/** Return SUID of root networks */
@GET
@Path("/")
@Produces(MediaType.APPLICATION_JSON + "; charset=UTF-8")
public Collection<Long> getCollectionsAsSUID(@QueryParam("subsuid") Long subsuid) {
if (subsuid == null) {
// Return all collection SUIDs
return getRootNetworks().stream().map(root -> root.getSUID()).collect(Collectors.toSet());
} else {
// Return parent collection's SUID
final CyNetwork subnetwork = networkManager.getNetwork(subsuid);
if (subnetwork == null) {
throw new NotFoundException();
}
final CyRootNetwork root = cyRootNetworkManager.getRootNetwork(subnetwork);
if (root == null) {
throw new NotFoundException();
} else {
final List<Long> rootId = new ArrayList<>();
rootId.add(root.getSUID());
return rootId;
}
}
}
private final CyRootNetwork getRootNetwork(final Long suid) {
final Set<CyRootNetwork> roots = getRootNetworks();
for (final CyRootNetwork root : roots) {
if (root.getSUID().equals(suid)) {
return root;
}
}
return null;
}
private final CyTable getTable(Long networkId, final String tableType) {
final CyRootNetwork root = getRootNetwork(networkId);
if (tableType.equals("default")) {
return root.getDefaultNetworkTable();
} else if (tableType.equals("shared")) {
return root.getSharedNetworkTable();
} else {
return null;
}
}
@GET
@Path("/{networkId}/subnetworks")
@Produces(MediaType.APPLICATION_JSON)
public Response getSubnetworks(@PathParam("networkId") Long networkId) {
final CyRootNetwork root = getRootNetwork(networkId);
final List<CySubNetwork> subnetworks = root.getSubNetworkList();
final Set<Long> subnetIds =
subnetworks.stream().map(subNet -> subNet.getSUID()).collect(Collectors.toSet());
return getResponse(subnetIds);
}
@GET
@Path("/{networkId}/tables")
@Produces(MediaType.APPLICATION_JSON)
public Response getRootTables(@PathParam("networkId") Long networkId) {
final CyRootNetwork root = getRootNetwork(networkId);
final CyTable table = root.getDefaultNetworkTable();
final CyTable shared = root.getSharedNetworkTable();
final Set<CyTable> tables = new HashSet<>();
tables.add(shared);
tables.add(table);
return getResponse(tables);
}
private static HashMap<String, CyRootNetwork> getRootNetworkMap(
CyNetworkManager cyNetworkManager, CyRootNetworkManager cyRootNetworkManager) {
HashMap<String, CyRootNetwork> name2RootMap = new HashMap<String, CyRootNetwork>();
for (CyNetwork net : cyNetworkManager.getNetworkSet()) {
final CyRootNetwork rootNet = cyRootNetworkManager.getRootNetwork(net);
if (!name2RootMap.containsValue(rootNet))
name2RootMap.put(rootNet.getRow(rootNet).get(CyRootNetwork.NAME, String.class), rootNet);
}
return name2RootMap;
}
private void extractNetworks(InputStream is, String entryName) throws Exception {
CyNetworkReader reader = networkReaderMgr.getReader(is, entryName);
reader.run(taskMonitor);
final CyNetwork[] netArray = reader.getNetworks();
for (final CyNetwork net : netArray) {
// Add its root-network to the lookup map first
final CyRootNetwork rootNet = rootNetworkManager.getRootNetwork(net);
if (!networkLookup.containsKey(rootNet.getSUID())) ;
networkLookup.put(rootNet.getSUID(), rootNet);
networkLookup.put(net.getSUID(), net);
networks.add(net); // Note: do NOT add the root-network to this set!
}
}
// Build the key-node map for the entire root network
// Note: The keyColName should start with "shared"
private void initNodeMap() {
String networkCollectionName = this.rootNetworkList.getSelectedValue().toString();
CyRootNetwork rootNetwork = this.name2RootMap.get(networkCollectionName);
if (networkCollectionName.equalsIgnoreCase(CRERATE_NEW_COLLECTION_STRING)) {
return;
}
String targetKeyColName = this.targetColumnList.getSelectedValue();
if (rootNetwork == null) {
return;
}
Iterator<CyNode> it = rootNetwork.getNodeList().iterator();
while (it.hasNext()) {
CyNode node = it.next();
Object keyValue = rootNetwork.getRow(node).getRaw(targetKeyColName);
this.nMap.put(keyValue, node);
}
}
private final String getNetworkViewsAsCX(final CyRootNetwork root) {
final CyNetworkViewWriterFactory cxWriterFactory =
viewWriterFactoryManager.getFactory(CyNetworkViewWriterFactoryManager.CX_WRITER_ID);
final ByteArrayOutputStream stream = new ByteArrayOutputStream();
CyWriter writer = cxWriterFactory.createWriter(stream, root.getSubNetworkList().get(0));
String jsonString = null;
try {
writer.run(null);
jsonString = stream.toString("UTF-8");
stream.close();
} catch (Exception e) {
throw getError(
"Failed to serialize network into CX: " + root, e, Response.Status.INTERNAL_SERVER_ERROR);
}
return jsonString;
}