/**
* write out the header of the report's content
*
* @param bw the writer to use
* @throws IOException if an error occurs
*/
protected void writeHtmlBodyHeader(BufferedWriter bw) throws IOException {
bw.write("<body>" + Dump.newLine());
bw.write(Dump.newLine());
bw.write("<h1>" + NAME + "</h1>" + Dump.newLine());
bw.write("<a href=\"../index.html\">Main</a>" + Dump.newLine());
bw.write("<p>" + Dump.newLine());
}
public static void main(String[] args) {
if (args.length == 0) {
help();
return;
}
// Consumes the command
String command = args[0];
String[] commandArgs = new String[args.length - 1];
System.arraycopy(args, 1, commandArgs, 0, args.length - 1);
if (command != null && !command.isEmpty()) {
switch (command.toLowerCase()) {
case "console":
Console.main(commandArgs);
break;
case "dump":
Dump.main(commandArgs);
break;
default:
help();
}
} else {
help();
}
}
/**
* 1：ANSI X9.8 Format(不带主账号) 06
*
* @param password
* @param pinKey
* @return
* @throws Exception
*/
public static String pinEncode(String password, byte[] pinKey) throws Exception {
int passwordLength = password.length();
String pin_fmt = StringUtils.rightPad("0" + passwordLength + password, 16, "F");
byte[] pinBLOCK = DumpUtils.hexToBytes(pin_fmt);
System.out.println("无主帐号pinBlock:" + Dump.getHexDump(pinBLOCK));
byte[] des3Info = DesUtils.tripDesEncrypt(pinBLOCK, pinKey);
return DumpUtils.bytesToHex(des3Info);
}
/**
* 1：ANSI X9.8 Format(带主账号)
*
* @param password
* @param pinKey
* @param pan
* @return
* @throws Exception
*/
public static String pinEncode(String password, byte[] pinKey, String pan) throws Exception {
int passwordLength = password.length();
int panLength = pan.length();
String pin_fmt = StringUtils.rightPad("0" + passwordLength + password, 16, "F");
byte[] pinBLOCK = DumpUtils.hexToBytes(pin_fmt);
String pin_str = "0000" + pan.substring(3, 15);
System.out.println("pinBlock:" + pin_str);
byte[] panByte = DumpUtils.hexToBytes(pin_str);
for (int i = 0; i < panByte.length; i++) {
pinBLOCK[i] ^= panByte[i];
}
System.out.println("有主帐号pinBlock:" + Dump.getHexDump(pinBLOCK));
byte[] des3Info = DesUtils.tripDesEncrypt(pinBLOCK, pinKey);
return DumpUtils.bytesToHex(des3Info);
}
public void packetReceived(byte[] packet) {
// XXX: hack: with the new packetsource format, packet does not
// contain a crc field, so numElements_data() will be wrong. But we
// access the data area via dataSet/dataGet, so we're ok.
// this is where the source comes in to create the correct packet
final TOSMsg msg = messageFactory.createTOSMsg(packet);
if (DEBUG) Dump.dump("Received message", packet);
if (drop_bad_crc && msg.get_crc() != 0x01) {
// Drop message
if (DISPLAY_ERROR_MSGS) Dump.dump("Dropping packet with bad CRC", packet);
return;
}
if (groupId == MoteIF.ANY_GROUP_ID || msg.get_group() == groupId) {
Integer type = new Integer(msg.get_type());
Vector vec = (Vector) templateTbl.get(type);
if (vec == null) {
if (DEBUG)
Dump.dump(
"Received packet with type " + msg.get_type() + ", but no listeners registered",
packet);
return;
}
int length = msg.get_length();
Enumeration en = vec.elements();
while (en.hasMoreElements()) {
msgTemplate temp = (msgTemplate) en.nextElement();
Message received;
// Erk - end up cloning the message multiple times in case
// different templates used for different listeners
try {
received = temp.template.clone(length);
received.dataSet(msg.dataGet(), msg.offset_data(0), 0, length);
} catch (ArrayIndexOutOfBoundsException e) {
/*
* Note: this will not catch messages whose length is
* incorrect, but less than DATA_LENGTH (see AM.h) + 2
*/
error(temp, "invalid length message received (too long)");
continue;
} catch (Exception e) {
error(temp, "couldn't clone message!");
continue;
}
/*
* Messages that are longer than the template might have a
* variable-sized array at their end
*/
if (temp.template.dataGet().length > length) {
error(temp, "invalid length message received (too short)");
continue;
}
temp.listener.messageReceived(msg.get_addr(), received);
}
} else {
if (DISPLAY_ERROR_MSGS) Dump.dump("Dropping packet with bad group ID", packet);
}
}
boolean dodata(ServletTest testcase) throws Exception {
boolean pass = true;
String baseline;
// Create request and response objects
Mocker mocker = new Mocker("dap4", testcase.makeurl(RequestMode.DAP), this);
byte[] byteresult = null; // output
// See if the servlet can process this
try {
byteresult = mocker.execute();
} catch (Throwable t) {
System.out.println(testcase.xfail ? "XFail" : "Fail");
t.printStackTrace();
return testcase.xfail;
}
if (prop_debug || DEBUG) {
DapDump.dumpbytestream(byteresult, ByteOrder.nativeOrder(), "TestServlet.dodata");
}
if (!testcase.xfail && prop_generate) {
// Dump the serialization into a file; this also includes the dmr
String target = testcase.generatepath + ".raw";
writefile(target, byteresult);
}
if (DEBUG) {
System.out.println("///////////////////");
ByteBuffer datab = ByteBuffer.wrap(byteresult).order(ByteOrder.nativeOrder());
DapDump.dumpbytes(datab, true);
System.out.println("///////////////////");
System.out.flush();
}
// Setup a ChunkInputStream
ByteArrayInputStream bytestream = new ByteArrayInputStream(byteresult);
ChunkInputStream reader =
new ChunkInputStream(bytestream, RequestMode.DAP, ByteOrder.nativeOrder());
String sdmr = reader.readDMR(); // Read the DMR
if (prop_visual) visual(testcase.title + ".dmr.dap", sdmr);
Dump printer = new Dump();
String sdata =
printer.dumpdata(reader, testcase.checksumming, reader.getByteOrder(), testcase.template);
if (prop_visual) visual(testcase.title + ".dap", sdata);
if (!testcase.xfail && prop_baseline) writefile(testcase.baselinepath + ".dap", sdata);
if (prop_diff) {
// compare with baseline
// Read the baseline file
System.out.println("Note Comparison:");
String baselinecontent = readfile(testcase.baselinepath + ".dap");
pass = compare(baselinecontent, sdata);
System.out.println(pass ? "Pass" : "Fail");
}
return pass;
}
/**
* write out the report's content
*
* @param bw the writer to use
* @throws IOException if an error occurs
*/
protected void writeHtmlBodyContent(BufferedWriter bw) throws IOException {
bw.write("<table>" + Dump.newLine());
bw.write(" <tr>" + Dump.newLine());
bw.write(" <th>Class</th>" + Dump.newLine());
bw.write(" <th>Depends On</th>" + Dump.newLine());
bw.write(" </tr>" + Dump.newLine());
SortedMap<String, SortedSet<String>> result = new TreeMap<String, SortedSet<String>>();
boolean odd = true;
for (Archive archive : archives) {
if (archive.getType() == ArchiveTypes.JAR) {
SortedMap<String, SortedSet<String>> classDependencies = archive.getClassDependencies();
Iterator<Map.Entry<String, SortedSet<String>>> dit =
classDependencies.entrySet().iterator();
while (dit.hasNext()) {
Map.Entry<String, SortedSet<String>> entry = dit.next();
String clz = entry.getKey();
SortedSet<String> deps = entry.getValue();
SortedSet<String> newDeps = new TreeSet<String>();
for (String dep : deps) {
if (!dep.equals(clz)) {
newDeps.add(dep);
}
}
result.put(clz, newDeps);
}
}
}
Iterator<Map.Entry<String, SortedSet<String>>> rit = result.entrySet().iterator();
while (rit.hasNext()) {
Map.Entry<String, SortedSet<String>> entry = rit.next();
String clz = entry.getKey();
SortedSet<String> deps = entry.getValue();
if (odd) {
bw.write(" <tr class=\"rowodd\">" + Dump.newLine());
} else {
bw.write(" <tr class=\"roweven\">" + Dump.newLine());
}
bw.write(" <td>" + clz + "</a></td>" + Dump.newLine());
bw.write(" <td>");
Iterator<String> sit = deps.iterator();
while (sit.hasNext()) {
String dep = sit.next();
bw.write(dep);
if (sit.hasNext()) {
bw.write(", ");
}
}
bw.write("</td>" + Dump.newLine());
bw.write(" </tr>" + Dump.newLine());
odd = !odd;
}
bw.write("</table>" + Dump.newLine());
}
/**
* Factory for command line tools to call different functions
*
* @author Muhammad Shamim
* @since 1/30/2015
*/
public class CLTFactory {
// Commenting some out because we're not going to release all these when we release CLT
private static final String[] commandLineToolUsages = {
// "addGWNorm", "addGWNorm <input_HiC_file> <min resolution>",
// "addNorm", "addNorm <input_HiC_file> [0 for no frag, 1 for no single frag]",
// "bigWig", "bigWig <bigWig path or URL> <window size in bp> [chr] [start base]
// [end base]",
// "binToPairs", "binToPairs <input_HiC_file> <output_HiC_file>",
// "bpToFrag", "bpToFrag <fragmentFile> <inputBedFile> <outputFile>",
// "calcKR", "calcKR <input_HiC_file>",
// "fragmentToBed","fragmentToBed <fragmentFile>",
// "pairsToBin", "pairsToBin <input_HiC_file> <output_HiC_file> <genomeID>",
// "db", "db <frag|annot|update> [items]",
Dump.getUsage(),
PreProcessing.getBasicUsage(),
APA.getBasicUsage(),
Arrowhead.getBasicUsage(),
HiCCUPS.getBasicUsage(),
HiCCUPSDiff.getBasicUsage(),
ValidateFile.getUsage()
};
public static void generalUsage() {
System.out.println("Juicebox and Juicer Command Line Tools Usage:");
for (String usage : commandLineToolUsages) {
System.out.println("\t\t" + usage);
}
System.out.println("Type juicebox <commandName> for more detailed usage instructions");
}
public static JuiceboxCLT getCLTCommand(String cmd) {
cmd = cmd.toLowerCase();
if (cmd.equals("pre")) {
return new PreProcessing();
} else if (cmd.equals("dump")) {
return new Dump();
} else if (cmd.equals("validate")) {
return new ValidateFile();
} else if (cmd.equals("addGWNorm".toLowerCase())) {
return new AddGWNorm();
} else if (cmd.equals("addNorm".toLowerCase())) {
return new AddNorm();
} else if (cmd.equals("apa")) {
return new APA();
} else if (cmd.equals("compare")) {
return new CompareLists();
} else if (cmd.equals("arrowhead")) {
return new Arrowhead();
} else if (cmd.equals("bigWig".toLowerCase())) {
return new BigWig();
} else if (cmd.equals("binToPairs".toLowerCase())) {
return new BinToPairs();
} else if (cmd.equals("bpToFrag".toLowerCase())) {
return new BPToFragment();
} else if (cmd.equals("calcKR".toLowerCase())) {
return new CalcKR();
} else if (cmd.equals("fragmentToBed".toLowerCase())) {
return new FragmentToBed();
} else if (cmd.equals("hiccups")) {
return new HiCCUPS();
} else if (cmd.equals("motifs")) {
return new MotifFinder();
} else if (cmd.equals("pairsToBin".toLowerCase())) {
return new PairsToBin();
} else if (cmd.equals("db")) {
return new SQLDatabase();
} else if (cmd.equals("hiccupsdiff")) {
return new HiCCUPSDiff();
} else if (cmd.equals("ab_compdiff")) {
return new ABCompartmentsDiff();
}
return null;
}
}
