@Override public Set<OntologyTerm> getAllParentsToRoot(boolean includeSynonyms) { return getAllParentsToRoot(this, includeSynonyms); }
public List<OntologyTerm> getParents() { return getParents(false); }
public List<OntologyTerm> getChildren() { return getChildren(false); }
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 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()); } }
protected Multimap<Integer, OntologyTerm> getChildren(OntologyTerm term, int currentDepth, int maxDepth) { if (currentDepth > maxDepth) { return HashMultimap.create(); } Multimap<Integer,OntologyTerm> terms = HashMultimap.create(); terms.put(currentDepth, term); for (OntologyTerm child : term.getChildren()) { terms.putAll(getChildren(child, currentDepth+1, maxDepth)); } return terms; }
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 Multimap<Integer, OntologyTerm> getChildren(OntologyTerm term, int currentDepth, int maxDepth) { if (currentDepth > maxDepth) { return HashMultimap.create(); } Multimap<Integer,OntologyTerm> terms = HashMultimap.create(); terms.put(currentDepth, term); for (OntologyTerm child : term.getChildren()) { terms.putAll(getChildren(child, currentDepth+1, maxDepth)); } return terms; }
public void enrich(Field field) throws SolrServerException { String db = field.get(CalimochoKeys.DB); if (fieldEnricher.isExpandableOntology(db)) { String id = field.get(CalimochoKeys.VALUE); OntologyTerm ontologyTerm = fieldEnricher.findOntologyTerm(id, null); field.set(CalimochoKeys.TEXT, ontologyTerm.getName()); } }
protected OntologyTerm newInternalOntologyTerm(OntologyIndexSearcher searcher, String id, String name, Collection<String> synonyms) { return new LazyLoadedOntologyTerm(searcher, id, name, synonyms); }
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; } }
protected Multimap<Integer, OntologyTerm> getChildren(OntologyTerm term, int currentDepth, int maxDepth) { if (currentDepth > maxDepth) { return HashMultimap.create(); } Multimap<Integer,OntologyTerm> terms = HashMultimap.create(); terms.put(currentDepth, term); for (OntologyTerm child : term.getChildren()) { terms.putAll(getChildren(child, currentDepth+1, maxDepth)); } return terms; }
public void enrich(CrossReference xref) throws SolrServerException { if (fieldEnricher.isExpandableOntology(xref.getDatabase())) { String id = xref.getIdentifier(); OntologyTerm ontologyTerm = fieldEnricher.findOntologyTerm(id, null); xref.setText(ontologyTerm.getName()); } }
public Set<OntologyTerm> getAllParentsToRoot() { return getAllParentsToRoot(this, false); }
public Collection<OntologyTerm> getChildrenAtDepth(int depth) { return getChildren(this, 0, depth).get(depth); }
public void enrich(CrossReference xref) throws SolrServerException { if (fieldEnricher.isExpandableOntology(xref.getDatabase())) { String id = xref.getIdentifier(); OntologyTerm ontologyTerm = fieldEnricher.findOntologyTerm(id, null); xref.setText(ontologyTerm.getName()); } }