How to use

getCurrentInstance

method

in

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

/**
 * @since 2.4.0
 */
public CoreDeleter getCoreDeleter() {
  return (CoreDeleter) IntactContext.getCurrentInstance().getSpringContext().getBean("coreDeleter");
}

  @Deprecated
  public CorePersister getCorePersister() {
    return IntactContext.getCurrentInstance().getCorePersister();
  }
}

  @Deprecated
  public CorePersister getCorePersister() {
    return IntactContext.getCurrentInstance().getCorePersister();
  }
}

private static CvFuzzyType createCvFuzzyType(String position) {
  if (position == null) {
    throw new IllegalArgumentException("The range position cannot be null.");
  }
  for (String key : rangeStatusMap.keySet()) {
    if (position.toLowerCase().contains(key)) {
      return rangeStatusMap.get(key);
    }
  }
  return CvObjectUtils.createCvObject(IntactContext.getCurrentInstance().getInstitution(), CvFuzzyType.class, CvFuzzyType.CERTAIN_MI_REF, CvFuzzyType.CERTAIN);
}

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> 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;
}

@Override
@Transactional
public Institution convertFromString(String str) {
  if (str == null) return null;
  return IntactContext.getCurrentInstance().getDaoFactory().getInstitutionDao().getByShortLabel(str);
}

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;
}

/**
 * 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 SearchableDao getDao() {
  if (searchableDao == null) {
    searchableDao = IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getSearchableDao();
  }
  return searchableDao;
}

private List<Publication> getPublicationsContainingComponents(Collection<String> intactAccession) throws DatasetException {
  // get the intact datacontext and daofactory
  final DataContext dataContext = IntactContext.getCurrentInstance().getDataContext();
  final DaoFactory daoFactory = dataContext.getDaoFactory();
  // This query is looking for all experiences with at least one interaction involving the component of interest
  String componentQuery = "select i.ac from InteractionImpl i join i.components as c " +
      "where c.ac in (:accession)";
  return getPublicationsWithSpecificSelection(componentQuery, intactAccession, daoFactory);
}

public Collection<String> getNucleicAcidMIs() {
   final CvObjectDao<CvInteractorType> itdao = IntactContext.getCurrentInstance().getDataContext()
        .getDaoFactory().getCvObjectDao( CvInteractorType.class);
  // 1. load the root term
  CvInteractorType root = itdao.getByPsiMiRef( CvInteractorType.NUCLEIC_ACID_MI_REF );
  Collection<String> collectedMIs = new ArrayList<String>( );
  if( root != null ) {
    // 2. traverse children and collect their MIs
    CvObjectUtils.getChildrenMIs( root, collectedMIs );
  }
  
  return collectedMIs;
}

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);
}

private Collection<Confidence> synchronizeConfidences( Collection<Confidence> confidencesToSynchronize, Interaction parentInteraction ) {
  List<Confidence> confidences = new ArrayList<Confidence>(confidencesToSynchronize.size());
  for ( Confidence confidence : confidencesToSynchronize ) {
    if (confidence.getAc() != null && IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getConfidenceDao().isTransient(confidence)) {
      confidence = IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getConfidenceDao().getByAc(confidence.getAc());
    }
    confidence.setCvConfidenceType( synchronize (confidence.getCvConfidenceType()));
    confidence.setInteraction((InteractionImpl)parentInteraction);
    confidences.add(confidence);
  }
  return confidences;
}

private Collection<Confidence> synchronizeConfidences( Collection<Confidence> confidencesToSynchronize, Interaction parentInteraction ) {
  List<Confidence> confidences = new ArrayList<Confidence>(confidencesToSynchronize.size());
  for ( Confidence confidence : confidencesToSynchronize ) {
    if (confidence.getAc() != null && IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getConfidenceDao().isTransient(confidence)) {
      confidence = IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getConfidenceDao().getByAc(confidence.getAc());
    }
    confidence.setCvConfidenceType( synchronize (confidence.getCvConfidenceType()));
    confidence.setInteraction((InteractionImpl)parentInteraction);
    confidences.add(confidence);
  }
  return confidences;
}

public Publication createPublication(String pmid) {
  Publication pub = new Publication(getInstitution(), pmid);
  IntactContext.getCurrentInstance().getLifecycleManager().getStartStatus().create(pub, "Mock builder");
  return pub;
}

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 Alias synchronizeAlias( Alias alias, AnnotatedObject parent ) {
  if (alias.getAc() != null) {
    return IntactContext.getCurrentInstance().getDataContext().getDaoFactory()
        .getAliasDao().getByAc(alias.getAc());
  }
  alias.setCvAliasType( synchronize( alias.getCvAliasType() ) );
  alias.setParent(parent);
  if (alias.getAc() == null && parent.getAc() != null) {
    annotatedObjectsToPersist.put(keyBuilder.keyForAlias(alias), alias);
  }
  return alias;
}

private static void addStartAndEndPercentIfNecessary( QueryTerm term ) {
  if ( term.hasModifier( QueryModifier.PHRASE_DELIM ) ) {
    return;
  }
  String acPrefix = IntactContext.getCurrentInstance().getConfig().getAcPrefix();
  if ( !term.startsWith( acPrefix ) && !term.hasModifier( QueryModifier.WILDCARD_START ) ) {
    term.addModifier( QueryModifier.WILDCARD_START );
  }
  if ( !term.startsWith( acPrefix ) && !term.hasModifier( QueryModifier.WILDCARD_END ) ) {
    term.addModifier( QueryModifier.WILDCARD_END );
  }
}