private JSONObject convertXMLToJSON(String xmlData) throws JSONException, JAXBException {
// Unmarshall the xml into a GraphML
ByteArrayInputStream baiStream = new ByteArrayInputStream(xmlData.getBytes());
JAXBContext jc = JAXBContext.newInstance(GraphMLUtil.GRAPHML_CLASSES);
Unmarshaller unmarshaller = jc.createUnmarshaller();
GraphML graphML = (GraphML) unmarshaller.unmarshal(baiStream);
// eventually check version for compatibility
s_logger.info("Importing chart version: {}", graphML.getversion());
Graph graph = graphML.getGraph();
JSONObject toReturn = new JSONObject(),
miscData = null,
columnJSON,
nodeJSON = null,
clusterJSON;
String cachedClusterJSON = null;
int columnIdx = -1, rowIdx = -1;
List<List<JSONObject>> allColumns = new ArrayList<List<JSONObject>>();
List<JSONObject> currColumn, outColumns = new ArrayList<JSONObject>();
// first, set up the column and misc JSON data contained in the graph
for (GraphDataXML data : graph.getdata()) {
if (data.getkey().startsWith("column")) {
columnJSON = XML.toJSONObject(data.getvalue());
columnIdx = Integer.parseInt(data.getkey().substring(6));
while (columnIdx >= outColumns.size()) {
outColumns.add(new JSONObject());
}
outColumns.set(columnIdx, columnJSON);
allColumns.add(new ArrayList<JSONObject>());
} else if (data.getkey().equals("miscData")) {
miscData = XML.toJSONObject(data.getvalue());
}
}
// next, iterate through the graph nodes and place the JSONObject for each into it's proper
// row/column
for (GraphNode node : graph.getnode()) {
for (GraphData data : node.getdata()) { // parse the goodies from each file node
if (data.getkey().equals("column")) {
columnIdx = Integer.parseInt(data.getvalue());
} else if (data.getkey().equals("row")) {
rowIdx = Integer.parseInt(data.getvalue());
}
}
for (GraphDataXML data : node.getnodedata()) { // parse the goodies from each data node
if (data.getkey().equals("fileJSON")) {
nodeJSON = XML.toJSONObject(data.getvalue());
} else if (data.getkey().equals("clusterJSON")) {
cachedClusterJSON = data.getvalue();
}
}
if (nodeJSON != null
&& nodeJSON.has("clusterUIObject")
&& !nodeJSON.get("clusterUIObject").toString().equals("null")) {
clusterJSON = nodeJSON.getJSONObject("clusterUIObject"); // do annoying cleanup
insertJSONArray(clusterJSON, "children");
insertJSONArray(clusterJSON.getJSONObject("spec"), "members");
}
if (cachedClusterJSON != null) {
PermitSet permits = new PermitSet();
try {
List<String> entityIds = new LinkedList<String>();
List<FL_Cluster> allClusters = ClusterHelper.listFromJson(cachedClusterJSON);
;
for (FL_Cluster cluster : allClusters) {
entityIds.addAll(cluster.getMembers());
for (FL_Property property : cluster.getProperties()) {
if (!(property.getRange() instanceof FL_SingletonRange)) continue;
FL_SingletonRange range = (FL_SingletonRange) property.getRange();
if (!range.getType().equals(FL_PropertyType.STRING)) continue;
property.setRange(
new SingletonRangeHelper(
StringEscapeUtils.unescapeXml((String) range.getValue())));
}
}
final ContextReadWrite contextRW =
contextCache.getReadWrite(nodeJSON.getString("xfId"), permits);
contextRW.getContext().addClusters(allClusters);
contextRW
.getContext()
.addEntities(entityAccess.getEntities(entityIds, FL_LevelOfDetail.SUMMARY));
contextRW.setSimplifiedContext(allClusters);
} catch (IOException e) {
throw new ResourceException(
Status.CLIENT_ERROR_BAD_REQUEST, "Exception during cluster cache processing.", e);
} finally {
permits.revoke();
}
}
currColumn = allColumns.get(columnIdx);
while (rowIdx >= currColumn.size()) {
currColumn.add(new JSONObject());
}
currColumn.set(rowIdx, nodeJSON);
}
// place the files as children in the outgoing columns array
for (int i = 0; i < allColumns.size(); i++) {
columnJSON = outColumns.get(i);
columnJSON.put("children", new JSONArray(allColumns.get(i)));
}
// finally, place the child columns and misc data in the resulting JSON object
toReturn.put("children", new JSONArray(outColumns));
for (String dataKey : JSONObject.getNames(miscData)) {
toReturn.put(dataKey, miscData.get(dataKey));
}
return toReturn;
}
@Override
public ClusterContext clusterEntities(
Collection<FL_Entity> entities,
Collection<FL_Cluster> immutableClusters,
Collection<FL_Cluster> clusters,
ClusterContext context) {
Map<String, FL_Entity> entityIndex = createEntityIndex(entities);
Map<String, FL_Cluster> immutableClusterIndex = createClusterIndex(immutableClusters);
Map<String, FL_Cluster> clusterIndex = createClusterIndex(clusters);
DataSet ds = createDataSet(entities, immutableClusters, context);
BaseClusterer clusterer = createNumericClusterer();
List<Cluster> existingClusters = new LinkedList<Cluster>();
for (FL_Cluster cluster : clusters) {
double val = 0;
PropertyHelper prop = getFirstProperty(cluster, toClusterPropertyName(clusterField));
if (prop != null) {
val = getDoubleValue(prop);
}
Cluster c = clusterer.createCluster();
c.setId(cluster.getUid());
NumericVectorFeature feature = new NumericVectorFeature("num");
feature.setValue(new double[] {val});
c.addFeature(feature);
existingClusters.add(c);
}
ClusterResult rs = null;
if (existingClusters.isEmpty()) {
rs = clusterer.doCluster(ds);
} else {
rs = clusterer.doIncrementalCluster(ds, existingClusters);
}
// clean up
clusterer.terminate();
Map<String, FL_Cluster> modifiedClusters = new HashMap<String, FL_Cluster>();
for (Cluster c : rs) {
List<FL_Cluster> subClusters = new LinkedList<FL_Cluster>();
List<FL_Entity> members = new LinkedList<FL_Entity>();
for (Instance inst : c.getMembers()) {
String id = inst.getId();
if (entityIndex.containsKey(id)) {
members.add(entityIndex.get(id));
} else if (immutableClusterIndex.containsKey(id)) {
subClusters.add(immutableClusterIndex.get(id));
}
}
FL_Cluster cluster = clusterIndex.get(c.getId());
if (cluster == null) {
cluster = clusterFactory.toCluster(members, subClusters);
// cache the cluster property
NumericVectorFeature feature = (NumericVectorFeature) c.getFeature("num");
double value = feature.getValue()[0];
addClusterProperty(cluster, clusterField, value);
} else {
ClusterHelper.addMembers(cluster, members);
EntityClusterFactory.setEntityCluster(members, cluster);
for (FL_Cluster subCluster : subClusters) {
ClusterHelper.addSubCluster(cluster, subCluster);
subCluster.setParent(cluster.getUid());
}
// cache the cluster property
NumericVectorFeature feature = (NumericVectorFeature) c.getFeature("num");
double value = feature.getValue()[0];
addClusterProperty(cluster, clusterField, value);
}
modifiedClusters.put(cluster.getUid(), cluster);
}
ClusterContext result = new ClusterContext();
result.roots.putAll(modifiedClusters);
result.clusters.putAll(modifiedClusters);
return result;
}