/** {@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[] mapFromTable(CyEdge edge, CyTable table) {
if (edge == null) throw new NullPointerException("edge cannot be null");
if (table == null) throw new NullPointerException("table cannot be null");
Set<String> nonAnnotationColumns =
new HashSet<String>(
asList(
CyNetwork.SUID,
NETWORK_SUID,
NETWORK_NAME,
EDGE_SUID,
BEL_STATEMENT,
SUMMARY_TEXT,
CITATION_ID,
CITATION_NAME,
CITATION_TYPE,
SPECIES));
Collection<CyRow> evidenceRows = table.getMatchingRows(EDGE_SUID, edge.getSUID());
List<Evidence> evidences = new ArrayList<Evidence>(evidenceRows.size());
if (!evidenceRows.isEmpty()) {
for (CyRow evRow : evidenceRows) {
Evidence e = new Evidence();
e.belStatement = evRow.get(BEL_STATEMENT, String.class);
e.summaryText = evRow.get(SUMMARY_TEXT, String.class);
e.citation = new Citation();
e.citation.id = evRow.get(CITATION_ID, String.class);
e.citation.name = evRow.get(CITATION_NAME, String.class);
e.citation.type = evRow.get(CITATION_TYPE, String.class);
e.biologicalContext = new BiologicalContext();
e.biologicalContext.speciesCommonName = evRow.get(SPECIES, String.class);
e.biologicalContext.variedAnnotations = new HashMap<String, Object>();
for (Entry<String, Object> columnValue : evRow.getAllValues().entrySet()) {
if (nonAnnotationColumns.contains(columnValue.getKey())) continue;
e.biologicalContext.variedAnnotations.put(columnValue.getKey(), columnValue.getValue());
}
evidences.add(e);
}
}
return evidences.toArray(new Evidence[evidences.size()]);
}
@Override
public void serialize(CyNetworkView networkView, JsonGenerator jgen, SerializerProvider provider)
throws IOException, JsonProcessingException {
jgen.useDefaultPrettyPrinter();
jgen.writeStartObject();
jgen.writeStringField(
CytoscapeJsNetworkModule.FORMAT_VERSION_TAG, CytoscapeJsNetworkModule.FORMAT_VERSION);
jgen.writeStringField(CytoscapeJsNetworkModule.GENERATED_BY_TAG, "cytoscape-" + version);
jgen.writeStringField(
CytoscapeJsNetworkModule.TARGET_CYJS_VERSION_TAG,
CytoscapeJsNetworkModule.CYTOSCAPEJS_VERSION);
final CyNetwork network = networkView.getModel();
// Serialize network data table
jgen.writeObjectFieldStart(DATA.getTag());
jgen.writeObject(network.getRow(network));
jgen.writeEndObject();
jgen.writeObjectFieldStart(ELEMENTS.getTag());
// Write array
final List<CyNode> nodes = network.getNodeList();
final List<CyEdge> edges = network.getEdgeList();
jgen.writeArrayFieldStart(NODES.getTag());
for (final CyNode node : nodes) {
jgen.writeStartObject();
// Data field
jgen.writeObjectFieldStart(DATA.getTag());
jgen.writeStringField(ID.getTag(), node.getSUID().toString());
// Write CyRow in "data" field
jgen.writeObject(network.getRow(node));
jgen.writeEndObject();
// Position and other visual props
jgen.writeObject(networkView.getNodeView(node));
// Special case for cytoscape.js format:
// - Selected
jgen.writeBooleanField(
CyNetwork.SELECTED, network.getRow(node).get(CyNetwork.SELECTED, Boolean.class));
jgen.writeEndObject();
}
jgen.writeEndArray();
jgen.writeArrayFieldStart(EDGES.getTag());
for (final CyEdge edge : edges) {
jgen.writeStartObject();
jgen.writeObjectFieldStart(DATA.getTag());
jgen.writeStringField(ID.getTag(), edge.getSUID().toString());
jgen.writeStringField(SOURCE.getTag(), edge.getSource().getSUID().toString());
jgen.writeStringField(TARGET.getTag(), edge.getTarget().getSUID().toString());
// Write CyRow in "data" field
jgen.writeObject(network.getRow(edge));
jgen.writeEndObject();
// Special case for cytoscape.js format:
// - Selected
jgen.writeBooleanField(
CyNetwork.SELECTED, network.getRow(edge).get(CyNetwork.SELECTED, Boolean.class));
jgen.writeEndObject();
}
jgen.writeEndArray();
jgen.writeEndObject();
}
