How to use

getSpringContext

method

in

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

private ConfigurationHandler getConfigurationHandler() {
  return (ConfigurationHandler) getSpringContext().getBean("configurationHandler");
}

private ConfigurationHandler getConfigurationHandler() {
  return (ConfigurationHandler) getSpringContext().getBean("configurationHandler");
}

public static CvUpdater createInstance(IntactContext intactContext) {
  return (CvUpdater) intactContext.getSpringContext().getBean("cvUpdater");
}

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

  public void destroy() throws Exception {
    getSpringContext().close();

    if (log.isDebugEnabled()) log.debug("Releasing LogFactory");
    LogFactory.release(Thread.currentThread().getContextClassLoader());

    if (log.isInfoEnabled()) log.debug("Destroying IntactContext");
    instance = null;
  }
}

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

  public void destroy() throws Exception {
    getSpringContext().close();

    if (log.isDebugEnabled()) log.debug("Releasing LogFactory");
    LogFactory.release(Thread.currentThread().getContextClassLoader());

    if (log.isInfoEnabled()) log.debug("Destroying IntactContext");
    instance = null;
  }
}

public static String nextUnassignedId(IntactContext intactContext) {
  SequenceManager sequenceManager = (SequenceManager) intactContext.getSpringContext().getBean("sequenceManager");
  return "unassigned" + sequenceManager.getNextValueForSequence("unassigned_seq");
}

public static String nextUnassignedId(IntactContext intactContext) {
  SequenceManager sequenceManager = (SequenceManager) intactContext.getSpringContext().getBean("sequenceManager");
  return "unassigned" + sequenceManager.getNextValueForSequence("unassigned_seq");
}

public static PsiEnricher createPsiEnricher(IntactContext intactContext) {
  return createPsiEnricher(intactContext.getSpringContext());
}

public CorePersister getCorePersister() {
  return (CorePersister) IntactContext.getCurrentInstance().getSpringContext().getBean("corePersister");
}

public static PsiExchange createPsiExchange(IntactContext intactContext) {
  return createPsiExchange(intactContext.getSpringContext());
}

public CorePersister getCorePersister() {
  return (CorePersister) IntactContext.getCurrentInstance().getSpringContext().getBean("corePersister");
}

public CorePersisterImpl() {
  this(IntactContext.getCurrentInstance(), (Finder)
      IntactContext.getCurrentInstance().getSpringContext().getBean("finder"));
}

public CorePersisterImpl() {
  this(IntactContext.getCurrentInstance(), (Finder)
      IntactContext.getCurrentInstance().getSpringContext().getBean("finder"));
}

/**
 * Creates a schema
 * @param initializeDatabase If false, do not initialize the database (e.g. don't create Institution)
 */
public static void createSchema(boolean initializeDatabase) {
  if (log.isDebugEnabled()) log.debug("Creating schema");
  SchemaExport se = newSchemaExport();
  se.create(false, true);
  if (initializeDatabase) {
    if (log.isDebugEnabled()) log.debug("Initializing database");
    IntactInitializer initializer = (IntactInitializer) IntactContext.getCurrentInstance()
        .getSpringContext().getBean("intactInitializer");
    try {
      initializer.init();
    } catch (Exception e) {
      throw new IntactException("Problem re-initializing core", e);
    }
  } 
}

protected static SchemaExport newSchemaExport() {
  LocalEntityManagerFactoryBean factoryBean = (LocalEntityManagerFactoryBean) IntactContext.getCurrentInstance().getSpringContext()
      .getBean("&entityFactoryManager");
  PersistenceUnitInfo persistenceUnitInfo = factoryBean.getPersistenceUnitInfo();
  Configuration config = new Ejb3Configuration().configure(persistenceUnitInfo, null).getHibernateConfiguration();
  
  SchemaExport se =  new SchemaExport(config);
  return se;
}

protected static SchemaExport newSchemaExport() {
  LocalEntityManagerFactoryBean factoryBean = (LocalEntityManagerFactoryBean) IntactContext.getCurrentInstance().getSpringContext()
      .getBean("&entityFactoryManager");
  PersistenceUnitInfo persistenceUnitInfo = factoryBean.getPersistenceUnitInfo();
  Configuration config = new Ejb3Configuration().configure(persistenceUnitInfo, null).getHibernateConfiguration();
  
  SchemaExport se =  new SchemaExport(config);
  return se;
}

/**
 * The local identity is created using a sequence. If the sequence does not exist, a new one is created
 * with initial value calculated using the maximum integer for the existing local CV identifiers.
 * @return The next value available
 * @throws SequenceCreationException thrown if the sequence cannot be created.
 */
protected String nextLocalIdentifier() throws SequenceCreationException {
  final IntactContext context = IntactContext.getCurrentInstance();
  String prefix = context.getConfig().getLocalCvPrefix();
  Integer max = context.getDataContext().getDaoFactory()
      .getCvObjectDao().getLastCvIdentifierWithPrefix(prefix);
  if (max == null) max = 0;
  SequenceManager seqManager = (SequenceManager) context.getSpringContext().getBean("sequenceManager");
  seqManager.createSequenceIfNotExists(IntactAuxiliaryConfigurator.CV_LOCAL_SEQ, max+1);
  String nextIntegerAsString = String.valueOf(seqManager.getNextValueForSequence(IntactAuxiliaryConfigurator.CV_LOCAL_SEQ));
  return prefix+":" + StringUtils.leftPad(nextIntegerAsString, 4, "0");
}

/**
 * The local identity is created using a sequence. If the sequence does not exist, a new one is created
 * with initial value calculated using the maximum integer for the existing local CV identifiers.
 * @return The next value available
 * @throws SequenceCreationException thrown if the sequence cannot be created.
 */
protected String nextLocalIdentifier() throws SequenceCreationException {
  final IntactContext context = IntactContext.getCurrentInstance();
  String prefix = context.getConfig().getLocalCvPrefix();
  Integer max = context.getDataContext().getDaoFactory()
      .getCvObjectDao().getLastCvIdentifierWithPrefix(prefix);
  if (max == null) max = 0;
  SequenceManager seqManager = (SequenceManager) context.getSpringContext().getBean("sequenceManager");
  seqManager.createSequenceIfNotExists(IntactAuxiliaryConfigurator.CV_LOCAL_SEQ, max+1);
  String nextIntegerAsString = String.valueOf(seqManager.getNextValueForSequence(IntactAuxiliaryConfigurator.CV_LOCAL_SEQ));
  return prefix+":" + StringUtils.leftPad(nextIntegerAsString, 4, "0");
}