/** {@inheritDoc} */
@Override
public Evidence[] mapEdgeToEvidence(Graph graph, Edge edge) {
if (graph == null) throw new NullPointerException("graph cannot be null");
if (edge == null) throw new NullPointerException("edge cannot be null");
if (edge.metadata == null) return new Evidence[0];
Object evidences = edge.metadata.get("evidences");
if (evidences == null || !(evidences instanceof List)) return new Evidence[0];
List<Map> evidenceMap = typedList(((List) evidences), Map.class);
List<Evidence> evidenceList = new ArrayList<Evidence>();
for (Map item : evidenceMap) {
@SuppressWarnings("unchecked")
Map<String, Object> evMap = (Map<String, Object>) item;
Evidence ev = new Evidence();
ev.belStatement = getOrEmptyString("bel_statement", evMap).replace("\\\"", "\"");
ev.summaryText = getOrEmptyString("summary_text", evMap);
Citation citation = new Citation();
@SuppressWarnings("unchecked")
Map<String, Object> citationMap = (Map<String, Object>) evMap.get("citation");
if (citationMap != null) {
citation.id = getOrEmptyString("id", citationMap);
citation.type = getOrEmptyString("type", citationMap);
citation.name = getOrEmptyString("name", citationMap);
}
ev.citation = citation;
BiologicalContext context = new BiologicalContext();
@SuppressWarnings("unchecked")
Map<String, Object> contextMap = (Map<String, Object>) evMap.get("biological_context");
if (contextMap != null) {
context.speciesCommonName = getOrEmptyString("species_common_name", contextMap);
context.ncbiTaxId = getOrZero("ncbi_tax_id", contextMap);
Set<String> varying = new HashSet<String>(contextMap.keySet());
varying.removeAll(asList("species_common_name", "ncbi_tax_id"));
for (String key : varying) {
context.variedAnnotations.put(key, contextMap.get(key));
}
ev.biologicalContext = context;
}
evidenceList.add(ev);
}
return evidenceList.toArray(new Evidence[evidenceList.size()]);
}
