private ClassLoaderStrategy getClassLoaderStrategy(String fullyQualifiedClassName)
throws Exception {
try {
// Get just the package name
StringBuffer sb = new StringBuffer(fullyQualifiedClassName);
sb.delete(sb.lastIndexOf("."), sb.length());
currentPackage = sb.toString();
// Retrieve the Java classpath from the system properties
String cp = System.getProperty("java.class.path");
String sepChar = System.getProperty("path.separator");
String[] paths = StringUtils.pieceList(cp, sepChar.charAt(0));
ClassLoaderStrategy cl =
ClassLoaderUtil.getClassLoader(ClassLoaderUtil.FILE_SYSTEM_CLASS_LOADER, new String[] {});
// Iterate through paths until class with the specified name is found
String classpath = StringUtils.replaceChar(currentPackage, '.', File.separatorChar);
for (int i = 0; i < paths.length; i++) {
Class[] classes = cl.getClasses(paths[i] + File.separatorChar + classpath, currentPackage);
for (int j = 0; j < classes.length; j++) {
if (classes[j].getName().equals(fullyQualifiedClassName)) {
return ClassLoaderUtil.getClassLoader(
ClassLoaderUtil.FILE_SYSTEM_CLASS_LOADER, new String[] {paths[i]});
}
}
}
throw new Exception("Class could not be found.");
} catch (Exception e) {
System.err.println("Exception creating class loader strategy.");
System.err.println(e.getMessage());
throw e;
}
}
// ## 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);
}
// #]
}
private static SAXParserFactory createFastSAXParserFactory()
throws ParserConfigurationException, SAXException {
if (fastParserFactoryClass == null) {
try {
fastParserFactoryClass =
Class.forName("org.apache.crimson.jaxp.SAXParserFactoryImpl"); // NOI18N
} catch (Exception ex) {
useFastSAXParserFactory = false;
if (System.getProperty("java.version").startsWith("1.4")) { // NOI18N
ErrorManager.getDefault().notify(ErrorManager.INFORMATIONAL, ex);
}
}
}
if (fastParserFactoryClass != null) {
try {
SAXParserFactory factory = (SAXParserFactory) fastParserFactoryClass.newInstance();
return factory;
} catch (Exception ex) {
useFastSAXParserFactory = false;
throw new ParserConfigurationException(ex.getMessage());
}
}
return SAXParserFactory.newInstance();
}
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);
}
// #]
}
// ## 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);
}
// #]
}
public static List<GenerationTarget> getTargets() {
if (m_targets != null) {
return m_targets;
}
m_targets = new ArrayList<GenerationTarget>();
URL location = getClassLocation();
if (location == null) return m_targets;
if (location.getProtocol().equals("file")) {
String encoded = location.getFile();
File classFileLocation = null;
try {
String decoded = URLDecoder.decode(encoded, "UTF-8"); // important
classFileLocation = new File(decoded);
} catch (UnsupportedEncodingException ex) {
ex.printStackTrace();
} // end try
if (classFileLocation != null) {
File root = classFileLocation;
String classname = GenerationTarget.class.getName();
int levels = countNbChars(classname, '.');
// iterate to the root
for (int i = 0; i < levels; i++) {
root = root.getParentFile();
} // end while
scanFolder(classFileLocation.getParentFile(), root, m_targets);
}
} else if (location.getProtocol().equals("jar")) {
String jarname = location.toExternalForm();
int index = jarname.indexOf(".jar!");
if (index > -1) jarname = jarname.substring(0, index + 4);
index = jarname.indexOf("jar:");
if (index > -1) {
jarname = jarname.substring(4);
}
index = jarname.indexOf("file:/");
if (index > -1) {
jarname = jarname.substring(6);
}
index = jarname.indexOf("file:");
if (index > -1) {
jarname = jarname.substring(5);
}
scanJar(new File(jarname), new File(System.getProperty("java.io.tmpdir")), m_targets);
}
return m_targets;
}
// ## 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);
}
}
// #]
}
@Test
public void parseRootElementWithFile() throws Exception {
String xml =
"<?xml version=\"1.0\"?><html><head /><body><p>Good morning</p><p>How are you?</p></body></html>";
File f = new File(System.getProperty("java.io.tmpdir"), "test.xml");
Utils.writeFile(f, xml);
f.deleteOnExit();
DocumentBuilder builder = builderFactory.newDocumentBuilder();
Document doc = builder.parse(f);
Element root = doc.getDocumentElement();
Assert.assertEquals("html", root.getNodeName());
}
public String toString() {
String endl = System.getProperty("line.separator");
String str = "";
if (numRunningJobs != -1) {
str += "running jobs: " + numRunningJobs + endl;
}
if (numWaitingJobs != -1) {
str += "waiting jobs: " + numWaitingJobs + endl;
}
if (usedProcessors != -1) {
str += "used processors: " + usedProcessors + endl;
}
return str;
}
@Test
public void testgetAttributesWithNamedNodeMap() throws Exception {
// builderFactory = DocumentBuilderFactory.newInstance();
builderFactory.setNamespaceAware(true);
File f = new File(System.getProperty("user.dir"), "src/test/resources/sample-springbeans.xml");
DocumentBuilder builder = builderFactory.newDocumentBuilder();
Document doc = builder.parse(f);
Element root = doc.getDocumentElement();
// System.out.println("* current impl: " + doc.getClass().getName());
// id, class
Map<String, String> actualMap = new HashMap<String, String>();
NodeList list = root.getChildNodes();
for (int i = 0; i < list.getLength(); i++) {
Node node = list.item(i);
if (node instanceof Element) {
Element elem = (Element) node;
if (elem.getTagName().equals("beans:bean")) {
// System.out.println("bean[" + elem.getAttribute("id") + "]");
NamedNodeMap map = elem.getAttributes();
String valueId = null;
String valueClass = null;
for (int x = 0; x < map.getLength(); x++) {
Node attr = map.item(x);
if (attr.getNodeName().equals("id")) valueId = attr.getNodeValue();
if (attr.getNodeName().equals("class")) valueClass = attr.getNodeValue();
}
if (valueId != null && valueClass != null) actualMap.put(valueId, valueClass);
}
}
}
Map<String, String> expected = new HashMap<String, String>();
expected.put("authenticationManager", "org.springframework.security.providers.ProviderManager");
expected.put(
"daoAuthenticationProvider",
"org.springframework.security.providers.dao.DaoAuthenticationProvider");
expected.put(
"loggerListener", "org.springframework.security.event.authentication.LoggerListener");
Assert.assertEquals("Attributes with NamedNodeMap", expected, actualMap);
}
/** Initialize the GUI */
private void initGUI() {
counts theApp_new_counts = new counts();
String sysPath =
System.getProperty("user.home") + File.separator + "SRSCKT" + File.separator + "pkg";
File sysDir = new File(sysPath);
// if our system folder doesn't exist it creates it
if (!sysDir.exists()) sysDir.mkdirs();
String[] SysPkgs = sysDir.list();
for (String x : SysPkgs) {
System.out.println(x);
package_cls defaultPkgs =
new package_cls(
x, theApp_new_counts, 1); // sysCall is 1 as System Packages will be installed
}
connections theApp_new_connections = new connections();
this.setFrame(theApp_new_counts, theApp_new_connections);
this.setPath(null);
this.setSaved(false); // default false
}
// ## operation Chemkin(double,double,String)
public Chemkin(double p_rtol, double p_atol, String p_reactorType) {
// #[ operation Chemkin(double,double,String)
if (p_rtol < 0 || p_atol < 0)
throw new InvalidChemkinParameterException("Negative rtol or atol!");
if (p_reactorType == null) throw new NullPointerException();
String dir = System.getProperty("RMG.workingDirectory");
// create the documentTypesDefinitions
File docFile = new File("chemkin/documentTypeDefinitions");
docFile.mkdir();
copyFiles(
dir + "/software/reactorModel/documentTypeDefinitions/reactorInput.dtd",
"chemkin/documentTypeDefinitions/reactorInput.dtd");
copyFiles(
dir + "/software/reactorModel/documentTypeDefinitions/reactorOutput.dtd",
"chemkin/documentTypeDefinitions/reactorOutput.dtd");
rtol = p_rtol;
atol = p_atol;
reactorType = p_reactorType;
}
// ## 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;
}
// #]
}
public static void main(String[] args) {
String specloc = System.getProperty("spec");
if (specloc == null) {
System.out.print("No spec file given, quitting");
System.exit(0);
}
DateFormat dateFormat = new SimpleDateFormat("yyyy/MM/dd HH:mm:ss z");
java.util.Date date = new java.util.Date();
String startstamp = dateFormat.format(date);
boolean firstrun = true;
while (true) {
System.out.println("Loading XML Spec file: " + specloc);
// BufferedWriter out = null;
SocketAcceptor acceptor = null;
SocketAcceptor statusacceptor = null;
Vector<MonitorThread> monitorlist = new Vector<MonitorThread>();
try {
DocumentBuilderFactory docBuilderFactory = DocumentBuilderFactory.newInstance();
DocumentBuilder docBuilder = docBuilderFactory.newDocumentBuilder();
Document doc = docBuilder.parse(new File(specloc));
doc.getDocumentElement().normalize();
String heartbeatportString = doc.getDocumentElement().getAttribute("heartbeatport");
String statusportString = doc.getDocumentElement().getAttribute("statusport");
String logfiledir = doc.getDocumentElement().getAttribute("logfiledir");
String masterlabel = doc.getDocumentElement().getAttribute("label");
String nodeid = doc.getDocumentElement().getAttribute("id");
String smtphost = doc.getDocumentElement().getAttribute("smtphost");
String l1mailto = doc.getDocumentElement().getAttribute("l1mailto");
String l2mailto = doc.getDocumentElement().getAttribute("l2mailto");
String l2threshold = doc.getDocumentElement().getAttribute("l2threshold");
if (heartbeatportString == null || heartbeatportString.equals("")) {
System.out.println("No heartbeat specified in spec, quitting");
System.exit(0);
}
if (statusportString == null || statusportString.equals("")) {
System.out.println("No status port specified in spec, quitting");
System.exit(0);
}
if (logfiledir == null || logfiledir.equals("")) {
System.out.println("No logfile directory location specified in spec, quitting");
System.exit(0);
}
int heartbeatport = Integer.valueOf(heartbeatportString).intValue();
System.out.println("This Monitor is using port " + heartbeatport + " for heartbeat");
int statusport = Integer.valueOf(statusportString).intValue();
System.out.println("This Monitor is using port " + statusport + " for status updates");
System.out.println("Logging to directory " + logfiledir);
Log log = new Log(logfiledir);
log.nodelabel = masterlabel;
log.setMailer(smtphost, l1mailto, l2mailto, convertStringToInt(l2threshold));
if (firstrun) {
firstrun = false;
log.logit("Monitor Node Started", "start", null);
}
log.logit("Logging started", "", null);
ThreadPing threadping = new ThreadPing(log, false);
Thread pinger = new Thread(threadping);
threadping.thisThread = pinger;
pinger.start();
log.pinger = threadping;
// ShutdownHook hook = new ShutdownHook(out);
// Runtime.getRuntime().addShutdownHook(hook);
// Starting Heartbeat server
acceptor = new NioSocketAcceptor();
acceptor.getSessionConfig().setReuseAddress(true);
acceptor.getSessionConfig().setTcpNoDelay(true);
acceptor.setReuseAddress(true);
// acceptor.getFilterChain().addLast("logger", new LoggingFilter());
acceptor
.getFilterChain()
.addLast(
"codec",
new ProtocolCodecFilter(new TextLineCodecFactory(Charset.forName("UTF-8"))));
acceptor.setReuseAddress(true);
// acceptor.setCloseOnDeactivation(true);
acceptor.getSessionConfig().setTcpNoDelay(true);
acceptor.setDefaultLocalAddress(new InetSocketAddress(heartbeatport));
Vector<IoSession> sessionlist = new Vector<IoSession>();
acceptor.setHandler(new HeartBeatHandler(sessionlist));
acceptor.bind();
// Starting Path Monitoring
NodeList listOfServers = doc.getElementsByTagName("check");
int totalServers = listOfServers.getLength();
System.out.println("Total # of checks: " + totalServers);
// Vector<PingMonitorThread> pinglist = new Vector<PingMonitorThread>();
// Vector<PortMonitorThread> portlist = new Vector<PortMonitorThread>();
// Vector<HeartbeatMonitorThread> heartbeatlist = new Vector<HeartbeatMonitorThread>();
System.out.println();
for (int i = 0; i < totalServers; i++) {
Node serverNode = listOfServers.item(i);
Element serverNodeElement = (Element) serverNode;
String checklabel = serverNodeElement.getAttribute("label");
String host =
serverNodeElement
.getElementsByTagName("host")
.item(0)
.getChildNodes()
.item(0)
.getNodeValue();
String checktype =
serverNodeElement
.getElementsByTagName("checktype")
.item(0)
.getChildNodes()
.item(0)
.getNodeValue();
boolean enabled = true;
if (serverNodeElement.getElementsByTagName("enabled").item(0) != null
&& serverNodeElement
.getElementsByTagName("enabled")
.item(0)
.getChildNodes()
.item(0)
.getNodeValue()
.toLowerCase()
.equals("false")) {
enabled = false;
}
String successrateString =
serverNodeElement
.getElementsByTagName("successrate")
.item(0)
.getChildNodes()
.item(0)
.getNodeValue();
String retryrateString =
serverNodeElement
.getElementsByTagName("retryrate")
.item(0)
.getChildNodes()
.item(0)
.getNodeValue();
// String l2thresholdoverride =
// serverNodeElement.getElementsByTagName("l2threshold").item(0).getChildNodes().item(0).getNodeValue();
String l2thresholdoverride = getElementValue("l2threshold", serverNodeElement);
// String l1mailtoadd =
// serverNodeElement.getElementsByTagName("l1mailto").item(0).getChildNodes().item(0).getNodeValue();
String l1mailtoadd = getElementValue("l1mailto", serverNodeElement);
// String l2mailtoadd =
// serverNodeElement.getElementsByTagName("l2mailto").item(0).getChildNodes().item(0).getNodeValue();
String l2mailtoadd = getElementValue("l2mailto", serverNodeElement);
int l2thresholdoverrideint = convertStringToInt(l2thresholdoverride);
String[] l1mailtoaddarray = new String[0];
String[] l2mailtoaddarray = new String[0];
if (!l1mailtoadd.equals("")) {
l1mailtoaddarray = l1mailtoadd.split(",");
}
if (!l2mailtoadd.equals("")) {
l2mailtoaddarray = l2mailtoadd.split(",");
}
// System.out.println(l1mailtoaddarray.length + "-" + l2mailtoaddarray.length);
int successrate = 30;
int retryrate = 30;
if (host == null || host.equals("")) {
System.out.println("No Host, skipping this path");
enabled = false;
}
if (successrateString == null || successrateString.equals("")) {
System.out.println(
"No Success Rate defined, using default (" + successrate + " seconds)");
} else {
successrate = Integer.valueOf(successrateString).intValue();
}
if (retryrateString == null || retryrateString.equals("")) {
System.out.println("No retry rate defined, using default (" + retryrate + " seconds)");
} else {
retryrate = Integer.valueOf(retryrateString).intValue();
}
System.out.println(checklabel);
if (checktype.equals("heartbeat")) {
String portString =
serverNodeElement
.getElementsByTagName("port")
.item(0)
.getChildNodes()
.item(0)
.getNodeValue();
if (portString == null || portString.equals("")) {
System.out.println("No Heartbeat, skipping this path");
} else {
int heartbeat = Integer.valueOf(portString).intValue();
System.out.println("Starting Heartbeat Check:");
System.out.println("Host: " + host);
System.out.println("Port: " + heartbeat);
System.out.println();
HeartbeatMonitorThread m =
new HeartbeatMonitorThread(
host, heartbeat, log, successrate, retryrate, checklabel);
m.setAlertOverride(l2thresholdoverrideint, l1mailtoaddarray, l2mailtoaddarray);
Thread t = new Thread(m);
m.thisthread = t;
if (enabled) {
t.start();
log.logit(
"Starting Heartbeat Check - " + host + ":" + heartbeat,
"enable-" + successrate + "-" + retryrate,
m.getStatus());
} else {
log.logit(
"Heartbeat Check - " + host + ":" + heartbeat + " Disabled on start",
"disable",
m.getStatus());
}
monitorlist.add(m);
}
} else if (checktype.equals("ping")) {
System.out.println("Starting Ping Check:");
System.out.println("Host: " + host);
System.out.println();
PingMonitorThread m =
new PingMonitorThread(host, log, successrate, retryrate, checklabel);
m.setAlertOverride(l2thresholdoverrideint, l1mailtoaddarray, l2mailtoaddarray);
Thread t = new Thread(m);
m.thisthread = t;
if (enabled) {
t.start();
log.logit(
"Starting Ping Check - " + host,
"enable-" + successrate + "-" + retryrate,
m.getStatus());
} else {
log.logit("Ping Check - " + host + " Disabled on start", "disable", m.getStatus());
}
monitorlist.add(m);
} else if (checktype.equals("port")) {
String portString =
serverNodeElement
.getElementsByTagName("port")
.item(0)
.getChildNodes()
.item(0)
.getNodeValue();
if (portString == null || portString.equals("")) {
System.out.println("No Port Given, skipping");
} else {
int heartbeat = Integer.valueOf(portString).intValue();
System.out.println("Starting Port Check:");
System.out.println("Host: " + host);
System.out.println("Port: " + heartbeat);
System.out.println();
PortMonitorThread m =
new PortMonitorThread(host, heartbeat, log, successrate, retryrate, checklabel);
m.setAlertOverride(l2thresholdoverrideint, l1mailtoaddarray, l2mailtoaddarray);
Thread t = new Thread(m);
m.thisthread = t;
if (enabled) {
t.start();
log.logit(
"Starting Port Check - " + host + ":" + heartbeat,
"enable-" + successrate + "-" + retryrate,
m.getStatus());
} else {
log.logit(
"Port Check - " + host + ":" + heartbeat + " Disabled on start",
"disable",
m.getStatus());
}
monitorlist.add(m);
}
}
}
statusacceptor = new NioSocketAcceptor();
statusacceptor.setReuseAddress(true);
// statusacceptor.getFilterChain().addLast("logger", new LoggingFilter());
statusacceptor.getSessionConfig().setTcpNoDelay(true);
statusacceptor.getSessionConfig().setKeepAlive(true);
statusacceptor.getSessionConfig().setBothIdleTime(5);
statusacceptor.getSessionConfig().setReaderIdleTime(5);
statusacceptor.getSessionConfig().setWriteTimeout(5);
// statusacceptor.setReuseAddress(true);
statusacceptor.setCloseOnDeactivation(true);
statusacceptor.setDefaultLocalAddress(new InetSocketAddress(statusport));
statusacceptor.setHandler(
new StatusHttpProtocolHandler(
monitorlist,
acceptor,
statusacceptor,
log,
masterlabel,
nodeid,
sessionlist,
startstamp));
statusacceptor.bind();
System.out.println("Status Listener activated...");
} catch (Exception e) {
e.printStackTrace();
try {
// out.flush();
// out.close();
} catch (Exception e2) {
}
try {
Thread.sleep(30000);
} catch (Exception e3) {
}
}
for (int x = 0; x < monitorlist.size(); x++) {
if (monitorlist.get(x).getThisThread() != null) {
try {
monitorlist.get(x).getThisThread().join();
} catch (Exception e) {
}
}
}
if (acceptor != null) {
while (acceptor.isActive() || !acceptor.isDisposed()) {
try {
Thread.sleep(1000);
} catch (Exception e) {
}
}
}
if (statusacceptor != null) {
while (statusacceptor.isActive() || !statusacceptor.isDisposed()) {
try {
Thread.sleep(1000);
} catch (Exception e) {
}
}
}
System.out.println("Main thread has reached end, reloading...");
/*
try
{
Thread.sleep(9999999);
}
catch (Exception e)
{
e.printStackTrace();
}
*/
}
}
/**
* This class wrapps WikiTableWriter
*
* @author shahzad bhatti
* <p>modification history date who what 1/9/06 SB created.
*/
public class WikiTableWriter implements ExtendedHierarchicalStreamWriter {
private final PointableWriter writer;
private final FastStack elementStack = new FastStack(16);
private final char[] lineIndenter;
private boolean useLineSeparateBetweenTags;
private boolean tagInProgress;
private int startPointer;
private int depth;
private boolean readyForNewLine;
private boolean tagIsEmpty;
private boolean quickNodeValue;
private boolean lastTagHadAttributes;
private static final char[] AMP = "&".toCharArray();
private static final char[] LT = "<".toCharArray();
private static final char[] GT = ">".toCharArray();
private static final char[] SLASH_R = "
".toCharArray();
private static final char[] QUOT = """.toCharArray();
private static final char[] APOS = "'".toCharArray();
private static final char[] CLOSE = "</".toCharArray();
private static final String LF = System.getProperty("line.separator");
/**
* WikiTableWriter constructor
*
* @param writer - output writer object
* @param lineIdenter - indentation
*/
public WikiTableWriter(Writer writer, char[] lineIndenter) {
this.writer = new PointableWriter(writer);
this.lineIndenter = lineIndenter;
this.useLineSeparateBetweenTags =
true; // context.getConfig().getBoolean("testplayer.fitnesse.use.line.separator.between.tags", true);
}
/**
* WikiTableWriter constructor
*
* @param writer - output writer object
* @param lineIdenter - indentation
*/
public WikiTableWriter(Writer writer, String lineIndenter) {
this(writer, lineIndenter.toCharArray());
}
/**
* WikiTableWriter constructor
*
* @param writer - print writer object
*/
public WikiTableWriter(PrintWriter writer) {
this(writer, new char[] {'|'});
}
/**
* WikiTableWriter constructor
*
* @param writer - writer object
*/
public WikiTableWriter(Writer writer) {
this(new PrintWriter(writer));
}
/**
* Marks start of XML node
*
* @param name - name of node
*/
public void startNode(String name, Class clazz) {
startNode(name);
}
public void startNode(String name) {
startPointer = writer.getPointer();
quickNodeValue = false;
lastTagHadAttributes = false;
tagIsEmpty = false;
finishTag();
if (depth != 0) writer.write(LF);
writer.write(
WikiTableDriver.DELIM
+ WikiTableDriver.QUOTES
+ WikiTableDriver.START_NODE
+ WikiTableDriver.QUOTES
+ WikiTableDriver.DELIM);
if (this.useLineSeparateBetweenTags) {
writer.write(LF + WikiTableDriver.DELIM);
}
writer.write(name + WikiTableDriver.DELIM);
elementStack.push(name);
tagInProgress = true;
depth++;
readyForNewLine = true;
tagIsEmpty = true;
}
/**
* Stores value of previously defined XML node
*
* @param text - value of node
*/
public void setValue(String text) {
readyForNewLine = false;
tagIsEmpty = false;
finishTag();
if (lastTagHadAttributes) {
writer.write(
LF
+ WikiTableDriver.DELIM
+ WikiTableDriver.QUOTES
+ WikiTableDriver.SET_VALUE
+ WikiTableDriver.QUOTES
+ WikiTableDriver.DELIM);
quickNodeValue = false;
} else {
String startTag =
StringHelper.replace(
writer.substring(startPointer),
WikiTableDriver.START_NODE,
WikiTableDriver.SET_NODE_VALUE);
if (this.useLineSeparateBetweenTags) {
writer.write(LF + WikiTableDriver.DELIM);
}
writer.setPointer(startPointer);
writer.write(startTag);
quickNodeValue = true;
}
writeText(writer, text);
writer.write(WikiTableDriver.DELIM);
}
/**
* Adds attribute for XML node
*
* @param key - name of attribute
* @param value - value of attribute
*/
public void addAttribute(String key, String value) {
writer.write(
LF
+ WikiTableDriver.DELIM
+ WikiTableDriver.QUOTES
+ WikiTableDriver.ADD_ATTRIBUTE
+ WikiTableDriver.QUOTES
+ WikiTableDriver.DELIM);
if (this.useLineSeparateBetweenTags) {
writer.write(LF + WikiTableDriver.DELIM);
}
writer.write(key + WikiTableDriver.DELIM);
writeAttributeValue(writer, value);
writer.write(WikiTableDriver.DELIM);
lastTagHadAttributes = true;
}
/** Marks end of node */
public void endNode() {
depth--;
if (tagIsEmpty) {
String prevTag = (String) elementStack.pop(); // Silently();
if (!quickNodeValue) {
writer.write(
LF
+ WikiTableDriver.DELIM
+ WikiTableDriver.QUOTES
+ WikiTableDriver.END_NODE
+ WikiTableDriver.QUOTES
+ WikiTableDriver.DELIM);
if (this.useLineSeparateBetweenTags) {
writer.write(LF + WikiTableDriver.DELIM);
}
writer.write(prevTag + WikiTableDriver.DELIM);
}
readyForNewLine = false;
} else {
String prevTag = (String) elementStack.pop();
if (!quickNodeValue) {
writer.write(
LF
+ WikiTableDriver.DELIM
+ WikiTableDriver.QUOTES
+ WikiTableDriver.END_NODE
+ WikiTableDriver.QUOTES
+ WikiTableDriver.DELIM);
if (this.useLineSeparateBetweenTags) {
writer.write(LF + WikiTableDriver.DELIM);
}
writer.write(prevTag + WikiTableDriver.DELIM);
}
}
finishTag();
readyForNewLine = true;
if (depth == 0) {
writer.flush();
}
quickNodeValue = false;
}
/** Flushes output */
public void flush() {
writer.flush();
}
/** Closes output */
public void close() {
writer.close();
}
/** Returns underlying writer */
public HierarchicalStreamWriter underlyingWriter() {
return this;
}
/////////////////////////////////////////////////////////////////////////
//
private void finishTag() {
tagInProgress = false;
readyForNewLine = false;
tagIsEmpty = false;
}
private void endOfLine() {
writer.write(LF);
for (int i = 0; i < depth; i++) {
writer.write(lineIndenter);
}
}
private void writeAttributeValue(PointableWriter writer, String text) {
int length = text.length();
for (int i = 0; i < length; i++) {
char c = text.charAt(i);
switch (c) {
case '&':
this.writer.write(AMP);
break;
case '<':
this.writer.write(LT);
break;
case '>':
this.writer.write(GT);
break;
case '"':
this.writer.write(QUOT);
break;
case '\'':
this.writer.write(APOS);
break;
case '\r':
this.writer.write(SLASH_R);
break;
default:
this.writer.write(c);
}
}
}
private void writeText(PointableWriter writer, String text) {
int length = text.length();
for (int i = 0; i < length; i++) {
char c = text.charAt(i);
switch (c) {
case '&':
this.writer.write(AMP);
break;
case '<':
this.writer.write(LT);
break;
case '>':
this.writer.write(GT);
break;
case '"':
this.writer.write(QUOT);
break;
case '\'':
this.writer.write(APOS);
break;
case '\r':
this.writer.write(SLASH_R);
break;
default:
this.writer.write(c);
}
}
}
}
/**
* 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 static MiningResult importFile(InputStream input) throws IOException {
try {
DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
Document doc;
// NodeList netNodes;
dbf.setValidating(false);
dbf.setIgnoringComments(true);
dbf.setIgnoringElementContentWhitespace(true);
// dbf.setExpandEntityReferences(false);
// dbf.setNamespaceAware(false);
DocumentBuilder db = dbf.newDocumentBuilder();
db.setEntityResolver(
new EntityResolver() {
public InputSource resolveEntity(String publicId, String systemId) {
if (systemId.indexOf("ARIS-Export") != -1) {
return new InputSource("file:" + About.EXTLIBLOCATION() + "ARIS-Export101.dtd");
} else {
return null;
}
}
});
InputSource inpStream = new InputSource(input);
inpStream.setSystemId("file:" + System.getProperty("user.dir", ""));
doc = db.parse(inpStream);
// check if root element is a aml tag
Message.add("parsing done" + doc, Message.DEBUG);
if (!(doc.getDocumentElement().getNodeName().equals("AML"))) {
Message.add("aml tag not found", Message.ERROR);
throw new Exception("aml tag not found");
} else {
Message.add("aml root element found");
}
EPCResult result = new EPCResult(null, (EPC) null);
HashMap ObjDef_LinkId = new HashMap();
HashMap modelid_net = new HashMap();
HashMap ObjDef_Name = new HashMap();
HashMap function_LinkId = new HashMap();
HashMap ModelId_ModelType = new HashMap();
traverseAMLforObjectNames(
ObjDef_Name, doc.getDocumentElement(), ObjDef_LinkId, ModelId_ModelType);
Iterator findLinkToEpc = ObjDef_LinkId.keySet().iterator();
while (findLinkToEpc.hasNext()) {
String currentObjDef = (String) findLinkToEpc.next();
String Links = (String) ObjDef_LinkId.get(currentObjDef);
StringTokenizer linkSet = new StringTokenizer(Links);
String realEpcLink = "";
while (linkSet.hasMoreTokens()) {
String currentLink = linkSet.nextToken();
if (ModelId_ModelType.get(currentLink).equals("MT_EEPC")) {
realEpcLink = currentLink;
break;
}
}
if (realEpcLink.equals(" ")) {
ObjDef_LinkId.remove(currentObjDef);
} else {
ObjDef_LinkId.put(currentObjDef, realEpcLink);
}
}
result =
traverseAML(
result,
doc.getDocumentElement(),
null,
ObjDef_Name,
ObjDef_LinkId,
modelid_net,
function_LinkId);
Iterator hierarchicalFunctions = function_LinkId.keySet().iterator();
while (hierarchicalFunctions.hasNext()) {
EPCSubstFunction f = (EPCSubstFunction) hierarchicalFunctions.next();
f.setSubstitutedEPC((EPC) modelid_net.get(function_LinkId.get(f)));
// Message.add(f.getSubstitutedEPC().getName());
}
return result;
} catch (Throwable x) {
Message.add(x.toString());
throw new IOException(x.getMessage());
}
}
/** @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);
}
// ## 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;
}
// #]
}
