/*
* public HashMap getLeafElements() { HashMap map = new HashMap(); Object[]
* elts = dataElements.values().toArray(); for (int j=0; j<elts.length; j++)
* { PDMDataElement data = (PDMDataElement) elts[j];
* map.put(data.getID(),data); } Object[] ops =
* operations.values().toArray(); for (int i=0; i<ops.length; i++){
* PDMOperation op = (PDMOperation) ops[i]; if
* (!(op.getInputElements().isEmpty())){ HashMap outs =
* op.getOutputElements(); Object[] outArray = outs.values().toArray(); for
* (int j=0; j<outArray.length; j++) { PDMDataElement d = (PDMDataElement)
* outArray[j]; map.remove(d.getID()); } } } return map; }
*/
public HashMap getLeafElements() {
HashMap result = new HashMap();
HashSet leafOps = getLeafOperations();
if (!(leafOps.isEmpty())) {
Iterator it = leafOps.iterator();
while (it.hasNext()) {
PDMOperation op = (PDMOperation) it.next();
PDMDataElement data = op.getOutputElement();
result.put(data.getID(), data);
}
} else {
Object[] elts = dataElements.values().toArray();
for (int j = 0; j < elts.length; j++) {
PDMDataElement data = (PDMDataElement) elts[j];
result.put(data.getID(), data);
}
Object[] ops = operations.values().toArray();
for (int i = 0; i < ops.length; i++) {
PDMOperation op = (PDMOperation) ops[i];
HashMap outs = op.getOutputElements();
Object[] outArray = outs.values().toArray();
for (int j = 0; j < outArray.length; j++) {
PDMDataElement d = (PDMDataElement) outArray[j];
result.remove(d.getID());
}
}
}
return result;
}
/**
* Writes the model to DOT.
*
* @param bw The writer
* @throws IOException If writing fails
*/
public void writeToDot(Writer bw) throws IOException {
// super.writeToDot(bw);
// Preamble of dot file
bw.write(
"digraph G {ranksep=\".3\"; fontsize=\"8\"; remincross=true; margin=\"0.0,0.0\"; rankdir=TB; ");
bw.write("fontname=\"Arial\"; \n");
bw.write("edge [arrowsize=\"0.5\"];\n");
bw.write("node [fontname=\"Arial\",fontsize=\"8\"];\n");
// Add the Data Element nodes
Iterator it = getVerticeList().iterator();
while (it.hasNext()) {
Object object = it.next();
if (object instanceof PDMDataElement) {
((PDMDataElement) object).writeToDot(bw, this);
}
}
// Add all edges
it = operations.values().iterator();
while (it.hasNext()) {
Object object = it.next();
if (object instanceof PDMOperation) {
((PDMOperation) object).writeToDot(bw, this);
}
}
bw.write("\n}\n");
}
public PDMState checkIfStateExists(
PDMStateSpace statespace, HashSet data, HashSet exec, HashSet failed) {
PDMState result = null;
boolean bool = false;
HashSet states = statespace.getStates();
Iterator it = states.iterator();
while (it.hasNext() && !bool) {
PDMState state2 = (PDMState) it.next();
boolean one = false;
boolean two = false;
boolean three = false;
HashSet data2 = state2.dataElements;
HashSet exec2 = state2.executedOperations;
HashSet failed2 = state2.failedOperations;
one = hashSetContainsSameDataElements(data, data2);
two = hashSetContainsSameOperations(exec, exec2);
three = hashSetContainsSameOperations(failed, failed2);
if (one && two && three) {
bool = true;
result = state2;
}
}
return result;
}
public void display(Graphics2D g, AffineTransform a_trans) {
Iterator i = createIterator();
while (i.hasNext()) {
GlyphObject object = (GlyphObject) i.next();
object.display(g, a_trans);
} // while
}
public static void exportThis(
String target_sea_state_set,
String target_sea_state_datum,
String[] sea_state_headings,
IntegerTargetTypeLookup states,
Element envElement,
Document doc) {
// ok, put us into the element
org.w3c.dom.Element itt = doc.createElement(target_sea_state_set);
// get on with the name attribute
Double unknown = states.getUnknownResult();
if (unknown != null) itt.setAttribute(UNKNOWN_TYPE, writeThis(unknown.doubleValue()));
// now the matrix of sea states
Collection<String> keys = states.getNames();
for (Iterator<String> iter = keys.iterator(); iter.hasNext(); ) {
String thisN = (String) iter.next();
// ok, cycle through the sea states for this participant
NamedList thisList = states.getThisSeries(thisN);
exportThisSeries(thisN, target_sea_state_datum, thisList, sea_state_headings, itt, doc);
}
envElement.appendChild(itt);
}
/**
* Returns a String representation of the <code><saml:Attribute></code> element.
*
* @param includeNS Determines whether or not the namespace qualifier is prepended to the Element
* when converted
* @param declareNS Determines whether or not the namespace is declared within the Element.
* @return A string containing the valid XML for this element
*/
public String toString(boolean includeNS, boolean declareNS) {
StringBuffer result = new StringBuffer(1000);
String prefix = "";
String uri = "";
if (includeNS) {
prefix = SAMLConstants.ASSERTION_PREFIX;
}
if (declareNS) {
uri = SAMLConstants.assertionDeclareStr;
}
result
.append("<")
.append(prefix)
.append("Attribute")
.append(uri)
.append(" AttributeName=\"")
.append(_attributeName)
.append("\" AttributeNamespace=\"")
.append(_attributeNameSpace)
.append("\">\n");
Iterator iter = _attributeValue.iterator();
while (iter.hasNext()) {
result.append(XMLUtils.printAttributeValue((Element) iter.next(), prefix)).append("\n");
}
result.append("</").append(prefix).append("Attribute>\n");
return result.toString();
}
/**
* Constructs an instance of <code>Attribute</code>.
*
* @param name A String representing <code>AttributeName</code> (the name of the attribute).
* @param nameSpace A String representing the namespace in which <code>AttributeName</code>
* elements are interpreted.
* @param values A List of DOM element representing the <code>AttributeValue</code> object.
* @exception SAMLException if there is an error in the sender or in the element definition.
*/
public Attribute(String name, String nameSpace, List values) throws SAMLException {
super(name, nameSpace);
if (values == null || values.isEmpty()) {
if (SAMLUtilsCommon.debug.messageEnabled()) {
SAMLUtilsCommon.debug.message("Attribute: AttributeValue is" + "required.");
}
throw new SAMLRequesterException(SAMLUtilsCommon.bundle.getString("nullInput"));
}
if (_attributeValue == null) {
_attributeValue = new ArrayList();
}
// Make sure this is a list of AttributeValue
Iterator iter = values.iterator();
String tag = null;
while (iter.hasNext()) {
tag = ((Element) iter.next()).getLocalName();
if ((tag == null) || (!tag.equals("AttributeValue"))) {
if (SAMLUtilsCommon.debug.messageEnabled()) {
SAMLUtilsCommon.debug.message("AttributeValue: wrong input.");
}
throw new SAMLRequesterException(SAMLUtilsCommon.bundle.getString("wrongInput"));
}
}
_attributeValue = values;
}
/**
* Reload the composite nodes of the circuit, this is recursive
*
* @param g the graphics that will paint the node
* @throws CircuitLoadingException if the internal circuit can not be loaded
*/
public void reloadCompositeNodes(Graphics g) throws CircuitLoadingException {
for (iterNodes = this.nodes.iterator(); iterNodes.hasNext(); ) {
Node n = iterNodes.next();
if (n.getCategoryID() == Node.COMPOSITE) ((CompositeNode) n).reload(g);
}
}
// ## operation writeChemkinReactions(ReactionModel)
// 10/26/07 gmagoon: changed to take temperature as parameter (it doesn't seem like this method is
// currently used anywhere)
public static String writeChemkinReactions(
ReactionModel p_reactionModel, Temperature p_temperature) {
// #[ operation writeChemkinReactions(ReactionModel)
StringBuilder result = new StringBuilder();
result.append("REACTIONS KCAL/MOLE\n");
CoreEdgeReactionModel cerm = (CoreEdgeReactionModel) p_reactionModel;
LinkedHashSet all = cerm.getReactedReactionSet();
HashSet hs = new HashSet();
int numfor = 0;
int numrev = 0;
int numdup = 0;
int numnorev = 0;
for (Iterator iter = all.iterator(); iter.hasNext(); ) {
Reaction rxn = (Reaction) iter.next();
if (rxn.isForward()) {
result.append(
" "
+ rxn.toChemkinString(p_temperature)
+ "\n"); // 10/26/07 gmagoon: changed to avoid use of Global.temperature
// result.append(" " + rxn.toChemkinString(Global.temperature) + "\n");
}
}
result.append("END\n");
return result.toString();
// #]
}
private String unirMapeos(LinkedHashMap<String, String> mapa, Object[] descripciones) {
// mapa(llave,punto)
// descripciones en el mismo orden que el mapeo
String comillas = "\"";
StringBuilder builder = new StringBuilder();
Iterator<String> iterador = mapa.keySet().iterator();
int indice = 0;
while (iterador.hasNext()) {
String llave = iterador.next();
String puntaje = mapa.get(llave);
String descripcion =
descripciones[indice].toString().equals("null") ? "" : descripciones[indice].toString();
builder.append(comillas + descripcion + comillas + "," + comillas + puntaje + comillas + ",");
indice++;
}
return builder.toString();
}
/**
* This method exports the single pattern decision instance to the XML. It MUST be called by an
* XML exporter, as this will not have a complete header.
*
* @param ratDoc The ratDoc generated by the XML exporter
* @return the SAX representation of the object.
*/
public Element toXML(Document ratDoc) {
Element decisionE;
RationaleDB db = RationaleDB.getHandle();
// Now, add pattern to doc
String entryID = db.getRef(this);
if (entryID == null) {
entryID = db.addPatternDecisionRef(this);
}
decisionE = ratDoc.createElement("DR:patternDecision");
decisionE.setAttribute("rid", entryID);
decisionE.setAttribute("name", name);
decisionE.setAttribute("type", type.toString());
decisionE.setAttribute("phase", devPhase.toString());
decisionE.setAttribute("status", status.toString());
// decisionE.setAttribute("artifact", artifact);
Element descE = ratDoc.createElement("description");
Text descText = ratDoc.createTextNode(description);
descE.appendChild(descText);
decisionE.appendChild(descE);
// Add child pattern references...
Iterator<Pattern> cpi = candidatePatterns.iterator();
while (cpi.hasNext()) {
Pattern cur = cpi.next();
Element curE = ratDoc.createElement("refChildPattern");
Text curText = ratDoc.createTextNode("p" + new Integer(cur.getID()).toString());
curE.appendChild(curText);
decisionE.appendChild(curE);
}
return decisionE;
}
private static void exportThisSeries(
String name,
String target_sea_state_datum,
NamedList thisList,
String[] sea_state_headings,
Element itt,
Document doc) {
// ok, put us into the element
org.w3c.dom.Element datum = doc.createElement(target_sea_state_datum);
datum.setAttribute("Type", name);
// and step through its values
Collection<Double> indices = thisList.getValues();
int ctr = 0;
for (Iterator<Double> iter = indices.iterator(); iter.hasNext(); ) {
Double val = (Double) iter.next();
if (val != null) {
datum.setAttribute(sea_state_headings[ctr], writeThis(val.doubleValue()));
ctr++;
} else break;
}
itt.appendChild(datum);
}
public void selectNext() {
Iterator i = new SelectionIterator(this);
if (m_actives.size() == 1) {
boolean isFound = false;
// loop the iterator in reverse order of drawing
while (i.hasNext()) {
GlyphObject object = (GlyphObject) i.next();
if (m_actives.isSelected(object)) {
isFound = true;
continue;
} // if
if (!isFound) {
continue;
} // if
m_actives.unselectAll();
m_actives.addActive(object);
return;
} // while i
} // if
i = new SelectionIterator(this);
if (i.hasNext()) {
GlyphObject object = (GlyphObject) i.next();
m_actives.unselectAll();
m_actives.addActive(object);
return;
} // if
}
public static void write() {
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
Document doc;
System.out.println("Writing patient data file\n");
try {
DocumentBuilder builder = factory.newDocumentBuilder();
doc = builder.newDocument();
Element root = doc.createElement("patientdata");
root.appendChild(XMLInterface.nl(doc));
// get first PatientData from DataStore
Iterator<PatientDataStore> pdsIt = GlobalVars.pds.iterator();
while (pdsIt.hasNext()) {
PatientDataStore pds = pdsIt.next();
Node n = pds.createXMLNode(doc);
XMLInterface.addNode(doc, root, n, 0);
}
root.normalize();
// create junk to write it out (see java xml tutorial)
TransformerFactory tFactory = TransformerFactory.newInstance();
Transformer transformer = tFactory.newTransformer();
DOMSource src = new DOMSource(root);
StreamResult result = new StreamResult(new File(GlobalVars.XMLDataFile));
transformer.transform(src, result);
} catch (Exception e) {
System.err.println("Error WRITING xml patient data file");
e.printStackTrace();
}
}
public static List list(NodeList self) {
List answer = new ArrayList();
Iterator it = DefaultGroovyMethods.iterator(self);
while (it.hasNext()) {
answer.add(it.next());
}
return answer;
}
public static Element appendNode(Element self, Object name, Map attributes, String value) {
Element result = appendNode(self, name, value);
for (Iterator iterator = attributes.entrySet().iterator(); iterator.hasNext(); ) {
Map.Entry e = (Map.Entry) iterator.next();
putAt(result, "@" + e.getKey().toString(), e.getValue());
}
return result;
}
public Collection hasRepositoryLocations(Collection repositoryLocationsToCheck) {
Vector v = new Vector();
for (Iterator en = repositoryLocationsToCheck.iterator(); en.hasNext(); ) {
IRepositoryLocation elt = (IRepositoryLocation) en.next();
v.addElement(new Boolean(hasRepositoryLocation(elt)));
}
return v;
}
public Collection hasSourceCodeFiles(Collection sourceCodeFilesToCheck) {
Vector v = new Vector();
for (Iterator en = sourceCodeFilesToCheck.iterator(); en.hasNext(); ) {
IJavaSourceFile elt = (IJavaSourceFile) en.next();
v.addElement(new Boolean(hasSourceCodeFile(elt)));
}
return v;
}
public Iterator getAllAttributes() {
Iterator i = getAllAttributesFrom(this);
ArrayList list = new ArrayList();
while (i.hasNext()) {
Name name = (Name) i.next();
if (!"xmlns".equalsIgnoreCase(name.getPrefix())) list.add(name);
}
return list.iterator();
}
public boolean hasAllRepositoryLocations(Collection repositoryLocationsToCheck) {
for (Iterator en = repositoryLocationsToCheck.iterator(); en.hasNext(); ) {
IRepositoryLocation elt = (IRepositoryLocation) en.next();
if (!hasRepositoryLocation(elt)) {
return false;
}
}
return true;
}
public boolean hasAllSourceCodeFiles(Collection sourceCodeFilesToCheck) {
for (Iterator en = sourceCodeFilesToCheck.iterator(); en.hasNext(); ) {
IJavaSourceFile elt = (IJavaSourceFile) en.next();
if (!hasSourceCodeFile(elt)) {
return false;
}
}
return true;
}
public void makeNSMappings(PrintWriter buffer) {
Set keys = prefixByUri_.keySet();
Iterator iter = keys.iterator();
while (iter.hasNext()) {
String uri = (String) iter.next();
buffer.print(makeNSMapping(uri));
}
}
public ActionDescriptor getAction(int id) {
// check global actions
for (Iterator iterator = globalActions.iterator(); iterator.hasNext(); ) {
ActionDescriptor actionDescriptor = (ActionDescriptor) iterator.next();
if (actionDescriptor.getId() == id) {
return actionDescriptor;
}
}
// check steps
for (Iterator iterator = steps.iterator(); iterator.hasNext(); ) {
StepDescriptor stepDescriptor = (StepDescriptor) iterator.next();
ActionDescriptor actionDescriptor = stepDescriptor.getAction(id);
if (actionDescriptor != null) {
return actionDescriptor;
}
}
// check initial actions, which we now must have unique id's
for (Iterator iterator = initialActions.iterator(); iterator.hasNext(); ) {
ActionDescriptor actionDescriptor = (ActionDescriptor) iterator.next();
if (actionDescriptor.getId() == id) {
return actionDescriptor;
}
}
return null;
}
public JoinDescriptor getJoin(int id) {
for (Iterator iterator = joins.iterator(); iterator.hasNext(); ) {
JoinDescriptor joinDescriptor = (JoinDescriptor) iterator.next();
if (joinDescriptor.getId() == id) {
return joinDescriptor;
}
}
return null;
}
public SplitDescriptor getSplit(int id) {
for (Iterator iterator = splits.iterator(); iterator.hasNext(); ) {
SplitDescriptor splitDescriptor = (SplitDescriptor) iterator.next();
if (splitDescriptor.getId() == id) {
return splitDescriptor;
}
}
return null;
}
private static String toString(NodeList self) {
StringBuffer sb = new StringBuffer();
sb.append("[");
Iterator it = DefaultGroovyMethods.iterator(self);
while (it.hasNext()) {
if (sb.length() > 1) sb.append(", ");
sb.append(it.next().toString());
}
sb.append("]");
return sb.toString();
}
public StepDescriptor getStep(int id) {
for (Iterator iterator = steps.iterator(); iterator.hasNext(); ) {
StepDescriptor step = (StepDescriptor) iterator.next();
if (step.getId() == id) {
return step;
}
}
return null;
}
public static byte[] convertToJSON(
IExtensionHelpers helpers, IHttpRequestResponse requestResponse) {
byte[] request = requestResponse.getRequest();
if (Objects.equals(helpers.analyzeRequest(request).getMethod(), "GET")) {
request = helpers.toggleRequestMethod(request);
}
IRequestInfo requestInfo = helpers.analyzeRequest(request);
int bodyOffset = requestInfo.getBodyOffset();
byte content_type = requestInfo.getContentType();
String body = new String(request, bodyOffset, request.length - bodyOffset);
String json = "";
Boolean success = true;
try {
if (content_type == 3) {
JSONObject xmlJSONObject = XML.toJSONObject(body);
json = xmlJSONObject.toString(2);
} else if (content_type == 0 || content_type == 1) {
Map<String, String> params = splitQuery(body);
Gson gson = new Gson();
json = gson.toJson(params);
} else {
json = body;
}
} catch (Exception e) {
success = false;
}
if (!success) {
return request;
} else {
List<String> headers;
headers = helpers.analyzeRequest(request).getHeaders();
Iterator<String> iter = headers.iterator();
while (iter.hasNext()) {
if (iter.next().contains("Content-Type")) iter.remove();
}
headers.add("Content-Type: application/json;charset=UTF-8");
return helpers.buildHttpMessage(headers, json.getBytes());
}
}
/**
* Get the inputable nodes of the circuit
*
* @return an hashset of the inputable nodes of the circuit
*/
public HashSet<Inputable> getInputables() {
HashSet<Inputable> inputs = new HashSet<Inputable>();
for (iterNodes = getNodesIterator(); iterNodes.hasNext(); ) {
Node n = iterNodes.next();
if (n.getCategoryID() == Node.INPUT) inputs.add((Inputable) n);
}
return inputs;
}
/**
* Get the outputable nodes of the circuit
*
* @return an hashset of the outputable nodes of the circuit
*/
public HashSet<Outputable> getOutputables() {
HashSet<Outputable> outputs = new HashSet<Outputable>();
for (iterNodes = getNodesIterator(); iterNodes.hasNext(); ) {
Node n = iterNodes.next();
if (n.getCategoryID() == Node.OUTPUT) outputs.add((Outputable) n);
}
return outputs;
}