/** {@inheritDoc} */
@Override
public void mapToTable(Graph graph, Edge edge, Evidence evidence, CyTable table) {
if (graph == null) throw new NullPointerException("graph cannot be null");
if (edge == null) throw new NullPointerException("edge cannot be null");
if (evidence == null) throw new NullPointerException("evidence cannot be null");
if (table == null) throw new NullPointerException("table cannot be null");
if (graph.cyNetwork == null)
throw new IllegalArgumentException("graph's cyNetwork cannot be null");
if (edge.cyEdge == null) throw new IllegalArgumentException("edge's cyEdge cannot be null");
CyNetwork cyN = graph.cyNetwork;
CyEdge cyE = edge.cyEdge;
CyRow networkRow = cyN.getRow(cyN);
String networkName = networkRow.get(CyNetwork.NAME, String.class);
CyRow row = table.getRow(SUIDFactory.getNextSUID());
row.set(NETWORK_SUID, cyN.getSUID());
row.set(NETWORK_NAME, networkName);
row.set(EDGE_SUID, cyE.getSUID());
row.set(BEL_STATEMENT, evidence.belStatement);
row.set(SUMMARY_TEXT, evidence.summaryText);
if (evidence.citation != null) {
row.set(CITATION_TYPE, evidence.citation.type);
row.set(CITATION_ID, evidence.citation.id);
row.set(CITATION_NAME, evidence.citation.name);
}
if (evidence.biologicalContext != null) {
// create any annotation columns that do not already exist
BiologicalContext bc = evidence.biologicalContext;
for (String varyingKey : bc.variedAnnotations.keySet()) {
getOrCreateColumn(varyingKey, String.class, false, table);
}
// set annotation values
row.set(SPECIES, bc.speciesCommonName);
Map<String, Object> varying = bc.variedAnnotations;
for (Entry<String, Object> entry : varying.entrySet()) {
row.set(entry.getKey(), getOrEmptyString(entry.getKey(), varying));
}
}
}
/** {@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()]);
}