public static void main(String[] args) {
System.out.println("Test 2");
Network net3 = new Network();
net3.addConnection(1, 2);
net3.addConnection(3, 1);
net3.addConnection(2, 4);
System.out.println(net3.addConnection(4, 3));
System.out.println(net3.addConnection(3, 3));
System.out.println(net3.addConnection(3, 3));
net3.addConnection(100, 4);
net3.addConnection(3, 100);
net3.addConnection(2, 5);
net3.addConnection(5, 6);
net3.addConnection(6, 7);
net3.findTree();
Collection switches3 = net3.getSwitches();
Iterator iter3 = switches3.iterator();
while (iter3.hasNext()) {
Switch y = (Switch) iter3.next();
System.out.println("Switch: Root, Parent, Hops to Root");
String output = " " + y.getMAC() + ": ";
output = output + y.getRoot().getMAC() + " ";
output = output + y.getParent().getMAC() + " ";
output = output + y.getDistance();
System.out.println(output);
}
}
/**
* create a 1-d String array from a network, for easy transmission to R. triples (source,
* edgeType, target) are filled in to an array of length 3 * # of interactions
*
* @param network a gaggle network
* @return the edge attributes of the network as a string array
*/
protected String[] networkEdgeAttributesToStringArray(Network network) {
Interaction[] interactions = network.getInteractions();
String source, target, type;
String[] attributeNames = network.getEdgeAttributeNames();
ArrayList<String> list = new ArrayList<String>();
for (Interaction interaction : interactions) {
source = interaction.getSource();
type = interaction.getType();
target = interaction.getTarget();
String edgeName = source + " (" + type + ") " + target;
String terseEdgeName = source + "::" + target + "::" + type;
for (String name : attributeNames) {
HashMap hash = network.getEdgeAttributes(name);
if (hash.containsKey(edgeName)) {
Object value = hash.get(edgeName);
StringBuffer sb = new StringBuffer();
sb.append(terseEdgeName);
sb.append("::");
sb.append(name);
sb.append("::");
sb.append(value.toString());
list.add(sb.toString());
} else {
System.out.println("no " + name + " attribute for " + edgeName);
}
} // for a
} // for r
return list.toArray(new String[0]);
} // networkEdgeAttributesToStringArray
// ----------------------------------------------------------------------------------------
public void handleNetwork(String source, Network newNetwork) {
System.out.println(
"network ready, node count "
+ newNetwork.getNodes().length
+ ", edges: "
+ newNetwork.edgeCount());
network = newNetwork;
defaultSpecies = newNetwork.getSpecies();
}
public static double getVertexCount(Network forest, Collection<Long> a0) {
int count = 0;
for (Long v : forest.getVertices()) {
if (!a0.contains(v)) {
count++;
}
}
return (double) count;
}
@Test
public void testHighLevelAccess() {
Link link = nw.getLinkById(3L);
Double val = 1.23;
dp.setVehiclesPerMeterOnLink(link, val);
assertEquals((Double) 1.23, dp.getVehiclesPerMeterOnLink(link));
}
private CompositeData getCompositeData(Network mo, String moName) throws Exception {
values = new Object[names.length];
values[0] = moName;
if (mo.getDiscover()) {
values[1] = "true"; // No I18N
} else {
values[1] = "false"; // No I18N
}
values[2] = new Integer(mo.getDiscoveryStatus());
String oid = agentName.getChildTableOID(mo.getClassname(), this.className);
values[3] = oid;
values[4] = agentName.getChildTableName(oid);
try {
return new CompositeData(null, names, values);
} catch (Exception e) {
return null;
}
}
/**
* create a 1-d String array from a network's node attributes, for easy transmission to R. use
* this format for each attribute of each node: nodeName::attributeName::value
*
* @param network a gaggle network
* @return the network's node attributes as a string array
*/
protected String[] networkNodeAttributesToStringArray(Network network) {
String[] attributeNames = network.getNodeAttributeNames();
// System.out.println (" nnatsa, attribute name count: " + attributeNames.length);
ArrayList<String> list = new ArrayList<String>();
for (String attributeName : attributeNames) {
// System.out.println (" nnatsa, attribute name: " + attributeName);
HashMap attributeHash = network.getNodeAttributes(attributeName);
// can't remove this warning until Network is genericized in next api release:
String[] nodeNames = (String[]) attributeHash.keySet().toArray(new String[0]);
for (String nodeName : nodeNames) {
// System.out.println (" nnatsa, node name: " + nodeName);
Object value = attributeHash.get(nodeName);
String terseForm = nodeName + "::" + attributeName + "::" + value.toString();
list.add(terseForm);
} // for n
} // for i
return list.toArray(new String[0]);
} // networkEdgeAttributesToStringArray
protected void addMetaDataToNetwork(Network network) {
if (networkMetadata.size() == 0) {
return;
}
Tuple metadata = new Tuple();
Set<String> keys = networkMetadata.keySet();
for (Iterator<String> it = keys.iterator(); it.hasNext(); ) {
String key = it.next();
metadata.addSingle(new Single(key, networkMetadata.get(key)));
}
network.setMetadata(metadata);
}
// ----------------------------------------------------------------------------------------
// is this called from anywhere? doesn't look like it
public void createAndBroadcastNetwork(
String sourceNode, String[] targetNodes, double[] weights, String[] targetTypes) {
// System.out.println ("createAndBroadcastNetwork, source: " + sourceNode);
Network network = new Network();
addMetaDataToNetwork(network);
network.setSpecies(defaultSpecies);
for (int i = 0; i < targetNodes.length; i++) {
Interaction interaction = new Interaction(sourceNode, targetNodes[i], targetTypes[i]);
network.add(interaction);
String edgeName = sourceNode + " (" + targetTypes[i] + ") " + targetNodes[i];
// System.out.println ("adding weight " + weights [i] + " for edge " + edgeName);
network.addEdgeAttribute(edgeName, "weight", weights[i]);
}
try {
gaggleBoss.broadcastNetwork(myGaggleName, targetGoose, network);
} catch (RemoteException rex) {
System.err.println("error broadcasting network from RShellGoose " + myGaggleName);
rex.printStackTrace();
}
} // createAndBroadcastNetwork
/**
* create a 1-d String array from a network, for easy transmission to R. each element in the array
* is a string, with format sourceNode::targetNode::edgeType
*
* @param network the network to convert to a string
* @return an array of strings representing a network
*/
protected String[] networkToStringArray(Network network) {
Interaction[] interactions = network.getInteractions();
ArrayList<String> list = new ArrayList<String>();
// System.out.println ("networkToStringArray, interaction ount: " + interactions.length);
for (Interaction interaction : interactions) {
String source = interaction.getSource();
String target = interaction.getTarget();
String type = interaction.getType();
String combined = source + "::" + target + "::" + type;
// System.out.println (" interaction: " + combined);
list.add(combined);
} // for i
String[] orphanNodes = network.getOrphanNodes();
// System.out.println ("networkToStringArray, orphanCount: " + orphanNodes.length);
for (String orphanNode : orphanNodes) {
// System.out.println (" orphan: " + orphanNodes [i]);
list.add(orphanNode);
}
return list.toArray(new String[0]);
} // networkToStringArray
@Transactional(propagation = Propagation.SUPPORTS)
public boolean hasAccessToNetwork(AccessKey accessKey, Network targetNetwork) {
Set<AccessKeyPermission> permissions = accessKey.getPermissions();
User user = accessKey.getUser();
boolean hasNullPermission =
permissions.stream().anyMatch(perm -> perm.getNetworkIdsAsSet() == null);
if (hasNullPermission) {
return userService.hasAccessToNetwork(user, targetNetwork);
} else {
Set<Long> allowedNetworks =
permissions
.stream()
.map(AccessKeyPermission::getNetworkIdsAsSet)
.flatMap(Collection::stream)
.collect(Collectors.toSet());
user = userService.findUserWithNetworks(user.getId());
return allowedNetworks.contains(targetNetwork.getId())
&& (user.isAdmin() || user.getNetworks().contains(targetNetwork));
}
}
public void runTest() {
BufferedReader in = null;
/*
* read input from file
*/
try {
in = new BufferedReader(new FileReader(file));
String read = null;
while ((read = in.readLine()) != null) {
list.add(read.trim());
count++;
}
for (int i = 0; i < count; i++) {
System.out.println(list.get(i));
}
} catch (Exception e) {
System.out.println("There was a problem: " + e);
e.printStackTrace();
} finally {
try {
in.close();
} catch (Exception e) {
System.out.println("There was a problem: " + e);
e.printStackTrace();
}
}
/*
* send list of test messages to server
*/
for (String command : list) {
try {
Thread.sleep(1000);
} catch (Exception e) {
e.printStackTrace();
}
net.sendMessage(new UserMessage(command, serverIp, serverPort, System.nanoTime()));
}
}
@Before
public void setup() {
nw = new Network();
nw.setName("test network");
dp = new DensityMap();
nw.setNodes(new ArrayList<edu.berkeley.path.model_elements_base.Node>());
nw.setLinks(new ArrayList<edu.berkeley.path.model_elements_base.Link>());
Node nd1;
Node nd2;
Link ln;
nd1 = new Node();
nd1.setId(1L);
nd1.setName("one");
nd1.setType("Highway");
nw.getNodes().add(nd1);
nd2 = new Node();
nd2.setId(2L);
nd2.setName("two");
nd2.setType("Highway");
nw.getNodes().add(nd2);
ln = new Link();
ln.setId(3L);
ln.setName("three");
ln.setType("Highway");
ln.setLaneCount(4.0);
ln.setLength(1000.0);
ln.setBegin(nd1);
ln.setEnd(nd2);
nw.getLinks().add(ln);
}
/**
* a network is a collection of (possibly degenerate) interactions. the R client should pass 3
* arrays of strings, having the following structure
*
* <p>edges consist of strings like "VNG0723G::VNG1233G::PhylogeneticProfile" node attributes:
* "VNG1233G::commonName::pepq2" edge attributes:
* "VNG0723G::VNG1233G::PhylogeneticProfile::confidence::0.533"
*/
public void createAndBroadcastNetwork(
String[] interactionStrings,
String[] nodeAttributeStrings,
String[] edgeAttributeStrings,
String name) {
Network network = new Network();
addMetaDataToNetwork(network);
network.setName(name);
network.setSpecies(defaultSpecies);
for (String interactionString : interactionStrings) {
String[] tokens = interactionString.split("::");
int tokenCount = tokens.length;
// for (int t=0; t < tokens.length; t++)
// System.out.println (" edge token " + t + ": " + tokens [t]);
if (tokenCount == 1 && tokens[0].trim().length() > 0) {
// System.out.println ("adding one orphan node to network: " + tokens [0]);
network.add(tokens[0]);
} else if (tokenCount == 3) {
String sourceNode = tokens[0];
String targetNode = tokens[1];
String interactionType = tokens[2];
network.add(new Interaction(sourceNode, targetNode, interactionType));
} // else: good interaction
} // for i
// System.out.println ("nodeAttributeStrings count: " + nodeAttributeStrings.length);
for (String nodeAttributeString : nodeAttributeStrings) {
// System.out.println (" " + nodeAttributeStrings [i]);
String[] tokens = nodeAttributeString.split("::");
if (tokens.length == 3) {
String nodeName = tokens[0].trim();
String attributeName = tokens[1].trim();
String rawValue = tokens[2].trim();
Object value = StringToObjectConverter.convert(rawValue);
network.addNodeAttribute(nodeName, attributeName, value);
} // if 3 tokens
} // for i
// System.out.println ("edgeAttributeStrings count: " + edgeAttributeStrings.length);
for (String edgeAttributeString : edgeAttributeStrings) {
// System.out.println (" " + edgeAttributeStrings [i]);
String[] tokens = edgeAttributeString.split("::");
if (tokens.length == 5) {
String sourceNode = tokens[0].trim();
String targetNode = tokens[1].trim();
String edgeType = tokens[2].trim();
String attributeName = tokens[3].trim();
String rawValue = tokens[4].trim();
Object value = StringToObjectConverter.convert(rawValue);
String edgeName = sourceNode + " (" + edgeType + ") " + targetNode;
network.addEdgeAttribute(edgeName, attributeName, value);
} // if 5 tokens
} // for i
// System.out.println ("RShellGoose, about to broadcast network");
// System.out.println (" node count: " + network.getNodes().length);
// System.out.println (" connected: " + network.getConnectedNodes ().size ());
// System.out.println (" orphan: " + network.getOrphanNodes().length);
try {
gaggleBoss.broadcastNetwork(myGaggleName, targetGoose, network);
} catch (RemoteException rex) {
System.err.println("error broadcasting network from RShellGoose " + myGaggleName);
rex.printStackTrace();
}
} // createAndBroadcastNetwork
public ChargerReader(Network network, EvData data) {
this.data = data;
links = network.getLinks();
}
/** Insert the method's description here. Creation date: (16/01/2002 9.53.37) */
public static boolean xor_evaluate(Organism organism) {
Network _net = null;
boolean success = false;
double errorsum = 0.0;
double[] out = new double[4]; // The four outputs
// int numnodes = 0;
int net_depth = 0; // The max depth of the network to be activated
int count = 0;
// The four possible input combinations to xor
// The first number is for biasing
double in[][] = {{1.0, 0.0, 0.0}, {1.0, 0.0, 1.0}, {1.0, 1.0, 0.0}, {1.0, 1.0, 1.0}};
_net = organism.net;
// numnodes = organism.genome.nodes.size();
net_depth = _net.max_depth();
// for each example , 'count', propagate signal .... and compute results
for (count = 0; count <= 3; count++) {
// first activation from sensor to first next levelof neurons
_net.load_sensors(in[count]);
success = _net.activate();
// next activation while last level is reached !
// use depth to ensure relaxation
for (int relax = 0; relax <= net_depth; relax++) success = _net.activate();
// ok : the propagation is completed : repeat until all examples are presented
out[count] = ((NNode) _net.getOutputs().firstElement()).getActivation();
_net.flush();
}
// control the result
if (success) {
errorsum =
(double)
(Math.abs(out[0])
+ Math.abs(1.0 - out[1])
+ Math.abs(1.0 - out[2])
+ Math.abs(out[3]));
organism.setFitness(Math.pow((4.0 - errorsum), 2));
organism.setError(errorsum);
} else {
errorsum = 999.0;
organism.setFitness(0.001);
organism.setError(errorsum);
}
String mask03 = "0.000";
DecimalFormat fmt03 = new DecimalFormat(mask03);
if ((out[0] < 0.5) && (out[1] >= 0.5) && (out[2] >= 0.5) && (out[3] < 0.5)) {
organism.setWinner(true);
return true;
} else {
organism.setWinner(false);
return false;
}
}
public boolean execute() {
if (CDState.getCycle() % period != 0) return false;
MycoCast mycocast = (MycoCast) Network.get(0).getProtocol(mycocastPid);
int bio = mycocast.countBiomass();
int ext = mycocast.countExtending();
int bra = mycocast.countBranching();
int imm = mycocast.countImmobile();
// Update vertices
Set<MycoNode> activeNodes = new HashSet<MycoNode>();
for (int i = 0; i < Network.size(); i++) {
MycoNode n = (MycoNode) Network.get(i);
activeNodes.add(n);
HyphaData data = n.getHyphaData();
// if (data.isBiomass()) { continue; }
if (graph.containsVertex(n)) {
graph.removeVertex(n);
}
if (!graph.containsVertex(n)) {
graph.addVertex(n);
}
}
Set<MycoNode> jungNodes = new HashSet<MycoNode>(graph.getVertices());
jungNodes.removeAll(activeNodes);
for (MycoNode n : jungNodes) {
graph.removeVertex(n);
}
// Update edges
for (int i = 0; i < Network.size(); i++) {
MycoNode n = (MycoNode) Network.get(i);
HyphaData data = n.getHyphaData();
HyphaLink link = n.getHyphaLink();
synchronized (graph) {
// We now add in all links and tune out display in Visualizer
java.util.List<MycoNode> neighbors = (java.util.List<MycoNode>) link.getNeighbors();
//// Adding only links to hypha thins out links to biomass
// (java.util.List<MycoNode>) link.getHyphae();
Collection<MycoNode> jungNeighbors = graph.getNeighbors(n);
// Remove edges from Jung graph that are not in peersim graph
for (MycoNode o : jungNeighbors) {
if (!neighbors.contains(o)) {
MycoEdge edge = graph.findEdge(n, o);
while (edge != null) {
graph.removeEdge(edge);
edge = graph.findEdge(n, o);
}
}
}
// Add missing edges to Jung graph that are in peersim graph
for (MycoNode o : neighbors) {
if (graph.findEdge(n, o) == null) {
MycoEdge edge = new MycoEdge();
graph.addEdge(edge, n, o, EdgeType.DIRECTED);
}
}
}
// log.finest("VERTICES: " + graph.getVertices());
// log.finest("EDGES: " + graph.getEdges());
}
for (ChangeListener cl : changeListeners) {
cl.stateChanged(new ChangeEvent(graph));
}
if (walking) {
try {
Thread.sleep(walkDelay);
} catch (InterruptedException e) {
}
stepBlocked = false;
}
try {
while (stepBlocked && !noBlock) {
synchronized (JungGraphObserver.class) {
JungGraphObserver.class.wait();
}
}
} catch (InterruptedException e) {
stepBlocked = true;
}
stepBlocked = true;
// System.out.println(graph.toString());
return false;
}
/**
* This is a test for compute depth of genome and trace all debug information for viewing all
* signal flowing is not necessary for network simulation
*/
public static void Experiment2(String xFileName) {
StringTokenizer st;
String curword;
String xline;
String fnamebuf;
IOseq xFile;
int id;
Genome g1 = null;
Network net = null;
System.out.println("------ Start experiment 2 -------");
xFile = new IOseq(xFileName);
boolean ret = xFile.IOseqOpenR();
if (ret) {
try {
System.out.println(" Start experiment 2");
System.out.println(" Read start genome..");
xline = xFile.IOseqRead();
st = new StringTokenizer(xline);
// skip
curword = st.nextToken();
// id of genome can be readed
curword = st.nextToken();
id = Integer.parseInt(curword);
g1 = new Genome(id, xFile);
// generate a link mutation
g1.mutate_link_weight(Neat.p_weight_mut_power, 1.0, NeatConstant.GAUSSIAN);
// generate from genome the phenotype
g1.genesis(id);
// view genotype
g1.op_view();
// assign reference to genotype
net = g1.phenotype;
// compute first the 'teorical' depth
int lx = net.max_depth();
// compute . after, the 'pratical' depth passing
// the virtual depth;
int dx = net.is_stabilized(lx);
// after reset all value of net
net.flush();
System.out.print("\n For genome : " + xFileName + " : max depth virtuale=" + lx);
System.out.print(", max depth reale=" + dx);
if (dx != lx) System.out.print("\n *ALERT* This net is NOT S T A B L E ");
net.flush();
double errorsum = 0.0;
double[] out = new double[4]; // The four outputs
int numnodes = 0;
int net_depth = 0; // The max depth of the network to be activated
int count = 0;
boolean success = false;
double in[] = {1.0, 1.0, 1.0};
count = 0;
// first activation from sensor to first next level of neurons
net.load_sensors(in);
// first activation....
success = net.activate();
// next activation while last level is reached !
// use depth to ensure relaxation
for (int relax = 1; relax <= dx; relax++) {
success = net.activate();
// System.out.print("\n -----TIME <"+relax+"> -----");
}
// ok : the propagation is completed
} catch (Throwable e) {
System.err.println(e + " : error during open " + xFileName);
}
xFile.IOseqCloseR();
} else System.err.print("\n : error during open " + xFileName);
System.out.println("\n\n End of experiment");
}
public static double getEdgeCount(Network forest) {
return (double) forest.getEdgeCount();
}
/**
* This is a test for compute depth of genome and compute if has a path from two nodes (is a test
* for new version of method is_recur()) --> has_a_path(..) is not necessary for network
* simulation
*/
public static void Experiment5(String xFileName, int potin, int potout) {
StringTokenizer st;
String curword;
String xline;
String fnamebuf;
IOseq xFile;
int id;
Genome g1 = null;
Network net = null;
xFile = new IOseq(xFileName);
boolean ret = xFile.IOseqOpenR();
if (ret) {
try {
System.out.println("------ Start experiment 5 -------");
// read genome A
System.out.println(" Read start genome..");
xline = xFile.IOseqRead();
st = new StringTokenizer(xline);
// skip
curword = st.nextToken();
// id of genome can be readed
curword = st.nextToken();
id = Integer.parseInt(curword);
g1 = new Genome(id, xFile);
// generate a link mutation
g1.mutate_link_weight(Neat.p_weight_mut_power, 1.0, NeatConstant.GAUSSIAN);
// generate from genome the phenotype
g1.genesis(id);
// view genotype
g1.op_view();
// assign reference to genotype
net = g1.phenotype;
// compute first the 'teorical' depth
int lx = net.max_depth();
// compute . after, the 'pratical' depth passing
// the virtual depth;
int dx = net.is_stabilized(lx);
System.out.print("\n Max depth virtuale=" + lx);
System.out.print(", max depth reale=" + dx);
// search the inode
NNode inode = null;
NNode onode = null;
NNode curnode = null;
boolean rc = false;
int cnt = 0;
for (int ix = 0; (ix < net.allnodes.size()) && (cnt < 2); ix++) {
curnode = (NNode) net.allnodes.elementAt(ix);
if (curnode.node_id == potin) {
inode = curnode;
cnt++;
}
if (curnode.node_id == potout) {
onode = curnode;
cnt++;
}
}
// if exist , point to exitsting version
if (cnt < 2) {
System.out.print("\n ERROR :nodes in e/o out wrong's : retype!");
} else {
net.status = 0;
rc = net.has_a_path(inode, onode, 0, 30);
System.out.print("\n Result for example " + xFileName + " for ipotetic path ");
System.out.print(
"\n inode[" + potin + "] ---> onode[" + potout + "] is return code=" + rc);
System.out.print(", status = " + net.status);
}
// after reset all value of net
net.flush();
// ok : the propagation is completed
} catch (Throwable e) {
System.err.println(e + " : error during read " + xFileName);
}
xFile.IOseqCloseR();
} else System.err.print("\n : error during open " + xFileName);
System.out.println("\n\n End of experiment");
}