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();
}
}
private byte[] readMultiPartChunk(ServletInputStream requestStream, String contentType)
throws IOException {
// fast forward stream past multi-part header
int boundaryOff = contentType.indexOf("boundary="); // $NON-NLS-1$
String boundary = contentType.substring(boundaryOff + 9);
BufferedReader reader =
new BufferedReader(new InputStreamReader(requestStream, "ISO-8859-1")); // $NON-NLS-1$
StringBuffer out = new StringBuffer();
// skip headers up to the first blank line
String line = reader.readLine();
while (line != null && line.length() > 0) line = reader.readLine();
// now process the file
char[] buf = new char[1000];
int read;
while ((read = reader.read(buf)) > 0) {
out.append(buf, 0, read);
}
// remove the boundary from the output (end of input is \r\n--<boundary>--\r\n)
out.setLength(out.length() - (boundary.length() + 8));
return out.toString().getBytes("ISO-8859-1"); // $NON-NLS-1$
}
// The main procedure
public static void main(String args[]) {
String s;
initGUI();
while (true) {
try { // Poll every ~10 ms
Thread.sleep(10);
} catch (InterruptedException e) {
}
switch (connectionStatus) {
case BEGIN_CONNECT:
try {
// Try to set up a server if host
if (isHost) {
hostServer = new ServerSocket(port);
socket = hostServer.accept();
}
// If guest, try to connect to the server
else {
socket = new Socket(hostIP, port);
}
in = new BufferedReader(new InputStreamReader(socket.getInputStream()));
out = new PrintWriter(socket.getOutputStream(), true);
changeStatusTS(CONNECTED, true);
}
// If error, clean up and output an error message
catch (IOException e) {
cleanUp();
changeStatusTS(DISCONNECTED, false);
}
break;
case CONNECTED:
try {
// Send data
if (toSend.length() != 0) {
out.print(toSend);
out.flush();
toSend.setLength(0);
changeStatusTS(NULL, true);
}
// Receive data
if (in.ready()) {
s = in.readLine();
if ((s != null) && (s.length() != 0)) {
// Check if it is the end of a trasmission
if (s.equals(END_CHAT_SESSION)) {
changeStatusTS(DISCONNECTING, true);
}
// Otherwise, receive what text
else {
appendToChatBox("INCOMING: " + s + "\n");
changeStatusTS(NULL, true);
}
}
}
} catch (IOException e) {
cleanUp();
changeStatusTS(DISCONNECTED, false);
}
break;
case DISCONNECTING:
// Tell other chatter to disconnect as well
out.print(END_CHAT_SESSION);
out.flush();
// Clean up (close all streams/sockets)
cleanUp();
changeStatusTS(DISCONNECTED, true);
break;
default:
break; // do nothing
}
}
}
// Checks the current state and sets the enables/disables
// accordingly
public void run() {
switch (connectionStatus) {
case DISCONNECTED:
connectButton.setEnabled(true);
disconnectButton.setEnabled(false);
ipField.setEnabled(true);
portField.setEnabled(true);
hostOption.setEnabled(true);
guestOption.setEnabled(true);
chatLine.setText("");
chatLine.setEnabled(false);
statusColor.setBackground(Color.red);
break;
case DISCONNECTING:
connectButton.setEnabled(false);
disconnectButton.setEnabled(false);
ipField.setEnabled(false);
portField.setEnabled(false);
hostOption.setEnabled(false);
guestOption.setEnabled(false);
chatLine.setEnabled(false);
statusColor.setBackground(Color.orange);
break;
case CONNECTED:
connectButton.setEnabled(false);
disconnectButton.setEnabled(true);
ipField.setEnabled(false);
portField.setEnabled(false);
hostOption.setEnabled(false);
guestOption.setEnabled(false);
chatLine.setEnabled(true);
statusColor.setBackground(Color.green);
break;
case BEGIN_CONNECT:
connectButton.setEnabled(false);
disconnectButton.setEnabled(false);
ipField.setEnabled(false);
portField.setEnabled(false);
hostOption.setEnabled(false);
guestOption.setEnabled(false);
chatLine.setEnabled(false);
chatLine.grabFocus();
statusColor.setBackground(Color.orange);
break;
}
// Make sure that the button/text field states are consistent
// with the internal states
ipField.setText(hostIP);
portField.setText((new Integer(port)).toString());
hostOption.setSelected(isHost);
guestOption.setSelected(!isHost);
statusField.setText(statusString);
chatText.append(toAppend.toString());
toAppend.setLength(0);
mainFrame.repaint();
}
// initiate either a server or a user session
public void run() {
if (isDaemon) {
daemon();
return;
}
;
boolean loggedIn = false;
int i, h1;
String di, str1, user = "******", user_id = "0";
InetAddress localNode;
byte dataBuffer[] = new byte[1024];
String command = null;
StringBuffer statusMessage = new StringBuffer(40);
File targetFile = null;
try {
// start mysql
Class.forName("com.mysql.jdbc.Driver").newInstance();
this.db_conn = DriverManager.getConnection(db_url);
this.db_stmt = this.db_conn.createStatement();
this.db_stmt.executeUpdate("INSERT INTO test_table (name) VALUES ('hello world')");
incoming.setSoTimeout(inactivityTimer); // enforce I/O timeout
remoteNode = incoming.getInetAddress();
localNode = InetAddress.getLocalHost();
BufferedReader in =
new BufferedReader(new InputStreamReader(incoming.getInputStream(), TELNET));
PrintWriter out =
new PrintWriter(new OutputStreamWriter(incoming.getOutputStream(), TELNET), true);
str1 = "220 Flickr FTP Server Ready";
out.println(str1);
if (log) System.out.println(remoteNode.getHostName() + " " + str1);
boolean done = false;
char dataType = 0;
while (!done) {
statusMessage.setLength(0);
// obtain and tokenize command
String str = in.readLine();
if (str == null) break; // EOS reached
i = str.indexOf(' ');
if (i == -1) i = str.length();
command = str.substring(0, i).toUpperCase().intern();
if (log)
System.out.print(
user
+ "@"
+ remoteNode.getHostName()
+ " "
+ (String) ((command != "PASS") ? str : "PASS ***"));
str = str.substring(i).trim();
try {
if (command == "USER") {
user = str;
statusMessage.append("331 Password");
} else if (command == "PASS") {
String pass = str;
String pass_md5 = md5(pass);
this.db_rs =
this.db_stmt.executeQuery(
"SELECT * FROM users WHERE email='"
+ user
+ "' AND password='******'");
if (this.db_rs.first()) {
loggedIn = true;
user_id = this.db_rs.getString("id");
System.out.println("Account id is " + user_id);
}
statusMessage.append(loggedIn ? "230 logged in User" : "530 Login Incorrect");
} else if (!loggedIn) {
statusMessage.append("530 Not logged in");
} else if (command == "RETR") {
statusMessage.append("999 Not likely");
} else if (command == "STOR") {
out.println(BINARY_XFER);
// trim a leading slash off the filename if there is one
if (str.substring(0, 1).equals("/")) str = str.substring(1);
String filename = user_id + "_" + str;
// TODO: sanitise filename
targetFile = new File(upload_root + "/" + filename);
RandomAccessFile dataFile = null;
InputStream inStream = null;
OutputStream outStream = null;
BufferedReader br = null;
PrintWriter pw = null;
try {
int amount;
dataSocket = setupDataLink();
// ensure timeout on reads.
dataSocket.setSoTimeout(inactivityTimer);
dataFile = new RandomAccessFile(targetFile, "rw");
inStream = dataSocket.getInputStream();
while ((amount = inStream.read(dataBuffer)) != -1)
dataFile.write(dataBuffer, 0, amount);
statusMessage.append(XFER_COMPLETE);
shell_exec(ingest_path + " " + user_id + " " + filename);
} finally {
try {
if (inStream != null) inStream.close();
} catch (Exception e1) {
}
;
try {
if (outStream != null) outStream.close();
} catch (Exception e1) {
}
;
try {
if (dataFile != null) dataFile.close();
} catch (Exception e1) {
}
;
try {
if (dataSocket != null) dataSocket.close();
} catch (Exception e1) {
}
;
dataSocket = null;
}
} else if (command == "REST") {
statusMessage.append("502 Sorry, no resuming");
} else if (command == "TYPE") {
if (Character.toUpperCase(str.charAt(0)) == 'I') {
statusMessage.append(COMMAND_OK);
} else {
statusMessage.append("504 Only binary baybee");
}
} else if (command == "DELE"
|| command == "RMD"
|| command == "XRMD"
|| command == "MKD"
|| command == "XMKD"
|| command == "RNFR"
|| command == "RNTO"
|| command == "CDUP"
|| command == "XCDUP"
|| command == "CWD"
|| command == "SIZE"
|| command == "MDTM") {
statusMessage.append("502 None of that malarky!");
} else if (command == "QUIT") {
statusMessage.append(COMMAND_OK).append("GOOD BYE");
done = true;
} else if (command == "PWD" | command == "XPWD") {
statusMessage.append("257 \"/\" is current directory");
} else if (command == "PORT") {
int lng, lng1, lng2, ip2;
String a1 = "", a2 = "";
lng = str.length() - 1;
lng2 = str.lastIndexOf(",");
lng1 = str.lastIndexOf(",", lng2 - 1);
for (i = lng1 + 1; i < lng2; i++) {
a1 = a1 + str.charAt(i);
}
for (i = lng2 + 1; i <= lng; i++) {
a2 = a2 + str.charAt(i);
}
remotePort = Integer.parseInt(a1);
ip2 = Integer.parseInt(a2);
remotePort = (remotePort << 8) + ip2;
statusMessage.append(COMMAND_OK).append(remotePort);
} else if (command == "LIST" | command == "NLST") {
try {
out.println("150 ASCII data");
dataSocket = setupDataLink();
PrintWriter out2 = new PrintWriter(dataSocket.getOutputStream(), true);
if ((command == "NLST")) {
out2.println(".");
out2.println("..");
} else {
out2.println("total 8.0k");
out2.println("dr--r--r-- 1 owner group 213 Aug 26 16:31 .");
out2.println("dr--r--r-- 1 owner group 213 Aug 26 16:31 ..");
}
// socket MUST be closed before signalling EOD
dataSocket.close();
dataSocket = null;
statusMessage.setLength(0);
statusMessage.append(XFER_COMPLETE);
} finally {
try {
if (dataSocket != null) dataSocket.close();
} catch (Exception e) {
}
;
dataSocket = null;
}
} else if (command == "NOOP") {
statusMessage.append(COMMAND_OK);
} else if (command == "SYST") {
statusMessage.append("215 UNIX"); // allows NS to do long dir
} else if (command == "MODE") {
if (Character.toUpperCase(str.charAt(0)) == 'S') {
statusMessage.append(COMMAND_OK);
} else {
statusMessage.append("504");
}
} else if (command == "STRU") {
if (str.equals("F")) {
statusMessage.append(COMMAND_OK);
} else {
statusMessage.append("504");
}
} else if (command == "PASV") {
try {
int num = 0, j = 0;
if (passiveSocket != null)
try {
passiveSocket.close();
} catch (Exception e) {
}
;
passiveSocket = new ServerSocket(0); // any port
// ensure timeout on reads.
passiveSocket.setSoTimeout(inactivityTimer);
statusMessage.append("227 Entering Passive Mode (");
String s = localNode.getHostAddress().replace('.', ','); // get host #
statusMessage.append(s).append(',');
num = passiveSocket.getLocalPort(); // get port #
j = (num >> 8) & 0xff;
statusMessage.append(j);
statusMessage.append(',');
j = num & 0xff;
statusMessage.append(j);
statusMessage.append(')');
} catch (Exception e) {
try {
if (passiveSocket != null) passiveSocket.close();
} catch (Exception e1) {
}
;
passiveSocket = null;
throw e;
}
} else {
statusMessage.append("502 unimplemented ").append(command);
}
}
// shutdown causes an interruption to be thrown
catch (InterruptedException e) {
throw (e);
} catch (Exception e) // catch all for any errors (including files)
{
statusMessage.append(FAULT).append(e.getMessage());
if (debug) {
System.out.println("\nFAULT - lastfile " + targetFile);
e.printStackTrace();
}
;
}
// send result status to remote
out.println(statusMessage);
if (log) System.out.println("\t" + statusMessage);
}
} catch (Exception e) // usually network errors (including timeout)
{
if (log) System.out.println("forced instance exit " + e);
if (debug) e.printStackTrace();
} finally // exiting server instance
{
// tear down mysql
if (this.db_rs != null) {
try {
this.db_rs.close();
} catch (SQLException SQLE) {;
}
}
if (this.db_stmt != null) {
try {
this.db_stmt.close();
} catch (SQLException SQLE) {;
}
}
if (this.db_pstmt != null) {
try {
this.db_pstmt.close();
} catch (SQLException SQLE) {;
}
}
if (this.db_conn != null) {
try {
this.db_conn.close();
} catch (SQLException SQLE) {;
}
}
forceClose();
}
}
// This uses the key to get the entire record from the web page
// For now the fields that compose the record will be hardcoded
// but these fields need to be checked with the advertisement
// in future releases. It then uses the parameter passed to it
// to decide which fields to return
// Also put's the field values in a Hashtable that can be later accessed
private synchronized String getRecordFields(String key, String param) {
fieldsTable = null;
String city = new String(key);
displayMessage("DEBUG", "WCNForecastWeatherQueryFn::getRecordFields " + "city = " + city);
// Add the URL extension corresponding to the city.
StringBuffer sbuf = new StringBuffer();
for (int i = 0; i < city.length(); i++) {
char ch = city.charAt(i);
if (ch != ' ' && ch != '\t' && ch != '\n') sbuf.append(ch);
}
String formURLString = siteURLString + new String(sbuf) + ".html";
URL infoURL = null;
try {
infoURL = new URL(formURLString);
} catch (MalformedURLException e) {
displayMessage(
"ERROR",
"WCNForecastWeatherQueryFn::getRecordFields " + "Malformed URL " + formURLString);
return null;
}
// displayMessage("DEBUG", "WCNForecastWeatherQueryFn::getRecordFields " +
// "Got URL for site: " + formURLString);
Object content = null;
try {
content = infoURL.getContent();
} catch (IOException e) {
displayMessage(
"ERROR",
"WCNForecastWeatherQueryFn::getRecordFields "
+ "Can't load content from "
+ formURLString);
return null;
}
InputStreamReader input = new InputStreamReader((InputStream) content);
BufferedReader reader = new BufferedReader(input);
sbuf.setLength(0);
boolean stillReading = true;
char[] cbuf = new char[100000];
int ccount = 0;
long startTime = System.currentTimeMillis();
while (stillReading) {
try {
ccount = reader.read(cbuf);
} catch (IOException e) {
displayMessage(
"ERROR",
"WCNForecastWeatherQueryFn::getRecordFields "
+ "IO error getting content from "
+ formURLString);
return null;
}
if (ccount > 0) sbuf.append(cbuf, 0, ccount);
if (ccount < 0) stillReading = false;
}
// displayMessage("DEBUG", "WCNForecastWeatherQueryFn::getRecordFields " +
// "Time to read content: " + ((System.currentTimeMillis() - startTime) / 1000.0) +
// " seconds");
String page = sbuf.toString();
StringBuffer day = new StringBuffer();
StringBuffer condition = new StringBuffer();
int pos = page.indexOf("<!-- forecast include");
int delimit;
pos = page.indexOf("<TR>", pos);
pos = page.indexOf("<TR>", pos + 1);
pos = page.indexOf("<TR>", pos + 1);
for (int n = 0; n < 10; n++) {
pos = page.indexOf("<TR>", pos + 1);
int daypos = page.indexOf("<BR>", pos) + 4;
delimit = page.indexOf("</B>", daypos);
day.append("(" + page.substring(daypos, delimit) + (n == 9 ? ")" : ") "));
pos = page.indexOf("<FONT", daypos);
int condpos = page.indexOf(">", pos) + 1;
delimit = page.indexOf("</FONT>", condpos);
condition.append("(" + page.substring(condpos, delimit) + (n == 9 ? ")" : ") "));
}
// Get the parser corresponding to the initial URL
/*
Parser infoParser = null;
try {
infoParser = new Parser(infoURL,true,display);
} catch (Exception ex) {
infoParser = null;
}
if (infoParser == null) {
displayMessage("ERROR", "WCNForecastWeatherQueryFn::getRecordFields " +
"Cannot initialize parser for page " + formURLString );
return null ;
}
if (FILE_WRITE) {
displayMessage("DEBUG", "WCNForecastWeatherQueryFn::getRecordFields " +
"Site URL: " + formURLString +
" Calling writeContent()." + FILE_WRITE_EXT_NUM);
writeContent(infoParser.getContent());
}
displayMessage("DEBUG", "WCNForecastWeatherQueryFn::getRecordFields " +
"ready to return record fields: " + param);
displayMessage("DEBUG", "WCNForecastWeatherQueryFn::getRecordFields " +
"city is: " + key);
String ct = null;
StringBuffer day = new StringBuffer();
StringBuffer condition = new StringBuffer();
String tag = null;
while ((tag = infoParser.nextTag("NONE")) != null) {
ct = infoParser.getContentBetween ();
if ((ct == null) || (ct.length() == 0)) continue;
ct = ct.replace('\n', ' ');
ct = ct.replace('\r', ' ');
if (ct.toLowerCase().indexOf("sunrise:") != -1) {
tag = infoParser.nextTag("NONE");
while (tag != null && !tag.equalsIgnoreCase("table"))
tag = infoParser.nextTag("NONE");
while (tag != null && !tag.equalsIgnoreCase("span"))
tag = infoParser.nextTag("NONE");
for ( int n = 0; n < 5; n++ ) {
if (tag != null) {
infoParser.removeContentBetween();
tag = infoParser.nextTag("NONE");
while (tag != null && !tag.equalsIgnoreCase("/span"))
tag = infoParser.nextTag("NONE");
if (tag != null) {
day.append(infoParser.getContentBetween() + (n == 4 ? "" : " "));
tag = infoParser.nextTag("IMG");
while (tag != null && !tag.equalsIgnoreCase("img"))
tag = infoParser.nextTag("IMG");
if (tag != null)
condition.append(infoParser.getParameterValue("ALT") + (n == 4 ? "" : " "));
}
}
tag = infoParser.nextTag("NONE");
while (tag != null && !tag.equalsIgnoreCase("img"))
tag = infoParser.nextTag("NONE");
while (tag != null && !tag.equalsIgnoreCase("span"))
tag = infoParser.nextTag("NONE");
System.out.println("Content after condition = " + infoParser.getContentBetween());
}
}
infoParser.removeContentBetween();
}
*/
// If we couldn't get at least a temperature from the page, it must
// have been an invalid URL, ie.e, a city not in CNN database or
// incorrectly spelled or designated.
if (day == null) {
displayMessage(
"ERROR",
"WCNForecastWeatherQueryFn::getRecordFields "
+ "URL "
+ formURLString
+ " is not a valid URL. "
+ "The \"CityCountry\" or \"CityState\" key may be wrong.");
return null;
}
String weather =
WEATHER_PERF_STRING
+ " "
+ ":"
+ DAY_STRING
+ " ("
+ day.toString()
+ ") "
+ ":"
+ CONDITION_STRING
+ " ("
+ condition.toString()
+ ")";
if (param.equalsIgnoreCase(ALL_FIELDS)) {
fieldsTable = new Hashtable();
if (key != null) {
fieldsTable.put(CITY_STRING, key);
}
if (day != null) {
fieldsTable.put(DAY_STRING, day);
}
if (condition != null) {
fieldsTable.put(CONDITION_STRING, condition);
}
if (formURLString != null) {
fieldsTable.put(WEATHER_URL_STRING, formURLString);
}
if (key == null) {
key = " ";
}
if (formURLString == null) {
formURLString = " ";
}
String reply =
"(reply :"
+ CITY_STRING
+ " ("
+ key
+ ") "
+ ":"
+ WEATHER_STRING
+ " ("
+ weather
+ ") "
+ ":"
+ WEATHER_URL_STRING
+ " ("
+ formURLString
+ "))";
displayMessage(
"DEBUG", "WCNForecastWeatherQueryFn::getRecordFields " + "Weather is: " + reply);
return reply;
} else if (param.equalsIgnoreCase(CITY_STRING)) {
fieldsTable = new Hashtable();
fieldsTable.put(CITY_STRING, key);
return key;
} else if (param.equalsIgnoreCase(WEATHER_STRING)) {
fieldsTable = new Hashtable();
fieldsTable.put(WEATHER_STRING, weather);
return weather;
} else if (param.equalsIgnoreCase(WEATHER_URL_STRING)) {
fieldsTable = new Hashtable();
fieldsTable.put(WEATHER_URL_STRING, formURLString);
return formURLString;
} else {
return null;
}
}
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]);
}
/**
* Gets the next token from a tokenizer.
*
* @param wantWhitespace If true, leading whitespace will be returned as a token.
* @param wantComment If true, comments are returned as tokens.
* @return The next token in the stream.
* @throws TextParseException The input was invalid.
* @throws IOException An I/O error occurred.
*/
public Token get(boolean wantWhitespace, boolean wantComment) throws IOException {
int type;
int c;
if (ungottenToken) {
ungottenToken = false;
if (current.type == WHITESPACE) {
if (wantWhitespace) return current;
} else if (current.type == COMMENT) {
if (wantComment) return current;
} else {
if (current.type == EOL) line++;
return current;
}
}
int skipped = skipWhitespace();
if (skipped > 0 && wantWhitespace) return current.set(WHITESPACE, null);
type = IDENTIFIER;
sb.setLength(0);
while (true) {
c = getChar();
if (c == -1 || delimiters.indexOf(c) != -1) {
if (c == -1) {
if (quoting) throw exception("EOF in " + "quoted string");
else if (sb.length() == 0) return current.set(EOF, null);
else return current.set(type, sb);
}
if (sb.length() == 0 && type != QUOTED_STRING) {
if (c == '(') {
multiline++;
skipWhitespace();
continue;
} else if (c == ')') {
if (multiline <= 0) throw exception("invalid " + "close " + "parenthesis");
multiline--;
skipWhitespace();
continue;
} else if (c == '"') {
if (!quoting) {
quoting = true;
delimiters = quotes;
type = QUOTED_STRING;
} else {
quoting = false;
delimiters = delim;
skipWhitespace();
}
continue;
} else if (c == '\n') {
return current.set(EOL, null);
} else if (c == ';') {
while (true) {
c = getChar();
if (c == '\n' || c == -1) break;
sb.append((char) c);
}
if (wantComment) {
ungetChar(c);
return current.set(COMMENT, sb);
} else if (c == -1 && type != QUOTED_STRING) {
checkUnbalancedParens();
return current.set(EOF, null);
} else if (multiline > 0) {
skipWhitespace();
sb.setLength(0);
continue;
} else return current.set(EOL, null);
} else throw new IllegalStateException();
} else ungetChar(c);
break;
} else if (c == '\\') {
c = getChar();
if (c == -1) throw exception("unterminated escape sequence");
sb.append('\\');
} else if (quoting && c == '\n') {
throw exception("newline in quoted string");
}
sb.append((char) c);
}
if (sb.length() == 0 && type != QUOTED_STRING) {
checkUnbalancedParens();
return current.set(EOF, null);
}
return current.set(type, sb);
}
