How to use

getConfig

method

in

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

public DefaultFinder(IntactContext intactContext) {
  config = intactContext.getConfig();
}

public DefaultFinder(IntactContext intactContext) {
  config = intactContext.getConfig();
}

public DefaultFinder() {
  config = IntactContext.getCurrentInstance().getConfig();
}

public DefaultFinder() {
  config = IntactContext.getCurrentInstance().getConfig();
}

/**
 * Update the shortlabel based on the data available in the database.
 */
public void synchronizeShortLabel() {
  if( IntactContext.currentInstanceExists() ) {
    if( IntactContext.getCurrentInstance().getConfig().isAutoUpdateInteractionLabel() ) {
      String shortLabel = getShortLabel();
      String newShortLabel = InteractionUtils.syncShortLabelWithDb(shortLabel);
      if (!shortLabel.equals(newShortLabel)) {
        if (log.isDebugEnabled()) log.debug("Interaction with label '"+shortLabel+"' renamed '"+newShortLabel+"'" );
        setShortLabel(newShortLabel);
      }
    }
  } else {
    log.warn( "There is no IntAct Context initialized, skipping interaction shortlabel synchronization." );
  }
}

/**
 * Update the shortlabel based on the data available in the database.
 */
public void synchronizeShortLabel() {
  if( IntactContext.currentInstanceExists() ) {
    if( IntactContext.getCurrentInstance().getConfig().isAutoUpdateInteractionLabel() ) {
      String shortLabel = getShortLabel();
      String newShortLabel = InteractionUtils.syncShortLabelWithDb(shortLabel);
      if (!shortLabel.equals(newShortLabel)) {
        if (log.isDebugEnabled()) log.debug("Interaction with label '"+shortLabel+"' renamed '"+newShortLabel+"'" );
        setShortLabel(newShortLabel);
      }
    }
  } else {
    log.warn( "There is no IntAct Context initialized, skipping interaction shortlabel synchronization." );
  }
}

@PrePersist
public void synchronizeShortLabel() {
  if( IntactContext.currentInstanceExists() ) {
    if( IntactContext.getCurrentInstance().getConfig().isAutoUpdateExperimentLabel() ) {
      String shortLabel = getShortLabel();
      String newShortLabel = shortLabel;
      try {
        newShortLabel = ExperimentUtils.syncShortLabelWithDb(shortLabel, ExperimentUtils.getPubmedId( this ));
      } catch (Exception e) {
        log.error("Exception synchronizing the label, probably due to an invalid format: "+newShortLabel, e);
      }
      if (!shortLabel.equals(newShortLabel)) {
        if (log.isDebugEnabled()) log.debug("Experiment with label '"+shortLabel+"' renamed '"+newShortLabel+"'" );
        setShortLabel(newShortLabel);
      }
    }
  } else {
    log.warn( "There is no IntAct Context initialized, skipping experiment shortlabel synchronization." );
  }
}

@PrePersist
public void synchronizeShortLabel() {
  if( IntactContext.currentInstanceExists() ) {
    if( IntactContext.getCurrentInstance().getConfig().isAutoUpdateExperimentLabel() ) {
      String shortLabel = getShortLabel();
      String newShortLabel = shortLabel;
      try {
        newShortLabel = ExperimentUtils.syncShortLabelWithDb(shortLabel, ExperimentUtils.getPubmedId( this ));
      } catch (Exception e) {
        log.error("Exception synchronizing the label, probably due to an invalid format: "+newShortLabel, e);
      }
      if (!shortLabel.equals(newShortLabel)) {
        if (log.isDebugEnabled()) log.debug("Experiment with label '"+shortLabel+"' renamed '"+newShortLabel+"'" );
        setShortLabel(newShortLabel);
      }
    }
  } else {
    log.warn( "There is no IntAct Context initialized, skipping experiment shortlabel synchronization." );
  }
}

@Before
public void prepareBasicTest() throws Exception {
  mockBuilder = new IntactMockBuilder(getIntactContext().getConfig().getDefaultInstitution());
}

/**
 * The ID is the concatenation of the prefix and a sequence provided by the database, separated
 * by a dash.
 *
 * @param sessionImplementor a hibernate session implementor
 * @param object             the object being persisted
 *
 * @return the new generated ID
 *
 * @throws HibernateException if something goes wrong
 */
@Override
public Serializable generate( SessionImplementor sessionImplementor, Object object ) throws HibernateException {
  String prefix;
  if (IntactContext.currentInstanceExists()) {
    prefix = IntactContext.getCurrentInstance().getConfig().getAcPrefix();
  } else {
    prefix = "UNK";
  }
  String id = prefix + "-" + super.generate( sessionImplementor, object );
  log.trace( "Assigning Id: " + id );
  return id;
}

@Before
public void prepareBasicTest() throws Exception {
  mockBuilder = new IntactMockBuilder(getIntactContext().getConfig().getDefaultInstitution());
}

/**
 * The ID is the concatenation of the prefix and a sequence provided by the database, separated
 * by a dash.
 *
 * @param sessionImplementor a hibernate session implementor
 * @param object             the object being persisted
 *
 * @return the new generated ID
 *
 * @throws HibernateException if something goes wrong
 */
@Override
public Serializable generate( SessionImplementor sessionImplementor, Object object ) throws HibernateException {
  String prefix;
  if (IntactContext.currentInstanceExists()) {
    prefix = IntactContext.getCurrentInstance().getConfig().getAcPrefix();
  } else {
    prefix = "UNK";
  }
  String id = prefix + "-" + super.generate( sessionImplementor, object );
  log.trace( "Assigning Id: " + id );
  return id;
}

/**
 * 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");
}

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 );
  }
}

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 );
  }
}