uk.ac.ebi.intact.core.context.IntactContext.getConfig java code examples

Common ways to obtain IntactContext

private void myMethod () {
 IntactContext i =IntactContext.getCurrentInstance()
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}

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 );
  }
}

Popular methods of IntactContext

getCurrentInstance
Gets the current (ThreadLocal) instance of IntactContext. If no such instance exist, IntAct Core wil
getDataContext
getInstitution
Gets the institution from the RuntimeConfig object. In addition, tries to refresh the instance from
getDaoFactory
getCorePersister
currentInstanceExists
Checks if an instance already exists.
getSpringContext
getLifecycleManager
Gets the lifecycle manager for publications.
getPersisterHelper
initContext
Initializes a standalone context.
bindToApplication
getApplication

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How to use getConfigmethodin uk.ac.ebi.intact.core.context.IntactContext

Best Java code snippets using uk.ac.ebi.intact.core.context.IntactContext.getConfig (Showing top 16 results out of 315)

How to use
getConfig
method
in
uk.ac.ebi.intact.core.context.IntactContext