private static void validateXMLWithURL(File nmlFile, String schemaUrl) {
try {
Source schemaFileSource = new StreamSource(schemaUrl);
SchemaFactory factory = SchemaFactory.newInstance(XMLConstants.W3C_XML_SCHEMA_NS_URI);
Schema schema = factory.newSchema(schemaFileSource);
Validator validator = schema.newValidator();
Source xmlFileSource = new StreamSource(nmlFile);
validator.validate(xmlFileSource);
System.out.println(
"**** File: " + nmlFile + " is VALID according to " + schemaUrl + "!!! ****");
} catch (Exception ex) {
System.err.println(
"Problem validating xml file: "
+ nmlFile.getAbsolutePath()
+ " according to "
+ schemaUrl
+ "!!!");
ex.printStackTrace();
System.exit(1);
}
}
public ArrayList<String> collectLinks(String p) {
ArrayList<String> PageLinks = new ArrayList<String>();
try {
URL url = new URL(p);
BufferedReader br3 = new BufferedReader(new InputStreamReader(url.openStream()));
String str = "";
while (null != (str = br3.readLine())) {
Pattern link =
Pattern.compile(
"<a target=\"_top\" href=\"/m/.*", Pattern.CASE_INSENSITIVE | Pattern.DOTALL);
Matcher match = link.matcher(str);
while (match.find()) {
String tmp = match.group();
int start = tmp.indexOf('/');
tmp = tmp.substring(start + 1, tmp.indexOf('\"', start + 1));
if (Crawl.contains("http://www.rottentomatoes.com/" + tmp)
|| ToCrawl.contains("http://www.rottentomatoes.com/" + tmp)
|| PageLinks.contains("http://www.rottentomatoes.com/" + tmp)) continue;
PageLinks.add("http://www.rottentomatoes.com/" + tmp);
// bw4.write("http://www.rottentomatoes.com/"+tmp+"\r\n");
}
}
br3.close();
} catch (Exception ex) {
ex.printStackTrace();
}
return PageLinks;
}
// ## operation runReactor()
public void runReactor() {
// #[ operation runReactor()
// run reactor
String dir = System.getProperty("RMG.workingDirectory");
try {
// system call for reactor
String[] command = {dir + "/software/reactorModel/reactor.exe"};
File runningDir = new File("chemkin");
Process reactor = Runtime.getRuntime().exec(command, null, runningDir);
InputStream ips = reactor.getInputStream();
InputStreamReader is = new InputStreamReader(ips);
BufferedReader br = new BufferedReader(is);
String line = null;
while ((line = br.readLine()) != null) {
// System.out.println(line);
}
int exitValue = reactor.waitFor();
} catch (Exception e) {
System.out.println("Error in running reactor!");
System.out.println(e.getMessage());
System.exit(0);
}
// #]
}
// ## operation checkChemkinMessage()
public void checkChemkinMessage() {
// #[ operation checkChemkinMessage()
try {
String dir = System.getProperty("RMG.workingDirectory");
String filename = "chemkin/chem.message";
FileReader fr = new FileReader(filename);
BufferedReader br = new BufferedReader(fr);
String line = br.readLine().trim();
if (line.startsWith("NO ERRORS FOUND ON INPUT")) {
return;
} else if (line.startsWith("WARNING...THERE IS AN ERROR IN THE LINKING FILE")) {
System.out.println("Error in chemkin linking to reactor!");
System.exit(0);
} else {
System.out.println("Unknown message in chem.message!");
System.exit(0);
}
} catch (Exception e) {
System.out.println("Can't read chem.message!");
System.out.println(e.getMessage());
System.exit(0);
}
// #]
}
public static void writeChemkinInputFile(ReactionSystem rs) {
// #[ operation writeChemkinInputFile(ReactionModel,SystemSnapshot)
StringBuilder result = new StringBuilder();
result.append(writeChemkinHeader());
result.append(writeChemkinElement());
double start = System.currentTimeMillis();
result.append(writeChemkinSpecies(rs.reactionModel, rs.initialStatus));
result.append(writeChemkinThermo(rs.reactionModel));
Global.chemkinThermo = Global.chemkinThermo + (System.currentTimeMillis() - start) / 1000 / 60;
start = System.currentTimeMillis();
result.append(writeChemkinPdepReactions(rs));
Global.chemkinReaction =
Global.chemkinReaction + (System.currentTimeMillis() - start) / 1000 / 60;
String dir = System.getProperty("RMG.workingDirectory");
if (!dir.endsWith("/")) dir += "/";
dir += "software/reactorModel/";
String file = "chemkin/chem.inp";
try {
FileWriter fw = new FileWriter(file);
fw.write(result.toString());
fw.close();
} catch (Exception e) {
System.out.println("Error in writing chemkin input file chem.inp!");
System.out.println(e.getMessage());
System.exit(0);
}
// #]
}
private void deflate(String tmpDir, String path) {
String tmpFile = "tmp-" + Utils.timestamp() + ".zip";
try {
ZipFile zipFile = new ZipFile(tmpFile);
ZipParameters parameters = new ZipParameters();
parameters.setCompressionMethod(Zip4jConstants.COMP_DEFLATE);
parameters.setCompressionLevel(Zip4jConstants.DEFLATE_LEVEL_NORMAL);
parameters.setIncludeRootFolder(false);
zipFile.addFolder(tmpDir, parameters);
} catch (Exception e) {
e.printStackTrace();
return;
}
File from = null;
File to = null;
try {
File target = new File(path);
if (target.exists()) FileUtils.forceDelete(target);
from = new File(tmpFile);
to = new File(path);
FileUtils.moveFile(from, to);
} catch (IOException e) {
Utils.onError(new Error.FileMove(tmpFile, path));
}
try {
FileUtils.deleteDirectory(new File(tmpDir));
} catch (IOException e) {
Utils.log("can't delete temporary folder");
}
}
// ## operation writeChemkinInputFile(ReactionModel,SystemSnapshot)
public static void writeChemkinInputFile(
final ReactionModel p_reactionModel, SystemSnapshot p_beginStatus) {
// #[ operation writeChemkinInputFile(ReactionModel,SystemSnapshot)
StringBuilder result = new StringBuilder();
result.append(writeChemkinHeader());
result.append(writeChemkinElement());
double start = System.currentTimeMillis();
result.append(writeChemkinSpecies(p_reactionModel, p_beginStatus));
result.append(writeChemkinThermo(p_reactionModel));
Global.chemkinThermo = Global.chemkinThermo + (System.currentTimeMillis() - start) / 1000 / 60;
start = System.currentTimeMillis();
result.append(
writeChemkinPdepReactions(
p_reactionModel, p_beginStatus)); // 10/26/07 gmagoon: changed to pass p_beginStatus
// result.append(writeChemkinPdepReactions(p_reactionModel));
Global.chemkinReaction =
Global.chemkinReaction + (System.currentTimeMillis() - start) / 1000 / 60;
String dir = System.getProperty("RMG.workingDirectory");
if (!dir.endsWith("/")) dir += "/";
dir += "software/reactorModel/";
String file = "chemkin/chem.inp";
try {
FileWriter fw = new FileWriter(file);
fw.write(result.toString());
fw.close();
} catch (Exception e) {
System.out.println("Error in writing chemkin input file chem.inp!");
System.out.println(e.getMessage());
System.exit(0);
}
if (PDepRateConstant.getMode() == Mode.CHEBYSHEV
|| PDepRateConstant.getMode() == Mode.PDEPARRHENIUS
|| PDepRateConstant.getMode() == Mode.RATE) {
StringBuilder gridOfRateCoeffs = new StringBuilder();
gridOfRateCoeffs.append(writeGridOfRateCoeffs(p_reactionModel));
String newFile = "chemkin/tableOfRateCoeffs.txt";
try {
FileWriter fw = new FileWriter(newFile);
fw.write(gridOfRateCoeffs.toString());
fw.close();
} catch (Exception e) {
System.out.println("Error in writing tableOfRateCoeffs.txt");
System.out.println(e.getMessage());
System.exit(0);
}
}
// #]
}
private String inflate(String path) {
if (!new File(path).canRead()) {
Utils.onError(new Error.FileRead(path));
return null;
}
String tmpDir = "tmp-" + Utils.timestamp();
try {
ZipFile zipFile = new ZipFile(path);
zipFile.extractAll(tmpDir);
} catch (Exception e) {
e.printStackTrace();
return null;
}
return tmpDir;
}
/**
* 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();
}
}
/**
* Gets the string of an XML document containing multiple words for saving purposes.
*
* @param words The words to save.
* @return String containing XML containing all words.
*/
public static String getMultipleWordXML(Word[] words) {
try {
DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
DocumentBuilder db = dbf.newDocumentBuilder();
Document doc = db.newDocument();
Element root = doc.createElement("Root");
for (int i = 0; i < words.length; i++) {
root.appendChild(words[i].getWordXMLNode(doc));
}
doc.appendChild(root);
return getStringFromDocument(doc);
} catch (Exception ex) {
ex.printStackTrace();
return null;
}
}
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());
}
}
/**
* 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 static Word[] getWordsFromFile(ByteArrayInputStream inputStream) {
try {
// now to parse the XML
DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
DocumentBuilder db = dbf.newDocumentBuilder();
Document doc = db.parse(inputStream);
removeEmptyTextNodes(doc);
NodeList wordList = doc.getElementsByTagName("WordDefinitions");
int wordCount = wordList.getLength();
Word[] returnWords = new Word[wordCount];
for (int wordi = 0; wordi < wordCount; wordi++) {
NodeList list = ((Element) wordList.item(wordi)).getElementsByTagName("Definition");
Element wordElement = (Element) wordList.item(wordi);
String word = wordElement.getAttribute("word");
String mainDefinition = wordElement.getAttribute("mainDefinition");
int numDefinitions = list.getLength();
Definition[] wordOtherDefinitions = 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 theWord = 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
wordOtherDefinitions[i] =
new Definition(dictionaryName, dictionaryId, definition, theWord);
}
if (wordOtherDefinitions.length == 0) {
wordOtherDefinitions =
new Definition[] {new Definition("nil", "nil", "NO DEFINITION FOUND", word)};
}
Word currentWord = new Word(word, mainDefinition);
currentWord.setOtherDefinitions(wordOtherDefinitions);
returnWords[wordi] = currentWord;
}
return returnWords;
} catch (Exception ex) {
ex.printStackTrace();
return null;
}
}
/** used for cut and paste. */
public void addObjectFromClipboard(String a_value) throws CircularIncludeException {
Reader reader = new StringReader(a_value);
Document document = null;
try {
document = UJAXP.getDocument(reader);
} catch (Exception e) {
e.printStackTrace();
return;
} // try-catch
Element root = document.getDocumentElement();
if (!root.getNodeName().equals("clipboard")) {
return;
} // if
Node child;
for (child = root.getFirstChild(); child != null; child = child.getNextSibling()) {
if (!(child instanceof Element)) {
continue;
} // if
Element element = (Element) child;
IGlyphFactory factory = GlyphFactory.getFactory();
if (XModule.isMatch(element)) {
EModuleInvoke module = (EModuleInvoke) factory.createXModule(element);
addModule(module);
continue;
} // if
if (XContour.isMatch(element)) {
EContour contour = (EContour) factory.createXContour(element);
addContour(contour);
continue;
} // if
if (XInclude.isMatch(element)) {
EIncludeInvoke include = (EIncludeInvoke) factory.createXInclude(element);
addInclude(include);
continue;
} // if
} // while
}
public static String errorMessage(Exception exception) {
String message = "";
try {
String addErrorMessage = getErrorStackString(exception.getStackTrace());
message = exception.toString();
return "<errortext>"
+ message
+ "</errortext>".replaceAll("\"", "'")
+ "<stack>"
+ addErrorMessage.replaceAll(">", "-").replaceAll("<", "-")
+ "</stack>\n\r";
} catch (Exception e) {
System.out.println(e);
e.printStackTrace();
return "";
}
}
/**
* Gets XML string for this definition so that it may be printed.
*
* @return XML node that can be saved of this word.
*/
public Element getWordXMLNode(Document doc) {
try {
Element rootWordElement = doc.createElement("WordDefinitions");
rootWordElement.setAttribute("word", this.word);
rootWordElement.setAttribute("mainDefinition", this.getMainDefinition());
if (this.otherDefinitions == null) {
this.getDefinitions();
}
for (int i = 0; i < this.otherDefinitions.length; i++) {
// main definition node
Element definition = doc.createElement("Definition");
// word
Element word = doc.createElement("Word");
word.setTextContent(otherDefinitions[i].getWord());
// dictionary
Element dictionary = doc.createElement("Dictionary");
Element id = doc.createElement("Id");
id.setTextContent(otherDefinitions[i].getId());
Element source = doc.createElement("Name");
source.setTextContent(otherDefinitions[i].getSource());
dictionary.appendChild(id);
dictionary.appendChild(source);
// definition
Element wordDefinition = doc.createElement("WordDefinition");
wordDefinition.setTextContent(otherDefinitions[i].getDefinition());
// append all the children
definition.appendChild(word);
definition.appendChild(dictionary);
definition.appendChild(wordDefinition);
rootWordElement.appendChild(definition);
}
return rootWordElement;
} catch (Exception ex) {
ex.printStackTrace();
return null;
}
}
/**
* Gets a ByteArrayInputStream to parse a word from the definition API.
*
* @return ByteArrayInputStream containing definition XML, null if trouble parsing or getting the
* definition.
*/
public ByteArrayInputStream getStreamFromOnlineXML() {
try {
// download the xml definition page of the word
String urlSafeWord = URLEncoder.encode(this.word, "UTF-8");
InputStream response = new URL(SERVICE_URL + urlSafeWord).openStream();
Scanner responseReader = new Scanner(response).useDelimiter("\\A");
if (responseReader.hasNext()) {
// gets a clean version of xml the document can parse
String xml = responseReader.next();
response.close();
xml = xml.trim().replaceFirst("^([\\W]+)<", "<");
ByteArrayInputStream stream = new ByteArrayInputStream(xml.getBytes("utf-8"));
return stream;
} else {
return null;
}
} catch (Exception ex) {
ex.printStackTrace();
return null;
}
}
/**
* 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;
}
}
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;
}
/** @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);
}
/**
* 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);
}
}
}
}
}
public StartProcess() {
super();
Hashtable jndiProps = new Hashtable();
jndiProps.put(Context.PROVIDER_URL, "t3://soaps3.alfa.local:8001/soa-infra");
jndiProps.put(Context.INITIAL_CONTEXT_FACTORY, "weblogic.jndi.WLInitialContextFactory");
jndiProps.put(Context.SECURITY_PRINCIPAL, "weblogic");
jndiProps.put(Context.SECURITY_CREDENTIALS, "weblogic1");
jndiProps.put("dedicated.connection", "true");
String inputPayload =
"<process xmlns=\"http://xmlns.oracle.com/HelloWorld/Helloworld/BPELProcess1\">"
+ " <input>hello</input>"
+ "</process>";
Locator locator = null;
try {
// connect to the soa server
locator = LocatorFactory.createLocator(jndiProps);
String compositeDN = "default/Helloworld!1.0";
// find composite
Composite composite = locator.lookupComposite("default/Helloworld!1.0");
System.out.println("Got Composite : " + composite.toString());
// find exposed service of the composite
Service service = composite.getService("ADFBindingService");
System.out.println("Got serviceName : " + service.toString());
// make the input request and add this to a operation of the service
NormalizedMessage input = new NormalizedMessageImpl();
String uuid = "uuid:" + UUID.randomUUID();
input.addProperty(NormalizedMessage.PROPERTY_CONVERSATION_ID, uuid);
// payload is the partname of the process operation
input.getPayload().put("payload", inputPayload);
// process is the operation of the employee service
NormalizedMessage res = null;
try {
res = service.request("process", input);
} catch (Exception e) {
e.printStackTrace();
}
Map payload = res.getPayload();
Element element = (Element) payload.get("payload");
TransformerFactory tFactory = TransformerFactory.newInstance();
Transformer transformer = tFactory.newTransformer();
transformer.setOutputProperty("indent", "yes");
StringWriter sw = new StringWriter();
StreamResult result = new StreamResult(sw);
DOMSource source = new DOMSource(element);
transformer.transform(source, result);
System.out.println("Result\n" + sw.toString());
System.out.println("instances");
CompositeInstanceFilter filter = new CompositeInstanceFilter();
filter.setMinCreationDate(new java.util.Date((System.currentTimeMillis() - 2000000)));
// get composite instances by filter ..
List<CompositeInstance> obInstances = composite.getInstances(filter);
// for each of the returned composite instances..
for (CompositeInstance instance : obInstances) {
System.out.println(
" DN: "
+ instance.getCompositeDN()
+ " Instance: "
+ instance.getId()
+ " creation-date: "
+ instance.getCreationDate()
+ " state ("
+ instance.getState()
+ "): "
+ getStateAsString(instance.getState()));
// setup a component filter
ComponentInstanceFilter cInstanceFilter = new ComponentInstanceFilter();
// get child component instances ..
List<ComponentInstance> childComponentInstances =
instance.getChildComponentInstances(cInstanceFilter);
// for each child component instance (e.g. a bpel process)
for (ComponentInstance cInstance : childComponentInstances) {
System.out.println(
" -> componentinstance: "
+ cInstance.getComponentName()
+ " type: "
+ cInstance.getServiceEngine().getEngineType()
+ " state: "
+ getStateAsString(cInstance.getState()));
System.out.println("State: " + cInstance.getNormalizedStateAsString());
}
}
} catch (Exception e) {
e.printStackTrace();
}
}
// ## operation writeReactorInputFile(ReactionModel,ReactionTime,ReactionTime,SystemSnapshot)
public boolean writeReactorInputFile(
ReactionModel p_reactionModel,
ReactionTime p_beginTime,
ReactionTime p_endTime,
SystemSnapshot p_beginStatus) {
// #[ operation writeReactorInputFile(ReactionModel,ReactionTime,ReactionTime,SystemSnapshot)
// construct "input" string
String input = "<?xml version=\"1.0\" standalone=\"no\"?>" + "\n";
String dir = System.getProperty("RMG.workingDirectory");
if (!dir.endsWith("/")) dir += "/";
String dtd = dir + "software/reactorModel/documentTypeDefinitions/reactorInput.dtd";
input += "<!DOCTYPE reactorinput SYSTEM \"" + dtd + "\">" + "\n";
input += "<reactorinput>" + "\n";
input += "<header>" + "\n";
input += "<title>Reactor Input File</title>" + "\n";
input +=
"<description>RMG-generated file used to call an external reactor model</description>"
+ "\n";
input += "</header>" + "\n";
input += "<inputvalues>" + "\n";
input += "<integrationparameters>" + "\n";
input += "<reactortype>" + reactorType + "</reactortype>" + "\n";
input +=
"<starttime units=\""
+ p_beginTime.getUnit()
+ "\">"
+ MathTool.formatDouble(p_beginTime.getTime(), 15, 6)
+ "</starttime>"
+ "\n";
input +=
"<endtime units=\""
+ p_endTime.getUnit()
+ "\">"
+ MathTool.formatDouble(p_endTime.getTime(), 15, 6)
+ "</endtime>"
+ "\n";
// input += "<starttime units=\"" + p_beginTime.unit + "\">" +
// MathTool.formatDouble(p_beginTime.time,15,6) + "</starttime>" + "\n";
// input += "<endtime units=\"" + p_endTime.unit + "\">" +
// MathTool.formatDouble(p_endTime.time,15,6) + "</endtime>" + "\n";
input += "<rtol>" + rtol + "</rtol>" + "\n";
input += "<atol>" + atol + "</atol>" + "\n";
input += "</integrationparameters>" + "\n";
input += "<chemistry>" + "\n";
input += "</chemistry>" + "\n";
input += "<systemstate>" + "\n";
input +=
"<temperature units=\"K\">"
+ MathTool.formatDouble(p_beginStatus.getTemperature().getK(), 15, 6)
+ "</temperature>"
+ "\n";
input +=
"<pressure units=\"Pa\">"
+ MathTool.formatDouble(p_beginStatus.getPressure().getPa(), 15, 6)
+ "</pressure>"
+ "\n";
for (Iterator iter = p_beginStatus.getSpeciesStatus(); iter.hasNext(); ) {
SpeciesStatus spcStatus = (SpeciesStatus) iter.next();
Species thisSpecies = spcStatus.getSpecies();
CoreEdgeReactionModel cerm = (CoreEdgeReactionModel) p_reactionModel;
if (cerm.containsAsReactedSpecies(thisSpecies)) {
String spcChemkinName = thisSpecies.getChemkinName();
double concentration = spcStatus.getConcentration();
input +=
"<amount units=\"molPerCm3\" speciesid=\""
+ spcChemkinName
+ "\">"
+ concentration
+ "</amount>"
+ "\n";
}
}
for (Iterator iter = p_beginStatus.getInertGas(); iter.hasNext(); ) {
String name = (String) iter.next();
double conc = p_beginStatus.getInertGas(name);
if (conc != 0.0)
input +=
"<amount units=\"molPerCm3\" speciesid=\"" + name + "\">" + conc + "</amount>" + "\n";
}
input += "</systemstate>" + "\n";
input += "</inputvalues>" + "\n";
input += "</reactorinput>" + "\n";
// write "input" string to file
try {
String file = "chemkin/reactorInput.xml";
FileWriter fw = new FileWriter(file);
fw.write(input);
fw.close();
return true;
} catch (Exception e) {
System.out.println("Error in writing reactorInput.xml!");
System.out.println(e.getMessage());
return false;
}
// #]
}
private void importItemActionPerformed(
java.awt.event.ActionEvent evt) { // GEN-FIRST:event_importItemActionPerformed
// Display a file chooser
File selectedFile;
Model m = null;
JFileChooser jfc = new JFileChooser(workingDirectory);
jfc.setFileFilter(
new FileFilter() {
public boolean accept(File f) {
return f.isDirectory() || f.getName().endsWith(".xmi");
}
public String getDescription() {
return "XMI UML files (*.xmi)";
}
});
jfc.setCurrentDirectory(workingDirectory);
jfc.showDialog(this, "Import");
selectedFile = jfc.getSelectedFile();
if (selectedFile != null) {
try {
m = importModel(selectedFile);
if (m != null) {
models.add(m);
JOptionPane.showMessageDialog(
this, "Model loaded successfully.", "Success!", JOptionPane.INFORMATION_MESSAGE);
workingDirectory = jfc.getSelectedFile().getParentFile();
getContentPane().remove(MTP);
MTP = new ModelTreePanel(m);
getContentPane().add(MTP, BorderLayout.CENTER);
try {
ObjectOutputStream Out =
new ObjectOutputStream(
new FileOutputStream(System.getProperty("user.home") + "/" + "WorkSpace.dat"));
Out.writeObject(new WorkSpace(workingDirectory.getAbsolutePath()));
Out.close();
} catch (Exception ex) {
ex.printStackTrace();
}
}
} catch (FileNotFoundException fnfe) {
JOptionPane.showMessageDialog(
this,
"Could not open the model file: " + fnfe.getMessage(),
"File not found",
JOptionPane.ERROR_MESSAGE);
} catch (ParseException pe) {
JOptionPane.showMessageDialog(
this,
"There was an error in parsing the given model: " + pe.getMessage(),
"Parse error",
JOptionPane.ERROR_MESSAGE);
} catch (LemException le) {
JOptionPane.showMessageDialog(
this,
"There was an error in parsing the given model: " + le.getMessage(),
"Parse error",
JOptionPane.ERROR_MESSAGE);
} catch (IOException ioe) {
JOptionPane.showMessageDialog(
this,
"An input/output error occured while trying to read the model: " + ioe.getMessage(),
"Read error",
JOptionPane.ERROR_MESSAGE);
} catch (Exception e) {
e.printStackTrace();
}
}
setVisible(true);
} // GEN-LAST:event_importItemActionPerformed
// ## 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;
}
// #]
}
public static void main(String args[]) {
try {
SeleniumHtmlClient client = new SeleniumHtmlClient();
String testFile = null;
String testSuite = null;
String resultsFilename = null;
for (int i = 0; i < args.length; i++) {
if (args[i].equals("--host")) {
i++;
if (i < args.length) {
client.setHost(args[i]);
} else {
throw new BadUsageException("--host must be followed by a hostname");
}
} else if (args[i].equals("--port")) {
i++;
if (i < args.length) {
client.setPort(Integer.parseInt(args[i]));
} else {
throw new BadUsageException("--port must be followed by a port number");
}
} else if (args[i].equals("--browser")) {
i++;
if (i < args.length) {
client.setBrowser(args[i]);
} else {
throw new BadUsageException("--browser must be followed by a browser spec");
}
} else if (args[i].equals("--out")) {
i++;
if (i < args.length) {
resultsFilename = args[i];
} else {
throw new BadUsageException("--out must be followed by a filename");
}
/*
} else if (args[i].equals("--outdir")) {
i++;
if (i < args.length) {
client.setResultsDir(new File(args[i]));
} else {
throw new BadUsageException("--outdir must be followed by a path");
}
*/
} else if (args[i].equals("--baseurl")) {
i++;
if (i < args.length) {
client.setBaseUrl(args[i]);
} else {
throw new BadUsageException("--baseurl must be followed by a URL");
}
} else if (args[i].equals("--test")) {
i++;
if (i < args.length) {
if (testFile == null) {
testFile = args[i];
} else {
throw new BadUsageException("only one test file permitted");
}
} else {
throw new BadUsageException("--test must be followed by a test filepath");
}
} else if (args[i].equals("--testsuite")) {
i++;
if (i < args.length) {
testSuite = args[i];
} else {
throw new BadUsageException("--testsuite must be followed by a testsuite filepath");
}
} else if (args[i].equals("--verbose") || args[i].equals("-v")) {
client.setVerbose(true);
} else if (args[i].equals("--help") || args[i].equals("-h")) {
printUsage();
System.exit(0);
} else {
throw new BadUsageException("Unknown parameter " + args[i]);
}
}
if (testFile == null && testSuite == null) {
throw new BadUsageException("No test or testsuite file specified");
} else if (testFile != null && testSuite != null) {
throw new BadUsageException("A test and testsuite file cannot both be specified");
}
Writer resultsWriter = null;
if (resultsFilename != null) {
resultsWriter = new FileWriter(resultsFilename);
} else /* if (client.resultsDir == null) */ {
resultsWriter = new OutputStreamWriter(System.out);
}
client.setResultsWriter(resultsWriter);
if (testFile != null) {
client.runTest(testFile);
} else {
client.runSuite(testSuite);
}
if (resultsWriter != null) resultsWriter.close();
} catch (BadUsageException e) {
System.err.println("Error: " + e.getMessage());
System.err.println();
printUsage();
System.exit(1);
} catch (Exception e) {
e.printStackTrace();
System.exit(1);
}
}
public void doGet(HttpServletRequest request, HttpServletResponse response)
throws IOException, ServletException {
try {
response.setHeader("Cache-Control", "no-cache");
response.setCharacterEncoding("UTF-8");
String task = request.getParameter("task");
Element data = null;
// process help request
if (request.getParameter("help") != null) data = getDescription(task);
// redirect to home page if there is no task
if (data == null && task == null) {
response.setContentType("text/html");
response
.getWriter()
.append(
"<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\"><html><head><meta http-equiv=\"REFRESH\" content=\"0;url="
+ context.getInitParameter("server_path")
+ "></head><body></body></html>");
return;
}
// process definition request
if (data == null && task.equals("define")) {
int id = resolveIntegerArg(request.getParameter("id"), -1);
int length = resolveIntegerArg(request.getParameter("length"), definer.getDefaultLength());
int format = resolveIntegerArg(request.getParameter("format"), definer.getDefaultFormat());
int maxImageWidth =
resolveIntegerArg(
request.getParameter("maxImageWidth"), definer.getDefaultMaxImageWidth());
int maxImageHeight =
resolveIntegerArg(
request.getParameter("maxImageHeight"), definer.getDefaultMaxImageHeight());
int linkDestination =
resolveIntegerArg(
request.getParameter("linkDestination"), definer.getDefaultLinkDestination());
boolean getImages = resolveBooleanArg(request.getParameter("getImages"), false);
data =
definer.getDefinition(
id, length, format, linkDestination, getImages, maxImageWidth, maxImageHeight);
}
// all of the remaining tasks require data to be cached, so lets make sure that is finished
// before continuing.
if (!cachingThread.isOk()) throw new ServletException("Could not cache wikipedia data");
double progress = cachingThread.getProgress();
if (data == null && (progress < 1 || task.equals("progress"))) {
// still caching up data, not ready to return a response yet.
data = doc.createElement("loading");
data.setAttribute("progress", df.format(progress));
task = "loading";
}
// process search request
if (data == null && task.equals("search")) {
String term = request.getParameter("term");
String id = request.getParameter("id");
int linkLimit =
resolveIntegerArg(request.getParameter("linkLimit"), searcher.getDefaultMaxLinkCount());
int senseLimit =
resolveIntegerArg(
request.getParameter("senseLimit"), searcher.getDefaultMaxSenseCount());
if (id == null) data = searcher.doSearch(term, linkLimit, senseLimit);
else data = searcher.doSearch(Integer.parseInt(id), linkLimit);
}
// process compare request
if (data == null && task.equals("compare")) {
String term1 = request.getParameter("term1");
String term2 = request.getParameter("term2");
int linkLimit =
resolveIntegerArg(request.getParameter("linkLimit"), comparer.getDefaultMaxLinkCount());
boolean details =
resolveBooleanArg(request.getParameter("details"), comparer.getDefaultShowDetails());
data = comparer.getRelatedness(term1, term2, details, linkLimit);
}
// process wikify request
if (data == null && task.equals("wikify")) {
if (this.wikifier == null)
throw new ServletException(
"Wikifier is not available. You must configure the servlet so that it has access to link detection and disambiguation models.");
String source = request.getParameter("source");
int sourceMode =
resolveIntegerArg(request.getParameter("sourceMode"), Wikifier.SOURCE_AUTODETECT);
String linkColor = request.getParameter("linkColor");
String baseColor = request.getParameter("baseColor");
double minProb =
resolveDoubleArg(
request.getParameter("minProbability"), wikifier.getDefaultMinProbability());
int repeatMode =
resolveIntegerArg(request.getParameter("repeatMode"), wikifier.getDefaultRepeatMode());
boolean showTooltips =
resolveBooleanArg(
request.getParameter("showTooltips"), wikifier.getDefaultShowTooltips());
String bannedTopics = request.getParameter("bannedTopics");
boolean wrapInXml = resolveBooleanArg(request.getParameter("wrapInXml"), true);
if (wrapInXml) {
data =
wikifier.wikifyAndWrapInXML(
source,
sourceMode,
minProb,
repeatMode,
bannedTopics,
baseColor,
linkColor,
showTooltips);
} else {
response.setContentType("text/html");
response
.getWriter()
.append(
wikifier.wikify(
source,
sourceMode,
minProb,
repeatMode,
bannedTopics,
baseColor,
linkColor,
showTooltips));
return;
}
}
if (data == null) throw new Exception("Unknown Task");
// wrap data
Element wrapper = doc.createElement("WikipediaMinerResponse");
wrapper.setAttribute("server_path", context.getInitParameter("server_path"));
wrapper.setAttribute("service_name", context.getInitParameter("service_name"));
wrapper.appendChild(data);
data = wrapper;
// Transform or serialize xml data as appropriate
Transformer tf = null;
if (request.getParameter("xml") == null) {
// we need to transform the data into html
tf = transformersByName.get(task);
if (request.getParameter("help") != null) tf = transformersByName.get("help");
}
if (tf == null) {
// we need to serialize the data as xml
tf = transformersByName.get("serializer");
response.setContentType("application/xml");
} else {
// output will be transformed to html
response.setContentType("text/html");
response
.getWriter()
.append(
"<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01//EN\" \"http://www.w3.org/TR/html4/strict.dtd\">\n");
}
tf.transform(new DOMSource(data), new StreamResult(response.getWriter()));
} catch (Exception error) {
response.reset();
response.setContentType("application/xml");
response.setHeader("Cache-Control", "no-cache");
response.setCharacterEncoding("UTF8");
Element xmlError = doc.createElement("Error");
if (error.getMessage() != null) xmlError.setAttribute("message", error.getMessage());
Element xmlStackTrace = doc.createElement("StackTrace");
xmlError.appendChild(xmlStackTrace);
for (StackTraceElement ste : error.getStackTrace()) {
Element xmlSte = doc.createElement("StackTraceElement");
xmlSte.setAttribute("message", ste.toString());
xmlStackTrace.appendChild(xmlSte);
}
try {
transformersByName
.get("serializer")
.transform(new DOMSource(xmlError), new StreamResult(response.getWriter()));
} catch (Exception e) {
// TODO: something for when an error is thrown processing an error????
}
;
}
}
/**
* Format this XML data as a String.
*
* @webref xml:method
* @brief Formats XML data as a String
* @param indent -1 for a single line (and no declaration), >= 0 for indents and newlines
* @return the content
* @see XML#toString()
*/
public String format(int indent) {
try {
// entities = doctype.getEntities()
boolean useIndentAmount = false;
TransformerFactory factory = TransformerFactory.newInstance();
if (indent != -1) {
try {
factory.setAttribute("indent-number", indent);
} catch (IllegalArgumentException e) {
useIndentAmount = true;
}
}
Transformer transformer = factory.newTransformer();
// Add the XML declaration at the top if this node is the root and we're
// not writing to a single line (indent = -1 means single line).
if (indent == -1 || parent == null) {
transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
} else {
transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "no");
}
// transformer.setOutputProperty(OutputKeys.DOCTYPE_SYSTEM, "sample.dtd");
transformer.setOutputProperty(OutputKeys.METHOD, "xml");
// transformer.setOutputProperty(OutputKeys.CDATA_SECTION_ELEMENTS, "yes"); // huh?
// transformer.setOutputProperty(OutputKeys.DOCTYPE_PUBLIC,
// "-//W3C//DTD XHTML 1.0 Transitional//EN");
// transformer.setOutputProperty(OutputKeys.DOCTYPE_SYSTEM,
// "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd");
// For Android, because (at least 2.3.3) doesn't like indent-number
if (useIndentAmount) {
transformer.setOutputProperty(
"{http://xml.apache.org/xslt}indent-amount", String.valueOf(indent));
}
// transformer.setOutputProperty(OutputKeys.ENCODING,"ISO-8859-1");
// transformer.setOutputProperty(OutputKeys.ENCODING,"UTF8");
transformer.setOutputProperty(OutputKeys.ENCODING, "UTF-8");
// transformer.setOutputProperty(OutputKeys.CDATA_SECTION_ELEMENTS
// Always indent, otherwise the XML declaration will just be jammed
// onto the first line with the XML code as well.
transformer.setOutputProperty(OutputKeys.INDENT, "yes");
// Properties p = transformer.getOutputProperties();
// for (Object key : p.keySet()) {
// System.out.println(key + " -> " + p.get(key));
// }
// If you smell something, that's because this code stinks. No matter
// the settings of the Transformer object, if the XML document already
// has whitespace elements, it won't bother re-indenting/re-formatting.
// So instead, transform the data once into a single line string.
// If indent is -1, then we're done. Otherwise re-run and the settings
// of the factory will kick in. If you know a better way to do this,
// please contribute. I've wasted too much of my Sunday on it. But at
// least the Giants are getting blown out by the Falcons.
final String decl = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>";
final String sep = System.getProperty("line.separator");
StringWriter tempWriter = new StringWriter();
StreamResult tempResult = new StreamResult(tempWriter);
transformer.transform(new DOMSource(node), tempResult);
String[] tempLines = PApplet.split(tempWriter.toString(), sep);
// PApplet.println(tempLines);
if (tempLines[0].startsWith("<?xml")) {
// Remove XML declaration from the top before slamming into one line
int declEnd = tempLines[0].indexOf("?>") + 2;
// if (tempLines[0].length() == decl.length()) {
if (tempLines[0].length() == declEnd) {
// If it's all the XML declaration, remove it
// PApplet.println("removing first line");
tempLines = PApplet.subset(tempLines, 1);
} else {
// PApplet.println("removing part of first line");
// If the first node has been moved to this line, be more careful
// tempLines[0] = tempLines[0].substring(decl.length());
tempLines[0] = tempLines[0].substring(declEnd);
}
}
String singleLine = PApplet.join(PApplet.trim(tempLines), "");
if (indent == -1) {
return singleLine;
}
// Might just be whitespace, which won't be valid XML for parsing below.
// https://github.com/processing/processing/issues/1796
// Since indent is not -1, that means they want valid XML,
// so we'll give them the single line plus the decl... Lame? sure.
if (singleLine.trim().length() == 0) {
// You want whitespace? I've got your whitespace right here.
return decl + sep + singleLine;
}
// Since the indent is not -1, bring back the XML declaration
// transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "no");
StringWriter stringWriter = new StringWriter();
StreamResult xmlOutput = new StreamResult(stringWriter);
// DOMSource source = new DOMSource(node);
Source source = new StreamSource(new StringReader(singleLine));
transformer.transform(source, xmlOutput);
String outgoing = stringWriter.toString();
// Add the XML declaration to the top if it's not there already
if (outgoing.startsWith(decl)) {
int declen = decl.length();
int seplen = sep.length();
if (outgoing.length() > declen + seplen
&& !outgoing.substring(declen, declen + seplen).equals(sep)) {
// make sure there's a line break between the XML decl and the code
return outgoing.substring(0, decl.length()) + sep + outgoing.substring(decl.length());
}
return outgoing;
} else {
return decl + sep + outgoing;
}
} catch (Exception e) {
e.printStackTrace();
}
return null;
}
public void run() {
// String a =
// "http://neuromorpho.org/neuroMorpho/dableFiles/borst/CNG%20version/dCH-cobalt.CNG.swc"; //
// For developer use
if (myArgs.length == 0) {
String usage =
"\nError, missing SWC file containing morphology!\n\nUsage: \n java -cp build cvapp.main swc_file [-test]"
+ "\n or:\n ./run.sh swc_file ["
+ TEST_FLAG
+ "|"
+ TEST_NOGUI_FLAG
+ "|"
+ NEUROML1_EXPORT_FLAG
+ "|"
+ NEUROML2_EXPORT_FLAG
+ "]\n\n"
+ "where swc_file is the file name or URL of the SWC morphology file\n";
System.out.println(usage);
System.exit(0);
}
String a = myArgs[0];
File baseDir = new File(".");
if ((new File(a)).exists()) {
baseDir = (new File(a)).getParentFile();
}
try {
File root =
new File(main.class.getProtectionDomain().getCodeSource().getLocation().toURI().getPath())
.getParentFile();
if (!a.startsWith("http://") && !a.startsWith("file://")) {
a = "file://" + (new File(a)).getCanonicalPath();
}
boolean supressGui = false;
if (myArgs.length == 2
&& (myArgs[1].equals(TEST_NOGUI_FLAG)
|| myArgs[1].equals(NEUROML1_EXPORT_FLAG)
|| myArgs[1].equals(NEUROML2_EXPORT_FLAG))) {
supressGui = true;
}
neuronEditorFrame nef = null;
nef = new neuronEditorFrame(700, 600, supressGui);
// nef.validate();
nef.pack();
centerWindow(nef);
nef.setVisible(!supressGui);
nef.setReadWrite(true, true);
int indexof = a.lastIndexOf('/') + 1;
String directory = a.substring(0, indexof);
String fileName = a.substring(indexof, a.length());
URL u = new URL(a);
String sdata[] = readStringArrayFromURL(u);
nef.setTitle("3DViewer (Modified from CVAPP with permission)-Neuron: " + fileName);
nef.loadFile(sdata, directory, fileName);
System.out.println("Loaded: " + fileName);
if (myArgs.length == 2 && myArgs[1].equals(TEST_ONE_FLAG)) {
// Thread.sleep(1000);
doTests(nef, fileName);
} else if (myArgs.length == 2 && myArgs[1].equals(NEUROML1_EXPORT_FLAG)) {
File rootFile = (new File(baseDir, fileName)).getAbsoluteFile();
String nml1FileName =
rootFile.getName().endsWith(".swc")
? rootFile.getName().substring(0, rootFile.getName().length() - 4) + ".xml"
: rootFile.getName() + ".xml";
File nml1File = new File(rootFile.getParentFile(), nml1FileName);
neuronEditorPanel nep = nef.getNeuronEditorPanel();
nep.writeStringToFile(nep.getCell().writeNeuroML_v1_8_1(), nml1File.getAbsolutePath());
System.out.println(
"Saved NeuroML representation of the file to: "
+ nml1File.getAbsolutePath()
+ ": "
+ nml1File.exists());
File v1schemaFile = new File(root, "Schemas/v1.8.1/Level3/NeuroML_Level3_v1.8.1.xsd");
validateXML(nml1File, v1schemaFile);
System.exit(0);
} else if (myArgs.length == 2 && myArgs[1].equals(NEUROML2_EXPORT_FLAG)) {
File rootFile = (new File(baseDir, fileName)).getAbsoluteFile();
String nml2FileName =
rootFile.getName().endsWith(".swc")
? rootFile.getName().substring(0, rootFile.getName().length() - 4) + ".cell.nml"
: rootFile.getName() + ".cell.nml";
if (Character.isDigit(nml2FileName.charAt(0))) {
nml2FileName = "Cell_" + nml2FileName;
}
File nml2File = new File(rootFile.getParentFile(), nml2FileName);
neuronEditorPanel nep = nef.getNeuronEditorPanel();
nep.writeStringToFile(nep.getCell().writeNeuroML_v2beta(), nml2File.getAbsolutePath());
System.out.println(
"Saved the NeuroML representation of the file to: "
+ nml2File.getAbsolutePath()
+ ": "
+ nml2File.exists());
validateXML(nml2File, new File(root, "Schemas/v2/NeuroML_v2beta4.xsd"));
System.exit(0);
} else if (myArgs.length == 2
&& (myArgs[1].equals(TEST_FLAG) || (myArgs[1].equals(TEST_NOGUI_FLAG)))) {
// Thread.sleep(1000);
doTests(nef, fileName);
File exampleDir = new File("twoCylSwc");
for (File f : exampleDir.listFiles()) {
if (f.getName().endsWith(".swc")) {
sdata = fileString.readStringArrayFromFile(f.getAbsolutePath());
nef.setTitle("3DViewer (Modified from CVAPP with permission)-Neuron: " + f.getName());
nef.loadFile(sdata, f.getParent(), f.getName());
doTests(nef, f.getAbsolutePath());
}
}
exampleDir = new File("spherSomaSwc");
for (File f : exampleDir.listFiles()) {
if (f.getName().endsWith(".swc")) {
sdata = fileString.readStringArrayFromFile(f.getAbsolutePath());
nef.setTitle("3DViewer (Modified from CVAPP with permission)-Neuron: " + f.getName());
nef.loadFile(sdata, f.getParent(), f.getName());
doTests(nef, f.getAbsolutePath());
}
}
exampleDir = new File("caseExamples");
for (File f : exampleDir.listFiles()) {
if (f.getName().endsWith(".swc")) {
sdata = fileString.readStringArrayFromFile(f.getAbsolutePath());
nef.setTitle("3DViewer (Modified from CVAPP with permission)-Neuron: " + f.getName());
nef.loadFile(sdata, f.getParent(), f.getName());
doTests(nef, f.getAbsolutePath());
}
}
if (supressGui) System.exit(0);
}
} catch (Exception exception) {
System.err.println("Error while handling SWC file (" + a + ")");
exception.printStackTrace();
}
}
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 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();
}
}