/**
* Unmarshall a Genotype instance from a given XML Element representation. Its population of
* Chromosomes will be unmarshalled from the Chromosome sub-elements.
*
* @param a_activeConfiguration the current active Configuration object that is to be used during
* construction of the Genotype and Chromosome instances
* @param a_xmlElement the XML Element representation of the Genotype
* @return a new Genotype instance, complete with a population of Chromosomes, setup with the data
* from the XML Element representation
* @throws ImproperXMLException if the given Element is improperly structured or missing data
* @throws InvalidConfigurationException if the given Configuration is in an inconsistent state
* @throws UnsupportedRepresentationException if the actively configured Gene implementation does
* not support the string representation of the alleles used in the given XML document
* @throws GeneCreationException if there is a problem creating or populating a Gene instance
* @author Neil Rotstan
* @author Klaus Meffert
* @since 1.0
*/
public static Genotype getGenotypeFromElement(
Configuration a_activeConfiguration, Element a_xmlElement)
throws ImproperXMLException, InvalidConfigurationException,
UnsupportedRepresentationException, GeneCreationException {
// Sanity check. Make sure the XML element isn't null and that it
// actually represents a genotype.
if (a_xmlElement == null || !(a_xmlElement.getTagName().equals(GENOTYPE_TAG))) {
throw new ImproperXMLException(
"Unable to build Genotype instance from XML Element: "
+ "given Element is not a 'genotype' element.");
}
// Fetch all of the nested chromosome elements and convert them
// into Chromosome instances.
// ------------------------------------------------------------
NodeList chromosomes = a_xmlElement.getElementsByTagName(CHROMOSOME_TAG);
int numChromosomes = chromosomes.getLength();
Population population = new Population(a_activeConfiguration, numChromosomes);
for (int i = 0; i < numChromosomes; i++) {
population.addChromosome(
getChromosomeFromElement(a_activeConfiguration, (Element) chromosomes.item(i)));
}
// Construct a new Genotype with the chromosomes and return it.
// ------------------------------------------------------------
return new Genotype(a_activeConfiguration, population);
}
// Gets the specified XML Schema doc if one is mentioned in the file
public static File getSchemaFile(Document xmlDoc) {
/** @todo Must be an easier way of doing this... */
logger.logComment("Getting schema file for: " + xmlDoc.getDocumentURI());
NodeList nl = xmlDoc.getChildNodes();
for (int j = 0; j < nl.getLength(); j++) {
Node node = nl.item(j);
logger.logComment("Type: " + node.getNodeType() + "Name: " + node.getNodeName());
if (node.getNodeName().equals(XML_STYLESHEET_NODE)) {
String nodeVal = node.getNodeValue();
logger.logComment("Looking at: " + nodeVal);
String xslFileName =
nodeVal.substring(nodeVal.indexOf("href=\"") + 6, nodeVal.length() - 1);
File xslFile = new File(xslFileName);
return xslFile;
}
if (node.getAttributes().getLength() > 0) {
logger.logComment("Attributes: " + node.getAttributes());
if (node.getAttributes().getNamedItem(XML_SCHEMA_LOC_ATTR) != null) {
String locString = node.getAttributes().getNamedItem(XML_SCHEMA_LOC_ATTR).getNodeValue();
logger.logComment("Loc string: " + locString);
String file = locString.split("\\s")[1];
return new File(file);
}
}
}
logger.logError("No node found with name: " + XML_STYLESHEET_NODE);
return null;
}
private void removeNodes(NodeList nl) {
int count = nl.getLength();
for (int i = 0; i < count; i++) {
Node node = nl.item(i);
Node parent = node.getParentNode();
if (parent == null) continue;
parent.removeChild(node);
}
}
/**
* Honey, can you just check on the kids? Thanks.
*
* <p>Internal function; not included in reference.
*/
protected void checkChildren() {
if (children == null) {
NodeList kids = node.getChildNodes();
int childCount = kids.getLength();
children = new XML[childCount];
for (int i = 0; i < childCount; i++) {
children[i] = new XML(this, kids.item(i));
}
}
}
private Node getTextNode() {
NodeList list = element.getChildNodes();
int length = list.getLength();
for (int i = 0; i < length; i++) {
Node node = list.item(i);
if (node.getNodeType() == Node.TEXT_NODE) {
return node;
}
}
return element.appendChild(element.getOwnerDocument().createTextNode(""));
}
/**
* The DOM API states that NodeLists are dynamic, this means that when we replace a circle in
* the NodeList with a group of circles, then the original NodeList updates itself to contain
* the newly added circles. As we want to replace all circles with a group that possibly
* contains circles, then we need to turn the NodeList into a non-dynamic structure.
*
* @param nl
* @return Either null if the input parameter is null, or a List representation of the NodeList.
*/
private List<Node> nodeListToList(NodeList nl) {
if (null == nl) {
return null;
}
List<Node> list = new ArrayList<Node>();
for (int i = 1; i < nl.getLength(); i++) {
list.add(nl.item(i));
}
return list;
}
public NodeList getImediateElementsByTagName(Element el, String tagname) {
NodeList list = el.getElementsByTagName(tagname);
SimpleNodeList result = new SimpleNodeList();
int length = list.getLength();
for (int i = 0; i < length; i++) {
Node node = list.item(i);
if ((Element) node.getParentNode() == el) {
result.add(node);
}
}
return result;
}
private void appendXmlEntry(Document doc, Node opAppend) {
NodeList targetNodes = findNodes(doc, opAppend);
NodeList valueNodes = getValueNodes(opAppend);
if (targetNodes == null) {
return;
}
int targetNodesCount = targetNodes.getLength();
for (int i = 0; i < targetNodesCount; i++) {
Node target = targetNodes.item(i);
appendNodes(doc, target, valueNodes);
}
}
public void deleteSubNode(String subnode) {
int pos = subnode.lastIndexOf(DELIM);
if (pos >= 0) {
XMLHelper helper = getSubNode(subnode.substring(0, pos));
helper.deleteSubNode(subnode.substring(pos + 1));
} else {
NodeList list = getImediateElementsByTagName(subnode);
try {
element.removeChild(list.item(0));
} catch (Exception e) {
}
}
}
private void setXmlEntry(Document doc, Node opSet) {
NodeList targetNodes = findNodes(doc, opSet);
NodeList valueNodes = getValueNodes(opSet);
if (targetNodes == null) {
return;
}
int targetNodesCount = targetNodes.getLength();
for (int i = 0; i < targetNodesCount; i++) {
Node target = targetNodes.item(i);
for (Node child; (child = target.getFirstChild()) != null; target.removeChild(child)) ;
appendNodes(doc, target, valueNodes);
}
}
public XMLHelper[] getSubNodeList(String subnode) {
int pos = subnode.lastIndexOf(DELIM);
if (pos >= 0) {
XMLHelper helper = getSubNode(subnode.substring(0, pos));
return helper.getSubNodeList(subnode.substring(pos + 1));
} else {
NodeList list = getImediateElementsByTagName(subnode);
XMLHelper[] results = new XMLHelper[list.getLength()];
int length = list.getLength();
for (int i = 0; i < length; i++) {
results[i] = new XMLHelper((Element) list.item(i));
}
return results;
}
}
public void read(Document doc) {
try {
Element root = doc.getDocumentElement();
NodeList nList = doc.getElementsByTagName("user");
for (int i = 0; i < nList.getLength(); i++) {
Node node = nList.item(i);
if (node.getNodeType() == Node.ELEMENT_NODE) {
Element element = (Element) node;
}
}
// Element e1 = (Element) nList.item(0);
} catch (Exception e) {
}
}
public XMLHelper getSubNode(String subnode) {
String nodes[] = subnode.split(REGEX);
Element sub = element;
boolean isnew = false;
for (int i = 0; i < nodes.length; i++) {
NodeList list = getImediateElementsByTagName(sub, nodes[i]);
if (list.getLength() > 0) {
sub = (Element) list.item(0);
} else {
sub = (Element) sub.appendChild(element.getOwnerDocument().createElement(nodes[i]));
isnew = true;
}
}
return new XMLHelper(sub, isnew);
}
private void replaceXmlEntry(Document doc, Node opReplace) {
NodeList targetNodes = findNodes(doc, opReplace);
NodeList valueNodes = getValueNodes(opReplace);
if (targetNodes == null) {
return;
}
int targetNodesCount = targetNodes.getLength();
for (int i = 0; i < targetNodesCount; i++) {
Node target = targetNodes.item(i);
Node parent = target.getParentNode();
if (parent == null) continue;
parent.removeChild(target);
appendNodes(doc, parent, valueNodes);
}
}
public void trim() {
try {
XPathFactory xpathFactory = XPathFactory.newInstance();
XPathExpression xpathExp =
xpathFactory.newXPath().compile("//text()[normalize-space(.) = '']");
NodeList emptyTextNodes = (NodeList) xpathExp.evaluate(node, XPathConstants.NODESET);
// Remove each empty text node from document.
for (int i = 0; i < emptyTextNodes.getLength(); i++) {
Node emptyTextNode = emptyTextNodes.item(i);
emptyTextNode.getParentNode().removeChild(emptyTextNode);
}
} catch (Exception e) {
throw new RuntimeException(e);
}
}
public void deleteSubNodes(String subnode) {
int pos = subnode.lastIndexOf(DELIM);
if (pos >= 0) {
XMLHelper helper = getSubNode(subnode.substring(0, pos));
helper.deleteSubNodes(subnode.substring(pos + 1));
} else {
NodeList list = getImediateElementsByTagName(subnode);
int length = list.getLength();
for (int i = 0; i < length; i++) {
try {
element.removeChild(list.item(i));
} catch (Exception e) {
}
}
}
}
/**
* Method that reads a XML-file, and returns a Model that contains the information
*
* @param file
* @return
* @return
*/
public static Model readXML(String file) {
// initialize table to be filled with content of XML file
Model t = new Model();
try {
// Create file to be parsed by document parser
File xmlfile = new File(file);
// create parser
DocumentBuilder parser = DocumentBuilderFactory.newInstance().newDocumentBuilder();
// parse the file
Document parsedfile = parser.parse(xmlfile);
// normalize the parsed file (make it more user-friendly)
parsedfile.getDocumentElement().normalize();
NodeList cells = parsedfile.getElementsByTagName("CELL");
for (int i = 0; i < cells.getLength(); i++) {
// Get cell at list index i
Node currentcell = cells.item(i);
// read the elements "location" attributes row/column
if (Node.ELEMENT_NODE == currentcell.getNodeType()) {
Element cellinfo = (Element) currentcell;
// get the row number from node attribute
int row = Integer.parseInt(cellinfo.getAttribute("row")) - 1;
// get the column number from the node attribute
int col = Integer.parseInt(cellinfo.getAttribute("column")) - 1;
// get content from node
String content = cellinfo.getTextContent();
if (content != null) {
content = content.replace("\n", "");
}
// Make the content an Integer (if it is a number), easier
// for
// using it later on
// put content in table, with row/column inserted as x/y
t.setContent(row, col, (String) content);
}
}
} catch (ParserConfigurationException e) {
System.out.println("Fileparser could not be made");
} catch (IOException f) {
System.out.println("File could not be parsed, did you enter the correct file name?");
} catch (SAXException g) {
System.out.println("Something went wrong in parsing the file");
}
return t;
}
/**
* Removes empty #text nodes from a document. From James Murty on this StackOverflow post:
* http://stackoverflow.com/questions/978810/how-to-strip-whitespace-only-text-nodes-from-a-dom-before-serialization
*
* @param doc The document to remove empty text nodes from.
*/
private static void removeEmptyTextNodes(Document doc) {
try {
XPathFactory xpathFactory = XPathFactory.newInstance();
// XPath to find empty text nodes.
XPathExpression xpathExp =
xpathFactory.newXPath().compile("//text()[normalize-space(.) = '']");
NodeList emptyTextNodes = (NodeList) xpathExp.evaluate(doc, XPathConstants.NODESET);
// Remove each empty text node from document.
for (int i = 0; i < emptyTextNodes.getLength(); i++) {
Node emptyTextNode = emptyTextNodes.item(i);
emptyTextNode.getParentNode().removeChild(emptyTextNode);
}
} catch (Exception ex) {
ex.printStackTrace();
}
}
public void apply(String path, NodeList[] operations)
throws ParserConfigurationException, TransformerConfigurationException {
File target = new File(path);
if (target.isDirectory()) {
String callerDir = this.targetDir;
this.targetDir = path;
for (NodeList ops : operations) {
for (int i = 0; i < ops.getLength(); i++) call(ops.item(i));
}
this.targetDir = callerDir;
} else {
String tmpDir = inflate(path);
if (tmpDir == null) return;
apply(tmpDir, operations);
deflate(tmpDir, path);
}
}
/**
* Gets the definitions of a word, sets the main one if necessary, and returns it.
*
* @param overwrite if true, then function will attempt to retrieve from online even if the
* definition is already set.
* @return String containing the main definition of the word.
*/
public String getDefinitions(ByteArrayInputStream inputStream, boolean overwrite) {
if (overwrite || (definition == null || definition.isEmpty())) {
// get definition from online service
// if not able to access internet, then do something
try {
// now to parse the XML
DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
DocumentBuilder db = dbf.newDocumentBuilder();
Document doc = db.parse(inputStream);
removeEmptyTextNodes(doc);
NodeList list = doc.getElementsByTagName("Definition");
int numDefinitions = list.getLength();
otherDefinitions = new Definition[numDefinitions];
for (int i = 0; i < numDefinitions; i++) {
Node node = list.item(i);
NodeList children = node.getChildNodes(); // gets each child node of the definition
// get all data
String definition = children.item(XML_DEFINITION_LOC).getTextContent();
String word = children.item(XML_WORD_LOC).getTextContent();
NodeList dictionaryNode = children.item(XML_DICTIONARY_BRANCH_LOC).getChildNodes();
String dictionaryId = dictionaryNode.item(XML_DICTIONARY_ID_LOC).getTextContent();
String dictionaryName = dictionaryNode.item(XML_DICTIONARY_NAME_LOC).getTextContent();
// now we've got all the data lets add it to the array
otherDefinitions[i] = new Definition(dictionaryName, dictionaryId, definition, word);
}
if (otherDefinitions.length == 0) {
otherDefinitions =
new Definition[] {new Definition("nil", "nil", "NO DEFINITION FOUND", word)};
}
this.setMainDefinition(otherDefinitions[0].getDefinition());
return otherDefinitions[0].getDefinition();
} catch (Exception ex) {
ex.printStackTrace();
return "ERROR! " + ex;
}
} else {
return this.definition;
}
}
private void call(String script)
throws ParserConfigurationException, TransformerConfigurationException {
File callerScript = this.currentScript;
Document doc = null;
try {
this.currentScript = new File(script);
DocumentBuilder db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
doc = db.parse(this.currentScript);
} catch (Exception ex) {
this.currentScript = callerScript;
Utils.onError(new Error.FileParse(script));
return;
}
NodeList operations = doc.getDocumentElement().getChildNodes();
for (int i = 0; i < operations.getLength(); i++) {
Node operation = operations.item(i);
if (operation.getNodeType() != Node.ELEMENT_NODE) continue;
call(operation);
}
this.currentScript = callerScript;
}
public static List<Tombstone> loadTombstone(String chestsPath, DeathChests plugin) {
LinkedList<Tombstone> deathChests = new LinkedList<>();
try {
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
DocumentBuilder builder = factory.newDocumentBuilder();
// Start the parser
Document doc = builder.parse(new File(chestsPath));
Element rootElement = doc.getDocumentElement();
String version = rootElement.getAttribute("version");
if (!Settings.getVersion().equals(version)) {
System.out.println(
"The version of the Deathchests-File changed. There are possible errors at loading them. (Probably not if your updated it)");
}
long timestamp = System.currentTimeMillis();
NodeList list = rootElement.getChildNodes();
int length = list.getLength();
for (int i = 0; i < length; i++) {
try {
Node node = list.item(i);
String name = node.getNodeName();
if (name.equalsIgnoreCase(Utils.DEATHCHEST_XML_TAG)) {
deathChests.add(new Tombstone((Element) node, timestamp, plugin));
}
} catch (XMLParseException ex) {
System.err.println("Corrupted deathchest! Skipping this one!");
ex.printStackTrace();
}
}
} catch (IOException | ParserConfigurationException | SAXException ex) {
System.err.println("Error while loading deathchest data:");
ex.printStackTrace();
}
return deathChests;
}
public Command executeStep(Element stepRow) throws Exception {
Command command = new Command();
NodeList stepFields = stepRow.getElementsByTagName("td");
String cmd = stepFields.item(0).getTextContent().trim();
command.cmd = cmd;
ArrayList<String> argList = new ArrayList<String>();
if (stepFields.getLength() == 1) {
// skip comments
command.result = "OK";
return command;
}
for (int i = 1; i < stepFields.getLength(); i++) {
String content = stepFields.item(i).getTextContent();
content = content.replaceAll(" +", " ");
content = content.replace('\u00A0', ' ');
content = content.trim();
argList.add(content);
}
String args[] = argList.toArray(new String[0]);
command.args = args;
if (this.verbose) {
System.out.println(cmd + " " + Arrays.asList(args));
}
try {
command.result = this.commandProcessor.doCommand(cmd, args);
command.error = false;
} catch (Exception e) {
command.result = e.getMessage();
command.error = true;
}
command.failure = command.error && !cmd.startsWith("verify");
if (this.verbose) {
System.out.println(command.result);
}
return command;
}
/**
* XML Circuit constructor
*
* @param file the file that contains the XML description of the circuit
* @param g the graphics that will paint the node
* @throws CircuitLoadingException if the internal circuit can not be loaded
*/
public CircuitUI(File file, Graphics g) throws CircuitLoadingException {
this("");
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
DocumentBuilder builder;
Document doc;
Element root;
Hashtable<Integer, Link> linkstable = new Hashtable<Integer, Link>();
try {
builder = factory.newDocumentBuilder();
doc = builder.parse(file);
} catch (SAXException sxe) {
throw new CircuitLoadingException("SAX exception raised, invalid XML file.");
} catch (ParserConfigurationException pce) {
throw new CircuitLoadingException(
"Parser exception raised, parser configuration is invalid.");
} catch (IOException ioe) {
throw new CircuitLoadingException("I/O exception, file cannot be loaded.");
}
root = (Element) doc.getElementsByTagName("Circuit").item(0);
this.setName(root.getAttribute("name"));
NodeList nl = root.getElementsByTagName("Node");
Element e;
Node n;
Class cl;
for (int i = 0; i < nl.getLength(); ++i) {
e = (Element) nl.item(i);
try {
cl = Class.forName(e.getAttribute("class"));
} catch (Exception exc) {
System.err.println(exc.getMessage());
throw new RuntimeException("Circuit creation from xml.");
}
try {
n = ((Node) cl.newInstance());
} catch (Exception exc) {
System.err.println(exc.getMessage());
throw new RuntimeException("Circuit creation from xml.");
}
this.nodes.add(n);
n.setLocation(new Integer(e.getAttribute("x")), new Integer(e.getAttribute("y")));
if (n instanceof giraffe.ui.Nameable) ((Nameable) n).setNodeName(e.getAttribute("node_name"));
if (n instanceof giraffe.ui.CompositeNode) {
try {
((CompositeNode) n)
.load(new File(file.getParent() + "/" + e.getAttribute("file_name")), g);
} catch (Exception exc) {
/* try to load from the lib */
((CompositeNode) n)
.load(new File(giraffe.Giraffe.PATH + "/lib/" + e.getAttribute("file_name")), g);
}
}
NodeList nlist = e.getElementsByTagName("Anchor");
Element el;
for (int j = 0; j < nlist.getLength(); ++j) {
el = (Element) nlist.item(j);
Anchor a = n.getAnchor(new Integer(el.getAttribute("id")));
NodeList linklist = el.getElementsByTagName("Link");
Element link;
Link l;
for (int k = 0; k < linklist.getLength(); ++k) {
link = (Element) linklist.item(k);
int id = new Integer(link.getAttribute("id"));
int index = new Integer(link.getAttribute("index"));
if (id >= this.linkID) linkID = id + 1;
if (linkstable.containsKey(id)) {
l = linkstable.get(id);
l.addLinkedAnchorAt(a, index);
a.addLink(l);
} else {
l = new Link(id);
l.addLinkedAnchorAt(a, index);
this.links.add(l);
linkstable.put(id, l);
a.addLink(l);
}
}
}
}
}
// ## operation readReactorOutputFile(ReactionModel)
public SystemSnapshot readReactorOutputFile(ReactionModel p_reactionModel) {
// #[ operation readReactorOutputFile(ReactionModel)
try {
// open output file and build the DOM tree
String dir = System.getProperty("RMG.workingDirectory");
String filename = "chemkin/reactorOutput.xml";
File inputFile = new File(filename);
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
factory.setValidating(true); // validate the document with the DTD
factory.setIgnoringElementContentWhitespace(true); // ignore whitespace
DocumentBuilder builder = factory.newDocumentBuilder();
Document doc = builder.parse(inputFile);
// get root element and its children
Element root = doc.getDocumentElement();
NodeList rootchildren = root.getChildNodes();
// header is rootchildren.item(0)
// get return message and check for successful run
Element returnmessageElement = (Element) rootchildren.item(1);
Text returnmessageText = (Text) returnmessageElement.getFirstChild();
String returnmessage = returnmessageText.toString();
returnmessage = returnmessage.trim();
if (!returnmessage.contains("SUCCESSFULLY COMPLETED RUN.")) {
System.out.println("External reactor model failed!");
System.out.println("Reactor model error message: " + returnmessage);
System.exit(0);
}
// get outputvalues element and its children
Element outputvaluesElement = (Element) rootchildren.item(2);
NodeList children = outputvaluesElement.getChildNodes();
// get time
Element timeElement = (Element) children.item(0);
Text timeText = (Text) timeElement.getFirstChild();
double time = Double.parseDouble(timeText.getData());
String timeUnits = timeElement.getAttribute("units");
// get systemstate element and its children
Element systemstateElement = (Element) children.item(1);
NodeList states = systemstateElement.getChildNodes();
// get temperature and its units
Element temperatureElement = (Element) states.item(0);
String tempUnits = temperatureElement.getAttribute("units");
Text temperatureText = (Text) temperatureElement.getFirstChild();
double temp = Double.parseDouble(temperatureText.getData());
Temperature T = new Temperature(temp, tempUnits);
// get pressure and its units
Element pressureElement = (Element) states.item(1);
String presUnits = pressureElement.getAttribute("units");
Text pressureText = (Text) pressureElement.getFirstChild();
double pres = Double.parseDouble(pressureText.getData());
Pressure P = new Pressure(pres, presUnits);
// get species amounts (e.g. concentrations)
ArrayList speciesIDs = new ArrayList();
ArrayList amounts = new ArrayList();
ArrayList fluxes = new ArrayList();
String amountUnits = null;
String fluxUnits = null;
// loop thru all the species
// begin at i=2, since T and P take already the first two position of states
int nSpe = (states.getLength() - 2) / 2;
int index = 0;
LinkedHashMap inertGas = new LinkedHashMap();
for (int i = 2; i < nSpe + 2; i++) {
// get amount element and the units
Element amountElement = (Element) states.item(i);
amountUnits = amountElement.getAttribute("units");
Element fluxElement = (Element) states.item(i + nSpe);
fluxUnits = fluxElement.getAttribute("units");
// get speciesid and store in an array list
String thisSpeciesID = amountElement.getAttribute("speciesid");
// get amount (e.g. concentraion) and store in an array list
Text amountText = (Text) amountElement.getFirstChild();
double thisAmount = Double.parseDouble(amountText.getData());
if (thisAmount < 0) {
double aTol = ReactionModelGenerator.getAtol();
// if (Math.abs(thisAmount) < aTol) thisAmount = 0;
// else throw new NegativeConcentrationException("Negative concentration in
// reactorOutput.xml: " + thisSpeciesID);
if (thisAmount < -100.0 * aTol)
throw new NegativeConcentrationException(
"Species "
+ thisSpeciesID
+ " has negative concentration: "
+ String.valueOf(thisAmount));
}
// get amount (e.g. concentraion) and store in an array list
Text fluxText = (Text) fluxElement.getFirstChild();
double thisFlux = Double.parseDouble(fluxText.getData());
if (thisSpeciesID.compareToIgnoreCase("N2") == 0
|| thisSpeciesID.compareToIgnoreCase("Ne") == 0
|| thisSpeciesID.compareToIgnoreCase("Ar") == 0) {
inertGas.put(thisSpeciesID, new Double(thisAmount));
} else {
speciesIDs.add(index, thisSpeciesID);
amounts.add(index, new Double(thisAmount));
fluxes.add(index, new Double(thisFlux));
index++;
}
}
// print results for debugging purposes
/**
* System.out.println(returnmessage); System.out.println("Temp = " + temp + " " + tempUnits);
* System.out.println("Pres = " + pres + " " + presUnits); for (int i = 0; i < amounts.size();
* i++) { System.out.println(speciesIDs.get(i) + " " + amounts.get(i) + " " + amountUnits); }
*/
ReactionTime rt = new ReactionTime(time, timeUnits);
LinkedHashMap speStatus = generateSpeciesStatus(p_reactionModel, speciesIDs, amounts, fluxes);
SystemSnapshot ss = new SystemSnapshot(rt, speStatus, T, P);
ss.inertGas = inertGas;
return ss;
} catch (Exception e) {
System.out.println("Error reading reactor model output: " + e.getMessage());
System.exit(0);
return null;
}
// #]
}
private void loadFromXml(String fileName)
throws ParserConfigurationException, SAXException, IOException, ParseException {
System.out.println("NeuralNetwork : loading network topology from file " + fileName);
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
DocumentBuilder parser = factory.newDocumentBuilder();
Document doc = parser.parse(fileName);
Node nodeNeuralNetwork = doc.getDocumentElement();
if (!nodeNeuralNetwork.getNodeName().equals("neuralNetwork"))
throw new ParseException(
"[Error] NN-Load: Parse error in XML file, neural network couldn't be loaded.", 0);
// nodeNeuralNetwork ok
// indexNeuralNetworkContent -> indexStructureContent -> indexLayerContent -> indexNeuronContent
// -> indexNeuralInputContent
NodeList nodeNeuralNetworkContent = nodeNeuralNetwork.getChildNodes();
for (int innc = 0; innc < nodeNeuralNetworkContent.getLength(); innc++) {
Node nodeStructure = nodeNeuralNetworkContent.item(innc);
if (nodeStructure.getNodeName().equals("structure")) { // for structure element
NodeList nodeStructureContent = nodeStructure.getChildNodes();
for (int isc = 0; isc < nodeStructureContent.getLength(); isc++) {
Node nodeLayer = nodeStructureContent.item(isc);
if (nodeLayer.getNodeName().equals("layer")) { // for layer element
NeuralLayer neuralLayer = new NeuralLayer(this);
this.listLayers.add(neuralLayer);
NodeList nodeLayerContent = nodeLayer.getChildNodes();
for (int ilc = 0; ilc < nodeLayerContent.getLength(); ilc++) {
Node nodeNeuron = nodeLayerContent.item(ilc);
if (nodeNeuron.getNodeName().equals("neuron")) { // for neuron in layer
Neuron neuron =
new Neuron(
Double.parseDouble(((Element) nodeNeuron).getAttribute("threshold")),
neuralLayer);
neuralLayer.listNeurons.add(neuron);
NodeList nodeNeuronContent = nodeNeuron.getChildNodes();
for (int inc = 0; inc < nodeNeuronContent.getLength(); inc++) {
Node nodeNeuralInput = nodeNeuronContent.item(inc);
// if (nodeNeuralInput==null) System.out.print("-"); else System.out.print("*");
if (nodeNeuralInput.getNodeName().equals("input")) {
// System.out.println("neuron at
// STR:"+innc+" LAY:"+isc+" NEU:"+ilc+" INP:"+inc);
NeuralInput neuralInput =
new NeuralInput(
Double.parseDouble(((Element) nodeNeuralInput).getAttribute("weight")),
neuron);
neuron.listInputs.add(neuralInput);
}
}
}
}
}
}
}
}
}
private void appendNodes(Document doc, Node target, NodeList nodes) {
for (int i = 0; i < nodes.getLength(); i++) {
Node node = nodes.item(i);
target.appendChild(doc.importNode(node, true));
}
}
public boolean runTest(Test test) throws Exception {
String filename = test.file.toString();
if (this.verbose) {
System.out.println(
"Running "
+ filename
+ " against "
+ this.host
+ ":"
+ this.port
+ " with "
+ this.browser);
}
this.document = parseDocument(filename);
if (this.baseUrl == null) {
NodeList links = this.document.getElementsByTagName("link");
if (links.getLength() != 0) {
Element link = (Element) links.item(0);
setBaseUrl(link.getAttribute("href"));
}
}
if (this.verbose) {
System.out.println("Base URL=" + this.baseUrl);
}
Node body = this.document.getElementsByTagName("body").item(0);
Element resultContainer = document.createElement("div");
resultContainer.setTextContent("Result: ");
Element resultElt = document.createElement("span");
resultElt.setAttribute("id", "result");
resultElt.setIdAttribute("id", true);
resultContainer.appendChild(resultElt);
body.insertBefore(resultContainer, body.getFirstChild());
Element executionLogContainer = document.createElement("div");
executionLogContainer.setTextContent("Execution Log:");
Element executionLog = document.createElement("div");
executionLog.setAttribute("id", "log");
executionLog.setIdAttribute("id", true);
executionLog.setAttribute("style", "white-space: pre;");
executionLogContainer.appendChild(executionLog);
body.appendChild(executionLogContainer);
NodeList tableRows = document.getElementsByTagName("tr");
Element theadRow = (Element) tableRows.item(0);
test.name = theadRow.getTextContent();
appendCellToRow(theadRow, "Result");
this.commandProcessor =
new HtmlCommandProcessor(this.host, this.port, this.browser, this.baseUrl);
String resultState;
String resultLog;
test.result = true;
try {
this.commandProcessor.start();
test.commands = new Command[tableRows.getLength() - 1];
for (int i = 1; i < tableRows.getLength(); i++) {
Element stepRow = (Element) tableRows.item(i);
Command command = executeStep(stepRow);
appendCellToRow(stepRow, command.result);
test.commands[i - 1] = command;
if (command.error) {
test.result = false;
}
if (command.failure) {
test.result = false;
// break;
}
}
resultState = test.result ? "PASSED" : "FAILED";
resultLog = (test.result ? "Test Complete" : "Error");
this.commandProcessor.stop();
} catch (Exception e) {
test.result = false;
resultState = "ERROR";
resultLog = "Failed to initialize session\n" + e;
e.printStackTrace();
}
document.getElementById("result").setTextContent(resultState);
Element log = document.getElementById("log");
log.setTextContent(log.getTextContent() + resultLog + "\n");
return test.result;
}
public boolean runSuite(String filename) throws Exception {
if (this.verbose) {
System.out.println(
"Running test suite "
+ filename
+ " against "
+ this.host
+ ":"
+ this.port
+ " with "
+ this.browser);
}
TestSuite suite = new TestSuite();
long start = System.currentTimeMillis();
suite.numTestPasses = 0;
suite.file = new File(filename);
File suiteDirectory = suite.file.getParentFile();
this.document = parseDocument(filename);
Element table = (Element) this.document.getElementsByTagName("table").item(0);
NodeList tableRows = table.getElementsByTagName("tr");
Element tableNameRow = (Element) tableRows.item(0);
suite.name = tableNameRow.getTextContent();
suite.result = true;
suite.tests = new Test[tableRows.getLength() - 1];
for (int i = 1; i < tableRows.getLength(); i++) {
Element tableRow = (Element) tableRows.item(i);
Element cell = (Element) tableRow.getElementsByTagName("td").item(0);
Element link = (Element) cell.getElementsByTagName("a").item(0);
Test test = new Test();
test.label = link.getTextContent();
test.file = new File(suiteDirectory, link.getAttribute("href"));
SeleniumHtmlClient subclient = new SeleniumHtmlClient();
subclient.setHost(this.host);
subclient.setPort(this.port);
subclient.setBrowser(this.browser);
// subclient.setResultsWriter(this.resultsWriter);
subclient.setBaseUrl(this.baseUrl);
subclient.setVerbose(this.verbose);
subclient.runTest(test);
if (test.result) {
suite.numTestPasses++;
}
suite.result &= test.result;
suite.tests[i - 1] = test;
}
long end = System.currentTimeMillis();
suite.totalTime = (end - start) / 1000;
if (this.resultsWriter != null) {
this.resultsWriter.write("<html><head>\n");
this.resultsWriter.write("<style type='text/css'>\n");
this.resultsWriter.write(
"body, table {font-family: Verdana, Arial, sans-serif;font-size: 12;}\n");
this.resultsWriter.write("table {border-collapse: collapse;border: 1px solid #ccc;}\n");
this.resultsWriter.write("th, td {padding-left: 0.3em;padding-right: 0.3em;}\n");
this.resultsWriter.write("a {text-decoration: none;}\n");
this.resultsWriter.write(".title {font-style: italic;}");
this.resultsWriter.write(".selected {background-color: #ffffcc;}\n");
this.resultsWriter.write(".status_done {background-color: #eeffee;}\n");
this.resultsWriter.write(".status_passed {background-color: #ccffcc;}\n");
this.resultsWriter.write(".status_failed {background-color: #ffcccc;}\n");
this.resultsWriter.write(
".breakpoint {background-color: #cccccc;border: 1px solid black;}\n");
this.resultsWriter.write("</style>\n");
this.resultsWriter.write("<title>" + suite.name + "</title>\n");
this.resultsWriter.write("</head><body>\n");
this.resultsWriter.write("<h1>Test suite results </h1>\n\n");
this.resultsWriter.write("<table>\n");
this.resultsWriter.write(
"<tr>\n<td>result:</td>\n<td>" + (suite.result ? "passed" : "failed") + "</td>\n</tr>\n");
this.resultsWriter.write(
"<tr>\n<td>totalTime:</td>\n<td>" + suite.totalTime + "</td>\n</tr>\n");
this.resultsWriter.write(
"<tr>\n<td>numTestTotal:</td>\n<td>" + suite.tests.length + "</td>\n</tr>\n");
this.resultsWriter.write(
"<tr>\n<td>numTestPasses:</td>\n<td>" + suite.numTestPasses + "</td>\n</tr>\n");
int numTestFailures = suite.tests.length - suite.numTestPasses;
this.resultsWriter.write(
"<tr>\n<td>numTestFailures:</td>\n<td>" + numTestFailures + "</td>\n</tr>\n");
this.resultsWriter.write("<tr>\n<td>numCommandPasses:</td>\n<td>0</td>\n</tr>\n");
this.resultsWriter.write("<tr>\n<td>numCommandFailures:</td>\n<td>0</td>\n</tr>\n");
this.resultsWriter.write("<tr>\n<td>numCommandErrors:</td>\n<td>0</td>\n</tr>\n");
this.resultsWriter.write("<tr>\n<td>Selenium Version:</td>\n<td>2.24</td>\n</tr>\n");
this.resultsWriter.write("<tr>\n<td>Selenium Revision:</td>\n<td>.1</td>\n</tr>\n");
// test suite
this.resultsWriter.write("<tr>\n<td>\n");
this.resultsWriter.write(
"<table id=\"suiteTable\" class=\"selenium\" border=\"1\" cellpadding=\"1\" cellspacing=\"1\"><tbody>\n");
this.resultsWriter.write(
"<tr class=\"title "
+ (suite.result ? "status_passed" : "status_failed")
+ "\"><td><b>Test Suite</b></td></tr>\n");
int i = 0;
for (Test test : suite.tests) {
this.resultsWriter.write(
"<tr class=\""
+ (test.result ? "status_passed" : "status_failed")
+ "\"><td><a href=\"#testresult"
+ i
+ "\">"
+ test.name
+ "</a></td></tr>");
i++;
}
this.resultsWriter.write(
"</tbody></table>\n</td>\n<td> </td>\n</tr>\n</table>\n<table>");
int j = 0;
for (Test test : suite.tests) {
this.resultsWriter.write(
"<tr><td><a name=\"testresult" + j + "\">" + test.file + "</a><br/><div>\n");
this.resultsWriter.write("<table border=\"1\" cellpadding=\"1\" cellspacing=\"1\">\n");
this.resultsWriter.write(
"<thead>\n<tr class=\"title "
+ (test.result ? "status_passed" : "status_failed")
+ "\"><td rowspan=\"1\" colspan=\"3\">"
+ test.name
+ "</td></tr>");
this.resultsWriter.write("</thead><tbody>\n");
for (Command command : test.commands) {
boolean result = command.result.startsWith("OK");
boolean isAssert = command.cmd.startsWith("assert") || command.cmd.startsWith("verify");
;
if (!isAssert) {
this.resultsWriter.write(
"<tr class=\"" + (result ? "status_done" : "") + "\">\n<td>\n");
} else {
this.resultsWriter.write(
"<tr class=\"" + (result ? "status_passed" : "status_failed") + "\">\n<td>\n");
}
this.resultsWriter.write(command.cmd);
this.resultsWriter.write("</td>\n");
if (command.args != null) {
for (String arg : Arrays.asList(command.args)) {
this.resultsWriter.write("<td>" + arg + "</td>\n");
}
}
}
this.resultsWriter.write("</tr>\n");
this.resultsWriter.write("</tbody></table>\n");
this.resultsWriter.write("</div></td>\n<td> </td>\n</tr>");
j++;
}
int k = 0;
for (Test test : suite.tests) {
k++;
}
this.resultsWriter.write("</tbody></table>\n</td><td> </td>\n</tr>\n</table>\n");
this.resultsWriter.write("</body></html>");
}
return suite.result;
}
void xml() {
try {
File file = new File("c:\\users\\jason\\desktop\\proxies.xml");
// Create instance of DocumentBuilderFactory
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
// Get the DocumentBuilder
DocumentBuilder docBuilder = factory.newDocumentBuilder();
// Using existing XML Document
Document doc = docBuilder.parse(file);
// normalize the text
doc.getDocumentElement().normalize();
// gets just the name of the root
String simple_root = doc.getDocumentElement().getNodeName();
Element root = doc.getDocumentElement();
// gets the ip elements
NodeList proxy = doc.getElementsByTagName("proxy");
// checks the make sure i got the ip elements by printing out the number of occurances
int total = proxy.getLength();
NodeList list = doc.getElementsByTagName("*");
System.out.println("\nElements in the proxy file:");
int proxy_num = 1;
for (int i = 0; i < list.getLength(); i++) {
Node num2 = proxy.item(i);
Element second = (Element) num2;
Element element2 = (Element) list.item(i);
NodeList text2 = element2.getChildNodes();
if (element2.getNodeName() != "proxies" && element2.getNodeName() != "proxy") {
if (element2.getNodeName() == "ip") {
System.out.println("");
System.out.println("Proxy #: " + proxy_num);
proxy_num++;
System.out.println(
element2.getNodeName() + ": " + ((Node) text2.item(0)).getNodeValue().trim());
} else
System.out.println(
element2.getNodeName() + ": " + ((Node) text2.item(0)).getNodeValue().trim());
if (element2.getNodeName() == "source-ip") {
ip = ((Node) text2.item(0)).getNodeValue().trim();
myArr.add(ip);
jComboBox.addItem(ip);
}
}
}
// set up a transformer
TransformerFactory transfac = TransformerFactory.newInstance();
Transformer trans = transfac.newTransformer();
// create string from xml tree
StringWriter sw = new StringWriter();
StreamResult result = new StreamResult(sw);
DOMSource source = new DOMSource(doc);
trans.transform(source, result);
String xmlString = sw.toString();
OutputStream f0;
byte buf[] = xmlString.getBytes();
f0 = new FileOutputStream("c:\\users\\jason\\desktop\\connections.xml");
for (int i = 0; i < buf.length; i++) {
f0.write(buf[i]);
}
f0.close();
buf = null;
} catch (SAXException e) {
e.printStackTrace();
} catch (IOException e) {
e.printStackTrace();
} catch (ParserConfigurationException e) {
e.printStackTrace();
} catch (TransformerConfigurationException e) {
e.printStackTrace();
} catch (TransformerException e) {
e.printStackTrace();
}
}