (CvObject cv : cvs){
    cv = factory.getEntityManager().merge(cv);
    Collection<Annotation> annotations = new ArrayList<Annotation>(cv.getAnnotations());
    for (Annotation annotation : annotations){
      if (annotation.getCvTopic() != null && CvTopic.HIDDEN.equalsIgnoreCase(annotation.getCvTopic().getShortLabel())){
        cv.removeAnnotation(annotation);
        annDao.delete(annotation);
      }
    }
  }
}

/**
 * Prints the most counts in the database.
 * @param ps The printStream to use
 *
 * @since 1.9.0
 */
public static void printDatabaseCounts(PrintStream ps) {
  final DaoFactory daoFactory = IntactContext.getCurrentInstance().getDataContext().getDaoFactory();
  ps.println("Publications: "+ daoFactory.getPublicationDao().countAll());
  ps.println("\tXrefs: "+ daoFactory.getXrefDao(PublicationXref.class).countAll());
  ps.println("\tAliases: "+ daoFactory.getAliasDao(PublicationAlias.class).countAll());
  ps.println("Experiments: "+ daoFactory.getExperimentDao().countAll());
  ps.println("\tXrefs: "+ daoFactory.getXrefDao(ExperimentXref.class).countAll());
  ps.println("\tAliases: "+ daoFactory.getAliasDao(ExperimentAlias.class).countAll());
  ps.println("Interactors: "+ daoFactory.getInteractorDao().countAll());
  ps.println("\tInteractions: "+ daoFactory.getInteractionDao().countAll());
  ps.println("\tPolymers: " + daoFactory.getPolymerDao().countAll());
  ps.println("\t\tProteins: "+ daoFactory.getProteinDao().countAll());
  ps.println("\t\tNucleic Acids: "+ daoFactory.getInteractorDao(NucleicAcidImpl.class).countAll());
  ps.println("\tSmall molecules: " + daoFactory.getInteractorDao(SmallMoleculeImpl.class).countAll());
  ps.println("\tInteractor Xrefs: "+ daoFactory.getXrefDao(InteractorXref.class).countAll());
  ps.println("\tInteractor Aliases: "+ daoFactory.getAliasDao(InteractorAlias.class).countAll());
  ps.println("Components: "+ daoFactory.getComponentDao().countAll());
  ps.println("Features: "+ daoFactory.getFeatureDao().countAll());
  ps.println("\tRanges: "+ daoFactory.getRangeDao().countAll());
  ps.println("CvObjects: "+ daoFactory.getCvObjectDao().countAll());
  ps.println("BioSources: "+ daoFactory.getBioSourceDao().countAll());
  ps.println("Annotations: "+ daoFactory.getAnnotationDao().countAll());
  ps.println("Institutions: "+ daoFactory.getInstitutionDao().countAll());
}

/**
 * Retrieves the annotations from an AnnotatedObject, initializing them if necessary.
 *
 * @param ao The annotated object instance with possibly non-initialized annotations
 * @return The returned annotations are ensured to be initialized
 * @since 2.4.0
 */
public static Collection<Annotation> ensureInitializedAnnotations(AnnotatedObject ao) {
  Collection<Annotation> annotations;
  if (IntactCore.isInitialized(ao.getAnnotations())) {
    annotations = ao.getAnnotations();
  } else {
    annotations = IntactContext.getCurrentInstance().getDaoFactory().getAnnotationDao().getByParentAc(ao.getClass(), ao.getAc());
  }
  return annotations;
}

IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getAnnotationDao().persist( annotation );
  IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getAnnotationDao().update( annotation );
IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getAnnotationDao().delete( annotation );

IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getAnnotationDao().update( annot );
containsAnnotation = true;
break;

private Annotation synchronizeAnnotation( Annotation annotation, AnnotatedObject parent ) {
  if (annotation.getAc() != null) {
    return IntactContext.getCurrentInstance().getDataContext().getDaoFactory()
        .getAnnotationDao().getByAc(annotation.getAc());
  }
  else {
  }
  annotation.setCvTopic( synchronize( annotation.getCvTopic() ) );
  if (annotation.getAc() == null && parent.getAc() != null) {
    annotatedObjectsToPersist.put(keyBuilder.keyForAnnotation(annotation, parent), annotation);
  }
  return annotation;
}

@Transactional(propagation = Propagation.REQUIRES_NEW)
/**
 * Hide all the given cvs with the given message
 */
public void hideTerms(Collection<CvObject> cvs, String message){
  DaoFactory factory = IntactContext.getCurrentInstance().getDaoFactory();
  AnnotationDao annDao = factory.getAnnotationDao();
  for (CvObject cv : cvs){
    cv = factory.getEntityManager().merge(cv);
    boolean hasHidden = false;
    for (Annotation annotation : cv.getAnnotations()){
      if (annotation.getCvTopic() != null && CvTopic.HIDDEN.equalsIgnoreCase(annotation.getCvTopic().getShortLabel())){
        hasHidden = true;
      }
    }
    if (!hasHidden){
      annDao.persist(CvUpdateUtils.hideTerm(cv, message));
    }
  }
}

annotationDao.update(updated);
annotationDao.persist(created);
annotationDao.delete(deleted);

private Annotation synchronizeAnnotation( Annotation annotation, AnnotatedObject parent ) {
  if (annotation.getAc() != null) {
    return IntactContext.getCurrentInstance().getDataContext().getDaoFactory()
        .getAnnotationDao().getByAc(annotation.getAc());
  }
  else {
  }
  annotation.setCvTopic( synchronize( annotation.getCvTopic() ) );
  if (annotation.getAc() == null && parent.getAc() != null) {
    annotatedObjectsToPersist.put(keyBuilder.keyForAnnotation(annotation, parent), annotation);
  }
  return annotation;
}

if ( ! experiment.getAnnotations().contains( annotation ) ) {
  IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getAnnotationDao().persist( annotation );
  experiment.addAnnotation( annotation );
  IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getExperimentDao().update( experiment );

log.info("annotation no_uniprot_update removed from the annotations of " + accession);
prot.removeAnnotation(a);
daoFactory.getAnnotationDao().delete(a);
log.info("caution removed from the annotations of " + accession);
prot.removeAnnotation(a2);
daoFactory.getAnnotationDao().delete(a2);

/**
 * Retrieves the annotations from an AnnotatedObject, initializing them if necessary.
 *
 * @param ao The annotated object instance with possibly non-initialized annotations
 * @return The returned annotations are ensured to be initialized
 * @since 2.4.0
 */
public static Collection<Annotation> ensureInitializedAnnotations(AnnotatedObject ao) {
  Collection<Annotation> annotations;
  if (IntactCore.isInitialized(ao.getAnnotations())) {
    annotations = ao.getAnnotations();
  } else {
    annotations = IntactContext.getCurrentInstance().getDaoFactory().getAnnotationDao().getByParentAc(ao.getClass(), ao.getAc());
  }
  return annotations;
}

/**
 * Prints the most counts in the database.
 * @param ps The printStream to use
 *
 * @since 1.9.0
 */
public static void printDatabaseCounts(PrintStream ps) {
  final DaoFactory daoFactory = IntactContext.getCurrentInstance().getDataContext().getDaoFactory();
  ps.println("Publications: "+ daoFactory.getPublicationDao().countAll());
  ps.println("\tXrefs: "+ daoFactory.getXrefDao(PublicationXref.class).countAll());
  ps.println("\tAliases: "+ daoFactory.getAliasDao(PublicationAlias.class).countAll());
  ps.println("Experiments: "+ daoFactory.getExperimentDao().countAll());
  ps.println("\tXrefs: "+ daoFactory.getXrefDao(ExperimentXref.class).countAll());
  ps.println("\tAliases: "+ daoFactory.getAliasDao(ExperimentAlias.class).countAll());
  ps.println("Interactors: "+ daoFactory.getInteractorDao().countAll());
  ps.println("\tInteractions: "+ daoFactory.getInteractionDao().countAll());
  ps.println("\tPolymers: " + daoFactory.getPolymerDao().countAll());
  ps.println("\t\tProteins: "+ daoFactory.getProteinDao().countAll());
  ps.println("\t\tNucleic Acids: "+ daoFactory.getInteractorDao(NucleicAcidImpl.class).countAll());
  ps.println("\tSmall molecules: " + daoFactory.getInteractorDao(SmallMoleculeImpl.class).countAll());
  ps.println("\tInteractor Xrefs: "+ daoFactory.getXrefDao(InteractorXref.class).countAll());
  ps.println("\tInteractor Aliases: "+ daoFactory.getAliasDao(InteractorAlias.class).countAll());
  ps.println("Components: "+ daoFactory.getComponentDao().countAll());
  ps.println("Features: "+ daoFactory.getFeatureDao().countAll());
  ps.println("\tRanges: "+ daoFactory.getRangeDao().countAll());
  ps.println("CvObjects: "+ daoFactory.getCvObjectDao().countAll());
  ps.println("BioSources: "+ daoFactory.getBioSourceDao().countAll());
  ps.println("Annotations: "+ daoFactory.getAnnotationDao().countAll());
  ps.println("Institutions: "+ daoFactory.getInstitutionDao().countAll());
}

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;
}