private void indexFields(SolrInputDocument solrDocument) throws SolrServerException { Interactor interactor = component.getInteractor(); if (interactor != null){ // index interactor ac indexInteractorAC(interactor, solrDocument); // index interactor names indexInteractorNames(interactor, solrDocument); // index interactor type enricher.enrichInteractorType(interactor.getCvInteractorType(), solrDocument); // index and enrich xrefs enricher.enrichInteractorXref(interactor.getXrefs(), solrDocument); } // index biological role if (component.getCvBiologicalRole() != null){ enricher.enrichBiologicalRole(component.getCvBiologicalRole(), solrDocument); } // index features indexfeatures(solrDocument); // enrich sons if necessary if (hasSons()){ for (TreeComponents t : sons){ t.indexFields(solrDocument); } } }
if ( component.getCvBiologicalRole() != null ) { CvObject2xmlFactory.getInstance( session ).create( session, element, component.getCvBiologicalRole() );
CvBiologicalRole bio = component.getCvBiologicalRole();
intactObject.setCvBiologicalRole((CvBiologicalRole) cvPersister.syncIfTransient(intactObject.getCvBiologicalRole())); intactObject.setCvExperimentalRole((CvExperimentalRole) cvPersister.syncIfTransient(intactObject.getCvExperimentalRole()));
sb.append(createUniquenessString(component.getCvBiologicalRole()));
sb.append(createUniquenessString(component.getCvBiologicalRole()));
if ( component.getCvBiologicalRole() != null ) { CvObject2xmlFactory.getInstance( session ).create( session, element, component.getCvBiologicalRole() );
if (participant.getCvBiologicalRole() != null){ bioRole = cvObjectConverter.toCrossReference(participant.getCvBiologicalRole());
component.setCvBiologicalRole( synchronize( component.getCvBiologicalRole() ) );
component.setCvBiologicalRole( synchronize( component.getCvBiologicalRole() ) );
if (intactObject.getCvBiologicalRole() == null) { throw new IllegalStateException("Found component without biological role: "+intactObject.getAc()); BiologicalRole bioRole = this.biologicalRoleConverter.intactToPsi(intactObject.getCvBiologicalRole()); participant.setBiologicalRole(bioRole);
protected void traverseComponent(Component component, IntactVisitor ... visitors) { if (component == null) return; for (IntactVisitor visitor : visitors) { visitor.visitComponent(component); } // check if this element has been traversed already, to avoid cyclic recursion if (recursionChecker.isAlreadyTraversed(component)) { return; } traverse(component.getInteraction(), visitors); traverse(component.getInteractor(), visitors); traverse(component.getCvBiologicalRole(), visitors); traverse(component.getExpressedIn(), visitors); traverse(component.getParameters(), visitors); traverse(component.getParticipantDetectionMethods(), visitors); traverse(component.getExperimentalPreparations(), visitors); traverse(component.getBindingDomains(), visitors); traverse(component.getExperimentalRoles(), visitors); }
protected void traverseComponent(Component component, IntactVisitor ... visitors) { if (component == null) return; for (IntactVisitor visitor : visitors) { visitor.visitComponent(component); } // check if this element has been traversed already, to avoid cyclic recursion if (recursionChecker.isAlreadyTraversed(component)) { return; } traverse(component.getInteraction(), visitors); traverse(component.getInteractor(), visitors); traverse(component.getCvBiologicalRole(), visitors); traverse(component.getExpressedIn(), visitors); traverse(component.getParameters(), visitors); traverse(component.getParticipantDetectionMethods(), visitors); traverse(component.getExperimentalPreparations(), visitors); traverse(component.getBindingDomains(), visitors); traverse(component.getExperimentalRoles(), visitors); }
@Override protected void saveOrUpdateAttributes(Component intactObject) throws PersisterException { super.saveOrUpdateAttributes(intactObject); if (intactObject.getExpressedIn() != null) { BioSourcePersister bioSourcePersister = BioSourcePersister.getInstance(); bioSourcePersister.saveOrUpdate(intactObject.getExpressedIn()); } CvObjectPersister cvPersister = CvObjectPersister.getInstance(); cvPersister.saveOrUpdate(intactObject.getCvBiologicalRole()); cvPersister.saveOrUpdate(intactObject.getCvExperimentalRole()); for (CvIdentification participantDetection : intactObject.getParticipantDetectionMethods()) { cvPersister.saveOrUpdate(participantDetection); } for (CvExperimentalPreparation experimentalPreparation : intactObject.getExperimentalPreparations()) { cvPersister.saveOrUpdate(experimentalPreparation); } InteractionPersister.getInstance().saveOrUpdate(intactObject.getInteraction()); InteractorPersister.getInstance().saveOrUpdate(intactObject.getInteractor()); for (Feature feature : intactObject.getBindingDomains()) { FeaturePersister.getInstance().saveOrUpdate(feature); } }
if (!biologicalRole.equals( component.getCvBiologicalRole() )){ return false; else if (component.getCvBiologicalRole() != null){ return false;
if (!biologicalRole.equals( component.getCvBiologicalRole() )){ return false; else if (component.getCvBiologicalRole() != null){ return false;
clone.setCvBiologicalRole(clone(component.getCvBiologicalRole()));
clone.setCvBiologicalRole(clone(component.getCvBiologicalRole()));