protected Set<OntologyTerm> getAllParentsToRoot(OntologyTerm ontologyTerm, boolean includeSynonyms) { Set<OntologyTerm> parents = new HashSet<OntologyTerm>(); for (OntologyTerm parent : ontologyTerm.getParents()) { parents.add(parent); if (includeSynonyms) { Set<OntologyTerm> synonyms = parent.getSynonyms(); parents.addAll(synonyms); } parents.addAll(getAllParentsToRoot(parent, includeSynonyms)); } return parents; }
protected Set<OntologyTerm> getAllParentsToRoot(OntologyTerm ontologyTerm, boolean includeSynonyms) { Set<OntologyTerm> parents = new HashSet<OntologyTerm>(); for (OntologyTerm parent : ontologyTerm.getParents()) { parents.add(parent); if (includeSynonyms) { Set<OntologyTerm> synonyms = parent.getSynonyms(); parents.addAll(synonyms); } parents.addAll(getAllParentsToRoot(parent, includeSynonyms)); } return parents; }
protected Set<OntologyTerm> getAllParentsToRoot(OntologyTerm ontologyTerm, boolean includeSynonyms) { Set<OntologyTerm> parents = new HashSet<OntologyTerm>(); for (OntologyTerm parent : ontologyTerm.getParents()) { parents.add(parent); if (includeSynonyms) { Set<OntologyTerm> synonyms = parent.getSynonyms(); parents.addAll(synonyms); } parents.addAll(getAllParentsToRoot(parent, includeSynonyms)); } return parents; }
private Collection<Field> convertTermToFieldIncludingSynonyms(String type, OntologyTerm term) { Collection<Field> fields = new ArrayList<Field>(); fields.add(convertTermToField(type, term)); for (OntologyTerm synonymField : term.getSynonyms()) { fields.add(convertTermToField(type, synonymField)); } return fields; } }
private Collection<Field> convertTermToFieldIncludingSynonyms(String type, OntologyTerm term) { Collection<Field> fields = new ArrayList<Field>(); fields.add(convertTermToField(type, term)); for (OntologyTerm synonymField : term.getSynonyms()) { fields.add(convertTermToField(type, synonymField)); } return fields; } }
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()); } }
for ( OntologyTerm synonym : ontologyTerm_aux.getSynonyms ( ) ) { solrDocument.addField ( xrefFieldExact, synonym.getName ( ) ) ; solrDocument.addField ( xrefFieldName, synonym.getName ( ) ) ; solrDocument.addField ( xrefFieldName, parent.getId() ) ; solrDocument.addField ( xrefFieldName, parent.getName ( ) ) ; for ( OntologyTerm synonym : parent.getSynonyms ( ) ) { solrDocument.addField ( xrefFieldName, synonym.getName ( ) ) ;