private void sendProcessingError(Throwable t, ServletResponse response) {
String stackTrace = getStackTrace(t);
if (stackTrace != null && !stackTrace.equals("")) {
try {
response.setContentType("text/html");
PrintStream ps = new PrintStream(response.getOutputStream());
PrintWriter pw = new PrintWriter(ps);
pw.print("<html>\n<head>\n</head>\n<body>\n"); // NOI18N
// PENDING! Localize this for next official release
pw.print("<h1>The resource did not process correctly</h1>\n<pre>\n");
pw.print(stackTrace);
pw.print("</pre></body>\n</html>"); // NOI18N
pw.close();
ps.close();
response.getOutputStream().close();
;
} catch (Exception ex) {
}
} else {
try {
PrintStream ps = new PrintStream(response.getOutputStream());
t.printStackTrace(ps);
ps.close();
response.getOutputStream().close();
;
} catch (Exception ex) {
}
}
}
/** ** Main client thread loop */
public void run() {
this.setRunStatus(THREAD_RUNNING);
this.threadStarted();
try {
this.openSocket();
this.inputThread = new InputThread(this.socket, this.readTimeout, this.ioThreadLock);
this.outputThread = new OutputThread(this.socket, this.ioThreadLock);
this.inputThread.start();
this.outputThread.start();
synchronized (this.ioThreadLock) {
while (this.inputThread.isRunning() || this.outputThread.isRunning()) {
try {
this.ioThreadLock.wait();
} catch (Throwable t) {
}
}
}
} catch (NoRouteToHostException nrthe) {
Print.logInfo("Client:ControlThread - Unable to reach " + this.host + ":" + this.port);
nrthe.printStackTrace();
} catch (Throwable t) {
Print.logInfo("Client:ControlThread - " + t);
t.printStackTrace();
} finally {
this.closeSocket();
}
this.setRunStatus(THREAD_STOPPED);
this.threadStopped();
}
public void runPreProcess() {
Authorization auth = new glguerin.authkit.imp.macosx.MacOSXAuthorization();
Privilege priv = new Privilege("system.privilege.admin");
// see kAuthorizationRightExecute in the AuthorizationTags.h from Security.framework
int count = 0;
boolean succeed = false;
do {
try {
auth.authorize(priv, true);
succeed = true;
break;
} catch (Throwable t) {
System.out.println("Throwable " + t);
}
count++;
} while (count <= 3);
if (succeed) {
String preinstallPath = createTemporaryPreinstallFile();
if (preinstallPath == null) return;
String[] progArray = {preinstallPath, System.getProperty("user.name")};
try {
Process p = auth.execPrivileged(progArray);
Thread.sleep(1000L);
} catch (Throwable t) {
System.out.println("Throwable " + t);
t.printStackTrace();
}
}
}
public void run() {
StringBuffer data = new StringBuffer();
Print.logDebug("Client:InputThread started");
while (true) {
data.setLength(0);
boolean timeout = false;
try {
if (this.readTimeout > 0L) {
this.socket.setSoTimeout((int) this.readTimeout);
}
ClientSocketThread.socketReadLine(this.socket, -1, data);
} catch (InterruptedIOException ee) { // SocketTimeoutException ee) {
// error("Read interrupted (timeout) ...");
if (getRunStatus() != THREAD_RUNNING) {
break;
}
timeout = true;
// continue;
} catch (Throwable t) {
Print.logError("Client:InputThread - " + t);
t.printStackTrace();
break;
}
if (!timeout || (data.length() > 0)) {
ClientSocketThread.this.handleMessage(data.toString());
}
}
synchronized (this.threadLock) {
this.isRunning = false;
Print.logDebug("Client:InputThread stopped");
this.threadLock.notify();
}
}
Object createGuiElement(Class cls, EntityPlayer player, World world, int x, int y, int z) {
try {
try {
if (debugGui)
System.out.printf(
"BaseMod.createGuiElement: Invoking create method of %s for %s in %s\n",
cls, player, world);
return cls.getMethod(
"create", EntityPlayer.class, World.class, int.class, int.class, int.class)
.invoke(null, player, world, x, y, z);
} catch (NoSuchMethodException e) {
if (debugGui)
System.out.printf("BaseMod.createGuiElement: Invoking constructor of %s\n", cls);
return cls.getConstructor(EntityPlayer.class, World.class, int.class, int.class, int.class)
.newInstance(player, world, x, y, z);
}
} catch (Exception e) {
Throwable cause = e.getCause();
System.out.printf("BaseMod.createGuiElement: %s: %s\n", e, cause);
if (cause != null) cause.printStackTrace();
else e.printStackTrace();
// throw new RuntimeException(e);
return null;
}
}
public static void main(String[] args) {
try {
COConfigurationManager.initialise();
boolean v6 = true;
// Test connectivity.
if (true) {
// System.out.println( "UDP: " + getSingleton().getExternalIpAddressUDP(null,0,v6));
// System.out.println( "TCP: " + getSingleton().getExternalIpAddressTCP(null,0,v6));
// System.out.println( "HTTP: " + getSingleton().getExternalIpAddressHTTP(v6));
}
Map data = constructVersionCheckMessage(VersionCheckClient.REASON_UPDATE_CHECK_START);
System.out.println("Sending (pre-initialisation):");
printDataMap(data);
System.out.println("-----------");
System.out.println("Receiving (pre-initialisation):");
printDataMap(
getSingleton().getVersionCheckInfo(VersionCheckClient.REASON_UPDATE_CHECK_START));
System.out.println("-----------");
System.out.println();
System.out.print("Initialising core... ");
/**
* Suppress all of these errors being displayed in the output.
*
* <p>These things should be temporary...
*/
AzureusCoreImpl.SUPPRESS_CLASSLOADER_ERRORS = true;
DownloadManagerStateImpl.SUPPRESS_FIXUP_ERRORS = true;
AzureusCore core = AzureusCoreFactory.create();
core.start();
System.out.println("done.");
System.out.println();
System.out.println("-----------");
data = constructVersionCheckMessage(VersionCheckClient.REASON_UPDATE_CHECK_START);
System.out.println("Sending (post-initialisation):");
printDataMap(data);
System.out.println("-----------");
System.out.println("Receiving (post-initialisation):");
printDataMap(
getSingleton().getVersionCheckInfo(VersionCheckClient.REASON_UPDATE_CHECK_START));
System.out.println("-----------");
System.out.println();
System.out.print("Shutting down core... ");
core.stop();
System.out.println("done.");
} catch (Throwable e) {
e.printStackTrace();
}
}
boolean _error(Throwable t) throws MongoException {
if (_allHosts != null) {
System.out.println("paired mode, switching master b/c of: " + t);
t.printStackTrace();
_pickCurrent();
}
return true;
}
private String lookupFarm() {
if (Response != null) {
if (Response.isStillValid()) {
return Response.getFarmID();
}
Response = null;
}
try {
InetAddress CDPServer;
DatagramSocket Socket;
CDPQuery Query;
byte[] Buffer;
DatagramPacket Packet;
/* Get the IP address of the CDP servers. */
CDPServer = InetAddress.getByName(CDPServerName);
/* Create a UDP socket for the CDP query. */
Socket = new DatagramSocket();
Socket.setSoTimeout(CDPTimeout);
/* Build the CDP query. */
Query = new CDPQuery(Constants.AZUREUS_NAME + " " + Constants.AZUREUS_VERSION);
Buffer = Query.getBytes();
Packet = new DatagramPacket(Buffer, Buffer.length, CDPServer, CDPPort);
/* Send the query to the CDP server. */
Socket.send(Packet);
/* Receive the CDP response. */
Buffer = new byte[CDPResponse.MaxSize];
Packet.setData(Buffer);
Socket.receive(Packet);
if (Packet.getAddress() != CDPServer || Packet.getPort() != CDPPort)
throw (new Exception("CDP server address mismatch on response"));
/* Parse the CDP response. */
Response = new CDPResponse(Packet.getData());
/* Return the farmID from the CDP response. */
return Response.getFarmID();
} catch (Throwable Excpt) {
if (Excpt instanceof UnknownHostException) {
} else {
Excpt.printStackTrace();
}
return "default";
}
}
protected void log(String str, Throwable e) {
if (device_manager == null) {
System.out.println(str);
e.printStackTrace();
} else {
device_manager.log("TiVo: " + str, e);
}
}
/**
* Fired when a control is clicked. This is the equivalent of
* ActionListener.actionPerformed(ActionEvent e).
*/
protected void actionPerformed(GuiButton par1GuiButton) {
if (par1GuiButton.enabled) {
if (par1GuiButton.id == 5) {
if (Minecraft.getOs() == EnumOS.MACOS) {
try {
this.mc.getLogAgent().logInfo(this.fileLocation);
Runtime.getRuntime().exec(new String[] {"/usr/bin/open", this.fileLocation});
return;
} catch (IOException var7) {
var7.printStackTrace();
}
} else if (Minecraft.getOs() == EnumOS.WINDOWS) {
String var2 =
String.format(
"cmd.exe /C start \"Open file\" \"%s\"", new Object[] {this.fileLocation});
try {
Runtime.getRuntime().exec(var2);
return;
} catch (IOException var6) {
var6.printStackTrace();
}
}
boolean var8 = false;
try {
Class var3 = Class.forName("java.awt.Desktop");
Object var4 =
var3.getMethod("getDesktop", new Class[0]).invoke((Object) null, new Object[0]);
var3.getMethod("browse", new Class[] {URI.class})
.invoke(
var4,
new Object[] {(new File(Minecraft.getMinecraftDir(), "texturepacks")).toURI()});
} catch (Throwable var5) {
var5.printStackTrace();
var8 = true;
}
if (var8) {
this.mc.getLogAgent().logInfo("Opening via system class!");
Sys.openURL("file://" + this.fileLocation);
}
} else if (par1GuiButton.id == 6) {
this.mc.displayGuiScreen(this.guiScreen);
} else {
this.guiTexturePackSlot.actionPerformed(par1GuiButton);
}
}
}
private String[] store(String names[], long size, int i, NameValueRecord nvr) {
// store file
boolean error1 = false;
while (true) {
boolean error = false;
try {
names = createFileAndStore(names, size, binary, metadata, nvr, true, times, 0);
// nvr = retrieveMetadata(names[1], times, 0);
} catch (HoneycombTestException e) {
flex("store size=" + size + " name=" + (names == null ? "null" : names[0]), e);
log.log("store problem: " + e.getMessage());
// e.printStackTrace();
error = true;
} catch (Throwable t) {
flex("store size=" + size + " name=" + (names == null ? "null" : names[0]), t);
log.log("store: got throwable");
t.printStackTrace();
error = true;
}
if (error) {
error1 = true;
store_retries++;
sleep(SLEEP);
continue;
}
break;
}
if (error1) flog("#E ok\n");
// save info
total_files++;
total_bytes += size;
store_bytes += size;
time_store += times[0];
total_store_time += times[0];
oids[i] = names[1];
shas[i] = names[2];
if (fo != null) {
String s =
"" + size + '\t' + names[0] + '\t' + // filename
names[1] + '\t' + // oid
names[2] + '\t' + // sha1
names[3] + '\t' + // store date
binary + '\t' + metadata + '\t' + times[0] + '\n';
flog(s);
}
return names;
}
/**
* Try to execute given method on given object. Handles invocation target exceptions. XXX nearly
* duplicates tryMethod in JGEngine.
*
* @return null means method does not exist or returned null/void
*/
static Object tryMethod(Object o, String name, Object[] args) {
try {
Method met = JREEngine.getMethod(o.getClass(), name, args);
if (met == null) return null;
return met.invoke(o, args);
} catch (InvocationTargetException ex) {
Throwable ex_t = ex.getTargetException();
ex_t.printStackTrace();
return null;
} catch (IllegalAccessException ex) {
System.err.println("Unexpected exception:");
ex.printStackTrace();
return null;
}
}
public static String getStackTrace(Throwable t) {
String stackTrace = null;
try {
StringWriter sw = new StringWriter();
PrintWriter pw = new PrintWriter(sw);
t.printStackTrace(pw);
pw.close();
sw.close();
stackTrace = sw.getBuffer().toString();
} catch (Exception ex) {
}
return stackTrace;
}
public static void main(String[] args) {
try {
TOTorrent torrent =
TOTorrentFactory.deserialiseFromBEncodedFile(new File("C:\\temp\\test.torrent"));
CachePeer[] peers = new CLCacheDiscovery().lookup(torrent);
System.out.println("peers=" + peers.length);
for (int i = 0; i < peers.length; i++) {
System.out.println(" cache: " + peers[i].getAddress() + ":" + peers[i].getPort());
}
} catch (Throwable e) {
e.printStackTrace();
}
}
public static boolean exec(String cmd) throws Exception {
int exitVal = -1;
try {
Runtime rt = Runtime.getRuntime();
Process proc = rt.exec(new String[] {"/bin/bash", "-c", cmd});
OutputHandler err = new OutputHandler(proc.getErrorStream(), cmd);
err.start();
OutputHandler out = new OutputHandler(proc.getInputStream(), cmd);
out.start();
exitVal = proc.waitFor();
} catch (Throwable t) {
t.printStackTrace();
}
return (exitVal == 0);
}
public void run() {
String command = null;
Print.logInfo("Client:OutputThread started");
while (true) {
/* wait for commands */
synchronized (this.cmdList) {
while ((this.cmdList.size() <= 0) && (getRunStatus() == THREAD_RUNNING)) {
try {
this.cmdList.wait(5000L);
} catch (Throwable t) {
/*ignore*/
}
}
if (getRunStatus() != THREAD_RUNNING) {
break;
}
command = this.cmdList.remove(0).toString();
}
/* send commands */
try {
ClientSocketThread.socketWriteLine(this.socket, command);
} catch (Throwable t) {
Print.logError("Client:OutputThread - " + t);
t.printStackTrace();
break;
}
}
if (getRunStatus() == THREAD_RUNNING) {
Print.logWarn("Client:OutputThread stopped due to error");
} else {
Print.logInfo("Client:OutputThread stopped");
}
synchronized (this.threadLock) {
this.isRunning = false;
Print.logInfo("Client:OutputThread stopped");
this.threadLock.notify();
}
}
//
// The main work loop
//
public void run() {
//
// Poll the Namenode (once every 5 minutes) to find the size of the
// pending edit log.
//
long period = 5 * 60; // 5 minutes
long lastCheckpointTime = 0;
if (checkpointPeriod < period) {
period = checkpointPeriod;
}
while (shouldRun) {
try {
Thread.sleep(1000 * period);
} catch (InterruptedException ie) {
// do nothing
}
if (!shouldRun) {
break;
}
try {
long now = System.currentTimeMillis();
long size = namenode.getEditLogSize();
if (size >= checkpointSize || now >= lastCheckpointTime + 1000 * checkpointPeriod) {
doCheckpoint();
lastCheckpointTime = now;
}
} catch (IOException e) {
LOG.error("Exception in doCheckpoint: ");
LOG.error(StringUtils.stringifyException(e));
e.printStackTrace();
checkpointImage.imageDigest = null;
} catch (Throwable e) {
LOG.error("Throwable Exception in doCheckpoint: ");
LOG.error(StringUtils.stringifyException(e));
e.printStackTrace();
Runtime.getRuntime().exit(-1);
}
}
}
public static void main(String[] pArgs) {
if (pArgs.length < 3) {
System.out.println("usage: java Client host port boardnum");
return;
}
try {
Socket lSocket = new Socket(pArgs[0], Integer.parseInt(pArgs[1]));
PrintWriter lOut = new PrintWriter(lSocket.getOutputStream());
BufferedReader lIn = new BufferedReader(new InputStreamReader(lSocket.getInputStream()));
lOut.println(pArgs[2]);
lOut.flush();
String lLine = lIn.readLine();
// read number of rows
int lNumRows = Integer.parseInt(lLine);
// now, we should find a path from the player to any goal
// we've found our solution
String lMySol =
SokobanSolver.findSolution(Matrix.tileMatrixFromBufferedReader(lIn, lNumRows));
// these formats are also valid:
// String lMySol="URRUULDLLULLDRRRRLDDRURUDLLUR";
// String lMySol="0 3 3 0 0 2 1 2 2 0 2 2 1 3 3 3 3 2 1 1 3 0 3 0 1 2 2 0 3";
// send the solution to the server
lOut.println(lMySol);
lOut.flush();
// read answer from the server
lLine = lIn.readLine();
System.out.println(lLine);
} catch (Throwable t) {
t.printStackTrace();
}
}
public void setData(String text) {
if (text != null && text.length() > 0) {
InputStream in = null;
try {
Object result = null;
Drawing drawing = createDrawing();
// Try to read the data using all known input formats.
for (InputFormat fmt : drawing.getInputFormats()) {
try {
fmt.read(in, drawing);
in = new ByteArrayInputStream(text.getBytes("UTF8"));
result = drawing;
break;
} catch (IOException e) {
result = e;
}
}
if (result instanceof IOException) {
throw (IOException) result;
}
setDrawing(drawing);
} catch (Throwable e) {
getDrawing().removeAllChildren();
SVGTextFigure tf = new SVGTextFigure();
tf.setText(e.getMessage());
tf.setBounds(new Point2D.Double(10, 10), new Point2D.Double(100, 100));
getDrawing().add(tf);
e.printStackTrace();
} finally {
if (in != null) {
try {
in.close();
} catch (IOException ex) {
ex.printStackTrace();
}
}
}
}
}
void insertButton(Document document, PrintWriter out) {
String fileName = "netnow3.gif";
String imgURLString =
"http://home.netscape.com/comprod/products/navigator/version_3.0/images/" + fileName;
writeImageToDisk(document, imgURLString, fileName);
try {
// Write the HTML for the button
Tag anchor = new Tag("A");
anchor.addAttribute("HREF", "http://www.netscape.com");
Tag anchorEnd = new Tag("A", false);
Tag img = new Tag("IMG");
URL imgURL = new URL(document.getWorkDirectoryURL(), fileName);
img.addAttribute("SRC", imgURL.toString());
out.print(anchor);
out.print(img);
out.print(anchorEnd);
} catch (Throwable t) {
t.printStackTrace();
}
}
public Integer handleError(ESXX esxx, Context cx, Throwable ex) {
String title = "ESXX Server Error";
int code = 500;
if (ex instanceof ESXXException) {
code = ((ESXXException) ex).getStatus();
}
StringWriter sw = new StringWriter();
PrintWriter out = new PrintWriter(sw);
out.println(esxx.getHTMLHeader());
out.println("<h2>" + title + "</h2>");
out.println("<h3>Unhandled exception: " + ex.getClass().getSimpleName() + "</h3>");
if (ex instanceof ESXXException
|| ex instanceof javax.xml.stream.XMLStreamException
|| ex instanceof javax.xml.transform.TransformerException) {
out.println("<p><tt>" + encodeXMLContent(ex.getMessage()) + "</tt></p>");
} else if (ex instanceof RhinoException) {
out.println("<pre>");
out.println(ex.getClass().getSimpleName() + ": " + encodeXMLContent(ex.getMessage()));
out.println(((RhinoException) ex).getScriptStackTrace(new ESXX.JSFilenameFilter()));
out.println("</pre>");
} else {
out.println("<pre>");
ex.printStackTrace(out);
out.println("</pre>");
}
out.println(esxx.getHTMLFooter());
out.close();
try {
return handleResponse(
esxx, cx, new Response(code, "text/html; charset=UTF-8", sw.toString(), null));
} catch (Exception ex2) {
// Hmm
return 20;
}
}
/** @param args command line arguments */
public static void main(String[] args) {
DConnect2 dc;
for (String url : args) {
try {
System.out.println("");
System.out.println("");
System.out.println("########################################################");
System.out.println("\nConnecting to " + url + "\n");
dc = new DConnect2(url);
System.out.println("\n- - - - - - - - - - - - - - - - - - -");
System.out.println("Retrieving DDS:\n");
DDS dds = dc.getDDS();
dds.print(System.out);
System.out.println("\n- - - - - - - - - - - - - - - - - - -");
System.out.println("Retrieving DAS:\n");
DAS das = dc.getDAS();
das.print(System.out);
System.out.println("\n- - - - - - - - - - - - - - - - - - -");
System.out.println("Retrieving DATA:\n");
dds = dc.getData("");
dds.printVal(System.out, "");
System.out.println("\n- - - - - - - - - - - - - - - - - - -");
System.out.println("Retrieving DDX:\n");
dds = dc.getDDX();
dds.printXML(System.out);
} catch (Throwable t) {
t.printStackTrace(System.err);
}
}
}
/** Stand alone testing. */
public static void main(String[] args) {
try {
JFrame frame = new JFrame("JargonTree");
JargonTree tree = new JargonTree(args, null);
JScrollPane pane = new JScrollPane(tree);
pane.setPreferredSize(new Dimension(800, 600));
frame.addWindowListener(
new WindowAdapter() {
public void windowClosing(WindowEvent we) {
System.exit(0);
}
});
frame.getContentPane().add(pane, BorderLayout.NORTH);
frame.pack();
frame.show();
frame.validate();
} catch (Throwable e) {
e.printStackTrace();
System.out.println(((SRBException) e).getStandardMessage());
}
}
private void readwrite(long s1[], long s2[], int pass) {
// oids[] should correspond to s1[] going in, s2[] going out
String[] names = null;
time_retrieve = 0;
store_bytes = 0;
time_store = 0;
String algorithm_id = algorithms[randIndex(algorithms.length)];
String content_type = content_types[randIndex(content_types.length)];
StringBuffer sb = new StringBuffer();
for (int i = 0; i < s1.length; i++) {
String retrieved = null;
boolean error1 = false;
long t1 = System.currentTimeMillis();
while (true) {
boolean error = false;
try {
retrieved = retrieve(oids[i], times, 0);
time_retrieve += times[0];
total_retrieve_time += times[0];
} catch (HoneycombTestException e) {
flex("retrv " + oids[i], e);
String s = "#e retrv " + oids[i] + ": " + e.getMessage();
log.log(s);
// flog(s + "\n");
// e.printStackTrace();
error = true;
} catch (Throwable t) {
flex("retrv " + oids[i], t);
log.log("retrieve got throwable");
t.printStackTrace();
error = true;
}
if (error) {
error1 = true;
retrieve_retries++;
if (System.currentTimeMillis() - t1 > GIVEUP) {
retrieve_failures++;
retrieved = null;
break;
}
sleep(SLEEP);
continue;
}
break;
}
if (retrieved == null) {
failed_rtrv.add(oids[i]);
} else {
if (error1) flog("#E ok\n");
dot("r");
// compare retrieved w/ original
File f = new File(retrieved);
if (f.length() != s1[i]) {
bad_file_errors++;
String s =
"#e size mismatch ["
+ oids[i]
+ "] store/retrieve: "
+ s1[i]
+ " / "
+ f.length()
+ "\n";
flog(s);
} else {
String sha1sum = null;
try {
sha1sum = shell.sha1sum(retrieved);
} catch (Exception e) {
e.printStackTrace();
}
if (sha1sum != null && !sha1sum.equals(shas[i])) {
bad_file_errors++;
String s =
"#e sha1 mismatch ["
+ oids[i]
+ "] store/retrieve: "
+ shas[i]
+ " / "
+ sha1sum
+ "\n";
flog(s);
}
}
deleteFile(retrieved);
}
// compare mdata
t1 = System.currentTimeMillis();
NameValueRecord nvr = null;
error1 = false;
while (true) {
boolean error = false;
try {
nvr = retrieveMetadata(oids[i], times, 0);
md_retrieve_time += times[0];
md_retrieves++;
} catch (HoneycombTestException e) {
flex("md retrv " + oids[i], e);
String s = "#e md retrv " + oids[i] + ": " + e.getMessage();
log.log(s);
// flog(s + "\n");
// e.printStackTrace();
error = true;
} catch (Throwable t) {
flex("md retrv " + oids[i], t);
log.log("md retrieve got throwable");
t.printStackTrace();
error = true;
}
if (error) {
error1 = true;
md_retrieve_retries++;
if (System.currentTimeMillis() - t1 > GIVEUP) {
md_retrieve_failures++;
nvr = null;
flog("#E " + oids[i] + ": giving up\n");
break;
}
sleep(SLEEP);
continue;
}
break;
}
if (nvr == null) {
failed_md_rtrv.add(oids[i]);
} else {
if (error1) flog("#E ok\n");
SystemRecord sr = nvr.getSystemRecord();
String stored_oid = sr.getObjectIdentifier().toString();
if (!oids[i].equals(stored_oid)) {
// one oid looked up another
sb.append("#e oid mismatch! ").append(oids[i]);
sb.append(" / ").append(stored_oid).append("\n");
}
String sha2 = nvr.getString("sha1");
if (sha2 == null) {
sb.append("#e no sha1 in metadata\n");
} else if (!sha2.equals(shas[i])) {
sb.append("#e original/md sha: ").append(shas[i]);
sb.append(" / ").append(sha2).append("\n");
}
checkMD(sb, nvr, "cedars_subject_id", subject_id);
checkMD(sb, nvr, "cedars_study_id", study_id);
checkMD(sb, nvr, "cedars_species_id", species_id);
checkMD(sb, nvr, "cedars_sample_id", sample_id);
checkMD(sb, nvr, "cedars_collection_date", collection_date);
checkMD(sb, nvr, "cedars_processing_date", processing_date);
checkMD(sb, nvr, "cedars_collected_by", collected_by);
checkMD(sb, nvr, "cedars_processed_by", processed_by);
checkMD(sb, nvr, "cedars_sample_type", sample_type);
checkMD(sb, nvr, "cedars_experiment_date", experiment_date);
checkMD(sb, nvr, "cedars_experiment_number", experiment_number);
checkMD(sb, nvr, "cedars_scan_number", Integer.toString(i));
if (pass > 2) {
checkMD(sb, nvr, "cedars_algorithm_id", prev_algorithm_id);
checkMD(sb, nvr, "cedars_content_type", prev_content_type);
}
if (sb.length() > 0) {
bad_md_errors++;
flog("#e md error " + oids[i] + "\n");
flog(sb.toString());
sb.setLength(0);
}
}
if (s2 != null) {
// store next smaller file and save oid
nvr = createRecord();
nvr.put("cedars_subject_id", subject_id);
nvr.put("cedars_study_id", study_id);
nvr.put("cedars_species_id", species_id);
nvr.put("cedars_sample_id", sample_id);
nvr.put("cedars_collection_date", collection_date);
nvr.put("cedars_processing_date", processing_date);
nvr.put("cedars_collected_by", collected_by);
nvr.put("cedars_processed_by", processed_by);
nvr.put("cedars_sample_type", sample_type);
nvr.put("cedars_experiment_date", experiment_date);
nvr.put("cedars_experiment_number", experiment_number);
nvr.put("cedars_pass", Long.toString(pass));
nvr.put("cedars_scan_number", Long.toString(i));
nvr.put("cedars_algorithm_id", algorithm_id);
nvr.put("cedars_content_type", content_type);
names = store(names, s2[i], i, nvr);
oids[i] = names[1];
dot("s");
}
}
prev_algorithm_id = algorithm_id;
prev_content_type = content_type;
if (names != null && names[0] != null) deleteFile(names[0]);
}
public InputStream upload() throws ResourceUploaderException {
try {
try {
URL url = new URL(target.toString().replaceAll(" ", "%20"));
// some authentications screw up without an explicit port number here
String protocol = url.getProtocol().toLowerCase();
if (url.getPort() == -1) {
int target_port;
if (protocol.equals("http")) {
target_port = 80;
} else {
target_port = 443;
}
try {
String str = target.toString().replaceAll(" ", "%20");
int pos = str.indexOf("://");
pos = str.indexOf("/", pos + 4);
// might not have a trailing "/"
if (pos == -1) {
url = new URL(str + ":" + target_port + "/");
} else {
url = new URL(str.substring(0, pos) + ":" + target_port + str.substring(pos));
}
} catch (Throwable e) {
Debug.printStackTrace(e);
}
}
url = AddressUtils.adjustURL(url);
try {
if (user_name != null) {
SESecurityManager.setPasswordHandler(url, this);
}
for (int i = 0; i < 2; i++) {
try {
HttpURLConnection con;
if (url.getProtocol().equalsIgnoreCase("https")) {
// see ConfigurationChecker for SSL client defaults
HttpsURLConnection ssl_con = (HttpsURLConnection) url.openConnection();
// allow for certs that contain IP addresses rather than dns names
ssl_con.setHostnameVerifier(
new HostnameVerifier() {
public boolean verify(String host, SSLSession session) {
return (true);
}
});
con = ssl_con;
} else {
con = (HttpURLConnection) url.openConnection();
}
con.setRequestMethod("POST");
con.setRequestProperty(
"User-Agent", Constants.AZUREUS_NAME + " " + Constants.AZUREUS_VERSION);
con.setDoOutput(true);
con.setDoInput(true);
OutputStream os = con.getOutputStream();
byte[] buffer = new byte[65536];
while (true) {
int len = data.read(buffer);
if (len <= 0) {
break;
}
os.write(buffer, 0, len);
}
con.connect();
int response = con.getResponseCode();
if ((response != HttpURLConnection.HTTP_ACCEPTED)
&& (response != HttpURLConnection.HTTP_OK)) {
throw (new ResourceUploaderException(
"Error on connect for '"
+ url.toString()
+ "': "
+ Integer.toString(response)
+ " "
+ con.getResponseMessage()));
}
return (con.getInputStream());
} catch (SSLException e) {
if (i == 0) {
if (SESecurityManager.installServerCertificates(url) != null) {
// certificate has been installed
continue; // retry with new certificate
}
}
throw (e);
}
}
throw (new ResourceUploaderException("Should never get here"));
} finally {
if (user_name != null) {
SESecurityManager.setPasswordHandler(url, null);
}
}
} catch (java.net.MalformedURLException e) {
throw (new ResourceUploaderException(
"Exception while parsing URL '" + target + "':" + e.getMessage(), e));
} catch (java.net.UnknownHostException e) {
throw (new ResourceUploaderException(
"Exception while initializing download of '"
+ target
+ "': Unknown Host '"
+ e.getMessage()
+ "'",
e));
} catch (java.io.IOException e) {
throw (new ResourceUploaderException(
"I/O Exception while downloading '" + target + "':" + e.toString(), e));
}
} catch (Throwable e) {
ResourceUploaderException rde;
if (e instanceof ResourceUploaderException) {
rde = (ResourceUploaderException) e;
} else {
rde = new ResourceUploaderException("Unexpected error", e);
}
throw (rde);
} finally {
try {
data.close();
} catch (Throwable e) {
e.printStackTrace();
}
}
}
public void run() {
// XXX - Support other IPs
String announce = meta.getAnnounce();
String infoHash = urlencode(meta.getInfoHash());
String peerID = urlencode(coordinator.getID());
long uploaded = coordinator.getUploaded();
long downloaded = coordinator.getDownloaded();
long left = coordinator.getLeft();
boolean completed = (left == 0);
try {
boolean started = false;
while (!started) {
try {
// Send start.
TrackerInfo info =
doRequest(announce, infoHash, peerID, uploaded, downloaded, left, STARTED_EVENT);
Iterator it = info.getPeers().iterator();
while (it.hasNext()) coordinator.addPeer((Peer) it.next());
started = true;
} catch (IOException ioe) {
// Probably not fatal (if it doesn't last to long...)
Snark.debug(
"WARNING: Could not contact tracker at '" + announce + "': " + ioe, Snark.WARNING);
}
if (!started && !stop) {
Snark.debug(" Retrying in one minute...", Snark.DEBUG);
try {
// Sleep one minutes...
Thread.sleep(60 * 1000);
} catch (InterruptedException interrupt) {
// ignore
}
}
}
while (!stop) {
try {
// Sleep some minutes...
Thread.sleep(SLEEP * 60 * 1000);
} catch (InterruptedException interrupt) {
// ignore
}
if (stop) break;
uploaded = coordinator.getUploaded();
downloaded = coordinator.getDownloaded();
left = coordinator.getLeft();
// First time we got a complete download?
String event;
if (!completed && left == 0) {
completed = true;
event = COMPLETED_EVENT;
} else event = NO_EVENT;
// Only do a request when necessary.
if (event == COMPLETED_EVENT
|| coordinator.needPeers()
|| System.currentTimeMillis() > lastRequestTime + interval) {
try {
TrackerInfo info =
doRequest(announce, infoHash, peerID, uploaded, downloaded, left, event);
Iterator it = info.getPeers().iterator();
while (it.hasNext()) coordinator.addPeer((Peer) it.next());
} catch (IOException ioe) {
// Probably not fatal (if it doesn't last to long...)
Snark.debug(
"WARNING: Could not contact tracker at '" + announce + "': " + ioe, Snark.WARNING);
}
}
}
} catch (Throwable t) {
Snark.debug("TrackerClient: " + t, Snark.ERROR);
t.printStackTrace();
} finally {
try {
TrackerInfo info =
doRequest(announce, infoHash, peerID, uploaded, downloaded, left, STOPPED_EVENT);
} catch (IOException ioe) {
/* ignored */
}
}
}
/**
* Construct the default version check message.
*
* @return message to send
*/
public static Map constructVersionCheckMessage(String reason) {
// only send if anonymous-check flag is not set
boolean send_info = COConfigurationManager.getBooleanParameter("Send Version Info");
Map message = new HashMap();
// always send
message.put("appid", SystemProperties.getApplicationIdentifier());
message.put("appname", SystemProperties.getApplicationName());
message.put("version", Constants.AZUREUS_VERSION);
String sub_ver = Constants.AZUREUS_SUBVER;
if (sub_ver.length() > 0) {
message.put("subver", sub_ver);
}
if (COConfigurationManager.getBooleanParameter("Beta Programme Enabled")) {
message.put("beta_prog", "true");
}
message.put("ui", COConfigurationManager.getStringParameter("ui", "unknown"));
message.put("os", Constants.OSName);
message.put("os_version", System.getProperty("os.version"));
message.put(
"os_arch", System.getProperty("os.arch")); // see http://lopica.sourceforge.net/os.html
boolean using_phe =
COConfigurationManager.getBooleanParameter("network.transport.encrypted.require");
message.put("using_phe", using_phe ? new Long(1) : new Long(0));
// swt stuff
try {
Class c = Class.forName("org.eclipse.swt.SWT");
String swt_platform =
(String) c.getMethod("getPlatform", new Class[] {}).invoke(null, new Object[] {});
message.put("swt_platform", swt_platform);
Integer swt_version =
(Integer) c.getMethod("getVersion", new Class[] {}).invoke(null, new Object[] {});
message.put("swt_version", new Long(swt_version.longValue()));
if (send_info) {
c = Class.forName("org.gudy.azureus2.ui.swt.mainwindow.MainWindow");
if (c != null) {
c.getMethod("addToVersionCheckMessage", new Class[] {Map.class})
.invoke(null, new Object[] {message});
}
}
} catch (ClassNotFoundException e) {
/* ignore */
} catch (NoClassDefFoundError er) {
/* ignore */
} catch (InvocationTargetException err) {
/* ignore */
} catch (Throwable t) {
t.printStackTrace();
}
int last_send_time = COConfigurationManager.getIntParameter("Send Version Info Last Time", -1);
int current_send_time = (int) (SystemTime.getCurrentTime() / 1000);
COConfigurationManager.setParameter("Send Version Info Last Time", current_send_time);
String id = COConfigurationManager.getStringParameter("ID", null);
if (id != null && send_info) {
message.put("id", id);
try {
byte[] id2 = CryptoManagerFactory.getSingleton().getSecureID();
message.put("id2", id2);
} catch (Throwable e) {
}
if (last_send_time != -1 && last_send_time < current_send_time) {
// time since last
message.put("tsl", new Long(current_send_time - last_send_time));
}
message.put("reason", reason);
String java_version = System.getProperty("java.version");
if (java_version == null) {
java_version = "unknown";
}
message.put("java", java_version);
String java_vendor = System.getProperty("java.vm.vendor");
if (java_vendor == null) {
java_vendor = "unknown";
}
message.put("javavendor", java_vendor);
long max_mem = Runtime.getRuntime().maxMemory() / (1024 * 1024);
message.put("javamx", new Long(max_mem));
String java_rt_name = System.getProperty("java.runtime.name");
if (java_rt_name != null) {
message.put("java_rt_name", java_rt_name);
}
String java_rt_version = System.getProperty("java.runtime.version");
if (java_rt_version != null) {
message.put("java_rt_version", java_rt_version);
}
OverallStats stats = StatsFactory.getStats();
if (stats != null) {
// long total_bytes_downloaded = stats.getDownloadedBytes();
// long total_bytes_uploaded = stats.getUploadedBytes();
long total_uptime = stats.getTotalUpTime();
// removed due to complaints about anonymous stats collection
// message.put( "total_bytes_downloaded", new Long( total_bytes_downloaded ) );
// message.put( "total_bytes_uploaded", new Long( total_bytes_uploaded ) );
message.put("total_uptime", new Long(total_uptime));
// message.put( "dlstats", stats.getDownloadStats());
}
try {
NetworkAdminASN current_asn = NetworkAdmin.getSingleton().getCurrentASN();
String as = current_asn.getAS();
message.put("ip_as", current_asn.getAS());
String asn = current_asn.getASName();
if (asn.length() > 64) {
asn = asn.substring(0, 64);
}
message.put("ip_asn", asn);
} catch (Throwable e) {
Debug.out(e);
}
// send locale, so we can determine which languages need attention
message.put("locale", Locale.getDefault().toString());
String originalLocale =
System.getProperty("user.language") + "_" + System.getProperty("user.country");
String variant = System.getProperty("user.variant");
if (variant != null && variant.length() > 0) {
originalLocale += "_" + variant;
}
message.put("orig_locale", originalLocale);
// We may want to reply differently if the user is in Beginner mode vs Advanced
message.put("user_mode", COConfigurationManager.getIntParameter("User Mode", -1));
Set<String> features = UtilitiesImpl.getFeaturesInstalled();
if (features.size() > 0) {
String str = "";
for (String f : features) {
str += (str.length() == 0 ? "" : ",") + f;
}
message.put("vzfeatures", str);
}
try {
if (AzureusCoreFactory.isCoreAvailable()) {
// installed plugin IDs
PluginInterface[] plugins =
AzureusCoreFactory.getSingleton().getPluginManager().getPluginInterfaces();
List pids = new ArrayList();
List vs_data = new ArrayList();
for (int i = 0; i < plugins.length; i++) {
PluginInterface plugin = plugins[i];
String pid = plugin.getPluginID();
String info = plugin.getPluginconfig().getPluginStringParameter("plugin.info");
// filter out built-in and core ones
if ((info != null && info.length() > 0)
|| (!pid.startsWith("<")
&& !pid.startsWith("azbp")
&& !pid.startsWith("azupdater")
&& !pid.startsWith("azplatform")
&& !pids.contains(pid))) {
if (info != null && info.length() > 0) {
if (info.length() < 256) {
pid += ":" + info;
} else {
Debug.out("Plugin '" + pid + "' reported excessive info string '" + info + "'");
}
}
pids.add(pid);
}
Map data =
plugin.getPluginconfig().getPluginMapParameter("plugin.versionserver.data", null);
if (data != null) {
Map payload = new HashMap();
byte[] data_bytes = BEncoder.encode(data);
if (data_bytes.length > 16 * 1024) {
Debug.out(
"Plugin '"
+ pid
+ "' reported excessive version server data (length="
+ data_bytes.length
+ ")");
payload.put("error", "data too long: " + data_bytes.length);
} else {
payload.put("data", data_bytes);
}
payload.put("id", pid);
payload.put("version", plugin.getPluginVersion());
vs_data.add(payload);
}
}
message.put("plugins", pids);
if (vs_data.size() > 0) {
message.put("plugin_data", vs_data);
}
}
} catch (Throwable e) {
Debug.out(e);
}
}
return message;
}
public static void main(String[] args) {
// Initialize the logger (saves to RMG.log file).
Logger.initialize();
initializeSystemProperties();
try {
ChemGraph.readForbiddenStructure();
} catch (IOException e1) {
System.err.println("PopulateReactions cannot locate forbiddenStructures.txt file");
e1.printStackTrace();
}
ArrheniusKinetics.setAUnits("moles");
ArrheniusKinetics.setEaUnits("kcal/mol");
// Creating a new ReactionModelGenerator so I can set the variable temp4BestKinetics
// and call the new readAndMakePTL and readAndMakePRL methods
ReactionModelGenerator rmg = new ReactionModelGenerator();
rmg.setSpeciesSeed(new LinkedHashSet());
// Set Global.lowTemp and Global.highTemp
// The values of the low/highTemp are not used in the function
// (to the best of my knowledge).
// They are necessary for the instances of additionalKinetics,
// e.g. H2C*-CH2-CH2-CH3 -> H3C-CH2-*CH-CH3
/*
* 7Apr2010: The input file will now ask the user for a TemperatureModel and PressureModel (same as the RMG
* module). The Global .lowTemperature and .highTemperature will automatically be determined
*/
// Global.lowTemperature = new Temperature(300,"K");
// Global.highTemperature = new Temperature(1500,"K");
// Define variable 'speciesSet' to store the species contained in the input file
LinkedHashSet speciesSet = new LinkedHashSet();
// Define variable 'reactions' to store all possible rxns between the species in speciesSet
LinkedHashSet reactions = new LinkedHashSet();
// Define two string variables 'listOfReactions' and 'listOfSpecies'
// These strings will hold the list of rxns (including the structure,
// modified Arrhenius parameters, and source/comments) and the list of
// species (including the chemkin name and graph), respectively
String listOfReactions =
"Arrhenius 'A' parameter has units of: "
+ ArrheniusEPKinetics.getAUnits()
+ ",cm3,s\n"
+ "Arrhenius 'n' parameter is unitless and assumes Tref = 1K\n"
+ "Arrhenius 'E' parameter has units of: "
+ ArrheniusEPKinetics.getEaUnits()
+ "\n\n";
String listOfSpecies = "";
// Open and read the input file
try {
FileReader fr_input = new FileReader(args[0]);
BufferedReader br_input = new BufferedReader(fr_input);
// Read in the Database field
String line = ChemParser.readMeaningfulLine(br_input, true);
if (line.toLowerCase().startsWith("database")) {
RMG.extractAndSetDatabasePath(line);
} else {
System.err.println("PopulateReactions: Could not" + " locate the Database field");
System.exit(0);
}
// Read in the first line of the input file
// This line should hold the temperature of the system, e.g.
// Temperature: 500 (K)
line = ChemParser.readMeaningfulLine(br_input, true);
/*
* Read max atom types (if they exist)
*/
line = rmg.readMaxAtomTypes(line, br_input);
/*
* Read primary thermo libraries (if they exist)
*/
if (line.toLowerCase().startsWith("primarythermolibrary")) {
rmg.readAndMakePTL(br_input);
} else {
System.err.println(
"PopulateReactions: Could not locate the PrimaryThermoLibrary field.\n"
+ "Line read was: "
+ line);
System.exit(0);
}
line = ChemParser.readMeaningfulLine(br_input, true);
// Read primary transport library
if (line.toLowerCase().startsWith("primarytransportlibrary"))
rmg.readAndMakePTransL(br_input);
else {
System.err.println(
"PopulateReactions: Could not locate the PrimaryTransportLibrary field.\n"
+ "Line read was: "
+ line);
System.exit(0);
}
/*
* Read the temperature model (must be of length one)
*/
line = ChemParser.readMeaningfulLine(br_input, true);
rmg.createTModel(line);
if (rmg.getTempList().size() > 1) {
System.out.println("Please list only one temperature in the TemperatureModel field.");
System.exit(0);
}
// Set the user's input temperature
LinkedList tempList = rmg.getTempList();
systemTemp = ((ConstantTM) tempList.get(0)).getTemperature();
rmg.setTemp4BestKinetics(systemTemp);
/*
* Read the pressure model (must be of length 1)
*/
line = ChemParser.readMeaningfulLine(br_input, true);
rmg.createPModel(line);
if (rmg.getPressList().size() > 1) {
System.out.println("Please list only one pressure in the PressureModel field.");
System.exit(0);
}
/*
* Read the solvation field (if present)
*/
line = ChemParser.readMeaningfulLine(br_input, true);
StringTokenizer st = new StringTokenizer(line);
// The first line should start with "Solvation", otherwise do nothing and display a message to
// the user
if (st.nextToken().startsWith("Solvation")) {
line = st.nextToken().toLowerCase();
// The options for the "Solvation" field are "on" or "off" (as of 18May2009), otherwise do
// nothing and
// display a message to the user
// Note: I use "Species.useInChI" because the "Species.useSolvation" updates were not yet
// committed.
if (line.equals("on")) {
Species.useSolvation = true;
// rmg.setUseDiffusion(true);
listOfReactions += "Solution-phase chemistry!\n\n";
} else if (line.equals("off")) {
Species.useSolvation = false;
// rmg.setUseDiffusion(false);
listOfReactions += "Gas-phase chemistry.\n\n";
} else {
System.out.println(
"Error in reading input.txt file:\nThe field 'Solvation' has the options 'on' or 'off'."
+ "\nPopulateReactions does not recognize: "
+ line);
return;
}
line = ChemParser.readMeaningfulLine(br_input, true);
}
/*
* Read in the species (name, concentration, adjacency list)
*/
if (line.toLowerCase().startsWith("speciesstatus")) {
LinkedHashMap lhm = new LinkedHashMap();
lhm = rmg.populateInitialStatusListWithReactiveSpecies(br_input);
speciesSet.addAll(lhm.values());
}
/*
* Read in the inert gas (name, concentration)
*/
line = ChemParser.readMeaningfulLine(br_input, true);
if (line.toLowerCase().startsWith("bathgas")) {
rmg.populateInitialStatusListWithInertSpecies(br_input);
}
/*
* Read in the p-dep options
*/
line = ChemParser.readMeaningfulLine(br_input, true);
if (line.toLowerCase().startsWith("spectroscopicdata")) {
rmg.setSpectroscopicDataMode(line);
line = ChemParser.readMeaningfulLine(br_input, true);
line = rmg.setPressureDependenceOptions(line, br_input);
}
/*
* Read primary kinetic libraries (if they exist)
*/
if (line.toLowerCase().startsWith("primarykineticlibrary")) {
rmg.readAndMakePKL(br_input);
} else {
System.err.println(
"PopulateReactions: Could not locate the PrimaryKineticLibrary field."
+ "Line read was: "
+ line);
System.exit(0);
}
line = ChemParser.readMeaningfulLine(br_input, true);
if (line.toLowerCase().startsWith("reactionlibrary")) {
rmg.readAndMakeReactionLibrary(br_input);
} else {
System.err.println(
"PopulateReactions: Could not locate the ReactionLibrary field."
+ "Line read was: "
+ line);
System.exit(0);
}
/*
* Read in verbosity field (if it exists)
*/
line = ChemParser.readMeaningfulLine(br_input, true);
if (line != null && line.toLowerCase().startsWith("verbose")) {
StringTokenizer st2 = new StringTokenizer(line);
String tempString = st2.nextToken();
tempString = st2.nextToken();
tempString = tempString.toLowerCase();
if (tempString.equals("on") || tempString.equals("true") || tempString.equals("yes"))
ArrheniusKinetics.setVerbose(true);
}
TemplateReactionGenerator rtLibrary = new TemplateReactionGenerator();
// / THE SERVERY BIT
ServerSocket Server = new ServerSocket(5000);
Logger.info("TCPServer Waiting for client on port 5000");
Logger.info("Switching to quiet mode - only WARNINGS and above will be logged...");
Logger.setConsoleLevel(jing.rxnSys.Logger.WARNING);
Logger.setFileLevel(jing.rxnSys.Logger.WARNING);
while (true) {
Socket connected = Server.accept();
Logger.warning(
" THE CLIENT"
+ " "
+ connected.getInetAddress()
+ ":"
+ connected.getPort()
+ " IS CONNECTED ");
BufferedReader inFromClient =
new BufferedReader(new InputStreamReader(connected.getInputStream()));
inFromClient.mark(4096); // so you can reset up to 4096 characters back.
PrintWriter outToClient = new PrintWriter(connected.getOutputStream(), true);
try {
listOfReactions =
"Arrhenius 'A' parameter has units of: "
+ ArrheniusEPKinetics.getAUnits()
+ ",cm3,s\n"
+ "Arrhenius 'n' parameter is unitless and assumes Tref = 1K\n"
+ "Arrhenius 'E' parameter has units of: "
+ ArrheniusEPKinetics.getEaUnits()
+ "\n\n";
listOfSpecies = "";
// clear old things
speciesSet.clear();
reactions.clear();
/*
* Read in the species (name, concentration, adjacency list)
*/
LinkedHashMap lhm = new LinkedHashMap();
lhm = rmg.populateInitialStatusListWithReactiveSpecies(inFromClient);
speciesSet.addAll(lhm.values());
// Check Reaction Library
ReactionLibrary RL = rmg.getReactionLibrary();
LibraryReactionGenerator lrg1 = new LibraryReactionGenerator(RL);
reactions = lrg1.react(speciesSet);
if (RL != null) {
System.out.println("Checking Reaction Library " + RL.getName() + " for reactions.");
Iterator ReactionIter = reactions.iterator();
while (ReactionIter.hasNext()) {
Reaction current_reaction = (Reaction) ReactionIter.next();
System.out.println("Library Reaction: " + current_reaction.toString());
}
}
// Add all reactions found from RMG template reaction generator
reactions.addAll(rtLibrary.react(speciesSet));
System.out.println("FINISHED generating template reactions");
if (!(rmg.getReactionModelEnlarger() instanceof RateBasedRME)) {
// NOT an instance of RateBasedRME therefore assume RateBasedPDepRME and we're doing
// pressure
// dependence
CoreEdgeReactionModel cerm = new CoreEdgeReactionModel(speciesSet, reactions);
rmg.setReactionModel(cerm);
rmg.setReactionGenerator(rtLibrary);
ReactionSystem rs =
new ReactionSystem(
(TemperatureModel) rmg.getTempList().get(0),
(PressureModel) rmg.getPressList().get(0),
rmg.getReactionModelEnlarger(),
new FinishController(),
null,
rmg.getPrimaryKineticLibrary(),
rmg.getReactionGenerator(),
speciesSet,
(InitialStatus) rmg.getInitialStatusList().get(0),
rmg.getReactionModel(),
rmg.getLibraryReactionGenerator(),
0,
"GasPhase");
PDepNetwork.reactionModel = rmg.getReactionModel();
PDepNetwork.reactionSystem = rs;
// If the reaction structure is A + B = C + D, we are not concerned w/pdep
Iterator iter = reactions.iterator();
LinkedHashSet nonPdepReactions = new LinkedHashSet();
while (iter.hasNext()) {
Reaction r = (Reaction) iter.next();
if (FastMasterEqn.isReactionPressureDependent(r)) {
cerm.categorizeReaction(r.getStructure());
PDepNetwork.addReactionToNetworks(r);
} else {
nonPdepReactions.add(r);
}
}
// Run fame calculation
PDepKineticsEstimator pDepKineticsEstimator =
((RateBasedPDepRME) rmg.getReactionModelEnlarger()).getPDepKineticsEstimator();
BathGas bathGas = new BathGas(rs);
for (int numNetworks = 0;
numNetworks < PDepNetwork.getNetworks().size();
++numNetworks) {
LinkedHashSet allSpeciesInNetwork = new LinkedHashSet();
PDepNetwork pdepnetwork = PDepNetwork.getNetworks().get(numNetworks);
LinkedList isomers = pdepnetwork.getIsomers();
for (int numIsomers = 0; numIsomers < isomers.size(); ++numIsomers) {
PDepIsomer currentIsomer = (PDepIsomer) isomers.get(numIsomers);
if (currentIsomer.getNumSpecies() == 2)
pdepnetwork.makeIsomerIncluded(currentIsomer);
}
pDepKineticsEstimator.runPDepCalculation(pdepnetwork, rs, cerm);
if (pdepnetwork.getNetReactions().size() > 0) {
String formatSpeciesName = "%1$-16s\t";
listOfReactions +=
"!PDepNetwork\n"
+ "!\tdeltaEdown = "
+ bathGas.getDeltaEdown().getAlpha()
+ "(T / "
+ bathGas.getDeltaEdown().getT0()
+ ")^"
+ bathGas.getDeltaEdown().getN()
+ " kJ/mol\n"
+ "!\tbathgas MW = "
+ bathGas.getMolecularWeight()
+ " amu\n"
+ "!\tbathgas LJ sigma = "
+ bathGas.getLJSigma()
+ " meters\n"
+ "!\tbathgas LJ epsilon = "
+ bathGas.getLJEpsilon()
+ " Joules\n"
+ "!Here are the species and their thermochemistry:\n";
LinkedList<PDepIsomer> allpdepisomers = pdepnetwork.getIsomers();
for (int numIsomers = 0; numIsomers < allpdepisomers.size(); ++numIsomers) {
LinkedList species = allpdepisomers.get(numIsomers).getSpeciesList();
for (int numSpecies = 0; numSpecies < species.size(); ++numSpecies) {
Species currentSpec = (Species) species.get(numSpecies);
if (!allSpeciesInNetwork.contains(currentSpec)) {
listOfReactions +=
"!\t"
+ String.format(formatSpeciesName, currentSpec.getFullName())
+ currentSpec.getThermoData().toString()
+ currentSpec.getThermoData().getSource()
+ "\n";
allSpeciesInNetwork.add(currentSpec);
}
}
speciesSet.addAll(species);
}
String formatRxnName = "%1$-32s\t";
listOfReactions +=
"!Here are the path reactions and their high-P limit kinetics:\n";
LinkedList<PDepReaction> pathRxns = pdepnetwork.getPathReactions();
for (int numPathRxns = 0; numPathRxns < pathRxns.size(); numPathRxns++) {
Kinetics[] currentKinetics = pathRxns.get(numPathRxns).getKinetics();
for (int numKinetics = 0; numKinetics < currentKinetics.length; ++numKinetics) {
listOfReactions +=
"!\t"
+ String.format(
formatRxnName,
pathRxns.get(numPathRxns).getStructure().toRestartString(true))
+ currentKinetics[numKinetics].toChemkinString(
pathRxns
.get(numPathRxns)
.calculateHrxn(new Temperature(298.0, "K")),
new Temperature(298.0, "K"),
false)
+ "\n";
}
}
listOfReactions += "\n";
LinkedList<PDepReaction> indivPDepRxns = pdepnetwork.getNetReactions();
for (int numPDepRxns = 0; numPDepRxns < indivPDepRxns.size(); numPDepRxns++) {
listOfReactions += indivPDepRxns.get(numPDepRxns).toRestartString(systemTemp);
}
LinkedList<PDepReaction> nonIncludedRxns = pdepnetwork.getNonincludedReactions();
for (int numNonRxns = 0; numNonRxns < nonIncludedRxns.size(); ++numNonRxns) {
listOfReactions += nonIncludedRxns.get(numNonRxns).toRestartString(systemTemp);
}
}
}
reactions = nonPdepReactions;
}
// Some of the reactions may be duplicates of one another
// (e.g. H+CH4=CH3+H2 as a forward reaction and reverse reaction)
// Create new LinkedHashSet which will store the non-duplicate rxns
LinkedHashSet nonDuplicateRxns = new LinkedHashSet();
int Counter = 0;
Iterator iter_rxns = reactions.iterator();
while (iter_rxns.hasNext()) {
++Counter;
Reaction r = (Reaction) iter_rxns.next();
// The first reaction is not a duplicate of any previous reaction
if (Counter == 1) {
nonDuplicateRxns.add(r);
listOfReactions += writeOutputString(r, rtLibrary);
speciesSet.addAll(r.getProductList());
}
// Check whether the current reaction (or its reverse) has the same structure
// of any reactions already reported in the output
else {
Iterator iterOverNonDup = nonDuplicateRxns.iterator();
boolean dupRxn = false;
while (iterOverNonDup.hasNext()) {
Reaction temp_Reaction = (Reaction) iterOverNonDup.next();
if (r.getStructure() == temp_Reaction.getStructure()) {
dupRxn = true;
break;
} else if (r.hasReverseReaction()) {
if (r.getReverseReaction().getStructure() == temp_Reaction.getStructure()) {
dupRxn = true;
break;
}
}
}
if (!dupRxn) {
nonDuplicateRxns.add(r);
// If Reaction is Not a Library Reaction
listOfReactions += writeOutputString(r, rtLibrary);
speciesSet.addAll(r.getProductList());
}
}
}
Iterator iter_species = speciesSet.iterator();
// Define dummy integer 'i' so our getChemGraph().toString()
// call only returns the graph
int i = 0;
while (iter_species.hasNext()) {
Species species = (Species) iter_species.next();
listOfSpecies +=
species.getFullName() + "\n" + species.getChemGraph().toStringWithoutH(i) + "\n";
}
// Write the output files
try {
File rxns = new File("PopRxnsOutput_rxns.txt");
FileWriter fw_rxns = new FileWriter(rxns);
fw_rxns.write(listOfReactions);
fw_rxns.close();
File spcs = new File("PopRxnsOutput_spcs.txt");
FileWriter fw_spcs = new FileWriter(spcs);
fw_spcs.write(listOfSpecies);
fw_spcs.close();
} catch (IOException e) {
System.err.println("Could not write PopRxnsOutput*.txt files");
}
// Display to the user that the program was successful and also
// inform them where the results may be located
System.out.println(
"Reaction population complete. "
+ "Results are stored in PopRxnsOutput_rxns.txt and PopRxnsOutput_spcs.txt");
// send output to client
System.out.println("SENDING RESPONSE TO CLIENT");
outToClient.println(listOfSpecies);
outToClient.println(listOfReactions);
} catch (Throwable t) {
Logger.error("Error in PopulateReactionsServer");
try {
inFromClient.reset();
Logger.error("Input:");
while (inFromClient.ready()) {
Logger.error(inFromClient.readLine());
}
} catch (IOException e) {
Logger.error("Couldn't read input stream");
}
Logger.logStackTrace(t);
outToClient.println("Error in PopulateReactionsServer");
t.printStackTrace(outToClient);
}
connected.close();
System.out.println("SOCKET CLOSED");
}
} catch (FileNotFoundException e) {
System.err.println("File was not found!\n");
} catch (IOException e) {
System.err.println(
"IOException: Something maybe wrong with ChemParser.readChemGraph.\n" + e.toString());
}
}
