/**
* Creates the logfile to write log-infos into.
*
* @return The writer object instance
*/
private static PrintWriter createLogFile() {
String tempDir = System.getProperty("java.io.tmpdir");
File tempDirFile = new File(tempDir);
try {
tempDirFile.mkdirs();
} catch (RuntimeException e) {
e.printStackTrace();
}
String logfilename = LOGFILENAME;
System.out.println("creating Logfile: '" + logfilename + "' in: '" + tempDir + "'");
File out = new File(tempDir, logfilename);
PrintWriter logfile;
if (tempDirFile.canWrite()) {
try {
BufferedWriter fw =
new BufferedWriter(new OutputStreamWriter(new FileOutputStream(out), "UTF-8"));
logfile = setLogFile(new PrintWriter(fw));
} catch (Exception e) {
logfile = null;
e.printStackTrace();
}
} else {
logfile = null;
System.err.println("Fatal: cannot write File: '" + logfilename + "' into: " + tempDirFile);
}
return logfile;
}
public static void doThis() {
try {
NonRTException.entry();
RTException.entry();
} catch (RuntimeException e) {
e.printStackTrace();
// } catch (IOException e) {
// e.printStackTrace();
}
}
public static void main(String[] args) {
String inputMaf = null;
String outputMaf = null;
// default config params
boolean useCache = true; // use cache or not
boolean sort = false; // sort output MAF cols or not
boolean addMissing = false; // add missing standard cols or not
// process program arguments
int i;
for (i = 0; i < args.length; i++) {
if (args[i].startsWith("-")) {
if (args[i].equalsIgnoreCase("-nocache")) {
useCache = false;
} else if (args[i].equalsIgnoreCase("-sort")) {
sort = true;
} else if (args[i].equalsIgnoreCase("-std")) {
addMissing = true;
}
} else {
break;
}
}
if (args.length - i < 2) {
System.out.println(
"command line usage: oncotateMaf.sh [-nocache] [-sort] [-std] "
+ "<input_maf_file> <output_maf_file>");
System.exit(1);
}
inputMaf = args[i];
outputMaf = args[i + 1];
int oncoResult = 0;
try {
oncoResult = driver(inputMaf, outputMaf, useCache, sort, addMissing);
} catch (RuntimeException e) {
System.out.println("Fatal error: " + e.getMessage());
e.printStackTrace();
System.exit(1);
} finally {
// check errors at the end
if (oncoResult != 0) {
// TODO produce different error codes, for different types of errors?
System.out.println("Process completed with " + oncoResult + " error(s).");
System.exit(2);
}
}
}
/**
* @param path
* @return byte or null
*/
public byte[] getFile(String path) {
Log.d(TAG, "get file " + path); // NON-NLS
File f = new File(getFullCachePath(path));
if (!f.exists()) {
Log.w(TAG, "file: " + f.toString() + " not exists"); // NON-NLS
return null;
}
try {
ByteArrayOutputStream out = new ByteArrayOutputStream();
FileInputStream fileInputStream = new FileInputStream(f);
byte[] buf = new byte[1024];
int numRead = 0;
while ((numRead = fileInputStream.read(buf)) != -1) out.write(buf, 0, numRead);
fileInputStream.close();
return out.toByteArray();
} catch (FileNotFoundException e) {
Log.w(TAG, e.getMessage());
e.printStackTrace();
absoluteDelete(path);
return null;
} catch (StreamCorruptedException e) {
Log.w(TAG, e.getMessage());
e.printStackTrace();
absoluteDelete(path);
return null;
} catch (IOException e) {
Log.w(TAG, e.getMessage());
e.printStackTrace();
absoluteDelete(path);
return null;
} catch (IllegalArgumentException e) {
Log.w(TAG, e.getMessage());
e.printStackTrace();
absoluteDelete(path);
return null;
} catch (RuntimeException e) {
// не позволим кэшу убить нашу программу
Log.w(TAG, e.getMessage());
e.printStackTrace();
absoluteDelete(path);
return null;
} catch (Exception e) {
// не позволим кэшу убить нашу программу
Log.w(TAG, e.getMessage());
e.printStackTrace();
absoluteDelete(path);
return null;
}
}
public void doFilter(ServletRequest request, ServletResponse response, FilterChain chain)
throws IOException, ServletException {
// session属于http范畴，所以要将ServletRequest转换成httpServletRequest
try {
HttpServletRequest req = (HttpServletRequest) request;
HttpSession session = req.getSession();
if (session.getAttribute("username") != null) {
chain.doFilter(request, response);
} else {
request.getRequestDispatcher("error.jsp").forward(request, response);
}
} catch (RuntimeException e) {
e.printStackTrace();
}
}
public JSSA(Type.Class c, DataInput in, ConstantPool cp) throws IOException {
super(c, in, cp);
local = new Expr[maxLocals];
stack = new Expr[maxStack];
int n = 0;
if (!isStatic()) local[n++] = new Argument("this", method.getDeclaringClass());
for (int i = 0; i < this.method.getNumArgs(); i++)
local[n++] = new Argument("arg" + i, this.method.getArgType(i));
for (int i = 0; i < size(); i++) {
int op = get(i);
Object arg = getArg(i);
try {
Object o = addOp(op, arg);
if (o != null) {
ops[numOps] = o;
ofs[numOps++] = i;
}
} catch (RuntimeException e) {
System.err.println("Had a problem at PC: " + i + " of " + method);
e.printStackTrace();
throw new IOException("invalid class file");
}
}
}
/**
* @param path
* @param t
* @return
*/
public List<?> getList(String path, java.lang.reflect.Type t) {
Log.d(TAG, "get list " + path); // NON-NLS
File f = new File(getFullCachePath(path));
if (!f.exists()) {
Log.w(TAG, "file: " + f.toString() + " not exists"); // NON-NLS
return null;
}
List<?> list;
try {
StringBuffer fileData = new StringBuffer();
BufferedReader reader = new BufferedReader(new FileReader(f));
char[] buf = new char[1024];
int numRead = 0;
while ((numRead = reader.read(buf)) != -1) {
String readData = String.valueOf(buf, 0, numRead);
fileData.append(readData);
}
reader.close();
String json = fileData.toString();
Log.d(TAG, "cache: " + json); // NON-NLS
list = gson.fromJson(json, t);
} catch (FileNotFoundException e) {
Log.w(TAG, e.getMessage());
e.printStackTrace();
absoluteDelete(path);
return null;
} catch (StreamCorruptedException e) {
Log.w(TAG, e.getMessage());
e.printStackTrace();
absoluteDelete(path);
return null;
} catch (IOException e) {
Log.w(TAG, e.getMessage());
e.printStackTrace();
absoluteDelete(path);
return null;
} catch (JsonSyntaxException e) {
Log.w(TAG, e.getMessage());
e.printStackTrace();
absoluteDelete(path);
return null;
} catch (IllegalArgumentException e) {
Log.w(TAG, e.getMessage());
e.printStackTrace();
absoluteDelete(path);
return null;
} catch (RuntimeException e) {
// не позволим кэшу убить нашу программу
Log.w(TAG, e.getMessage());
e.printStackTrace();
absoluteDelete(path);
return null;
} catch (Exception e) {
// не позволим кэшу убить нашу программу
Log.w(TAG, e.getMessage());
e.printStackTrace();
absoluteDelete(path);
return null;
}
return list;
}
public <T> T get(String path, Class<T> c) {
Log.d(TAG, "get " + path); // NON-NLS
File f = new File(getFullCachePath(path));
if (!f.exists()) {
Log.w(TAG, "file: " + f.toString() + " not exists"); // NON-NLS
return null;
}
T object;
try {
StringBuffer fileData = new StringBuffer();
BufferedReader reader = new BufferedReader(new FileReader(f));
char[] buf = new char[1024];
int numRead = 0;
while ((numRead = reader.read(buf)) != -1) {
String readData = String.valueOf(buf, 0, numRead);
fileData.append(readData);
}
reader.close();
String json = fileData.toString();
Log.d(TAG, "cache: " + json); // NON-NLS
object = getGson().fromJson(json, c);
} catch (FileNotFoundException e) {
Log.w(TAG, e.getMessage());
e.printStackTrace();
absoluteDelete(path);
return null;
} catch (StreamCorruptedException e) {
Log.w(TAG, e.getMessage());
e.printStackTrace();
absoluteDelete(path);
return null;
} catch (IOException e) {
Log.w(TAG, e.getMessage());
e.printStackTrace();
absoluteDelete(path);
return null;
} catch (JsonSyntaxException e) {
Log.w(TAG, e.getMessage());
e.printStackTrace();
absoluteDelete(path);
return null;
} catch (IllegalArgumentException e) {
Log.w(TAG, e.getMessage());
e.printStackTrace();
absoluteDelete(path);
return null;
} catch (RuntimeException e) {
// не позволим кэшу убить нашу программу
Log.w(TAG, e.getMessage());
e.printStackTrace();
absoluteDelete(path);
return null;
} catch (Exception e) {
// не позволим кэшу убить нашу программу
Log.w(TAG, e.getMessage());
e.printStackTrace();
absoluteDelete(path);
return null;
}
if (object.getClass().toString().equals(c.toString())) return object;
else return null;
}
// private static final ArrayList<String> ignoreSuffixes = new
// ArrayList<>(Arrays.asList("Customizer", "BeanInfo"));
// private static final int ignoreSuffixesSize = ignoreSuffixes.size();
// TODO: does this need synchronized? slows it down...
private Class<?> loadClassInternal(String className, boolean resolve)
throws ClassNotFoundException {
/* This may not be a good idea, Groovy looks for all sorts of bogus class name but there may be a reason so not doing this or looking for other patterns:
for (int i = 0; i < ignoreSuffixesSize; i++) {
String ignoreSuffix = ignoreSuffixes.get(i);
if (className.endsWith(ignoreSuffix)) {
ClassNotFoundException cfne = new ClassNotFoundException("Ignoring Groovy style bogus class name " + className);
classCache.put(className, cfne);
throw cfne;
}
}
*/
Class<?> c = null;
try {
// classes handled opposite of resources, try parent first (avoid java.lang.LinkageError)
try {
ClassLoader cl = getParent();
c = cl.loadClass(className);
} catch (ClassNotFoundException | NoClassDefFoundError e) {
// do nothing, common that class won't be found if expected in additional JARs and class
// directories
} catch (RuntimeException e) {
e.printStackTrace();
throw e;
}
if (c == null) {
try {
if (trackKnown) {
File classFile = knownClassFiles.get(className);
if (classFile != null) c = makeClass(className, classFile);
if (c == null) {
JarEntryInfo jei = knownClassJarEntries.get(className);
if (jei != null) c = makeClass(className, jei.file, jei.entry, jei.jarLocation);
}
}
// not found in known? search through all
c = findJarClass(className);
} catch (Exception e) {
System.out.println(
"Error loading class [" + className + "] from additional jars: " + e.toString());
e.printStackTrace();
}
}
// System.out.println("Loading class name [" + className + "] got class: " + c);
if (c == null) {
ClassNotFoundException cnfe =
new ClassNotFoundException("Class " + className + " not found.");
if (rememberClassNotFound) {
// Groovy seems to look, then re-look, for funny names like:
// groovy.lang.GroovyObject$java$io$org$moqui$entity$EntityListIterator
// java.io.org$moqui$entity$EntityListIterator
// groovy.util.org$moqui$context$ExecutionContext
// org$moqui$context$ExecutionContext
// Groovy does similar with *Customizer and *BeanInfo; so just don't remember any of these
// In general it seems that anything with a '$' needs to be excluded
if (!className.contains("$")
&& !className.endsWith("Customizer")
&& !className.endsWith("BeanInfo")) {
ClassNotFoundException existingExc = notFoundCache.putIfAbsent(className, cnfe);
if (existingExc != null) throw existingExc;
}
}
throw cnfe;
} else {
classCache.put(className, c);
}
return c;
} finally {
if (c != null && resolve) resolveClass(c);
}
}