How to use

getId

method

in

uk.ac.ebi.intact.bridges.ontologies.term.OntologyTerm

private List<Field> convertTermsToFieldsIncludingSynonyms(String type, Set<OntologyTerm> terms) {
  List<Field> fields = new ArrayList<Field>();
  if (terms != null) {
    for ( OntologyTerm term : terms ) {
      if (!getOntologyTermsToIgnore().contains(term.getId())){
        Collection<Field> fieldsWithSynonyms = convertTermToFieldIncludingSynonyms(type, term);
        fields.addAll( fieldsWithSynonyms );
      }
    }
  }
  return fields;
}

private Field convertTermToField(String type, OntologyTerm term) {
  return new Field( type, term.getId(), term.getName() );
}

private Field convertTermToField(String type, OntologyTerm term) {
  Field field = new DefaultField( );
  field.set(CalimochoKeys.DB, type);
  field.set(CalimochoKeys.VALUE, term.getId());
  field.set(CalimochoKeys.TEXT, term.getName());
  return field;
}

public void enrichOrganism(Interaction interaction, SolrInputDocument solrDocument) throws SolrServerException {
  // retrieve the ontology term for this interaction (using BioSource)
  final OntologyTerm ontologyTerm = findOrganism(interaction) ;
  // add name, all synonyms and tax id to complex_organism
  if ( ontologyTerm != null ) {
    // enrich exact organism
    enrichOrganism(ComplexFieldNames.COMPLEX_ORGANISM_EXACT, null, solrDocument, ontologyTerm);
    // enrich organism for query
    enrichOrganism(ComplexFieldNames.COMPLEX_ORGANISM, ComplexFieldNames.COMPLEX_ORGANISM_F, solrDocument, ontologyTerm);
    // sort field
    solrDocument.addField(ComplexFieldNames.COMPLEX_ORGANISM_SORT, ontologyTerm.getId());
    // stored field to retrieve from the index
    solrDocument.addField(ComplexFieldNames.ORGANISM_NAME, ontologyTerm.getName()+"; "+ontologyTerm.getId());
    // add parents to complex_organism_ontology
    for ( OntologyTerm parent : ontologyTerm.getAllParentsToRoot ( true ) ) {
      enrichOrganism(ComplexFieldNames.COMPLEX_ORGANISM, null, solrDocument, parent);
    }
  }
}

protected void enrichOrganism(String fieldName, String facetField, SolrInputDocument solrDocument, OntologyTerm ontologyTerm) {
  // name
  solrDocument.addField ( fieldName, ontologyTerm.getName( ) ) ;
  // synonyms
  for ( OntologyTerm synonym : ontologyTerm.getSynonyms ( ) ) {
    solrDocument.addField ( fieldName, synonym.getName() ) ;
  }
  // taxid
  solrDocument.addField ( fieldName, ontologyTerm.getId() ) ;
  // facet field
  if (facetField != null){
    solrDocument.addField(facetField, ontologyTerm.getName());
  }
}

solrDocument.addField ( xrefFieldName, parent.getId() ) ;
solrDocument.addField ( xrefFieldName, parent.getName ( ) ) ;
for ( OntologyTerm synonym : parent.getSynonyms ( ) ) {