public void saveToXml(String fileName)
throws ParserConfigurationException, FileNotFoundException, TransformerException,
TransformerConfigurationException {
System.out.println("Saving network topology to file " + fileName);
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
DocumentBuilder parser = factory.newDocumentBuilder();
Document doc = parser.newDocument();
Element root = doc.createElement("neuralNetwork");
root.setAttribute("dateOfExport", new Date().toString());
Element layers = doc.createElement("structure");
layers.setAttribute("numberOfLayers", Integer.toString(this.numberOfLayers()));
for (int il = 0; il < this.numberOfLayers(); il++) {
Element layer = doc.createElement("layer");
layer.setAttribute("index", Integer.toString(il));
layer.setAttribute("numberOfNeurons", Integer.toString(this.getLayer(il).numberOfNeurons()));
for (int in = 0; in < this.getLayer(il).numberOfNeurons(); in++) {
Element neuron = doc.createElement("neuron");
neuron.setAttribute("index", Integer.toString(in));
neuron.setAttribute(
"NumberOfInputs", Integer.toString(this.getLayer(il).getNeuron(in).numberOfInputs()));
neuron.setAttribute(
"threshold", Double.toString(this.getLayer(il).getNeuron(in).threshold));
for (int ii = 0; ii < this.getLayer(il).getNeuron(in).numberOfInputs(); ii++) {
Element input = doc.createElement("input");
input.setAttribute("index", Integer.toString(ii));
input.setAttribute(
"weight", Double.toString(this.getLayer(il).getNeuron(in).getInput(ii).weight));
neuron.appendChild(input);
}
layer.appendChild(neuron);
}
layers.appendChild(layer);
}
root.appendChild(layers);
doc.appendChild(root);
// save
File xmlOutputFile = new File(fileName);
FileOutputStream fos;
Transformer transformer;
fos = new FileOutputStream(xmlOutputFile);
// Use a Transformer for output
TransformerFactory transformerFactory = TransformerFactory.newInstance();
transformer = transformerFactory.newTransformer();
DOMSource source = new DOMSource(doc);
StreamResult result = new StreamResult(fos);
// transform source into result will do save
transformer.setOutputProperty("encoding", "iso-8859-2");
transformer.setOutputProperty("indent", "yes");
transformer.transform(source, result);
}
Document parseDocument(String filename) throws Exception {
FileReader reader = new FileReader(filename);
String firstLine = new BufferedReader(reader).readLine();
reader.close();
Document document = null;
if (firstLine.startsWith("<?xml")) {
System.err.println("XML detected; using default XML parser.");
} else {
try {
Class nekoParserClass = Class.forName("org.cyberneko.html.parsers.DOMParser");
Object parser = nekoParserClass.newInstance();
Method parse = nekoParserClass.getMethod("parse", new Class[] {String.class});
Method getDocument = nekoParserClass.getMethod("getDocument", new Class[0]);
parse.invoke(parser, filename);
document = (Document) getDocument.invoke(parser);
} catch (Exception e) {
System.err.println("NekoHTML HTML parser not found; HTML4 support disabled.");
}
}
if (document == null) {
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
try { // http://www.w3.org/blog/systeam/2008/02/08/w3c_s_excessive_dtd_traffic
factory.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd", false);
} catch (ParserConfigurationException e) {
System.err.println("Warning: Could not disable external DTD loading");
}
DocumentBuilder builder = factory.newDocumentBuilder();
document = builder.parse(filename);
}
return document;
}
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);
}
}
}
}
}
}
}
}
}
protected void doGet(HttpServletRequest req, HttpServletResponse res)
throws ServletException, IOException {
try {
DateFormat df = DateFormat.getDateTimeInstance();
String titleStr = "C3P0 Status - " + df.format(new Date());
DocumentBuilderFactory fact = DocumentBuilderFactory.newInstance();
DocumentBuilder db = fact.newDocumentBuilder();
Document doc = db.newDocument();
Element htmlElem = doc.createElement("html");
Element headElem = doc.createElement("head");
Element titleElem = doc.createElement("title");
titleElem.appendChild(doc.createTextNode(titleStr));
Element bodyElem = doc.createElement("body");
Element h1Elem = doc.createElement("h1");
h1Elem.appendChild(doc.createTextNode(titleStr));
Element h3Elem = doc.createElement("h3");
h3Elem.appendChild(doc.createTextNode("PooledDataSources"));
Element pdsDlElem = doc.createElement("dl");
pdsDlElem.setAttribute("class", "PooledDataSources");
for (Iterator ii = C3P0Registry.getPooledDataSources().iterator(); ii.hasNext(); ) {
PooledDataSource pds = (PooledDataSource) ii.next();
StatusReporter sr = findStatusReporter(pds, doc);
pdsDlElem.appendChild(sr.reportDtElem());
pdsDlElem.appendChild(sr.reportDdElem());
}
headElem.appendChild(titleElem);
htmlElem.appendChild(headElem);
bodyElem.appendChild(h1Elem);
bodyElem.appendChild(h3Elem);
bodyElem.appendChild(pdsDlElem);
htmlElem.appendChild(bodyElem);
res.setContentType("application/xhtml+xml");
TransformerFactory tf = TransformerFactory.newInstance();
Transformer transformer = tf.newTransformer();
Source src = new DOMSource(doc);
Result result = new StreamResult(res.getOutputStream());
transformer.transform(src, result);
} catch (IOException e) {
throw e;
} catch (Exception e) {
throw new ServletException(e);
}
}
public XMLHelper(String root) {
this();
try {
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
DocumentBuilder builder = factory.newDocumentBuilder();
Document document = builder.newDocument();
setElement((Element) document.appendChild(document.createElement(root)));
} catch (ParserConfigurationException e) {
// Not quite sure when this would happen
severe("Could not extantiate XML builder: " + e.getMessage());
}
}
/**
* Advanced users only; use loadXML() in PApplet.
*
* <p>Added extra code to handle \u2028 (Unicode NLF), which is sometimes inserted by web browsers
* (Safari?) and not distinguishable from a "real" LF (or CRLF) in some text editors (i.e.
* TextEdit on OS X). Only doing this for XML (and not all Reader objects) because LFs are
* essential. https://github.com/processing/processing/issues/2100
*
* @nowebref
*/
public XML(final Reader reader, String options)
throws IOException, ParserConfigurationException, SAXException {
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
// Prevent 503 errors from www.w3.org
try {
factory.setAttribute("http://apache.org/xml/features/nonvalidating/load-external-dtd", false);
} catch (IllegalArgumentException e) {
// ignore this; Android doesn't like it
}
// without a validating DTD, this doesn't do anything since it doesn't know what is ignorable
// factory.setIgnoringElementContentWhitespace(true);
factory.setExpandEntityReferences(false);
// factory.setExpandEntityReferences(true);
// factory.setCoalescing(true);
// builderFactory.setFeature("http://apache.org/xml/features/disallow-doctype-decl", true);
DocumentBuilder builder = factory.newDocumentBuilder();
// builder.setEntityResolver()
// SAXParserFactory spf = SAXParserFactory.newInstance();
// spf.setFeature("http://apache.org/xml/features/disallow-doctype-decl", true);
// SAXParser p = spf.newSAXParser();
// builder = DocumentBuilderFactory.newDocumentBuilder();
// builder = new SAXBuilder();
// builder.setValidation(validating);
Document document =
builder.parse(
new InputSource(
new Reader() {
@Override
public int read(char[] cbuf, int off, int len) throws IOException {
int count = reader.read(cbuf, off, len);
for (int i = 0; i < count; i++) {
if (cbuf[off + i] == '\u2028') {
cbuf[off + i] = '\n';
}
}
return count;
}
@Override
public void close() throws IOException {
reader.close();
}
}));
node = document.getDocumentElement();
}
/** @param name creates a node with this name */
public XML(String name) {
try {
// TODO is there a more efficient way of doing this? wow.
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
DocumentBuilder builder = factory.newDocumentBuilder();
Document document = builder.newDocument();
node = document.createElement(name);
this.parent = null;
} catch (ParserConfigurationException pce) {
throw new RuntimeException(pce);
}
}
public static void main(String[] args) {
try {
// Find the implementation
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
factory.setNamespaceAware(true);
DocumentBuilder builder = factory.newDocumentBuilder();
DOMImplementation impl = builder.getDOMImplementation();
// Create the document
DocumentType svgDOCTYPE =
impl.createDocumentType(
"svg",
"-//W3C//DTD SVG 1.0//EN",
"http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd");
Document doc = impl.createDocument("http://www.w3.org/2000/svg", "svg", svgDOCTYPE);
// Fill the document
Node rootElement = doc.getDocumentElement();
ProcessingInstruction xmlstylesheet =
doc.createProcessingInstruction(
"xml-stylesheet", "type=\"text/css\" href=\"standard.css\"");
Comment comment = doc.createComment("An example from Chapter 10 of Processing XML with Java");
doc.insertBefore(comment, rootElement);
doc.insertBefore(xmlstylesheet, rootElement);
Node desc = doc.createElementNS("http://www.w3.org/2000/svg", "desc");
rootElement.appendChild(desc);
Text descText = doc.createTextNode("An example from Processing XML with Java");
desc.appendChild(descText);
// Serialize the document onto System.out
TransformerFactory xformFactory = TransformerFactory.newInstance();
Transformer idTransform = xformFactory.newTransformer();
Source input = new DOMSource(doc);
Result output = new StreamResult(System.out);
idTransform.transform(input, output);
} catch (FactoryConfigurationError e) {
System.out.println("Could not locate a JAXP factory class");
} catch (ParserConfigurationException e) {
System.out.println("Could not locate a JAXP DocumentBuilder class");
} catch (DOMException e) {
System.err.println(e);
} catch (TransformerConfigurationException e) {
System.err.println(e);
} catch (TransformerException e) {
System.err.println(e);
}
}
/**
* Writes a table to a XML-file
*
* @param t - Output Model
* @param destination - File Destination
*/
public static void writeXML(Model t, String destination) {
try {
// Create the XML document builder, and document that will be used
DocumentBuilderFactory xmlBuilder = DocumentBuilderFactory.newInstance();
DocumentBuilder Builder = xmlBuilder.newDocumentBuilder();
Document xmldoc = Builder.newDocument();
// create Document node, and get it into the file
Element Documentnode = xmldoc.createElement("SPREADSHEET");
xmldoc.appendChild(Documentnode);
// create element nodes, and their attributes (Cells, and row/column
// data) and their content
for (int row = 1; row < t.getRows(); row++) {
for (int col = 1; col < t.getCols(col); col++) {
Element cell = xmldoc.createElement("CELL");
// set attributes
cell.setAttribute("column", Integer.toString(col));
cell.setAttribute("row", Integer.toString(col));
// set content
cell.appendChild(xmldoc.createTextNode((String) t.getContent(row, col)));
// append node to document node
Documentnode.appendChild(cell);
}
}
// Creating a datastream for the DOM tree
TransformerFactory transformerFactory = TransformerFactory.newInstance();
Transformer transformer = transformerFactory.newTransformer();
// Indentation to make the XML file look better
transformer.setOutputProperty(OutputKeys.METHOD, "xml");
transformer.setOutputProperty(OutputKeys.INDENT, "yes");
// remove the java version
transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
DOMSource stream = new DOMSource(xmldoc);
StreamResult target = new StreamResult(new File(destination));
// write the file
transformer.transform(stream, target);
} catch (ParserConfigurationException e) {
System.out.println("Can't create the XML document builder");
} catch (TransformerConfigurationException e) {
System.out.println("Can't create transformer");
} catch (TransformerException e) {
System.out.println("Can't write to file");
}
}
public static void main(String[] args) {
try {
// open existing file
File xmlFile = new File(userFile);
DocumentBuilderFactory dbfac = DocumentBuilderFactory.newInstance();
DocumentBuilder dbuild = dbfac.newDocumentBuilder();
Document doc = dbuild.parse(xmlFile);
// DocumentBuilderFactory dbfac2 = DocumentBuilderFactory.newInstance();
// DocumentBuilder docBuilder = dbfac2.newDocumentBuilder();
// Document doc2 = docBuilder.parse(xmlFile);
// doc.getDocumentElement().normalize();
} catch (Exception e) {
System.err.println(e.getMessage());
}
}
/**
* Unlike the loadXML() method in PApplet, this version works with files that are not in UTF-8
* format.
*
* @nowebref
*/
public XML(InputStream input, String options)
throws IOException, ParserConfigurationException, SAXException {
// this(PApplet.createReader(input), options); // won't handle non-UTF8
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
try {
// Prevent 503 errors from www.w3.org
factory.setAttribute("http://apache.org/xml/features/nonvalidating/load-external-dtd", false);
} catch (IllegalArgumentException e) {
// ignore this; Android doesn't like it
}
factory.setExpandEntityReferences(false);
DocumentBuilder builder = factory.newDocumentBuilder();
Document document = builder.parse(new InputSource(input));
node = document.getDocumentElement();
}
// Gets the specified XML Schema doc if one is mentioned in the file
public static File getSchemaFile(File xmlDoc) {
/** @todo Must be an easier way of doing this... */
logger.logComment("Getting schema file for: " + xmlDoc);
try {
// File xslFile = null;
DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
DocumentBuilder db = dbf.newDocumentBuilder();
Document doc = db.parse(xmlDoc);
return getSchemaFile(doc);
} catch (Exception e) {
GuiUtils.showErrorMessage(logger, "Error when looking at the XML file: " + xmlDoc, e, null);
return null;
}
}
public XMLHelper(String filename, String root) {
this();
try {
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
DocumentBuilder builder = factory.newDocumentBuilder();
try {
Document document = builder.parse(new File(filename));
setElement((Element) document.getElementsByTagName(root).item(0));
} catch (Exception e) {
Document document = builder.newDocument();
setElement((Element) document.appendChild(document.createElement(root)));
warning("Could not load XML file: " + e.getMessage());
}
} catch (ParserConfigurationException e) {
// Not quite sure when this would happen
severe("Could not extantiate XML builder: " + e.getMessage());
}
}
public static boolean saveTombstones(List<Tombstone> deathChests, String chestsPath) {
long timestamp = System.currentTimeMillis();
try {
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
DocumentBuilder builder = factory.newDocumentBuilder();
// Create the writer
Document xmlDoc = builder.newDocument();
Element rootNode = xmlDoc.createElement("deathchestList");
// String pluginName = Settings.getPluginName();
String version = Settings.getVersion();
rootNode.setAttribute("version", version);
xmlDoc.appendChild(rootNode);
for (Tombstone tombstone : deathChests) {
rootNode.appendChild(
tombstone.createXmlNode(
xmlDoc.createElement(Utils.DEATHCHEST_XML_TAG), xmlDoc, timestamp));
}
// Put the XML file into domSource
DOMSource domSource = new DOMSource(xmlDoc);
// PrintStream will be responsible for writing
// the text data to the file
PrintStream ps = new PrintStream(chestsPath);
StreamResult fileWriter = new StreamResult(ps);
TransformerFactory transformerFactory = TransformerFactory.newInstance();
Transformer transformer = transformerFactory.newTransformer();
// Finally save the file
transformer.transform(domSource, fileWriter);
return true;
} catch (ParserConfigurationException | TransformerException | FileNotFoundException ex) {
System.err.println("Error while writing deathchest data:");
ex.printStackTrace();
}
return false;
}
/**
* Save the XML description of the circuit
*
* @param output an output stream to write in
* @return true if the dump was successful, false either
*/
public boolean dumpToXml(OutputStream output) {
Document doc;
Element root;
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
DocumentBuilder builder;
try {
builder = factory.newDocumentBuilder();
doc = builder.newDocument();
} catch (ParserConfigurationException pce) {
System.err.println("dumpToXmlFile: unable to write XML save file.");
return false;
}
root = doc.createElement("Circuit");
root.setAttribute("name", this.getName());
for (iterNodes = this.nodes.iterator(); iterNodes.hasNext(); )
iterNodes.next().dumpToXml(doc, root);
root.normalize();
doc.appendChild(root);
try {
TransformerFactory tffactory = TransformerFactory.newInstance();
Transformer transformer = tffactory.newTransformer();
transformer.setOutputProperty(OutputKeys.INDENT, "yes");
DOMSource source = new DOMSource(doc);
StreamResult result = new StreamResult(output);
transformer.transform(source, result);
} catch (TransformerConfigurationException tce) {
System.err.println("dumpToXmlFile: Configuration Transformer exception.");
return false;
} catch (TransformerException te) {
System.err.println("dumpToXmlFile: Transformer exception.");
return false;
}
return true;
}
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;
}
/** @param args the command line arguments */
public static void main(String[] args) {
// TODO code application logic here
Model model;
String insertstmt;
String insertmodel = "",
insertspecies = "",
insertcompartment = "",
insertfunction = "",
insertunitdef = "",
insertunits = "",
insertreaction = "",
insertreactant = "",
insertproduct = "";
String insertmodifier = "",
insertklaw = "",
insertrules = "",
insertconstraint = "",
insertdelay = "",
inserttrigger = "",
insertevent = "",
inserteventassign = "",
insertparameter = "";
String insertstatement = "";
String server, user, password, dbname, filepath;
String Filedata = "";
String cwd = System.getProperty("user.dir");
if (args.length == 0) {
server = "localhost";
user = "******";
password = "******";
dbname = "sbmldb2";
/**
* Path to extract the SBML files from database, where cwd is
* "github\db2sbml\dbtosbml_standalone_Project\dbtosbml" so add a folder in this directory and
* mention folder name instead of extractedbm folder
*/
filepath = cwd + "\\extractedbm\\";
} else {
server = args[0];
user = args[1];
password = args[2];
dbname = args[3];
filepath = args[4];
}
try {
Filedata = readFileAsString(cwd + "\\sbmldbschema.sql");
} catch (Exception e) {
e.printStackTrace();
}
Mysqlconn sql = new Mysqlconn(server, user, password, dbname);
// String modelids.getId() = "MorrisonAllegra" ;
ASTNode math = null;
int level = 0, version = 0;
ArrayList<modellist> modelidlist = sql.getmodels();
insertstatement =
"LOCK TABLES `model` WRITE,`species` WRITE,`compartment` WRITE,`functiondefinition` WRITE,";
insertstatement =
insertstatement
+ "`listofunitdefinitions` WRITE,`listofunits` WRITE,`reaction` WRITE,`simplespeciesreference` WRITE,";
insertstatement =
insertstatement
+ "`modifierspeciesreference` WRITE,`kineticlaw` WRITE,`parameter` WRITE,`sbmlconstraint` WRITE,";
insertstatement =
insertstatement
+ "`event` WRITE,`sbmltrigger` WRITE,`delay` WRITE,`eventassignment` WRITE,`rules` WRITE"
+ ";";
for (modellist modelids : modelidlist) {
ArrayList<modellist> modellevel = sql.getmodeldetails(modelids.getId());
for (modellist modellv : modellevel) {
level = modellv.getlevel();
version = modellv.getversion();
}
SBMLDocument doc = new SBMLDocument(level, version);
ArrayList<modellist> modellists = sql.getmodeldetails(modelids.getId());
if (!modellists.isEmpty())
insertmodel =
insertmodel
+ "\nInsert Into model (id, name,SBML_level,version,notes,annotation) Values";
for (modellist models : modellists) {
insertmodel =
insertmodel
+ "(\'"
+ models.getId()
+ "\',\'"
+ models.getName()
+ "\',"
+ models.getlevel()
+ ","
+ models.getversion()
+ ",\'"
+ models.getnotes()
+ "\',\'"
+ models.getannotation().toString()
+ "\'),";
model = doc.createModel(models.getId());
model.setName(models.getName());
// System.out.println("model : " + models.getId());
// model.setNotes(models.getnotes()); // there is some null exception is command line run
// but run perfectly from netbeans so ommented out
if (!models.getannotation().equals("")) {
Annotation annot = new Annotation(models.getannotation().toString());
model.setAnnotation(annot);
}
doc.setModel(model);
}
if (!modellists.isEmpty()) {
insertmodel = insertmodel.substring(0, insertmodel.length() - 1);
insertmodel = insertmodel + ';';
}
// insertmodel = insertmodel + "\nUNLOCK TABLES;";
// System.out.println(insertmodel);
ArrayList<SpeciesList> specieslist = sql.getspecies(modelids.getId());
if (!specieslist.isEmpty())
insertspecies =
insertspecies
+ "\nInsert Into species (id, name, compartment, initialAmount, initialConcentration,substanceUnits,hasOnlySubstanceUnits,boundaryCondition,constant,conversionFactor,model_id,annotation) Values";
for (SpeciesList species : specieslist) {
insertspecies =
insertspecies
+ "(\'"
+ species.getId()
+ "\',\'"
+ species.getName()
+ "\',\'"
+ species.getcompartment()
+ "\',"
+ species.getia()
+ ","
+ species.getic()
+ ",\'"
+ species.getsu()
+ "\',"
+ species.gethosu()
+ ","
+ species.getbc()
+ ","
+ species.getconstant()
+ ","
+ species.getcf()
+ ",\'"
+ modelids.getId()
+ "\',\'"
+ species.getannotation()
+ "\'),";
Species sp = doc.getModel().createSpecies(species.getId());
sp.setName(species.getName());
sp.setCompartment(species.getcompartment());
sp.setConstant(species.getconstant());
sp.setInitialAmount(species.getia());
sp.setInitialConcentration(species.getic());
sp.setHasOnlySubstanceUnits(species.gethosu());
if (doc.getModel().getLevel() == 3) sp.setConversionFactor(species.getcf());
sp.setBoundaryCondition(species.getbc());
sp.setSubstanceUnits(species.getsu());
if (!species.getannotation().equals("")) {
Annotation annot = new Annotation(species.getannotation().toString());
sp.setAnnotation(annot);
}
// doc.getModel().addSpecies(sp) ;
}
if (!specieslist.isEmpty()) {
insertspecies = insertspecies.substring(0, insertspecies.length() - 1);
insertspecies = insertspecies + ';';
}
ArrayList<CompartmentList> complist = sql.getcompartments(modelids.getId());
if (!complist.isEmpty())
insertcompartment =
insertcompartment
+ "\nInsert Into compartment (id, name,constant,model_id,spacialDimensions,size,units) Values";
for (CompartmentList comp : complist) {
insertcompartment =
insertcompartment
+ "(\'"
+ comp.getId()
+ "\',\'"
+ comp.getName()
+ "\',"
+ comp.getconstant()
+ ",\'"
+ modelids.getId()
+ "\',"
+ comp.getspatialdimensions()
+ ","
+ comp.getsize()
+ ","
+ comp.getunits()
+ "\'),";
Compartment c = doc.getModel().createCompartment(comp.getId());
c.setName(comp.getName());
c.setConstant(comp.getconstant());
c.setSize(comp.getsize());
c.setSpatialDimensions(comp.getspatialdimensions());
if (comp.getspatialdimensions() != 0) c.setUnits(comp.getunits());
// doc.getModel().addSpecies(sp) ;
}
if (!complist.isEmpty()) {
insertcompartment = insertcompartment.substring(0, insertcompartment.length() - 1);
insertcompartment = insertcompartment + ';';
}
ArrayList<functionList> funclist = sql.getfunctions(modelids.getId());
if (!funclist.isEmpty())
insertfunction =
insertfunction + "\nInsert Into functiondefinition (id, xmlns,model_id) Values";
for (functionList func : funclist) {
insertfunction =
insertfunction
+ "(\'"
+ func.getId()
+ "\',\'"
+ func.getxmlns()
+ "\',\'"
+ modelids.getId()
+ "\'),";
FunctionDefinition fd = doc.getModel().createFunctionDefinition(func.getId());
try {
math = ASTNode.parseFormula(func.getxmlns());
fd.setMath(math);
} catch (Exception e) {
e.printStackTrace();
}
}
if (!funclist.isEmpty()) {
insertfunction = insertfunction.substring(0, insertfunction.length() - 1);
insertfunction = insertfunction + ';';
}
ArrayList<unitList> unitlist = sql.getunitlist(modelids.getId());
if (!unitlist.isEmpty())
insertunitdef =
insertunitdef + "\nInsert Into listofunitdefinitions (id,name,model_id) Values";
for (unitList units : unitlist) {
insertunitdef =
insertunitdef
+ "(\'"
+ units.getId()
+ "\',\'"
+ units.getName()
+ "\',\'"
+ modelids.getId()
+ "\'),";
UnitDefinition ud = doc.getModel().createUnitDefinition(units.getId());
ud.setName(units.getName());
ArrayList<unitList> unitdeflist = sql.getunitdef(units.getId());
if (!unitdeflist.isEmpty())
insertunits =
insertunits
+ "\nInsert Into listofunits (listofunitdefinitions_id,kind, scale,exponent,multiplier) Values";
for (unitList unitdef : unitdeflist) {
insertunits =
insertunits
+ "(\'"
+ units.getId()
+ "\',\'"
+ unitdef.getkind()
+ "\',"
+ unitdef.getscale()
+ ","
+ unitdef.getexponent()
+ ","
+ unitdef.getmultiplier()
+ "),";
Unit u = ud.createUnit(Unit.Kind.valueOf(unitdef.getkind()));
u.setScale(unitdef.getscale());
u.setExponent(unitdef.getexponent());
u.setMultiplier(unitdef.getmultiplier());
}
// doc.getModel().addSpecies(sp) ;
if (!unitdeflist.isEmpty()) {
insertunits = insertunits.substring(0, insertunits.length() - 1);
insertunits = insertunits + ';';
}
}
if (!unitlist.isEmpty()) {
insertunitdef = insertunitdef.substring(0, insertunitdef.length() - 1);
insertunitdef = insertunitdef + ';';
}
ArrayList<reactionList> reactionlist = sql.getreactons(modelids.getId());
if (!reactionlist.isEmpty())
insertreaction =
insertreaction
+ "\nInsert Into reaction (id,name, reversible,fast,model_id,compartment,annotation) Values";
for (reactionList reaction : reactionlist) {
insertreaction =
insertreaction
+ "(\'"
+ reaction.getId()
+ "\',\'"
+ reaction.getName()
+ "\',"
+ reaction.getreversible()
+ ","
+ reaction.getfast()
+ ",\'"
+ modelids.getId()
+ "\',\'"
+ reaction.getcompartment()
+ "\',\'"
+ reaction.getannotation()
+ "\'),";
Reaction rn = doc.getModel().createReaction(reaction.getId());
rn.setName(reaction.getName());
if (doc.getModel().getLevel() == 3) rn.setCompartment(reaction.getcompartment());
rn.setFast(reaction.getfast());
rn.setReversible(reaction.getreversible());
if (!reaction.getannotation().equals("")) {
Annotation annot = new Annotation(reaction.getannotation().toString());
rn.setAnnotation(annot);
}
ArrayList<reactionList> reactantlist = sql.getreactants(reaction.getId());
if (!reactantlist.isEmpty())
insertreactant =
insertreactant
+ "\nInsert Into simplespeciesreference (reaction_id,species, sboTerm,stoichiometry,speciestype,constant) Values";
for (reactionList reactant : reactantlist) {
insertreactant =
insertreactant
+ "(\'"
+ reaction.getId()
+ "\',\'"
+ reactant.getspecies()
+ "\',\'"
+ reactant.getsboTerm()
+ "\',"
+ reactant.getstoichometry()
+ ","
+ reactant.getconstant()
+ ",\'reactants\'),";
SpeciesReference rt = new SpeciesReference();
rt.setName(reactant.getspecies());
rt.setSpecies(reactant.getspecies());
// rt.setSBOTerm(reactant.getsboTerm());
rt.setStoichiometry(reactant.getstoichometry());
// rt.setConstant(reactant.getconstant());
rn.addReactant(rt);
}
if (!reactantlist.isEmpty()) {
insertreactant = insertreactant.substring(0, insertreactant.length() - 1);
insertreactant = insertreactant + ';';
}
ArrayList<reactionList> productlist = sql.getproducts(reaction.getId());
if (!productlist.isEmpty())
insertproduct =
insertproduct
+ "\nInsert Into simplespeciesreference (reaction_id,species, sboTerm,stoichiometry,constant,speciestype) Values";
for (reactionList product : productlist) {
insertproduct =
insertproduct
+ "(\'"
+ reaction.getId()
+ "\',\'"
+ product.getspecies()
+ "\',\'"
+ product.getsboTerm()
+ "\',"
+ product.getstoichometry()
+ ","
+ product.getconstant()
+ ",\'products\'),";
SpeciesReference pr = new SpeciesReference();
pr.setName(product.getspecies());
pr.setSpecies(product.getspecies());
// pr.setSBOTerm(product.getsboTerm());
pr.setStoichiometry(product.getstoichometry());
// pr.setConstant(product.getconstant());
rn.addProduct(pr);
}
if (!productlist.isEmpty()) {
insertproduct = insertproduct.substring(0, insertproduct.length() - 1);
insertproduct = insertproduct + ';';
}
ArrayList<reactionList> modifierlist = sql.getmodifiers(reaction.getId());
if (!modifierlist.isEmpty())
insertmodifier =
insertmodifier
+ "\nInsert Into modifierspeciesreference (reaction_id,species, sboTerm,speciestype) Values";
for (reactionList modifier : modifierlist) {
insertmodifier =
insertmodifier
+ "(\'"
+ reaction.getId()
+ "\',\'"
+ modifier.getspecies()
+ "\',\'"
+ modifier.getsboTerm()
+ "\',\'modifiers\'),";
ModifierSpeciesReference m = new ModifierSpeciesReference();
m.setName(modifier.getspecies());
m.setSpecies(modifier.getspecies());
// m.setSBOTerm(modifier.getsboTerm());
rn.addModifier(m);
}
if (!modifierlist.isEmpty()) {
insertmodifier = insertmodifier.substring(0, insertmodifier.length() - 1);
insertmodifier = insertmodifier + ';';
}
ArrayList<reactionList> klawlist = sql.getkineticlaws(reaction.getId());
if (!klawlist.isEmpty())
insertklaw =
insertklaw + "\nInsert Into kineticlaw (reaction_id,kid, math,annotation) Values";
for (reactionList klaw : klawlist) {
insertklaw =
insertklaw
+ "(\'"
+ reaction.getId()
+ "\',\'"
+ klaw.getId()
+ "\',\'"
+ klaw.getmath()
+ "\',\'"
+ klaw.getannotation()
+ "\'),";
KineticLaw kl = rn.createKineticLaw();
try {
math = ASTNode.parseFormula(klaw.getmath());
kl.setMath(math);
if (!klaw.getannotation().equals("")) {
Annotation annot = new Annotation(klaw.getannotation().toString());
kl.setAnnotation(annot);
}
} catch (Exception e) {
e.printStackTrace();
}
}
if (!klawlist.isEmpty()) {
insertklaw = insertklaw.substring(0, insertklaw.length() - 1);
insertklaw = insertklaw + ';';
}
}
if (!reactionlist.isEmpty()) {
insertreaction = insertreaction.substring(0, insertreaction.length() - 1);
insertreaction = insertreaction + ';';
}
ArrayList<parameterList> paralist = sql.getparameters(modelids.getId());
if (!paralist.isEmpty())
insertparameter =
insertparameter
+ "\nInsert Into parameter (id,name,value,units,constant,model_id) Values";
for (parameterList para : paralist) {
insertparameter =
insertparameter
+ "(\'"
+ para.getId()
+ "\',\'"
+ para.getName()
+ "\',"
+ para.getvalue()
+ ","
+ para.getunits()
+ ","
+ para.getconstant()
+ ",\'"
+ modelids.getId()
+ "\'),";
Parameter par = doc.getModel().createParameter(para.getId());
par.setName(para.getId());
par.setConstant(para.getconstant());
par.setUnits(para.getunits());
par.setValue(para.getvalue());
}
if (!paralist.isEmpty()) {
insertparameter = insertparameter.substring(0, insertparameter.length() - 1);
insertparameter = insertparameter + ';';
}
ArrayList<constraintList> conslist = sql.getconstraints(modelids.getId());
if (!conslist.isEmpty())
insertconstraint =
insertconstraint + "\nInsert Into sbmlconstraint (math,message,model_id) Values";
for (constraintList constraint : conslist) {
insertconstraint =
insertconstraint
+ "(\'"
+ constraint.getmath()
+ "\',\'"
+ constraint.getmessage()
+ "\',\'"
+ modelids.getId()
+ "\'),";
Constraint cons = doc.getModel().createConstraint();
try {
math = ASTNode.parseFormula(constraint.getmath());
cons.setMath(math);
cons.setMessage(constraint.getmessage());
} catch (Exception e) {
e.printStackTrace();
}
}
if (!conslist.isEmpty()) {
insertconstraint = insertconstraint.substring(0, insertconstraint.length() - 1);
insertconstraint = insertconstraint + ';';
}
ArrayList<eventsList> eventlist = sql.getevents(modelids.getId());
if (!eventlist.isEmpty())
insertevent =
insertevent + "\nInsert Into event (id,name,UseValuesFromTriggerTime,model_id) Values";
for (eventsList events : eventlist) {
insertevent =
insertevent
+ "(\'"
+ events.getId()
+ "\',\'"
+ events.getName()
+ "\',"
+ events.getuservalues()
+ ",\'"
+ modelids.getId()
+ "\'),";
Event ev = doc.getModel().createEvent(events.getId());
ev.setName(events.getName());
// ev.setUseValuesFromTriggerTime(events.getuservalues());
ArrayList<eventsList> triggerlist = sql.gettriggers(events.getId());
if (!triggerlist.isEmpty())
inserttrigger =
inserttrigger
+ "\nInsert Into sbmltrigger (event_id,initialvalue,persisent,math) Values";
for (eventsList triggers : triggerlist) {
Trigger tr = doc.getModel().createTrigger();
try {
math = ASTNode.parseFormula(triggers.getmath());
tr.setMath(math);
tr.setInitialValue(triggers.getinitialval());
tr.setPersistent(triggers.getpersistent());
} catch (Exception e) {
e.printStackTrace();
}
}
if (!triggerlist.isEmpty()) {
inserttrigger = inserttrigger.substring(0, insertmodel.length() - 1);
inserttrigger = inserttrigger + ';';
}
ArrayList<eventsList> delaylist = sql.getdelays(events.getId());
if (!delaylist.isEmpty())
insertdelay = insertdelay + "\nInsert Into delay (event_id,math) Values";
for (eventsList delays : delaylist) {
Delay d = doc.getModel().createDelay();
try {
math = ASTNode.parseFormula(delays.getmath());
d.setMath(math);
} catch (Exception e) {
e.printStackTrace();
}
}
if (!delaylist.isEmpty()) {
insertdelay = insertdelay.substring(0, insertdelay.length() - 1);
insertdelay = insertdelay + ';';
}
ArrayList<eventsList> evasslist = sql.geteventassignments(events.getId());
if (!evasslist.isEmpty())
inserteventassign =
inserteventassign + "\nInsert Into eventassignment (event_id,variable,math) Values";
for (eventsList evassign : evasslist) {
EventAssignment ea = doc.getModel().createEventAssignment();
try {
math = ASTNode.parseFormula(evassign.getmath());
ea.setMath(math);
} catch (Exception e) {
e.printStackTrace();
}
}
if (!evasslist.isEmpty()) {
inserteventassign = inserteventassign.substring(0, inserteventassign.length() - 1);
inserteventassign = inserteventassign + ';';
}
}
if (!eventlist.isEmpty()) {
insertevent = insertevent.substring(0, insertevent.length() - 1);
insertevent = insertevent + ';';
}
ArrayList<ruleslist> rulelist = sql.getrules(modelids.getId());
if (!rulelist.isEmpty())
insertrules = insertrules + "\nInsert Into rules (id,math,ruletype,model_id) Values";
for (ruleslist rules : rulelist) {
insertrules =
insertrules
+ "(\'"
+ rules.getId()
+ "\',\'"
+ rules.getmath()
+ "\',\'"
+ rules.getruletype()
+ "\',\'"
+ modelids.getId()
+ "\'),";
if (rules.getruletype().equals("assignmentrule")) {
Rule r = doc.getModel().createAssignmentRule();
r.setMetaId(rules.getId());
try {
math = ASTNode.parseFormula(rules.getmath());
r.setMath(math);
} catch (Exception e) {
e.printStackTrace();
}
}
}
if (!rulelist.isEmpty()) {
insertrules = insertrules.substring(0, insertrules.length() - 1);
insertrules = insertrules + ';';
}
SBMLWriter writer = new SBMLWriter();
try {
String Path = filepath + modelids.getId() + ".xml";
writer.write(doc, Path);
DocumentBuilderFactory documentBuilderFactory = DocumentBuilderFactory.newInstance();
DocumentBuilder documentBuilder = documentBuilderFactory.newDocumentBuilder();
Document document = documentBuilder.parse(Path);
Element root = document.getDocumentElement();
Element newdataset = document.createElement("dataset");
root.appendChild(newdataset);
ArrayList<dataset> datasetlist = sql.getdataset(modelids.getId());
for (dataset ds : datasetlist) {
// System.out.println(ds.getexpcond());
Element name = document.createElement("experimentalcondition");
name.setAttribute("bioelement", ds.getbioel());
name.setAttribute("name", ds.getName());
name.setAttribute("descr", ds.getdescr());
name.setAttribute("expcond", ds.getexpcond());
name.setAttribute("value", String.valueOf(ds.getvalue()));
name.setAttribute("type", ds.gettype());
name.setAttribute("uri", ds.geturi());
newdataset.appendChild(name);
}
root.appendChild(newdataset);
DOMSource source = new DOMSource(document);
TransformerFactory transformerFactory = TransformerFactory.newInstance();
Transformer transformer = transformerFactory.newTransformer();
transformer.setOutputProperty(OutputKeys.INDENT, "yes");
transformer.setOutputProperty(OutputKeys.METHOD, "xml");
transformer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "4");
StreamResult result = new StreamResult(filepath + modelids.getId() + "d.xml");
transformer.transform(source, result);
System.out.println(
"Files : "
+ modelids.getId()
+ ".xml and "
+ modelids.getId()
+ "d.xml have been generated successfully !!!");
} catch (Exception e) {
e.printStackTrace();
}
insertstatement =
insertstatement
+ "\n\n"
+ insertmodel
+ "\n"
+ insertspecies
+ "\n"
+ insertcompartment
+ "\n"
+ insertfunction;
insertstatement =
insertstatement
+ "\n"
+ insertparameter
+ "\n"
+ insertreaction
+ "\n"
+ insertreactant
+ "\n"
+ insertproduct;
insertstatement =
insertstatement
+ "\n"
+ insertmodifier
+ "\n"
+ insertklaw
+ "\n"
+ insertunitdef
+ "\n"
+ insertunits;
insertstatement =
insertstatement
+ "\n"
+ insertrules
+ "\n"
+ insertconstraint
+ "\n"
+ insertevent
+ "\n"
+ inserttrigger
+ "\n"
+ insertdelay
+ "\n"
+ inserteventassign;
insertcompartment = "";
insertmodel = "";
insertspecies = "";
// System.out.println("document : " + doc);
}
insertstatement = insertstatement + "\nUNLOCK TABLES;";
Filedata = Filedata + "\n\n\n" + insertstatement;
try {
wrtireStringToFile(Filedata, filepath + "sbmldb.sql");
} catch (IOException e) {
e.printStackTrace();
}
// System.out.println(insertstatement);
}
public WriteXML(String name) throws ParserConfigurationException {
filename = name;
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
DocumentBuilder builder = factory.newDocumentBuilder();
document = builder.newDocument();
}
/**
* 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;
}
// #]
}
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();
}
}
public void CollectData(String link) {
try {
// Creating an empty XML Document
DocumentBuilderFactory dbfac = DocumentBuilderFactory.newInstance();
DocumentBuilder docBuilder = dbfac.newDocumentBuilder();
Document doc = docBuilder.newDocument();
int flag = 0;
// create the root element and add it to the document
Element movie = doc.createElement("movie");
doc.appendChild(movie);
movie.setAttribute("id", String.valueOf(n));
n++;
// create sub elements
Element genres = doc.createElement("genres");
Element actors = doc.createElement("actors");
Element reviews = doc.createElement("reviews");
URL movieUrl = new URL(link);
URL reviewsURL = new URL(link + "reviews/#type=top_critics");
BufferedWriter bw3 = new BufferedWriter(new FileWriter("movies.xml", true));
int count = -1;
String auth = "";
BufferedReader br3 = new BufferedReader(new InputStreamReader(movieUrl.openStream()));
String str2 = "";
String info = "";
while (null != (str2 = br3.readLine())) {
// start reading the html document
if (str2.isEmpty()) continue;
if (count == 14) break;
if (count == 12) {
if (!str2.contains("<h3>Cast</h3>")) continue;
else count++;
}
if (count == 13) {
if (str2.contains(">ADVERTISEMENT</p>")) {
count++;
movie.appendChild(actors);
continue;
} else {
if (str2.contains("itemprop=\"name\">")) {
Element actor = doc.createElement("actor");
actors.appendChild(actor);
Text text = doc.createTextNode(Jsoup.parse(str2.toString()).text());
actor.appendChild(text);
} else continue;
}
}
if (count <= 11) {
switch (count) {
case -1:
{
if (!str2.contains("property=\"og:image\"")) continue;
else {
Pattern image =
Pattern.compile("http://.*.jpg", Pattern.CASE_INSENSITIVE | Pattern.DOTALL);
Matcher match = image.matcher(str2);
while (match.find()) {
Element imageLink = doc.createElement("imageLink");
movie.appendChild(imageLink);
Text text = doc.createTextNode(match.group());
imageLink.appendChild(text);
count++;
}
}
break;
}
case 0:
{
if (str2.contains("<title>")) {
Element name = doc.createElement("name");
movie.appendChild(name);
Text text =
doc.createTextNode(
Jsoup.parse(str2.toString().replace(" - Rotten Tomatoes", "")).text());
name.appendChild(text);
count++;
}
break;
}
case 1:
{
if (!str2.contains("itemprop=\"ratingValue\"")) break;
else {
Element score = doc.createElement("score");
movie.appendChild(score);
Text text = doc.createTextNode(Jsoup.parse(str2.toString()).text());
score.appendChild(text);
count++;
}
break;
}
case 2:
{
if (!str2.contains("itemprop=\"description\">")) continue;
else count++;
break;
}
case 3:
{
if (!str2.contains("itemprop=\"duration\"")) info = info.concat(str2);
else {
Element MovieInfo = doc.createElement("MovieInfo");
movie.appendChild(MovieInfo);
Text text = doc.createTextNode(Jsoup.parse(info.toString()).text());
MovieInfo.appendChild(text);
info = str2;
count++;
}
break;
}
case 4:
{
if (!str2.contains("itemprop=\"genre\"")) info = info.concat(str2);
else {
Element duration = doc.createElement("duration");
movie.appendChild(duration);
Text text = doc.createTextNode(Jsoup.parse(info.toString()).text());
duration.appendChild(text);
info = str2;
count++;
}
break;
}
case 5:
{
if (info.contains("itemprop=\"genre\"")) {
Element genre = doc.createElement("genre");
genres.appendChild(genre);
Text text = doc.createTextNode(Jsoup.parse(info.toString()).text());
genre.appendChild(text);
info = "";
}
if (str2.contains(">Directed By:<")) {
count++;
movie.appendChild(genres);
continue;
} else {
if (str2.contains("itemprop=\"genre\"")) {
Element genre = doc.createElement("genre");
genres.appendChild(genre);
Text text = doc.createTextNode(Jsoup.parse(str2.toString()).text());
genre.appendChild(text);
} else continue;
}
break;
}
case 6:
{
if (!str2.contains(">Written By:<")) {
if (str2.contains(">In Theaters:<")) {
Element director = doc.createElement("director");
movie.appendChild(director);
Text text =
doc.createTextNode(
Jsoup.parse(info.toString().replace("Directed By: ", "")).text());
director.appendChild(text);
info = str2;
count += 2;
break;
}
info = info.concat(str2);
} else {
Element director = doc.createElement("director");
movie.appendChild(director);
Text text =
doc.createTextNode(
Jsoup.parse(info.toString().replace("Directed By: ", "")).text());
director.appendChild(text);
info = "";
count++;
}
break;
}
case 7:
{
if (!str2.contains(">In Theaters:<")) {
if (str2.contains(">On DVD:<")) {
Element writer = doc.createElement("writer");
movie.appendChild(writer);
Text text = doc.createTextNode(Jsoup.parse(info.toString()).text());
writer.appendChild(text);
info = str2;
count += 2;
break;
}
info = info.concat(str2);
} else {
Element writer = doc.createElement("writer");
movie.appendChild(writer);
Text text = doc.createTextNode(Jsoup.parse(info.toString()).text());
writer.appendChild(text);
info = str2;
count++;
}
break;
}
case 8:
{
if (!str2.contains(">On DVD:<")) info = info.concat(str2);
else {
Element TheatreRelease = doc.createElement("TheatreRelease");
movie.appendChild(TheatreRelease);
Text text =
doc.createTextNode(
Jsoup.parse(info.toString().replace("In Theaters:", "")).text());
TheatreRelease.appendChild(text);
info = str2;
count++;
}
break;
}
case 9:
{
if (!str2.contains(">US Box Office:<")) {
if (str2.contains("itemprop=\"productionCompany\"")) {
Element DvdRelease = doc.createElement("DvdRelease");
movie.appendChild(DvdRelease);
Text text =
doc.createTextNode(
Jsoup.parse(info.toString().replace("On DVD:", "")).text());
DvdRelease.appendChild(text);
info = str2;
count += 2;
break;
}
info = info.concat(str2);
} else {
Element DvdRelease = doc.createElement("DvdRelease");
movie.appendChild(DvdRelease);
Text text =
doc.createTextNode(
Jsoup.parse(info.toString().replace("On DVD:", "")).text());
DvdRelease.appendChild(text);
info = str2;
count++;
}
break;
}
case 10:
{
if (!str2.contains("itemprop=\"productionCompany\"")) info = info.concat(str2);
else {
Element BOCollection = doc.createElement("BOCollection");
movie.appendChild(BOCollection);
Text text =
doc.createTextNode(
Jsoup.parse(info.toString().replace("US Box Office:", "")).text());
BOCollection.appendChild(text);
info = str2;
count++;
}
break;
}
case 11:
{
if (!str2.contains(">Official Site")) info = info.concat(str2);
else {
Element Production = doc.createElement("Production");
movie.appendChild(Production);
Text text = doc.createTextNode(Jsoup.parse(info.toString()).text());
Production.appendChild(text);
info = str2;
count++;
}
break;
}
default:
break;
}
}
}
BufferedReader br4 = new BufferedReader(new InputStreamReader(reviewsURL.openStream()));
String str3 = "";
String info2 = "";
int count2 = 0;
while (null != (str3 = br4.readLine())) {
if (count2 == 0) {
if (!str3.contains("<div class=\"reviewsnippet\">")) continue;
else count2++;
}
if (count2 == 1) {
if (!str3.contains("<p class=\"small subtle\">")) info2 = info2.concat(str3);
else {
Element review = doc.createElement("review");
reviews.appendChild(review);
Text text = doc.createTextNode(Jsoup.parse(info2.toString()).text());
review.appendChild(text);
info2 = "";
count2 = 0;
}
}
}
movie.appendChild(reviews);
TransformerFactory transfac = TransformerFactory.newInstance();
Transformer trans = transfac.newTransformer();
trans.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
trans.setOutputProperty(OutputKeys.INDENT, "yes");
// 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();
bw3.write(xmlString);
br3.close();
br4.close();
bw3.close();
} catch (Exception ex) {
ex.printStackTrace();
}
}