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

Common ways to obtain IntactContext

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

@Deprecated
public CvXrefQualifier createIdentityCvXrefQualifier(IntactContext intactContext) {
  return createIdentityCvXrefQualifier(intactContext.getInstitution());
}

@Deprecated
public CvXrefQualifier createIdentityCvXrefQualifier(IntactContext intactContext) {
  return createIdentityCvXrefQualifier(intactContext.getInstitution());
}

@Deprecated
public CvDatabase createPsiMiCvDatabase(IntactContext intactContext) {
  return createPsiMiCvDatabase(intactContext.getInstitution());
}

@Deprecated
public CvDatabase createPsiMiCvDatabase(IntactContext intactContext) {
  return createPsiMiCvDatabase(intactContext.getInstitution());
}

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);
}

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);
}

@PostConstruct
private void init() {
  this.nonMiCvDatabase = CvObjectUtils.createCvObject( IntactContext.getCurrentInstance().getInstitution(),
                             CvDatabase.class, CvDatabase.INTACT_MI_REF, CvDatabase.INTACT );
}

public CvObjectOntologyBuilder( OBOSession oboSession_ ) {
  oboSession = oboSession_;
  this.nonMiCvDatabase = CvObjectUtils.createCvObject( IntactContext.getCurrentInstance().getInstitution(),
                             CvDatabase.class, CvDatabase.INTACT_MI_REF, CvDatabase.INTACT );
  this.psimod = CvObjectUtils.createCvObject( IntactContext.getCurrentInstance().getInstitution(),
                        CvDatabase.class, CvDatabase.PSI_MOD_MI_REF, CvDatabase.PSI_MOD );
  this.processed = Maps.newHashMap();
  this.map4misWithMoreParent = Maps.newHashMap();
  map4misWithMoreParent = initializeMisWithMoreParents();
  if ( log.isDebugEnabled() ) {
    log.debug( "map4misWithMoreParent size " + map4misWithMoreParent.size() );
  }
}

protected Alias toAlias( CvObject cvobj, String aliasName ) {
  Institution owner = IntactContext.getCurrentInstance().getInstitution();
  CvAliasType alias = getCvObjectByLabel( CvAliasType.class, CvAliasType.GO_SYNONYM );
  if ( alias == null ) {
    if ( log.isTraceEnabled() ) log.trace( "alias ==null creating new" );
    alias = CvObjectUtils.createCvObject( owner, CvAliasType.class, CvAliasType.GO_SYNONYM_MI_REF, CvAliasType.GO_SYNONYM );
  }
  return AliasUtils.createAlias( cvobj, aliasName, alias );
}

protected Annotation toAnnotation( String cvTopic, String annotation ) {
  Institution owner = IntactContext.getCurrentInstance().getInstitution();
  CvTopic topic = getCvObjectByLabel( CvTopic.class, cvTopic );
  if ( topic == null ) {
    if ( CvTopic.URL.equalsIgnoreCase( cvTopic ) ) {
      topic = CvObjectUtils.createCvObject( owner, CvTopic.class, CvTopic.URL_MI_REF, CvTopic.URL );
    } else if ( CvTopic.SEARCH_URL.equalsIgnoreCase( cvTopic ) ) {
      topic = CvObjectUtils.createCvObject( owner, CvTopic.class, CvTopic.SEARCH_URL_MI_REF, CvTopic.SEARCH_URL );
    } else if ( CvTopic.XREF_VALIDATION_REGEXP.equalsIgnoreCase( cvTopic ) ) {
      topic = CvObjectUtils.createCvObject( owner, CvTopic.class, CvTopic.XREF_VALIDATION_REGEXP_MI_REF, CvTopic.XREF_VALIDATION_REGEXP );
    } else if ( CvTopic.COMMENT.equalsIgnoreCase( cvTopic ) ) {
      topic = CvObjectUtils.createCvObject( owner, CvTopic.class, CvTopic.COMMENT_MI_REF, CvTopic.COMMENT );
    } else if ( CvTopic.OBSOLETE.equalsIgnoreCase( cvTopic ) ) {
      topic = CvObjectUtils.createCvObject( owner, CvTopic.class, CvTopic.OBSOLETE_MI_REF, CvTopic.OBSOLETE );
      topic.setFullName( CvTopic.OBSOLETE );
    } else {
      log.error( "Unexpected topic found on annotation: " + cvTopic );
      return null;
    }
  }
  if ( log.isTraceEnabled() )
    log.debug( "Returning from toAnnotation: owner: " + owner + "  topic: " + topic + " annotation  " + annotation );
  return new Annotation( owner, topic, annotation );
}

public Institution getDefaultInstitutionForAcs() {
  if (defaultInstitutionForAcs == null && IntactContext.currentInstanceExists()) {
    defaultInstitutionForAcs = IntactContext.getCurrentInstance().getInstitution();
    if (defaultInstitutionForAcs != null) {
      InstitutionXref xref = XrefUtils.getPsiMiIdentityXref(defaultInstitutionForAcs);
      if (xref != null) {
        defaultInstitutionPrimaryIdForAcs = xref.getPrimaryId();
      }
    }
  }
  return defaultInstitutionForAcs;
}

/**
 *
 * @param xref the xref to check
 * @return
 */
private boolean xrefPointsToOwnAc(Xref xref) {
  if (xref.getPrimaryId().startsWith(config.getAcPrefix())) {
    return true;
  } else {
    for (InstitutionXref institutionXref : IntactContext.getCurrentInstance().getInstitution().getXrefs()) {
      if (institutionXref.getPrimaryId().equals(xref.getCvDatabase().getIdentifier())) {
        return true;
      }
    }
    return false;
  }
}

/**
 *
 * @param xref the xref to check
 * @return
 */
private boolean xrefPointsToOwnAc(Xref xref) {
  if (xref.getPrimaryId().startsWith(config.getAcPrefix())) {
    return true;
  } else {
    for (InstitutionXref institutionXref : IntactContext.getCurrentInstance().getInstitution().getXrefs()) {
      if (institutionXref.getPrimaryId().equals(xref.getCvDatabase().getIdentifier())) {
        return true;
      }
    }
    return false;
  }
}

public static <X extends Xref> X createIdentityXref(AnnotatedObject<X, ?> parent, String primaryId, CvXrefQualifier identityQual, CvDatabase cvDatabase) {
  X xref = (X) newXrefInstanceFor(parent.getClass());
  Institution owner = parent.getOwner();
  if (owner == null) {
    owner = IntactContext.getCurrentInstance().getInstitution();
  }
  xref.setOwner(owner);
  xref.setCvDatabase(cvDatabase);
  xref.setCvXrefQualifier(identityQual);
  xref.setPrimaryId(primaryId);
  xref.setParent(parent);
  return xref;
}

public static <X extends Xref> X createIdentityXref(AnnotatedObject<X, ?> parent, String primaryId, CvXrefQualifier identityQual, CvDatabase cvDatabase) {
  X xref = (X) newXrefInstanceFor(parent.getClass());
  Institution owner = parent.getOwner();
  if (owner == null) {
    owner = IntactContext.getCurrentInstance().getInstitution();
  }
  xref.setOwner(owner);
  xref.setCvDatabase(cvDatabase);
  xref.setCvXrefQualifier(identityQual);
  xref.setPrimaryId(primaryId);
  xref.setParent(parent);
  return xref;
}

/**
 * Create a new InteractorXref for the protein
 * @param uniprotAc : the uniprot accession
 * @return the InteractorXref with the uniprot ac and qualifier identity
 */
private InteractorXref createIdentityInteractorXrefForUniprotAc(String uniprotAc){
  IntactContext intactContext = IntactContext.getCurrentInstance();
  if (uniprotAc == null){
    return null;
  }
  final CvDatabase uniprot = intactContext.getDaoFactory().getCvObjectDao(CvDatabase.class).getByPsiMiRef( CvDatabase.UNIPROT_MI_REF );
  final CvXrefQualifier identity = intactContext.getDaoFactory().getCvObjectDao(CvXrefQualifier.class).getByPsiMiRef(CvXrefQualifier.IDENTITY_MI_REF);
  InteractorXref xRef = new InteractorXref(intactContext.getInstitution(), uniprot, uniprotAc, identity);
  return xRef;
}

public static CvObjectXref createSecondaryXref(CvDagObject term, String database, String identifier) {
  DaoFactory factory = IntactContext.getCurrentInstance().getDaoFactory();
  CvObjectXref cvXref;
  CvXrefQualifier secondary = factory.getCvObjectDao(CvXrefQualifier.class).getByPsiMiRef(CvXrefQualifier.SECONDARY_AC_MI_REF);
  CvDatabase db = factory.getCvObjectDao(CvDatabase.class).getByPsiMiRef(database);
  if (secondary == null){
    secondary = CvObjectUtils.createCvObject(IntactContext.getCurrentInstance().getInstitution(), CvXrefQualifier.class, CvXrefQualifier.SECONDARY_AC_MI_REF, CvXrefQualifier.SECONDARY_AC);
    IntactContext.getCurrentInstance().getCorePersister().saveOrUpdate(secondary);
  }
  if (db == null){
    db = CvObjectUtils.createCvObject(IntactContext.getCurrentInstance().getInstitution(), CvDatabase.class, database, database);
    IntactContext.getCurrentInstance().getCorePersister().saveOrUpdate(db);
  }
  // create identity xref
  cvXref = XrefUtils.createIdentityXref(term, identifier, secondary, db);
  term.addXref(cvXref);
  return cvXref;
}

public static CvObjectXref createIdentityXref(CvDagObject term, String database, String identifier) {
  DaoFactory factory = IntactContext.getCurrentInstance().getDaoFactory();
  CvObjectXref cvXref;
  CvXrefQualifier identity = factory.getCvObjectDao(CvXrefQualifier.class).getByPsiMiRef(CvXrefQualifier.IDENTITY_MI_REF);
  CvDatabase db = factory.getCvObjectDao(CvDatabase.class).getByPsiMiRef(database);
  if (identity == null){
    identity = CvObjectUtils.createCvObject(IntactContext.getCurrentInstance().getInstitution(), CvXrefQualifier.class, CvXrefQualifier.IDENTITY_MI_REF, CvXrefQualifier.IDENTITY);
    IntactContext.getCurrentInstance().getCorePersister().saveOrUpdate(identity);
  }
  if (db == null){
    db = CvObjectUtils.createCvObject(IntactContext.getCurrentInstance().getInstitution(), CvDatabase.class, database, database);
    IntactContext.getCurrentInstance().getCorePersister().saveOrUpdate(db);
  }
  // create identity xref
  cvXref = XrefUtils.createIdentityXref(term, identifier, identity, db);
  term.addXref(cvXref);
  return cvXref;
}

public static Annotation hideTerm(CvObject c, String message){
  DaoFactory factory = IntactContext.getCurrentInstance().getDaoFactory();
  CvTopic topicFromDb = factory.getCvObjectDao(CvTopic.class).getByShortLabel(CvTopic.HIDDEN);
  if (topicFromDb == null){
    topicFromDb = CvObjectUtils.createCvObject(IntactContext.getCurrentInstance().getInstitution(), CvTopic.class, null, CvTopic.HIDDEN);
    IntactContext.getCurrentInstance().getCorePersister().saveOrUpdate(topicFromDb);
  }
  Annotation newAnnotation = new Annotation(topicFromDb, message);
  c.addAnnotation(newAnnotation);
  return newAnnotation;
}

private CvTopic createCvTopicObsolete() {
  final DaoFactory daoFactory = IntactContext.getCurrentInstance().getDataContext().getDaoFactory();
  if ( obsoleteTopic != null ) {
    if (daoFactory.getBaseDao().isTransient(obsoleteTopic) && obsoleteTopic.getAc() != null) {
      obsoleteTopic = daoFactory.getCvObjectDao( CvTopic.class ).getByAc( obsoleteTopic.getAc() );
    }
  } else {
    obsoleteTopic = daoFactory.getCvObjectDao( CvTopic.class ).getByPsiMiRef( CvTopic.OBSOLETE_MI_REF );
  }
  if ( obsoleteTopic == null ) {
    // create the obsolete term (which is obsolete too!)
    obsoleteTopic = CvObjectUtils.createCvObject( IntactContext.getCurrentInstance().getInstitution(), CvTopic.class, CvTopic.OBSOLETE_MI_REF, CvTopic.OBSOLETE );
    obsoleteTopic.setFullName( "obsolete term" );
    addObsoleteAnnotation( obsoleteTopic, "Deprecated CV term that should not be used to annotate entries" );
  }
  return obsoleteTopic;
}

Javadoc

Gets the institution from the RuntimeConfig object. In addition, tries to refresh the instance from the database if it is detached.

Popular methods of IntactContext

getCurrentInstance
Gets the current (ThreadLocal) instance of IntactContext. If no such instance exist, IntAct Core wil
getDataContext
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
getConfig

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

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