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[GNUnet-SVN] r23981 - in monkey/trunk/pathologist/src: include pathologi


From: gnunet
Subject: [GNUnet-SVN] r23981 - in monkey/trunk/pathologist/src: include pathologist
Date: Mon, 24 Sep 2012 20:49:45 +0200

Author: teichm
Date: 2012-09-24 20:49:45 +0200 (Mon, 24 Sep 2012)
New Revision: 23981

Added:
   monkey/trunk/pathologist/src/include/gnunet_common.h
   monkey/trunk/pathologist/src/include/gnunet_getopt_lib.h
   monkey/trunk/pathologist/src/include/platform.h
   monkey/trunk/pathologist/src/pathologist/getopt.c
   monkey/trunk/pathologist/src/pathologist/getopt_helpers.c
Modified:
   monkey/trunk/pathologist/src/pathologist/Makefile.am
Log:
added gnunet getopt files and modified them to compile.
they are not used yet however.



Added: monkey/trunk/pathologist/src/include/gnunet_common.h
===================================================================
--- monkey/trunk/pathologist/src/include/gnunet_common.h                        
        (rev 0)
+++ monkey/trunk/pathologist/src/include/gnunet_common.h        2012-09-24 
18:49:45 UTC (rev 23981)
@@ -0,0 +1,889 @@
+/*
+     This file is part of GNUnet.
+     (C) 2006, 2009 Christian Grothoff (and other contributing authors)
+
+     GNUnet is free software; you can redistribute it and/or modify
+     it under the terms of the GNU General Public License as published
+     by the Free Software Foundation; either version 2, or (at your
+     option) any later version.
+
+     GNUnet is distributed in the hope that it will be useful, but
+     WITHOUT ANY WARRANTY; without even the implied warranty of
+     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+     General Public License for more details.
+
+     You should have received a copy of the GNU General Public License
+     along with GNUnet; see the file COPYING.  If not, write to the
+     Free Software Foundation, Inc., 59 Temple Place - Suite 330,
+     Boston, MA 02111-1307, USA.
+*/
+
+/**
+ * @file include/gnunet_common.h
+ * @brief commonly used definitions; globals in this file
+ *        are exempt from the rule that the module name ("common")
+ *        must be part of the symbol name.
+ *
+ * @author Christian Grothoff
+ * @author Nils Durner
+ */
+#ifndef GNUNET_COMMON_H
+#define GNUNET_COMMON_H
+
+#if HAVE_SYS_SOCKET_H
+#include <sys/socket.h>
+#endif
+#if HAVE_NETINET_IN_H
+#include <netinet/in.h>
+#endif
+#ifdef MINGW
+#include "winproc.h"
+#endif
+#ifdef HAVE_STDINT_H
+#include <stdint.h>
+#endif
+#ifdef HAVE_STDARG_H
+#include <stdarg.h>
+#endif
+
+#ifdef __cplusplus
+extern "C"
+{
+#if 0                           /* keep Emacsens' auto-indent happy */
+}
+#endif
+#endif
+
+/**
+ * Version of the API (for entire gnunetutil.so library).
+ */
+#define GNUNET_UTIL_VERSION 0x00090200
+
+/**
+ * Named constants for return values.  The following
+ * invariants hold: "GNUNET_NO == 0" (to allow "if (GNUNET_NO)")
+ * "GNUNET_OK != GNUNET_SYSERR", "GNUNET_OK != GNUNET_NO", "GNUNET_NO != 
GNUNET_SYSERR"
+ * and finally "GNUNET_YES != GNUNET_NO".
+ */
+#define GNUNET_OK      1
+#define GNUNET_SYSERR -1
+#define GNUNET_YES     1
+#define GNUNET_NO      0
+
+#define GNUNET_MIN(a,b) (((a) < (b)) ? (a) : (b))
+
+#define GNUNET_MAX(a,b) (((a) > (b)) ? (a) : (b))
+
+/* some systems use one underscore only, and mingw uses no underscore... */
+#ifndef __BYTE_ORDER
+#ifdef _BYTE_ORDER
+#define __BYTE_ORDER _BYTE_ORDER
+#else
+#ifdef BYTE_ORDER
+#define __BYTE_ORDER BYTE_ORDER
+#endif
+#endif
+#endif
+#ifndef __BIG_ENDIAN
+#ifdef _BIG_ENDIAN
+#define __BIG_ENDIAN _BIG_ENDIAN
+#else
+#ifdef BIG_ENDIAN
+#define __BIG_ENDIAN BIG_ENDIAN
+#endif
+#endif
+#endif
+#ifndef __LITTLE_ENDIAN
+#ifdef _LITTLE_ENDIAN
+#define __LITTLE_ENDIAN _LITTLE_ENDIAN
+#else
+#ifdef LITTLE_ENDIAN
+#define __LITTLE_ENDIAN LITTLE_ENDIAN
+#endif
+#endif
+#endif
+
+/**
+ * Endian operations
+ */
+
+# if __BYTE_ORDER == __LITTLE_ENDIAN
+#  define GNUNET_htobe16(x) __bswap_16 (x)
+#  define GNUNET_htole16(x) (x)
+#  define GNUNET_be16toh(x) __bswap_16 (x)
+#  define GNUNET_le16toh(x) (x)
+
+#  define GNUNET_htobe32(x) __bswap_32 (x)
+#  define GNUNET_htole32(x) (x)
+#  define GNUNET_be32toh(x) __bswap_32 (x)
+#  define GNUNET_le32toh(x) (x)
+
+#  define GNUNET_htobe64(x) __bswap_64 (x)
+#  define GNUNET_htole64(x) (x)
+#  define GNUNET_be64toh(x) __bswap_64 (x)
+#  define GNUNET_le64toh(x) (x)
+#endif
+# if __BYTE_ORDER == __BIG_ENDIAN
+#  define GNUNET_htobe16(x) (x)
+#  define GNUNET_htole16(x) __bswap_16 (x)
+#  define GNUNET_be16toh(x) (x)
+#  define GNUNET_le16toh(x) __bswap_16 (x)
+
+#  define GNUNET_htobe32(x) (x)
+#  define GNUNET_htole32(x) __bswap_32 (x)
+#  define GNUNET_be32toh(x) (x)
+#  define GNUNET_le32toh(x) __bswap_32 (x)
+
+#  define GNUNET_htobe64(x) (x)
+#  define GNUNET_htole64(x) __bswap_64 (x)
+#  define GNUNET_be64toh(x) (x)
+#  define GNUNET_le64toh(x) __bswap_64 (x)
+#endif
+
+
+
+
+/**
+ * gcc-ism to get packed structs.
+ */
+#define GNUNET_PACKED __attribute__((packed))
+
+/**
+ * gcc-ism to get gcc bitfield layout when compiling with -mms-bitfields
+ */
+#if MINGW
+#define GNUNET_GCC_STRUCT_LAYOUT __attribute__((gcc_struct))
+#else
+#define GNUNET_GCC_STRUCT_LAYOUT
+#endif
+
+/**
+ * gcc-ism to force alignment; we use this to align char-arrays
+ * that may then be cast to 'struct's.  See also gcc
+ * bug #33594.
+ */
+#ifdef __BIGGEST_ALIGNMENT__
+#define GNUNET_ALIGN __attribute__((aligned (__BIGGEST_ALIGNMENT__)))
+#else
+#define GNUNET_ALIGN __attribute__((aligned (8)))
+#endif
+
+/**
+ * gcc-ism to document unused arguments
+ */
+#define GNUNET_UNUSED __attribute__((unused))
+
+/**
+ * gcc-ism to document functions that don't return
+ */
+#define GNUNET_NORETURN __attribute__((noreturn))
+
+#if MINGW
+#if __GNUC__ > 3
+/**
+ * gcc 4.x-ism to pack structures even on W32 (to be used before structs);
+ * Using this would cause structs to be unaligned on the stack on Sparc,
+ * so we *only* use this on W32 (see #670578 from Debian); fortunately,
+ * W32 doesn't run on sparc anyway.
+ */
+#define GNUNET_NETWORK_STRUCT_BEGIN \
+  _Pragma("pack(push)") \
+  _Pragma("pack(1)")
+
+/**
+ * gcc 4.x-ism to pack structures even on W32 (to be used after structs)
+ * Using this would cause structs to be unaligned on the stack on Sparc,
+ * so we *only* use this on W32 (see #670578 from Debian); fortunately,
+ * W32 doesn't run on sparc anyway.
+ */
+#define GNUNET_NETWORK_STRUCT_END _Pragma("pack(pop)")
+
+#else
+#error gcc 4.x or higher required on W32 systems
+#endif
+#else
+/**
+ * Define as empty, GNUNET_PACKED should suffice, but this won't work on W32
+ */
+#define GNUNET_NETWORK_STRUCT_BEGIN 
+
+/**
+ * Define as empty, GNUNET_PACKED should suffice, but this won't work on W32;
+ */
+#define GNUNET_NETWORK_STRUCT_END
+#endif
+
+/* ************************ super-general types *********************** */
+
+GNUNET_NETWORK_STRUCT_BEGIN
+
+/**
+ * Header for all communications.
+ */
+struct GNUNET_MessageHeader
+{
+
+  /**
+   * The length of the struct (in bytes, including the length field itself),
+   * in big-endian format.
+   */
+  uint16_t size GNUNET_PACKED;
+
+  /**
+   * The type of the message (GNUNET_MESSAGE_TYPE_XXXX), in big-endian format.
+   */
+  uint16_t type GNUNET_PACKED;
+
+};
+
+
+/**
+ * @brief 512-bit hashcode
+ */
+struct GNUNET_HashCode
+{
+  uint32_t bits[512 / 8 / sizeof (uint32_t)];   /* = 16 */
+};
+
+
+/**
+ * The identity of the host (basically the SHA-512 hashcode of
+ * it's public key).
+ */
+struct GNUNET_PeerIdentity
+{
+  struct GNUNET_HashCode hashPubKey;
+};
+GNUNET_NETWORK_STRUCT_END
+
+/**
+ * Function called with a filename.
+ *
+ * @param cls closure
+ * @param filename complete filename (absolute path)
+ * @return GNUNET_OK to continue to iterate,
+ *  GNUNET_SYSERR to abort iteration with error!
+ */
+typedef int (*GNUNET_FileNameCallback) (void *cls, const char *filename);
+
+
+/* ****************************** logging ***************************** */
+
+/**
+ * Types of errors.
+ */
+enum GNUNET_ErrorType
+{
+  GNUNET_ERROR_TYPE_UNSPECIFIED = -1,
+  GNUNET_ERROR_TYPE_NONE = 0,
+  GNUNET_ERROR_TYPE_ERROR = 1,
+  GNUNET_ERROR_TYPE_WARNING = 2,
+  GNUNET_ERROR_TYPE_INFO = 4,
+  GNUNET_ERROR_TYPE_DEBUG = 8,
+  GNUNET_ERROR_TYPE_INVALID = 16,
+  GNUNET_ERROR_TYPE_BULK = 32
+};
+
+
+/**
+ * User-defined handler for log messages.
+ *
+ * @param cls closure
+ * @param kind severeity
+ * @param component what component is issuing the message?
+ * @param date when was the message logged?
+ * @param message what is the message
+ */
+typedef void (*GNUNET_Logger) (void *cls, enum GNUNET_ErrorType kind,
+                               const char *component, const char *date,
+                               const char *message);
+
+
+/**
+ * Get the number of log calls that are going to be skipped
+ *
+ * @return number of log calls to be ignored
+ */
+int
+GNUNET_get_log_skip ();
+
+#if !defined(GNUNET_CULL_LOGGING)
+int
+GNUNET_get_log_call_status (int caller_level, const char *comp,
+                            const char *file, const char *function, int line);
+#endif
+/**
+ * Main log function.
+ *
+ * @param kind how serious is the error?
+ * @param message what is the message (format string)
+ * @param ... arguments for format string
+ */
+void
+GNUNET_log_nocheck (enum GNUNET_ErrorType kind, const char *message, ...);
+
+/* from glib */
+#if defined(__GNUC__) && (__GNUC__ > 2) && defined(__OPTIMIZE__)
+#define _GNUNET_BOOLEAN_EXPR(expr)              \
+ __extension__ ({                               \
+   int _gnunet_boolean_var_;                    \
+   if (expr)                                    \
+      _gnunet_boolean_var_ = 1;                 \
+   else                                         \
+      _gnunet_boolean_var_ = 0;                 \
+   _gnunet_boolean_var_;                        \
+})
+#define GN_LIKELY(expr) (__builtin_expect (_GNUNET_BOOLEAN_EXPR(expr), 1))
+#define GN_UNLIKELY(expr) (__builtin_expect (_GNUNET_BOOLEAN_EXPR(expr), 0))
+#else
+#define GN_LIKELY(expr) (expr)
+#define GN_UNLIKELY(expr) (expr)
+#endif
+
+#if !defined(GNUNET_LOG_CALL_STATUS)
+#define GNUNET_LOG_CALL_STATUS -1
+#endif
+
+/**
+ * Log function that specifies an alternative component.
+ * This function should be used by plugins.
+ *
+ * @param kind how serious is the error?
+ * @param comp component responsible for generating the message
+ * @param message what is the message (format string)
+ * @param ... arguments for format string
+ */
+void
+GNUNET_log_from_nocheck (enum GNUNET_ErrorType kind, const char *comp,
+                         const char *message, ...);
+
+#if !defined(GNUNET_CULL_LOGGING)
+#define GNUNET_log_from(kind,comp,...) do { int log_line = __LINE__;\
+  static int log_call_enabled = GNUNET_LOG_CALL_STATUS;\
+  if ((GNUNET_EXTRA_LOGGING > 0) || ((GNUNET_ERROR_TYPE_DEBUG & (kind)) == 0)) 
{ \
+    if (GN_UNLIKELY(log_call_enabled == -1))\
+      log_call_enabled = GNUNET_get_log_call_status ((kind) & 
(~GNUNET_ERROR_TYPE_BULK), (comp), __FILE__, __FUNCTION__, log_line); \
+    if (GN_UNLIKELY(GNUNET_get_log_skip () > 0)) { GNUNET_log_skip (-1, 
GNUNET_NO); }\
+    else {\
+      if (GN_UNLIKELY(log_call_enabled))\
+        GNUNET_log_from_nocheck ((kind), comp, __VA_ARGS__);   \
+    }\
+  }\
+} while (0)
+
+#define GNUNET_log(kind,...) do { int log_line = __LINE__;\
+  static int log_call_enabled = GNUNET_LOG_CALL_STATUS;\
+  if ((GNUNET_EXTRA_LOGGING > 0) || ((GNUNET_ERROR_TYPE_DEBUG & (kind)) == 0)) 
{ \
+    if (GN_UNLIKELY(log_call_enabled == -1))\
+      log_call_enabled = GNUNET_get_log_call_status ((kind) & 
(~GNUNET_ERROR_TYPE_BULK), NULL, __FILE__, __FUNCTION__, log_line);\
+    if (GN_UNLIKELY(GNUNET_get_log_skip () > 0)) { GNUNET_log_skip (-1, 
GNUNET_NO); }\
+    else {\
+      if (GN_UNLIKELY(log_call_enabled))\
+        GNUNET_log_nocheck ((kind), __VA_ARGS__);      \
+    }\
+  }\
+} while (0)
+#else
+#define GNUNET_log(...)
+#define GNUNET_log_from(...)
+#endif
+
+
+/**
+ * Abort the process, generate a core dump if possible.
+ */
+void
+GNUNET_abort (void) GNUNET_NORETURN;
+
+/**
+ * Ignore the next n calls to the log function.
+ *
+ * @param n number of log calls to ignore (could be negative)
+ * @param check_reset GNUNET_YES to assert that the log skip counter is 
currently zero
+ */
+void
+GNUNET_log_skip (int n, int check_reset);
+
+
+/**
+ * Setup logging.
+ *
+ * @param comp default component to use
+ * @param loglevel what types of messages should be logged
+ * @param logfile change logging to logfile (use NULL to keep stderr)
+ * @return GNUNET_OK on success, GNUNET_SYSERR if logfile could not be opened
+ */
+int
+GNUNET_log_setup (const char *comp, const char *loglevel, const char *logfile);
+
+
+/**
+ * Add a custom logger.
+ *
+ * @param logger log function
+ * @param logger_cls closure for logger
+ */
+void
+GNUNET_logger_add (GNUNET_Logger logger, void *logger_cls);
+
+
+/**
+ * Remove a custom logger.
+ *
+ * @param logger log function
+ * @param logger_cls closure for logger
+ */
+void
+GNUNET_logger_remove (GNUNET_Logger logger, void *logger_cls);
+
+
+/**
+ * Convert a hash value to a string (for printing debug messages).
+ * This is one of the very few calls in the entire API that is
+ * NOT reentrant!
+ *
+ * @param hc the hash code
+ * @return string
+ */
+const char *
+GNUNET_h2s (const struct GNUNET_HashCode * hc);
+
+
+/**
+ * Convert a hash value to a string (for printing debug messages).
+ * This prints all 104 characters of a hashcode!
+ * This is one of the very few calls in the entire API that is
+ * NOT reentrant!
+ *
+ * @param hc the hash code
+ * @return string
+ */
+const char *
+GNUNET_h2s_full (const struct GNUNET_HashCode * hc);
+
+
+/**
+ * Convert a peer identity to a string (for printing debug messages).
+ * This is one of the very few calls in the entire API that is
+ * NOT reentrant!
+ *
+ * @param pid the peer identity
+ * @return string form of the pid; will be overwritten by next
+ *         call to GNUNET_i2s.
+ */
+const char *
+GNUNET_i2s (const struct GNUNET_PeerIdentity *pid);
+
+/**
+ * Convert a peer identity to a string (for printing debug messages).
+ * This is one of the very few calls in the entire API that is
+ * NOT reentrant!
+ *
+ * @param pid the peer identity
+ * @return string form of the pid; will be overwritten by next
+ *         call to GNUNET_i2s.
+ */
+const char *
+GNUNET_i2s_full (const struct GNUNET_PeerIdentity *pid);
+
+/**
+ * Convert a "struct sockaddr*" (IPv4 or IPv6 address) to a string
+ * (for printing debug messages).  This is one of the very few calls
+ * in the entire API that is NOT reentrant!
+ *
+ * @param addr the address
+ * @param addrlen the length of the address
+ * @return nicely formatted string for the address
+ *  will be overwritten by next call to GNUNET_a2s.
+ */
+const char *
+GNUNET_a2s (const struct sockaddr *addr, socklen_t addrlen);
+
+/**
+ * Convert error type to string.
+ *
+ * @param kind type to convert
+ * @return string corresponding to the type
+ */
+const char *
+GNUNET_error_type_to_string (enum GNUNET_ErrorType kind);
+
+
+/**
+ * Use this for fatal errors that cannot be handled
+ */
+#define GNUNET_assert(cond) do { if (! (cond)) { 
GNUNET_log(GNUNET_ERROR_TYPE_ERROR, _("Assertion failed at %s:%d.\n"), 
__FILE__, __LINE__); GNUNET_abort(); } } while(0)
+
+/**
+ * Use this for fatal errors that cannot be handled
+ */
+#define GNUNET_assert_at(cond, f, l) do { if (! (cond)) { 
GNUNET_log(GNUNET_ERROR_TYPE_ERROR, _("Assertion failed at %s:%d.\n"), f, l); 
GNUNET_abort(); } } while(0)
+
+/**
+ * Use this for internal assertion violations that are
+ * not fatal (can be handled) but should not occur.
+ */
+#define GNUNET_break(cond)  do { if (! (cond)) { 
GNUNET_log(GNUNET_ERROR_TYPE_ERROR, _("Assertion failed at %s:%d.\n"), 
__FILE__, __LINE__); } } while(0)
+
+/**
+ * Use this for assertion violations caused by other
+ * peers (i.e. protocol violations).  We do not want to
+ * confuse end-users (say, some other peer runs an
+ * older, broken or incompatible GNUnet version), but
+ * we still want to see these problems during
+ * development and testing.  "OP == other peer".
+ */
+#define GNUNET_break_op(cond)  do { if (! (cond)) { 
GNUNET_log(GNUNET_ERROR_TYPE_WARNING | GNUNET_ERROR_TYPE_BULK, _("External 
protocol violation detected at %s:%d.\n"), __FILE__, __LINE__); } } while(0)
+
+/**
+ * Log an error message at log-level 'level' that indicates
+ * a failure of the command 'cmd' with the message given
+ * by strerror(errno).
+ */
+#define GNUNET_log_strerror(level, cmd) do { GNUNET_log(level, _("`%s' failed 
at %s:%d with error: %s\n"), cmd, __FILE__, __LINE__, STRERROR(errno)); } 
while(0)
+
+/**
+ * Log an error message at log-level 'level' that indicates
+ * a failure of the command 'cmd' with the message given
+ * by strerror(errno).
+ */
+#define GNUNET_log_from_strerror(level, component, cmd) do { GNUNET_log_from 
(level, component, _("`%s' failed at %s:%d with error: %s\n"), cmd, __FILE__, 
__LINE__, STRERROR(errno)); } while(0)
+
+/**
+ * Log an error message at log-level 'level' that indicates
+ * a failure of the command 'cmd' with the message given
+ * by strerror(errno).
+ */
+#define GNUNET_log_strerror_file(level, cmd, filename) do { GNUNET_log(level, 
_("`%s' failed on file `%s' at %s:%d with error: %s\n"), cmd, 
filename,__FILE__, __LINE__, STRERROR(errno)); } while(0)
+
+/**
+ * Log an error message at log-level 'level' that indicates
+ * a failure of the command 'cmd' with the message given
+ * by strerror(errno).
+ */
+#define GNUNET_log_from_strerror_file(level, component, cmd, filename) do { 
GNUNET_log_from (level, component, _("`%s' failed on file `%s' at %s:%d with 
error: %s\n"), cmd, filename,__FILE__, __LINE__, STRERROR(errno)); } while(0)
+
+/* ************************* endianess conversion ****************** */
+
+/**
+ * Convert unsigned 64-bit integer to host-byte-order.
+ * @param n the value in network byte order
+ * @return the same value in host byte order
+ */
+uint64_t
+GNUNET_ntohll (uint64_t n);
+
+/**
+ * Convert unsigned 64-bit integer to network-byte-order.
+ * @param n the value in host byte order
+ * @return the same value in network byte order
+ */
+uint64_t
+GNUNET_htonll (uint64_t n);
+
+/**
+ * Convert double to network-byte-order.
+ * @param d the value in network byte order
+ * @return the same value in host byte order
+ */
+double 
+GNUNET_hton_double (double d);
+
+/**
+ * Convert double to host-byte-order
+ * @param d the value in network byte order
+ * @return the same value in host byte order
+ */
+double 
+GNUNET_ntoh_double (double d);
+
+/* ************************* allocation functions ****************** */
+
+/**
+ * Maximum allocation with GNUNET_malloc macro.
+ */
+#define GNUNET_MAX_MALLOC_CHECKED (1024 * 1024 * 40)
+
+/**
+ * Wrapper around malloc. Allocates size bytes of memory.
+ * The memory will be zero'ed out.
+ *
+ * @param size the number of bytes to allocate, must be
+ *        smaller than 40 MB.
+ * @return pointer to size bytes of memory, never NULL (!)
+ */
+#define GNUNET_malloc(size) GNUNET_xmalloc_(size, __FILE__, __LINE__)
+
+/**
+ * Allocate and initialize a block of memory.
+ *
+ * @param buf data to initalize the block with
+ * @param size the number of bytes in buf (and size of the allocation)
+ * @return pointer to size bytes of memory, never NULL (!)
+ */
+#define GNUNET_memdup(buf,size) GNUNET_xmemdup_(buf, size, __FILE__, __LINE__)
+
+/**
+ * Wrapper around malloc. Allocates size bytes of memory.
+ * The memory will be zero'ed out.
+ *
+ * @param size the number of bytes to allocate
+ * @return pointer to size bytes of memory, NULL if we do not have enough 
memory
+ */
+#define GNUNET_malloc_large(size) GNUNET_xmalloc_unchecked_(size, __FILE__, 
__LINE__)
+
+/**
+ * Wrapper around realloc. Rellocates size bytes of memory.
+ *
+ * @param ptr the pointer to reallocate
+ * @param size the number of bytes to reallocate
+ * @return pointer to size bytes of memory
+ */
+#define GNUNET_realloc(ptr, size) GNUNET_xrealloc_(ptr, size, __FILE__, 
__LINE__)
+
+/**
+ * Wrapper around free. Frees the memory referred to by ptr.
+ * Note that is is generally better to free memory that was
+ * allocated with GNUNET_array_grow using GNUNET_array_grow(mem, size, 0) 
instead of GNUNET_free.
+ *
+ * @param ptr location where to free the memory. ptr must have
+ *     been returned by GNUNET_strdup, GNUNET_strndup, GNUNET_malloc or 
GNUNET_array_grow earlier.
+ */
+#define GNUNET_free(ptr) GNUNET_xfree_(ptr, __FILE__, __LINE__)
+
+/**
+ * Free the memory pointed to by ptr if ptr is not NULL.
+ * Equivalent to if (ptr!=null)GNUNET_free(ptr).
+ *
+ * @param ptr the location in memory to free
+ */
+#define GNUNET_free_non_null(ptr) do { void * __x__ = ptr; if (__x__ != NULL) 
{ GNUNET_free(__x__); } } while(0)
+
+/**
+ * Wrapper around GNUNET_strdup.  Makes a copy of the zero-terminated string
+ * pointed to by a.
+ *
+ * @param a pointer to a zero-terminated string
+ * @return a copy of the string including zero-termination
+ */
+#define GNUNET_strdup(a) GNUNET_xstrdup_(a,__FILE__,__LINE__)
+
+/**
+ * Wrapper around GNUNET_strndup.  Makes a partial copy of the string
+ * pointed to by a.
+ *
+ * @param a pointer to a string
+ * @param length of the string to duplicate
+ * @return a partial copy of the string including zero-termination
+ */
+#define GNUNET_strndup(a,length) GNUNET_xstrndup_(a,length,__FILE__,__LINE__)
+
+/**
+ * Grow a well-typed (!) array.  This is a convenience
+ * method to grow a vector <tt>arr</tt> of size <tt>size</tt>
+ * to the new (target) size <tt>tsize</tt>.
+ * <p>
+ *
+ * Example (simple, well-typed stack):
+ *
+ * <pre>
+ * static struct foo * myVector = NULL;
+ * static int myVecLen = 0;
+ *
+ * static void push(struct foo * elem) {
+ *   GNUNET_array_grow(myVector, myVecLen, myVecLen+1);
+ *   memcpy(&myVector[myVecLen-1], elem, sizeof(struct foo));
+ * }
+ *
+ * static void pop(struct foo * elem) {
+ *   if (myVecLen == 0) die();
+ *   memcpy(elem, myVector[myVecLen-1], sizeof(struct foo));
+ *   GNUNET_array_grow(myVector, myVecLen, myVecLen-1);
+ * }
+ * </pre>
+ *
+ * @param arr base-pointer of the vector, may be NULL if size is 0;
+ *        will be updated to reflect the new address. The TYPE of
+ *        arr is important since size is the number of elements and
+ *        not the size in bytes
+ * @param size the number of elements in the existing vector (number
+ *        of elements to copy over)
+ * @param tsize the target size for the resulting vector, use 0 to
+ *        free the vector (then, arr will be NULL afterwards).
+ */
+#define GNUNET_array_grow(arr,size,tsize) GNUNET_xgrow_((void**)&arr, 
sizeof(arr[0]), &size, tsize, __FILE__, __LINE__)
+
+/**
+ * Append an element to a list (growing the
+ * list by one).
+ */
+#define GNUNET_array_append(arr,size,element) do { 
GNUNET_array_grow(arr,size,size+1); arr[size-1] = element; } while(0)
+
+/**
+ * Like snprintf, just aborts if the buffer is of insufficient size.
+ *
+ * @param buf pointer to buffer that is written to
+ * @param size number of bytes in buf
+ * @param format format strings
+ * @param ... data for format string
+ * @return number of bytes written to buf or negative value on error
+ */
+int
+GNUNET_snprintf (char *buf, size_t size, const char *format, ...);
+
+
+/**
+ * Like asprintf, just portable.
+ *
+ * @param buf set to a buffer of sufficient size (allocated, caller must free)
+ * @param format format string (see printf, fprintf, etc.)
+ * @param ... data for format string
+ * @return number of bytes in "*buf" excluding 0-termination
+ */
+int
+GNUNET_asprintf (char **buf, const char *format, ...);
+
+
+/* ************** internal implementations, use macros above! ************** */
+
+/**
+ * Allocate memory. Checks the return value, aborts if no more
+ * memory is available.  Don't use GNUNET_xmalloc_ directly. Use the
+ * GNUNET_malloc macro.
+ * The memory will be zero'ed out.
+ *
+ * @param size number of bytes to allocate
+ * @param filename where is this call being made (for debugging)
+ * @param linenumber line where this call is being made (for debugging)
+ * @return allocated memory, never NULL
+ */
+void *
+GNUNET_xmalloc_ (size_t size, const char *filename, int linenumber);
+
+
+/**
+ * Allocate and initialize memory. Checks the return value, aborts if no more
+ * memory is available.  Don't use GNUNET_xmemdup_ directly. Use the
+ * GNUNET_memdup macro.
+ *
+ * @param buf buffer to initialize from (must contain size bytes)
+ * @param size number of bytes to allocate
+ * @param filename where is this call being made (for debugging)
+ * @param linenumber line where this call is being made (for debugging)
+ * @return allocated memory, never NULL
+ */
+void *
+GNUNET_xmemdup_ (const void *buf, size_t size, const char *filename,
+                 int linenumber);
+
+
+/**
+ * Allocate memory.  This function does not check if the allocation
+ * request is within reasonable bounds, allowing allocations larger
+ * than 40 MB.  If you don't expect the possibility of very large
+ * allocations, use GNUNET_malloc instead.  The memory will be zero'ed
+ * out.
+ *
+ * @param size number of bytes to allocate
+ * @param filename where is this call being made (for debugging)
+ * @param linenumber line where this call is being made (for debugging)
+ * @return pointer to size bytes of memory, NULL if we do not have enough 
memory
+ */
+void *
+GNUNET_xmalloc_unchecked_ (size_t size, const char *filename, int linenumber);
+
+/**
+ * Reallocate memory. Checks the return value, aborts if no more
+ * memory is available.
+ */
+void *
+GNUNET_xrealloc_ (void *ptr, size_t n, const char *filename, int linenumber);
+
+/**
+ * Free memory. Merely a wrapper for the case that we
+ * want to keep track of allocations.  Don't use GNUNET_xfree_
+ * directly. Use the GNUNET_free macro.
+ *
+ * @param ptr pointer to memory to free
+ * @param filename where is this call being made (for debugging)
+ * @param linenumber line where this call is being made (for debugging)
+ */
+void
+GNUNET_xfree_ (void *ptr, const char *filename, int linenumber);
+
+
+/**
+ * Dup a string. Don't call GNUNET_xstrdup_ directly. Use the GNUNET_strdup 
macro.
+ * @param str string to duplicate
+ * @param filename where is this call being made (for debugging)
+ * @param linenumber line where this call is being made (for debugging)
+ * @return the duplicated string
+ */
+char *
+GNUNET_xstrdup_ (const char *str, const char *filename, int linenumber);
+
+/**
+ * Dup partially a string. Don't call GNUNET_xstrndup_ directly. Use the 
GNUNET_strndup macro.
+ *
+ * @param str string to duplicate
+ * @param len length of the string to duplicate
+ * @param filename where is this call being made (for debugging)
+ * @param linenumber line where this call is being made (for debugging)
+ * @return the duplicated string
+ */
+char *
+GNUNET_xstrndup_ (const char *str, size_t len, const char *filename,
+                  int linenumber);
+
+/**
+ * Grow an array, the new elements are zeroed out.
+ * Grows old by (*oldCount-newCount)*elementSize
+ * bytes and sets *oldCount to newCount.
+ *
+ * Don't call GNUNET_xgrow_ directly. Use the GNUNET_array_grow macro.
+ *
+ * @param old address of the pointer to the array
+ *        *old may be NULL
+ * @param elementSize the size of the elements of the array
+ * @param oldCount address of the number of elements in the *old array
+ * @param newCount number of elements in the new array, may be 0 (then *old 
will be NULL afterwards)
+ * @param filename where is this call being made (for debugging)
+ * @param linenumber line where this call is being made (for debugging)
+ */
+void
+GNUNET_xgrow_ (void **old, size_t elementSize, unsigned int *oldCount,
+               unsigned int newCount, const char *filename, int linenumber);
+
+
+/**
+ * Create a copy of the given message.
+ *
+ * @param msg message to copy
+ * @return duplicate of the message
+ */
+struct GNUNET_MessageHeader *
+GNUNET_copy_message (const struct GNUNET_MessageHeader *msg);
+
+
+#if __STDC_VERSION__ < 199901L
+#if __GNUC__ >= 2
+#define __func__ __FUNCTION__
+#else
+#define __func__ "<unknown>"
+#endif
+#endif
+
+
+
+
+#if 0                           /* keep Emacsens' auto-indent happy */
+{
+#endif
+#ifdef __cplusplus
+}
+#endif
+
+
+
+
+#endif /*GNUNET_COMMON_H_ */

Added: monkey/trunk/pathologist/src/include/gnunet_getopt_lib.h
===================================================================
--- monkey/trunk/pathologist/src/include/gnunet_getopt_lib.h                    
        (rev 0)
+++ monkey/trunk/pathologist/src/include/gnunet_getopt_lib.h    2012-09-24 
18:49:45 UTC (rev 23981)
@@ -0,0 +1,367 @@
+/*
+     This file is part of GNUnet.
+     (C) 2001, 2002, 2003, 2004, 2005, 2006, 2009, 2011 Christian Grothoff 
(and other contributing authors)
+
+     GNUnet is free software; you can redistribute it and/or modify
+     it under the terms of the GNU General Public License as published
+     by the Free Software Foundation; either version 2, or (at your
+     option) any later version.
+
+     GNUnet is distributed in the hope that it will be useful, but
+     WITHOUT ANY WARRANTY; without even the implied warranty of
+     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+     General Public License for more details.
+
+     You should have received a copy of the GNU General Public License
+     along with GNUnet; see the file COPYING.  If not, write to the
+     Free Software Foundation, Inc., 59 Temple Place - Suite 330,
+     Boston, MA 02111-1307, USA.
+*/
+
+/**
+ * @file include/gnunet_getopt_lib.h
+ * @brief command line parsing and --help formatting
+ *
+ * @author Christian Grothoff
+ */
+
+#ifndef GNUNET_GETOPT_LIB_H
+#define GNUNET_GETOPT_LIB_H
+
+#ifdef __cplusplus
+extern "C"
+{
+#if 0                           /* keep Emacsens' auto-indent happy */
+}
+#endif
+#endif
+
+//#include "gnunet_configuration_lib.h"
+
+/**
+ * @brief General context for command line processors.
+ */
+struct GNUNET_GETOPT_CommandLineProcessorContext
+{
+
+  /**
+   * Name of the application
+   */
+  const char *binaryName;
+
+  /**
+   * Name of application with option summary
+   */
+  const char *binaryOptions;
+
+  /**
+   * Array with all command line options.
+   */
+  const struct GNUNET_GETOPT_CommandLineOption *allOptions;
+
+  /**
+   * Original command line
+   */
+  char *const *argv;
+
+  /**
+   * Total number of argv's.
+   */
+  unsigned int argc;
+
+  /**
+   * Current argument.
+   */
+  unsigned int currentArgument;
+
+};
+
+/**
+ * @brief Process a command line option
+ *
+ * @param ctx context for all options
+ * @param scls specific closure (for this processor)
+ * @param option long name of the option (i.e. "config" for --config)
+ * @param value argument, NULL if none was given
+ * @return GNUNET_OK to continue processing other options, GNUNET_SYSERR to 
abort
+ */
+typedef int (*GNUNET_GETOPT_CommandLineOptionProcessor) (struct
+                                                         
GNUNET_GETOPT_CommandLineProcessorContext
+                                                         * ctx, void *scls,
+                                                         const char *option,
+                                                         const char *value);
+
+/**
+ * @brief Definition of a command line option.
+ */
+struct GNUNET_GETOPT_CommandLineOption
+{
+
+  /**
+   * Short name of the option (use '\\0' for none).
+   */
+  const char shortName;
+
+  /**
+   * Long name of the option (may not be NULL)
+   */
+  const char *name;
+
+  /**
+   * Name of the argument for the user in help text
+   */
+  const char *argumentHelp;
+
+  /**
+   * Help text for the option (description)
+   */
+  const char *description;
+
+  /**
+   * Is an argument required?  0: GNUNET_NO (includes optional), 1: GNUNET_YES.
+   */
+  int require_argument;
+
+  /**
+   * Handler for the option.
+   */
+  GNUNET_GETOPT_CommandLineOptionProcessor processor;
+
+  /**
+   * Specific closure to pass to the processor.
+   */
+  void *scls;
+
+};
+
+/**
+ * Macro defining the option to print the command line
+ * help text (-h option).
+ *
+ * @param about string with brief description of the application
+ */
+#define GNUNET_GETOPT_OPTION_HELP(about) \
+  { 'h', "help", (const char *) NULL, gettext_noop("print this help"), 0, 
&GNUNET_GETOPT_format_help_, (void *) about }
+
+
+/**
+ * Macro defining the option to print the version of
+ * the application (-v option)
+ *
+ * @param version string with the version number
+ */
+#define GNUNET_GETOPT_OPTION_VERSION(version) \
+  { 'v', "version", (const char *) NULL, gettext_noop("print the version 
number"), 0, &GNUNET_GETOPT_print_version_, (void *) version }
+
+
+/**
+ * Allow user to specify log file name (-l option)
+ *
+ * @param logfn set to the name of the logfile
+ */
+#define GNUNET_GETOPT_OPTION_LOGFILE(logfn)                            \
+  { 'l', "logfile", "LOGFILE", gettext_noop("configure logging to write logs 
to LOGFILE"), 1, &GNUNET_GETOPT_set_string, (void *) logfn }
+
+
+/**
+ * Allow user to specify log level (-L option)
+ *
+ * @param loglev set to the log level
+ */
+#define GNUNET_GETOPT_OPTION_LOGLEVEL(loglev)                          \
+  { 'L', "log", "LOGLEVEL", gettext_noop("configure logging to use LOGLEVEL"), 
1, &GNUNET_GETOPT_set_string, (void *) loglev }
+
+
+/**
+ * Get number of verbose (-V) flags
+ *
+ * @param level where to store the verbosity level (should be an 'int')
+ */
+#define GNUNET_GETOPT_OPTION_VERBOSE(level)                            \
+  { 'V', "verbose", (const char *) NULL, gettext_noop("be verbose"), 0, 
&GNUNET_GETOPT_increment_value, (void *) level }
+
+
+/**
+ * Get configuration file name (-c option)
+ *
+ * @param fn set to the configuration file name
+ */
+#define GNUNET_GETOPT_OPTION_CFG_FILE(fn)                              \
+  { 'c', "config", "FILENAME", gettext_noop("use configuration file 
FILENAME"), 1, &GNUNET_GETOPT_set_string, (void *) fn }
+
+
+/**
+ * Marker for the end of the list of options.
+ */
+#define GNUNET_GETOPT_OPTION_END \
+  { '\0', NULL, NULL, NULL, 0, NULL, NULL }
+
+
+/**
+ * Parse the command line.
+ *
+ * @param binaryOptions Name of application with option summary
+ * @param allOptions defined options and handlers
+ * @param argc number of arguments
+ * @param argv actual arguments
+ * @return index into argv with first non-option
+ *   argument, or GNUNET_SYSERR on error
+ */
+int
+GNUNET_GETOPT_run (const char *binaryOptions,
+                   const struct GNUNET_GETOPT_CommandLineOption *allOptions,
+                   unsigned int argc, char *const *argv);
+
+
+/**
+ * Set an option of type 'unsigned long long' from the command line.
+ * A pointer to this function should be passed as part of the
+ * 'struct GNUNET_GETOPT_CommandLineOption' array to initialize options
+ * of this type.  It should be followed by a pointer to a value of
+ * type 'unsigned long long'.
+ *
+ * @param ctx command line processing context
+ * @param scls additional closure (will point to the 'unsigned long long')
+ * @param option name of the option
+ * @param value actual value of the option as a string.
+ * @return GNUNET_OK if parsing the value worked
+ */
+int
+GNUNET_GETOPT_set_ulong (struct GNUNET_GETOPT_CommandLineProcessorContext *ctx,
+                         void *scls, const char *option, const char *value);
+
+
+/**
+ * Set an option of type 'struct GNUNET_TIME_Relative' from the command line.
+ * A pointer to this function should be passed as part of the
+ * 'struct GNUNET_GETOPT_CommandLineOption' array to initialize options
+ * of this type.  It should be followed by a pointer to a value of
+ * type 'struct GNUNET_TIME_Relative'.
+ *
+ * @param ctx command line processing context
+ * @param scls additional closure (will point to the 'struct 
GNUNET_TIME_Relative')
+ * @param option name of the option
+ * @param value actual value of the option as a string.
+ * @return GNUNET_OK if parsing the value worked
+ */
+int
+GNUNET_GETOPT_set_relative_time (struct 
GNUNET_GETOPT_CommandLineProcessorContext *ctx,
+                                void *scls, const char *option, const char 
*value);
+
+
+/**
+ * Set an option of type 'unsigned int' from the command line.
+ * A pointer to this function should be passed as part of the
+ * 'struct GNUNET_GETOPT_CommandLineOption' array to initialize options
+ * of this type.  It should be followed by a pointer to a value of
+ * type 'unsigned int'.
+ *
+ * @param ctx command line processing context
+ * @param scls additional closure (will point to the 'unsigned int')
+ * @param option name of the option
+ * @param value actual value of the option as a string.
+ * @return GNUNET_OK if parsing the value worked
+ */
+int
+GNUNET_GETOPT_set_uint (struct GNUNET_GETOPT_CommandLineProcessorContext *ctx,
+                        void *scls, const char *option, const char *value);
+
+
+/**
+ * Set an option of type 'int' from the command line to 1 if the
+ * given option is present.
+ * A pointer to this function should be passed as part of the
+ * 'struct GNUNET_GETOPT_CommandLineOption' array to initialize options
+ * of this type.  It should be followed by a pointer to a value of
+ * type 'int'.
+ *
+ * @param ctx command line processing context
+ * @param scls additional closure (will point to the 'int')
+ * @param option name of the option
+ * @param value not used (NULL)
+ * @return GNUNET_OK
+ */
+int
+GNUNET_GETOPT_set_one (struct GNUNET_GETOPT_CommandLineProcessorContext *ctx,
+                       void *scls, const char *option, const char *value);
+
+
+/**
+ * Set an option of type 'char *' from the command line.
+ * A pointer to this function should be passed as part of the
+ * 'struct GNUNET_GETOPT_CommandLineOption' array to initialize options
+ * of this type.  It should be followed by a pointer to a value of
+ * type 'char *'.
+ *
+ * @param ctx command line processing context
+ * @param scls additional closure (will point to the 'char *',
+ *             which will be allocated)
+ * @param option name of the option
+ * @param value actual value of the option (a string)
+ * @return GNUNET_OK
+ */
+int
+GNUNET_GETOPT_set_string (struct GNUNET_GETOPT_CommandLineProcessorContext 
*ctx,
+                          void *scls, const char *option, const char *value);
+
+/**
+ * Set an option of type 'unsigned int' from the command line. Each
+ * time the option flag is given, the value is incremented by one.
+ * A pointer to this function should be passed as part of the
+ * 'struct GNUNET_GETOPT_CommandLineOption' array to initialize options
+ * of this type.  It should be followed by a pointer to a value of
+ * type 'int'.
+ *
+ * @param ctx command line processing context
+ * @param scls additional closure (will point to the 'int')
+ * @param option name of the option
+ * @param value not used (NULL)
+ * @return GNUNET_OK
+ */
+int
+GNUNET_GETOPT_increment_value (struct GNUNET_GETOPT_CommandLineProcessorContext
+                               *ctx, void *scls, const char *option,
+                               const char *value);
+
+
+/* *************** internal prototypes - use macros above! ************* */
+
+/**
+ * Print out details on command line options (implements --help).
+ *
+ * @param ctx command line processing context
+ * @param scls additional closure (points to about text)
+ * @param option name of the option
+ * @param value not used (NULL)
+ * @return GNUNET_SYSERR (do not continue)
+ */
+int
+GNUNET_GETOPT_format_help_ (struct GNUNET_GETOPT_CommandLineProcessorContext
+                            *ctx, void *scls, const char *option,
+                            const char *value);
+
+/**
+ * Print out program version (implements --version).
+ *
+ * @param ctx command line processing context
+ * @param scls additional closure (points to version string)
+ * @param option name of the option
+ * @param value not used (NULL)
+ * @return GNUNET_SYSERR (do not continue)
+ */
+int
+GNUNET_GETOPT_print_version_ (struct GNUNET_GETOPT_CommandLineProcessorContext
+                              *ctx, void *scls, const char *option,
+                              const char *value);
+
+#if 0                           /* keep Emacsens' auto-indent happy */
+{
+#endif
+#ifdef __cplusplus
+}
+#endif
+
+
+/* ifndef GNUNET_GETOPT_LIB_H */
+#endif
+/* end of gnunet_getopt_lib.h */

Added: monkey/trunk/pathologist/src/include/platform.h
===================================================================
--- monkey/trunk/pathologist/src/include/platform.h                             
(rev 0)
+++ monkey/trunk/pathologist/src/include/platform.h     2012-09-24 18:49:45 UTC 
(rev 23981)
@@ -0,0 +1,266 @@
+/*
+     This file is part of GNUnet.
+     (C) 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2009 Christian Grothoff 
(and other contributing authors)
+
+     GNUnet is free software; you can redistribute it and/or modify
+     it under the terms of the GNU General Public License as published
+     by the Free Software Foundation; either version 2, or (at your
+     option) any later version.
+
+     GNUnet is distributed in the hope that it will be useful, but
+     WITHOUT ANY WARRANTY; without even the implied warranty of
+     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+     General Public License for more details.
+
+     You should have received a copy of the GNU General Public License
+     along with GNUnet; see the file COPYING.  If not, write to the
+     Free Software Foundation, Inc., 59 Temple Place - Suite 330,
+     Boston, MA 02111-1307, USA.
+*/
+
+/**
+ * @file include/platform.h
+ * @brief plaform specifics
+ *
+ * @author Nils Durner
+ *
+ * This file should never be included by installed
+ * header files (thos starting with "gnunet_").
+ */
+
+#ifndef PLATFORM_H
+#define PLATFORM_H
+
+#ifndef HAVE_USED_CONFIG_H
+#define HAVE_USED_CONFIG_H
+#if HAVE_CONFIG_H
+//#include "gnunet_config.h"
+#endif
+#endif
+
+#ifdef WINDOWS
+#define BREAKPOINT asm("int $3;");
+#define GNUNET_SIGCHLD 17
+#else
+#define BREAKPOINT
+#define GNUNET_SIGCHLD SIGCHLD
+#endif
+
+#ifdef HAVE_SYS_TYPES_H
+#include <sys/types.h>
+#endif
+
+#define ALLOW_EXTRA_CHECKS GNUNET_NO
+
+/**
+ * For strptime (glibc2 needs this).
+ */
+#ifndef _XOPEN_SOURCE
+#define _XOPEN_SOURCE
+#endif
+
+#ifndef _REENTRANT
+#define _REENTRANT
+#endif
+
+/* configuration options */
+
+#define VERBOSE_STATS 0
+
+#ifdef CYGWIN
+#include <sys/reent.h>
+#endif
+
+#ifdef _MSC_VER
+#ifndef FD_SETSIZE
+#define FD_SETSIZE 1024
+#endif
+#include <Winsock2.h>
+#include <ws2tcpip.h>
+#else
+#ifndef MINGW
+#include <netdb.h>
+#include <sys/socket.h>
+#include <sys/un.h>
+#if HAVE_NETINET_IN_H
+#include <netinet/in.h>
+#endif
+#if HAVE_NETINET_IN_SYSTM_H
+#include <netinet/in_systm.h>
+#endif
+#include <netinet/ip.h>         /* superset of previous */
+#include <arpa/inet.h>
+#include <netinet/tcp.h>
+#include <pwd.h>
+#include <sys/ioctl.h>
+#include <sys/wait.h>
+#include <grp.h>
+#else
+#include "winproc.h"
+#endif
+#endif
+
+#include <string.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <stdint.h>
+#include <stdarg.h>
+#include <errno.h>
+#include <signal.h>
+#include <libgen.h>
+#ifdef WINDOWS
+#include <malloc.h>             /* for alloca(), on other OSes it's in 
stdlib.h */
+#endif
+#ifndef _MSC_VER
+#include <unistd.h>             /* KLB_FIX */
+#endif
+#include <sys/stat.h>
+#include <sys/types.h>
+#ifndef _MSC_VER
+#include <dirent.h>             /* KLB_FIX */
+#endif
+#include <fcntl.h>
+#include <math.h>
+#if HAVE_SYS_PARAM_H
+#include <sys/param.h>
+#endif
+#if TIME_WITH_SYS_TIME
+#include <sys/time.h>
+#include <time.h>
+#else
+#if HAVE_SYS_TIME_H
+#include <sys/time.h>
+#else
+#include <time.h>
+#endif
+#endif
+
+#ifdef SOMEBSD
+#include <net/if.h>
+#endif
+#ifdef GNUNET_freeBSD
+#include <semaphore.h>
+#endif
+#ifdef DARWIN
+#include <dlfcn.h>
+#include <semaphore.h>
+#include <net/if.h>
+#endif
+#if defined(LINUX) || defined(GNU)
+#include <net/if.h>
+#endif
+#ifdef SOLARIS
+#include <sys/sockio.h>
+#include <sys/filio.h>
+#include <sys/loadavg.h>
+#include <semaphore.h>
+#endif
+#if HAVE_UCRED_H
+#include <ucred.h>
+#endif
+#ifdef CYGWIN
+#include <windows.h>
+#include <cygwin/if.h>
+#endif
+#if HAVE_IFADDRS_H
+#include <ifaddrs.h>
+#endif
+#include <errno.h>
+#include <limits.h>
+
+#if HAVE_VFORK_H
+#include <vfork.h>
+#endif
+
+#include <ctype.h>
+#if HAVE_SYS_RESOURCE_H
+#include <sys/resource.h>
+#endif
+
+#if HAVE_ENDIAN_H
+#include <endian.h>
+#endif
+#if HAVE_SYS_ENDIAN_H
+#include <sys/endian.h>
+#endif
+
+#include "plibc.h"
+
+//#include <locale.h>
+//#ifndef FRAMEWORK_BUILD
+//#include "gettext.h"
+///**
+// * GNU gettext support macro.
+// */
+//#define _(String) dgettext("gnunet",String)
+//#define LIBEXTRACTOR_GETTEXT_DOMAIN "libextractor"
+//#else
+//#include "libintlemu.h"
+//#define _(String) dgettext("org.gnunet.gnunet",String)
+//#define LIBEXTRACTOR_GETTEXT_DOMAIN "org.gnunet.libextractor"
+//#endif
+
+#ifdef CYGWIN
+#define SIOCGIFCONF     _IOW('s', 100, struct ifconf)   /* get if list */
+#define SIOCGIFFLAGS    _IOW('s', 101, struct ifreq)    /* Get if flags */
+#define SIOCGIFADDR     _IOW('s', 102, struct ifreq)    /* Get if addr */
+#endif
+
+#ifndef MINGW
+#include <sys/mman.h>
+#endif
+
+#ifdef FREEBSD
+#define __BYTE_ORDER BYTE_ORDER
+#define __BIG_ENDIAN BIG_ENDIAN
+#endif
+
+#ifdef DARWIN
+#define __BYTE_ORDER BYTE_ORDER
+#define __BIG_ENDIAN BIG_ENDIAN
+ /* not available on darwin, override configure */
+#undef HAVE_STAT64
+#undef HAVE_MREMAP
+#endif
+
+
+#if !HAVE_ATOLL
+long long
+atoll (const char *nptr);
+#endif
+
+#if ENABLE_NLS
+#include "langinfo.h"
+#endif
+
+#ifndef SIZE_MAX
+#define SIZE_MAX ((size_t)(-1))
+#endif
+
+#ifndef O_LARGEFILE
+#define O_LARGEFILE 0
+#endif
+
+/**
+ * AI_NUMERICSERV not defined in windows.  Then we just do without.
+ */
+#ifndef AI_NUMERICSERV
+#define AI_NUMERICSERV 0
+#endif
+
+
+#if defined(__sparc__)
+#define MAKE_UNALIGNED(val) ({ __typeof__((val)) __tmp; memmove(&__tmp, 
&(val), sizeof((val))); __tmp; })
+#else
+#define MAKE_UNALIGNED(val) val
+#endif
+
+#if WINDOWS
+#define FDTYPE HANDLE
+#define SOCKTYPE SOCKET
+#else
+#define FDTYPE int
+#define SOCKTYPE int
+#endif
+
+#endif

Modified: monkey/trunk/pathologist/src/pathologist/Makefile.am
===================================================================
--- monkey/trunk/pathologist/src/pathologist/Makefile.am        2012-09-24 
12:59:42 UTC (rev 23980)
+++ monkey/trunk/pathologist/src/pathologist/Makefile.am        2012-09-24 
18:49:45 UTC (rev 23981)
@@ -50,6 +50,8 @@
 
 pathologist_SOURCES = \
  pathologist.c \
+ getopt.c \
+ getopt_helpers.c \
  mail_sender.c
 
 pathologist_LDADD = \

Added: monkey/trunk/pathologist/src/pathologist/getopt.c
===================================================================
--- monkey/trunk/pathologist/src/pathologist/getopt.c                           
(rev 0)
+++ monkey/trunk/pathologist/src/pathologist/getopt.c   2012-09-24 18:49:45 UTC 
(rev 23981)
@@ -0,0 +1,1047 @@
+/* Getopt for GNU.
+   NOTE: getopt is now part of the C library, so if you don't know what
+   "Keep this file name-space clean" means, talk to address@hidden
+   before changing it!
+
+   Copyright (C) 1987, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97
+     Free Software Foundation, Inc.
+
+NOTE: The canonical source of this file is maintained with the GNU C Library.
+Bugs can be reported to address@hidden
+
+This program is free software; you can redistribute it and/or modify it
+under the terms of the GNU General Public License as published by the
+Free Software Foundation; either version 2, or (at your option) any
+later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program; if not, write to the Free Software
+Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307,
+USA.
+
+
+This code was heavily modified for GNUnet.
+Copyright (C) 2006 Christian Grothoff
+*/
+
+/**
+ * @file util/getopt.c
+ * @brief GNU style option parsing
+ *
+ * TODO: get rid of statics (make reentrant) and
+ * replace main GNU getopt parser with one that
+ * actually fits our API.
+ */
+
+#include "platform.h"
+#include "gnunet_common.h"
+#include "gnunet_getopt_lib.h"
+
+#ifdef VMS
+#include <unixlib.h>
+#if HAVE_STRING_H - 0
+#include <string.h>
+#endif
+#endif
+
+#define LOG(kind,...) GNUNET_log_from (kind, "util", __VA_ARGS__)
+
+#define LOG_STRERROR(kind,syscall) GNUNET_log_from_strerror (kind, "util", 
syscall)
+
+#if defined (WIN32) && !defined (__CYGWIN32__)
+/* It's not Unix, really.  See?  Capital letters.  */
+#include <windows.h>
+#define getpid() GetCurrentProcessId()
+#endif
+
+#ifndef _
+/* This is for other GNU distributions with internationalized messages.
+   When compiling libc, the _ macro is predefined.  */
+#ifdef HAVE_LIBINTL_H
+#include <libintl.h>
+#define _(msgid)  gettext (msgid)
+#else
+#define _(msgid)  (msgid)
+#endif
+#endif
+
+/* Describe the long-named options requested by the application.
+   The LONG_OPTIONS argument to getopt_long or getopt_long_only is a vector
+   of `struct GNoption' terminated by an element containing a name which is
+   zero.
+
+   The field `has_arg' is:
+   no_argument         (or 0) if the option does not take an argument,
+   required_argument  (or 1) if the option requires an argument,
+   optional_argument   (or 2) if the option takes an optional argument.
+
+   If the field `flag' is not NULL, it points to a variable that is set
+   to the value given in the field `val' when the option is found, but
+   left unchanged if the option is not found.
+
+   To have a long-named option do something other than set an `int' to
+   a compiled-in constant, such as set a value from `GNoptarg', set the
+   option's `flag' field to zero and its `val' field to a nonzero
+   value (the equivalent single-letter option character, if there is
+   one).  For long options that have a zero `flag' field, `getopt'
+   returns the contents of the `val' field.  */
+
+struct GNoption
+{
+  const char *name;
+  /* has_arg can't be an enum because some compilers complain about
+   * type mismatches in all the code that assumes it is an int.  */
+  int has_arg;
+  int *flag;
+  int val;
+};
+
+
+/* This version of `getopt' appears to the caller like standard Unix `getopt'
+   but it behaves differently for the user, since it allows the user
+   to intersperse the options with the other arguments.
+
+   As `getopt' works, it permutes the elements of ARGV so that,
+   when it is done, all the options precede everything else.  Thus
+   all application programs are extended to handle flexible argument order.
+
+   Setting the environment variable POSIXLY_CORRECT disables permutation.
+   Then the behavior is completely standard.
+
+   GNU application programs can use a third alternative mode in which
+   they can distinguish the relative order of options and other arguments.  */
+
+/* For communication from `getopt' to the caller.
+   When `getopt' finds an option that takes an argument,
+   the argument value is returned here.
+   Also, when `ordering' is RETURN_IN_ORDER,
+   each non-option ARGV-element is returned here.  */
+
+static char *GNoptarg = NULL;
+
+/* Index in ARGV of the next element to be scanned.
+   This is used for communication to and from the caller
+   and for communication between successive calls to `getopt'.
+
+   On entry to `getopt', zero means this is the first call; initialize.
+
+   When `getopt' returns -1, this is the index of the first of the
+   non-option elements that the caller should itself scan.
+
+   Otherwise, `GNoptind' communicates from one call to the next
+   how much of ARGV has been scanned so far.  */
+
+/* 1003.2 says this must be 1 before any call.  */
+static int GNoptind = 1;
+
+/* The next char to be scanned in the option-element
+   in which the last option character we returned was found.
+   This allows us to pick up the scan where we left off.
+
+   If this is zero, or a null string, it means resume the scan
+   by advancing to the next ARGV-element.  */
+
+static char *nextchar;
+
+
+/* Describe how to deal with options that follow non-option ARGV-elements.
+
+   If the caller did not specify anything,
+   the default is REQUIRE_ORDER if the environment variable
+   POSIXLY_CORRECT is defined, PERMUTE otherwise.
+
+   REQUIRE_ORDER means don't recognize them as options;
+   stop option processing when the first non-option is seen.
+   This is what Unix does.
+   This mode of operation is selected by either setting the environment
+   variable POSIXLY_CORRECT, or using `+' as the first character
+   of the list of option characters.
+
+   PERMUTE is the default.  We GNUNET_CRYPTO_random_permute the contents of 
ARGV as we scan,
+   so that eventually all the non-options are at the end.  This allows options
+   to be given in any order, even with programs that were not written to
+   expect this.
+
+   RETURN_IN_ORDER is an option available to programs that were written
+   to expect GNoptions and other ARGV-elements in any order and that care about
+   the ordering of the two.  We describe each non-option ARGV-element
+   as if it were the argument of an option with character code 1.
+   Using `-' as the first character of the list of option characters
+   selects this mode of operation.
+
+   The special argument `--' forces an end of option-scanning regardless
+   of the value of `ordering'.  In the case of RETURN_IN_ORDER, only
+   `--' can cause `getopt' to return -1 with `GNoptind' != ARGC.  */
+
+static enum
+{
+  REQUIRE_ORDER, PERMUTE, RETURN_IN_ORDER
+} ordering;
+
+/* Value of POSIXLY_CORRECT environment variable.  */
+static char *posixly_correct;
+
+#ifdef  __GNU_LIBRARY__
+/* We want to avoid inclusion of string.h with non-GNU libraries
+   because there are many ways it can cause trouble.
+   On some systems, it contains special magic macros that don't work
+   in GCC.  */
+#include <string.h>
+#define  my_index      strchr
+#else
+
+/* Avoid depending on library functions or files
+   whose names are inconsistent.  */
+
+char *
+getenv ();
+
+static char *
+my_index (const char *str,
+         int chr)
+{
+  while (*str)
+  {
+    if (*str == chr)
+      return (char *) str;
+    str++;
+  }
+  return 0;
+}
+
+/* If using GCC, we can safely declare strlen this way.
+   If not using GCC, it is ok not to declare it.  */
+#ifdef __GNUC__
+/* Note that Motorola Delta 68k R3V7 comes with GCC but not stddef.h.
+   That was relevant to code that was here before.  */
+#if !defined (__STDC__) || !__STDC__
+/* gcc with -traditional declares the built-in strlen to return int,
+   and has done so at least since version 2.4.5. -- rms.  */
+extern int
+strlen (const char *);
+#endif /* not __STDC__ */
+#endif /* __GNUC__ */
+
+#endif /* not __GNU_LIBRARY__ */
+
+/* Handle permutation of arguments.  */
+
+/* Describe the part of ARGV that contains non-options that have
+   been skipped.  `first_nonopt' is the index in ARGV of the first of them;
+   `last_nonopt' is the index after the last of them.  */
+
+static int first_nonopt;
+static int last_nonopt;
+
+#ifdef _LIBC
+/* Bash 2.0 gives us an environment variable containing flags
+   indicating ARGV elements that should not be considered arguments.  */
+
+/* Defined in getopt_init.c  */
+extern char *__getopt_nonoption_flags;
+
+static int nonoption_flags_max_len;
+static int nonoption_flags_len;
+
+static int original_argc;
+static char *const *original_argv;
+
+extern pid_t __libc_pid;
+
+/* Make sure the environment variable bash 2.0 puts in the environment
+   is valid for the getopt call we must make sure that the ARGV passed
+   to getopt is that one passed to the process.  */
+static void GNUNET_UNUSED
+store_args_and_env (int argc, char *const *argv)
+{
+  /* XXX This is no good solution.  We should rather copy the args so
+   * that we can compare them later.  But we must not use malloc(3).  */
+  original_argc = argc;
+  original_argv = argv;
+}
+
+text_set_element (__libc_subinit, store_args_and_env);
+
+#define SWAP_FLAGS(ch1, ch2) \
+  if (nonoption_flags_len > 0)                                               \
+    {                                                                        \
+      char __tmp = __getopt_nonoption_flags[ch1];                    \
+      __getopt_nonoption_flags[ch1] = __getopt_nonoption_flags[ch2];        \
+      __getopt_nonoption_flags[ch2] = __tmp;                         \
+    }
+#else /* !_LIBC */
+#define SWAP_FLAGS(ch1, ch2)
+#endif /* _LIBC */
+
+/* Exchange two adjacent subsequences of ARGV.
+   One subsequence is elements [first_nonopt,last_nonopt)
+   which contains all the non-options that have been skipped so far.
+   The other is elements [last_nonopt,GNoptind), which contains all
+   the options processed since those non-options were skipped.
+
+   `first_nonopt' and `last_nonopt' are relocated so that they describe
+   the new indices of the non-options in ARGV after they are moved.  */
+
+#if defined (__STDC__) && __STDC__
+static void
+exchange (char **);
+#endif
+
+static void
+exchange (char **argv)
+{
+  int bottom = first_nonopt;
+  int middle = last_nonopt;
+  int top = GNoptind;
+  char *tem;
+
+  /* Exchange the shorter segment with the far end of the longer segment.
+   * That puts the shorter segment into the right place.
+   * It leaves the longer segment in the right place overall,
+   * but it consists of two parts that need to be swapped next.  */
+
+#ifdef _LIBC
+  /* First make sure the handling of the `__getopt_nonoption_flags'
+   * string can work normally.  Our top argument must be in the range
+   * of the string.  */
+  if (nonoption_flags_len > 0 && top >= nonoption_flags_max_len)
+  {
+    /* We must extend the array.  The user plays games with us and
+     * presents new arguments.  */
+    char *new_str = malloc (top + 1);
+
+    if (new_str == NULL)
+      nonoption_flags_len = nonoption_flags_max_len = 0;
+    else
+    {
+      memcpy (new_str, __getopt_nonoption_flags, nonoption_flags_max_len);
+      memset (&new_str[nonoption_flags_max_len], '\0',
+              top + 1 - nonoption_flags_max_len);
+      nonoption_flags_max_len = top + 1;
+      __getopt_nonoption_flags = new_str;
+    }
+  }
+#endif
+
+  while (top > middle && middle > bottom)
+  {
+    if (top - middle > middle - bottom)
+    {
+      /* Bottom segment is the short one.  */
+      int len = middle - bottom;
+      register int i;
+
+      /* Swap it with the top part of the top segment.  */
+      for (i = 0; i < len; i++)
+      {
+        tem = argv[bottom + i];
+        argv[bottom + i] = argv[top - (middle - bottom) + i];
+        argv[top - (middle - bottom) + i] = tem;
+        SWAP_FLAGS (bottom + i, top - (middle - bottom) + i);
+      }
+      /* Exclude the moved bottom segment from further swapping.  */
+      top -= len;
+    }
+    else
+    {
+      /* Top segment is the short one.  */
+      int len = top - middle;
+      register int i;
+
+      /* Swap it with the bottom part of the bottom segment.  */
+      for (i = 0; i < len; i++)
+      {
+        tem = argv[bottom + i];
+        argv[bottom + i] = argv[middle + i];
+        argv[middle + i] = tem;
+        SWAP_FLAGS (bottom + i, middle + i);
+      }
+      /* Exclude the moved top segment from further swapping.  */
+      bottom += len;
+    }
+  }
+
+  /* Update records for the slots the non-options now occupy.  */
+
+  first_nonopt += (GNoptind - last_nonopt);
+  last_nonopt = GNoptind;
+}
+
+/* Initialize the internal data when the first call is made.  */
+
+#if defined (__STDC__) && __STDC__
+static const char *
+_getopt_initialize (int, char *const *, const char *);
+#endif
+static const char *
+_getopt_initialize (int argc,
+                   char *const *argv,
+                   const char *optstring)
+{
+  /* Start processing options with ARGV-element 1 (since ARGV-element 0
+   * is the program name); the sequence of previously skipped
+   * non-option ARGV-elements is empty.  */
+
+  first_nonopt = last_nonopt = GNoptind;
+
+  nextchar = NULL;
+
+  posixly_correct = getenv ("POSIXLY_CORRECT");
+
+  /* Determine how to handle the ordering of options and nonoptions.  */
+
+  if (optstring[0] == '-')
+  {
+    ordering = RETURN_IN_ORDER;
+    ++optstring;
+  }
+  else if (optstring[0] == '+')
+  {
+    ordering = REQUIRE_ORDER;
+    ++optstring;
+  }
+  else if (posixly_correct != NULL)
+    ordering = REQUIRE_ORDER;
+  else
+    ordering = PERMUTE;
+
+#ifdef _LIBC
+  if (posixly_correct == NULL && argc == original_argc && argv == 
original_argv)
+  {
+    if (nonoption_flags_max_len == 0)
+    {
+      if (__getopt_nonoption_flags == NULL ||
+          __getopt_nonoption_flags[0] == '\0')
+        nonoption_flags_max_len = -1;
+      else
+      {
+        const char *orig_str = __getopt_nonoption_flags;
+        int len = nonoption_flags_max_len = strlen (orig_str);
+
+        if (nonoption_flags_max_len < argc)
+          nonoption_flags_max_len = argc;
+        __getopt_nonoption_flags = (char *) malloc (nonoption_flags_max_len);
+        if (__getopt_nonoption_flags == NULL)
+          nonoption_flags_max_len = -1;
+        else
+        {
+          memcpy (__getopt_nonoption_flags, orig_str, len);
+          memset (&__getopt_nonoption_flags[len], '\0',
+                  nonoption_flags_max_len - len);
+        }
+      }
+    }
+    nonoption_flags_len = nonoption_flags_max_len;
+  }
+  else
+    nonoption_flags_len = 0;
+#endif
+
+  return optstring;
+}
+
+/* Scan elements of ARGV (whose length is ARGC) for option characters
+   given in OPTSTRING.
+
+   If an element of ARGV starts with '-', and is not exactly "-" or "--",
+   then it is an option element.  The characters of this element
+   (aside from the initial '-') are option characters.  If `getopt'
+   is called repeatedly, it returns successively each of the option characters
+   from each of the option elements.
+
+   If `getopt' finds another option character, it returns that character,
+   updating `GNoptind' and `nextchar' so that the next call to `getopt' can
+   resume the scan with the following option character or ARGV-element.
+
+   If there are no more option characters, `getopt' returns -1.
+   Then `GNoptind' is the index in ARGV of the first ARGV-element
+   that is not an option.  (The ARGV-elements have been permuted
+   so that those that are not options now come last.)
+
+   OPTSTRING is a string containing the legitimate option characters.
+   If an option character is seen that is not listed in OPTSTRING,
+   return '?' after printing an error message.  If you set `GNopterr' to
+   zero, the error message is suppressed but we still return '?'.
+
+   If a char in OPTSTRING is followed by a colon, that means it wants an arg,
+   so the following text in the same ARGV-element, or the text of the following
+   ARGV-element, is returned in `GNoptarg'.  Two colons mean an option that
+   wants an optional arg; if there is text in the current ARGV-element,
+   it is returned in `GNoptarg', otherwise `GNoptarg' is set to zero.
+
+   If OPTSTRING starts with `-' or `+', it requests different methods of
+   handling the non-option ARGV-elements.
+   See the comments about RETURN_IN_ORDER and REQUIRE_ORDER, above.
+
+   Long-named options begin with `--' instead of `-'.
+   Their names may be abbreviated as long as the abbreviation is unique
+   or is an exact match for some defined option.  If they have an
+   argument, it follows the option name in the same ARGV-element, separated
+   from the option name by a `=', or else the in next ARGV-element.
+   When `getopt' finds a long-named option, it returns 0 if that option's
+   `flag' field is nonzero, the value of the option's `val' field
+   if the `flag' field is zero.
+
+   The elements of ARGV aren't really const, because we 
GNUNET_CRYPTO_random_permute them.
+   But we pretend they're const in the prototype to be compatible
+   with other systems.
+
+   LONGOPTS is a vector of `struct GNoption' terminated by an
+   element containing a name which is zero.
+
+   LONGIND returns the index in LONGOPT of the long-named option found.
+   It is only valid when a long-named option has been found by the most
+   recent call.
+
+   If LONG_ONLY is nonzero, '-' as well as '--' can introduce
+   long-named options.  */
+
+static int
+GN_getopt_internal (int argc, char *const *argv, const char *optstring,
+                    const struct GNoption *longopts, int *longind,
+                    int long_only)
+{
+  static int __getopt_initialized = 0;
+  static int GNopterr = 1;
+
+  GNoptarg = NULL;
+
+  if (GNoptind == 0 || !__getopt_initialized)
+  {
+    if (GNoptind == 0)
+      GNoptind = 1;             /* Don't scan ARGV[0], the program name.  */
+    optstring = _getopt_initialize (argc, argv, optstring);
+    __getopt_initialized = 1;
+  }
+
+  /* Test whether ARGV[GNoptind] points to a non-option argument.
+   * Either it does not have option syntax, or there is an environment flag
+   * from the shell indicating it is not an option.  The later information
+   * is only used when the used in the GNU libc.  */
+#ifdef _LIBC
+#define NONOPTION_P (argv[GNoptind][0] != '-' || argv[GNoptind][1] == '\0'     
   \
+            || (GNoptind < nonoption_flags_len                       \
+                && __getopt_nonoption_flags[GNoptind] == '1'))
+#else
+#define NONOPTION_P (argv[GNoptind][0] != '-' || argv[GNoptind][1] == '\0')
+#endif
+
+  if (nextchar == NULL || *nextchar == '\0')
+  {
+    /* Advance to the next ARGV-element.  */
+
+    /* Give FIRST_NONOPT & LAST_NONOPT rational values if GNoptind has been
+     * moved back by the user (who may also have changed the arguments).  */
+    if (last_nonopt > GNoptind)
+      last_nonopt = GNoptind;
+    if (first_nonopt > GNoptind)
+      first_nonopt = GNoptind;
+
+    if (ordering == PERMUTE)
+    {
+      /* If we have just processed some options following some non-options,
+       * exchange them so that the options come first.  */
+
+      if (first_nonopt != last_nonopt && last_nonopt != GNoptind)
+        exchange ((char **) argv);
+      else if (last_nonopt != GNoptind)
+        first_nonopt = GNoptind;
+
+      /* Skip any additional non-options
+       * and extend the range of non-options previously skipped.  */
+
+      while (GNoptind < argc && NONOPTION_P)
+        GNoptind++;
+      last_nonopt = GNoptind;
+    }
+
+    /* The special ARGV-element `--' means premature end of options.
+     * Skip it like a null option,
+     * then exchange with previous non-options as if it were an option,
+     * then skip everything else like a non-option.  */
+    if (GNoptind != argc && !strcmp (argv[GNoptind], "--"))
+    {
+      GNoptind++;
+
+      if (first_nonopt != last_nonopt && last_nonopt != GNoptind)
+        exchange ((char **) argv);
+      else if (first_nonopt == last_nonopt)
+        first_nonopt = GNoptind;
+      last_nonopt = argc;
+
+      GNoptind = argc;
+    }
+
+    /* If we have done all the ARGV-elements, stop the scan
+     * and back over any non-options that we skipped and permuted.  */
+
+    if (GNoptind == argc)
+    {
+      /* Set the next-arg-index to point at the non-options
+       * that we previously skipped, so the caller will digest them.  */
+      if (first_nonopt != last_nonopt)
+        GNoptind = first_nonopt;
+      return -1;
+    }
+
+    /* If we have come to a non-option and did not permute it,
+     * either stop the scan or describe it to the caller and pass it by.  */
+
+    if (NONOPTION_P)
+    {
+      if (ordering == REQUIRE_ORDER)
+        return -1;
+      GNoptarg = argv[GNoptind++];
+      return 1;
+    }
+
+    /* We have found another option-ARGV-element.
+     * Skip the initial punctuation.  */
+
+    nextchar =
+        (argv[GNoptind] + 1 + (longopts != NULL && argv[GNoptind][1] == '-'));
+  }
+
+  /* Decode the current option-ARGV-element.  */
+
+  /* Check whether the ARGV-element is a long option.
+   *
+   * If long_only and the ARGV-element has the form "-f", where f is
+   * a valid short option, don't consider it an abbreviated form of
+   * a long option that starts with f.  Otherwise there would be no
+   * way to give the -f short option.
+   *
+   * On the other hand, if there's a long option "fubar" and
+   * the ARGV-element is "-fu", do consider that an abbreviation of
+   * the long option, just like "--fu", and not "-f" with arg "u".
+   *
+   * This distinction seems to be the most useful approach.  */
+
+  if (longopts != NULL &&
+      (argv[GNoptind][1] == '-' ||
+       (long_only &&
+        (argv[GNoptind][2] || !my_index (optstring, argv[GNoptind][1])))))
+  {
+    char *nameend;
+    const struct GNoption *p;
+    const struct GNoption *pfound = NULL;
+    int exact = 0;
+    int ambig = 0;
+    int indfound = -1;
+    int option_index;
+
+    for (nameend = nextchar; *nameend && *nameend != '='; nameend++)
+      /* Do nothing.  */ ;
+
+    /* Test all long options for either exact match
+     * or abbreviated matches.  */
+    for (p = longopts, option_index = 0; p->name; p++, option_index++)
+      if (!strncmp (p->name, nextchar, nameend - nextchar))
+      {
+        if ((unsigned int) (nameend - nextchar) ==
+            (unsigned int) strlen (p->name))
+        {
+          /* Exact match found.  */
+          pfound = p;
+          indfound = option_index;
+          exact = 1;
+          break;
+        }
+        else if (pfound == NULL)
+        {
+          /* First nonexact match found.  */
+          pfound = p;
+          indfound = option_index;
+        }
+        else
+          /* Second or later nonexact match found.  */
+          ambig = 1;
+      }
+
+    if (ambig && !exact)
+    {
+      if (GNopterr)
+        FPRINTF (stderr, _("%s: option `%s' is ambiguous\n"), argv[0],
+                 argv[GNoptind]);
+      nextchar += strlen (nextchar);
+      GNoptind++;
+      return '?';
+    }
+
+    if (pfound != NULL)
+    {
+      option_index = indfound;
+      GNoptind++;
+      if (*nameend)
+      {
+        /* Don't test has_arg with >, because some C compilers don't
+         * allow it to be used on enums.  */
+        if (pfound->has_arg)
+          GNoptarg = nameend + 1;
+        else
+        {
+          if (GNopterr)
+          {
+            if (argv[GNoptind - 1][1] == '-')
+              /* --option */
+              FPRINTF (stderr,
+                       _("%s: option `--%s' does not allow an argument\n"),
+                       argv[0], pfound->name);
+            else
+              /* +option or -option */
+              FPRINTF (stderr,
+                       _("%s: option `%c%s' does not allow an argument\n"),
+                       argv[0], argv[GNoptind - 1][0], pfound->name);
+          }
+          nextchar += strlen (nextchar);
+          return '?';
+        }
+      }
+      else if (pfound->has_arg == 1)
+      {
+        if (GNoptind < argc)
+        {
+          GNoptarg = argv[GNoptind++];
+        }
+        else
+        {
+          if (GNopterr)
+          {
+            FPRINTF (stderr, _("%s: option `%s' requires an argument\n"),
+                     argv[0], argv[GNoptind - 1]);
+          }
+          nextchar += strlen (nextchar);
+          return (optstring[0] == ':') ? ':' : '?';
+        }
+      }
+      nextchar += strlen (nextchar);
+      if (longind != NULL)
+        *longind = option_index;
+      if (pfound->flag)
+      {
+        *(pfound->flag) = pfound->val;
+        return 0;
+      }
+      return pfound->val;
+    }
+
+    /* Can't find it as a long option.  If this is not getopt_long_only,
+     * or the option starts with '--' or is not a valid short
+     * option, then it's an error.
+     * Otherwise interpret it as a short option.  */
+    if (!long_only || argv[GNoptind][1] == '-' ||
+        my_index (optstring, *nextchar) == NULL)
+    {
+      if (GNopterr)
+      {
+        if (argv[GNoptind][1] == '-')
+          /* --option */
+          FPRINTF (stderr, _("%s: unrecognized option `--%s'\n"), argv[0],
+                   nextchar);
+        else
+          /* +option or -option */
+          FPRINTF (stderr, _("%s: unrecognized option `%c%s'\n"), argv[0],
+                   argv[GNoptind][0], nextchar);
+      }
+      nextchar = (char *) "";
+      GNoptind++;
+      return '?';
+    }
+  }
+
+  /* Look at and handle the next short option-character.  */
+
+  {
+    char c = *nextchar++;
+    char *temp = my_index (optstring, c);
+
+    /* Increment `GNoptind' when we start to process its last character.  */
+    if (*nextchar == '\0')
+      ++GNoptind;
+
+    if (temp == NULL || c == ':')
+    {
+      if (GNopterr)
+      {
+        if (posixly_correct)
+          /* 1003.2 specifies the format of this message.  */
+          FPRINTF (stderr, _("%s: illegal option -- %c\n"), argv[0], c);
+        else
+          FPRINTF (stderr, _("%s: invalid option -- %c\n"), argv[0], c);
+      }
+      return '?';
+    }
+    /* Convenience. Treat POSIX -W foo same as long option --foo */
+    if (temp[0] == 'W' && temp[1] == ';')
+    {
+      char *nameend;
+      const struct GNoption *p;
+      const struct GNoption *pfound = NULL;
+      int exact = 0;
+      int ambig = 0;
+      int indfound = 0;
+      int option_index;
+
+      /* This is an option that requires an argument.  */
+      if (*nextchar != '\0')
+      {
+        GNoptarg = nextchar;
+        /* If we end this ARGV-element by taking the rest as an arg,
+         * we must advance to the next element now.  */
+        GNoptind++;
+      }
+      else if (GNoptind == argc)
+      {
+        if (GNopterr)
+        {
+          /* 1003.2 specifies the format of this message.  */
+          FPRINTF (stderr, _("%s: option requires an argument -- %c\n"),
+                   argv[0], c);
+        }
+        if (optstring[0] == ':')
+          c = ':';
+        else
+          c = '?';
+        return c;
+      }
+      else
+        /* We already incremented `GNoptind' once;
+         * increment it again when taking next ARGV-elt as argument.  */
+        GNoptarg = argv[GNoptind++];
+
+      /* GNoptarg is now the argument, see if it's in the
+       * table of longopts.  */
+
+      for (nextchar = nameend = GNoptarg; *nameend && *nameend != '=';
+           nameend++)
+        /* Do nothing.  */ ;
+
+      /* Test all long options for either exact match
+       * or abbreviated matches.  */
+      if (longopts != NULL)
+        for (p = longopts, option_index = 0; p->name; p++, option_index++)
+          if (!strncmp (p->name, nextchar, nameend - nextchar))
+          {
+            if ((unsigned int) (nameend - nextchar) == strlen (p->name))
+            {
+              /* Exact match found.  */
+              pfound = p;
+              indfound = option_index;
+              exact = 1;
+              break;
+            }
+            else if (pfound == NULL)
+            {
+              /* First nonexact match found.  */
+              pfound = p;
+              indfound = option_index;
+            }
+            else
+              /* Second or later nonexact match found.  */
+              ambig = 1;
+          }
+      if (ambig && !exact)
+      {
+        if (GNopterr)
+          FPRINTF (stderr, _("%s: option `-W %s' is ambiguous\n"), argv[0],
+                   argv[GNoptind]);
+        nextchar += strlen (nextchar);
+        GNoptind++;
+        return '?';
+      }
+      if (pfound != NULL)
+      {
+        option_index = indfound;
+        if (*nameend)
+        {
+          /* Don't test has_arg with >, because some C compilers don't
+           * allow it to be used on enums.  */
+          if (pfound->has_arg)
+            GNoptarg = nameend + 1;
+          else
+          {
+            if (GNopterr)
+              FPRINTF (stderr, _("\
+%s: option `-W %s' does not allow an argument\n"), argv[0], pfound->name);
+
+            nextchar += strlen (nextchar);
+            return '?';
+          }
+        }
+        else if (pfound->has_arg == 1)
+        {
+          if (GNoptind < argc)
+            GNoptarg = argv[GNoptind++];
+          else
+          {
+            if (GNopterr)
+              FPRINTF (stderr, _("%s: option `%s' requires an argument\n"),
+                       argv[0], argv[GNoptind - 1]);
+            nextchar += strlen (nextchar);
+            return optstring[0] == ':' ? ':' : '?';
+          }
+        }
+        nextchar += strlen (nextchar);
+        if (longind != NULL)
+          *longind = option_index;
+        if (pfound->flag)
+        {
+          *(pfound->flag) = pfound->val;
+          return 0;
+        }
+        return pfound->val;
+      }
+      nextchar = NULL;
+      return 'W';               /* Let the application handle it.   */
+    }
+    if (temp[1] == ':')
+    {
+      if (temp[2] == ':')
+      {
+        /* This is an option that accepts an argument optionally.  */
+        if (*nextchar != '\0')
+        {
+          GNoptarg = nextchar;
+          GNoptind++;
+        }
+        else
+          GNoptarg = NULL;
+        nextchar = NULL;
+      }
+      else
+      {
+        /* This is an option that requires an argument.  */
+        if (*nextchar != '\0')
+        {
+          GNoptarg = nextchar;
+          /* If we end this ARGV-element by taking the rest as an arg,
+           * we must advance to the next element now.  */
+          GNoptind++;
+        }
+        else if (GNoptind == argc)
+        {
+          if (GNopterr)
+          {
+            /* 1003.2 specifies the format of this message.  */
+            FPRINTF (stderr, _("%s: option requires an argument -- %c\n"),
+                     argv[0], c);
+          }
+          if (optstring[0] == ':')
+            c = ':';
+          else
+            c = '?';
+        }
+        else
+          /* We already incremented `GNoptind' once;
+           * increment it again when taking next ARGV-elt as argument.  */
+          GNoptarg = argv[GNoptind++];
+        nextchar = NULL;
+      }
+    }
+    return c;
+  }
+}
+
+static int
+GNgetopt_long (int argc, char *const *argv, const char *options,
+               const struct GNoption *long_options, int *opt_index)
+{
+  return GN_getopt_internal (argc, argv, options, long_options, opt_index, 0);
+}
+
+/* ******************** now the GNUnet specific modifications... 
********************* */
+
+/**
+ * Parse the command line.
+ *
+ * @param binaryOptions Name of application with option summary
+ * @param allOptions defined options and handlers
+ * @param argc number of arguments
+ * @param argv actual arguments
+ * @return index into argv with first non-option
+ *   argument, or -1 on error
+ */
+int
+GNUNET_GETOPT_run (const char *binaryOptions,
+                   const struct GNUNET_GETOPT_CommandLineOption *allOptions,
+                   unsigned int argc, char *const *argv)
+{
+  struct GNoption *long_options;
+  struct GNUNET_GETOPT_CommandLineProcessorContext clpc;
+  int count;
+  int i;
+  char *shorts;
+  int spos;
+  int cont;
+  int c;
+
+//  GNUNET_assert (argc > 0);
+  GNoptind = 0;
+  clpc.binaryName = argv[0];
+  clpc.binaryOptions = binaryOptions;
+  clpc.allOptions = allOptions;
+  clpc.argv = argv;
+  clpc.argc = argc;
+  count = 0;
+  while (allOptions[count].name != NULL)
+    count++;
+  long_options = malloc (sizeof (struct GNoption) * (count + 1));
+  shorts = malloc (count * 2 + 1);
+  spos = 0;
+  for (i = 0; i < count; i++)
+  {
+    long_options[i].name = allOptions[i].name;
+    long_options[i].has_arg = allOptions[i].require_argument;
+    long_options[i].flag = NULL;
+    long_options[i].val = allOptions[i].shortName;
+    shorts[spos++] = allOptions[i].shortName;
+    if (allOptions[i].require_argument != 0)
+      shorts[spos++] = ':';
+  }
+  long_options[count].name = NULL;
+  long_options[count].has_arg = 0;
+  long_options[count].flag = NULL;
+  long_options[count].val = '\0';
+  shorts[spos] = '\0';
+  cont = GNUNET_OK;
+  /* main getopt loop */
+  while (cont == GNUNET_OK)
+  {
+    int option_index = 0;
+
+    c = GNgetopt_long (argc, argv, shorts, long_options, &option_index);
+
+    if (c == GNUNET_SYSERR)
+      break;                    /* No more flags to process */
+
+    for (i = 0; i < count; i++)
+    {
+      clpc.currentArgument = GNoptind - 1;
+      if ((char) c == allOptions[i].shortName)
+      {
+        cont =
+            allOptions[i].processor (&clpc, allOptions[i].scls,
+                                     allOptions[i].name, GNoptarg);
+        break;
+      }
+    }
+    if (i == count)
+    {
+      FPRINTF (stderr, _("Use %s to get a list of options.\n"), "--help");
+      cont = GNUNET_SYSERR;
+    }
+  }
+
+  free (shorts);
+  free (long_options);
+  if (cont == GNUNET_SYSERR)
+    return GNUNET_SYSERR;
+  return GNoptind;
+}
+
+/* end of getopt.c */

Added: monkey/trunk/pathologist/src/pathologist/getopt_helpers.c
===================================================================
--- monkey/trunk/pathologist/src/pathologist/getopt_helpers.c                   
        (rev 0)
+++ monkey/trunk/pathologist/src/pathologist/getopt_helpers.c   2012-09-24 
18:49:45 UTC (rev 23981)
@@ -0,0 +1,294 @@
+/*
+     This file is part of GNUnet
+     (C) 2006, 2011 Christian Grothoff (and other contributing authors)
+
+     GNUnet is free software; you can redistribute it and/or modify
+     it under the terms of the GNU General Public License as published
+     by the Free Software Foundation; either version 2, or (at your
+     option) any later version.
+
+     GNUnet is distributed in the hope that it will be useful, but
+     WITHOUT ANY WARRANTY; without even the implied warranty of
+     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+     General Public License for more details.
+
+     You should have received a copy of the GNU General Public License
+     along with GNUnet; see the file COPYING.  If not, write to the
+     Free Software Foundation, Inc., 59 Temple Place - Suite 330,
+     Boston, MA 02111-1307, USA.
+*/
+
+/**
+ * @file src/util/getopt_helpers.c
+ * @brief implements command line that sets option
+ * @author Christian Grothoff
+ */
+
+#include <string.h>
+#include "platform.h"
+#include "gnunet_common.h"
+#include "gnunet_getopt_lib.h"
+
+#define LOG(kind,...) GNUNET_log_from (kind, "util", __VA_ARGS__)
+
+
+/**
+ * Print out program version (implements --version).
+ *
+ * @param ctx command line processing context
+ * @param scls additional closure (points to version string)
+ * @param option name of the option
+ * @param value not used (NULL)
+ * @return GNUNET_SYSERR (do not continue)
+ */
+int
+GNUNET_GETOPT_print_version_ (struct GNUNET_GETOPT_CommandLineProcessorContext
+                              *ctx, void *scls, const char *option,
+                              const char *value)
+{
+  const char *version = scls;
+
+  printf ("%s v%s\n", ctx->binaryName, version);
+  return GNUNET_SYSERR;
+}
+
+
+
+#define BORDER 29
+
+/**
+ * Print out details on command line options (implements --help).
+ *
+ * @param ctx command line processing context
+ * @param scls additional closure (points to about text)
+ * @param option name of the option
+ * @param value not used (NULL)
+ * @return GNUNET_SYSERR (do not continue)
+ */
+int
+GNUNET_GETOPT_format_help_ (struct GNUNET_GETOPT_CommandLineProcessorContext
+                            *ctx, void *scls, const char *option,
+                            const char *value)
+{
+  const char *about = scls;
+  size_t slen;
+  unsigned int i;
+  int j;
+  size_t ml;
+  size_t p;
+  char *scp;
+  const char *trans;
+  const struct GNUNET_GETOPT_CommandLineOption *opt;
+
+  if (NULL != about)
+  {
+    printf ("%s\n%s\n", ctx->binaryOptions, about);
+    printf ("Arguments mandatory for long options are also mandatory for short 
options.\n");
+  }
+  i = 0;
+  opt = ctx->allOptions;
+  while (opt[i].description != NULL)
+  {
+    if (opt[i].shortName == '\0')
+      printf ("      ");
+    else
+      printf ("  -%c, ", opt[i].shortName);
+    printf ("--%s", opt[i].name);
+    slen = 8 + strlen (opt[i].name);
+    if (opt[i].argumentHelp != NULL)
+    {
+      printf ("=%s", opt[i].argumentHelp);
+      slen += 1 + strlen (opt[i].argumentHelp);
+    }
+    if (slen > BORDER)
+    {
+      printf ("\n%*s", BORDER, "");
+      slen = BORDER;
+    }
+    if (slen < BORDER)
+    {
+      printf ("%*s", (int) (BORDER - slen), "");
+      slen = BORDER;
+    }
+    if (0 < strlen (opt[i].description))
+      trans = opt[i].description;
+    else
+      trans = "";
+    ml = strlen (trans);
+    p = 0;
+OUTER:
+    while (ml - p > 78 - slen)
+    {
+      for (j = p + 78 - slen; j > p; j--)
+      {
+        if (isspace ((unsigned char) trans[j]))
+        {
+          scp = malloc (j - p + 1);
+          memcpy (scp, &trans[p], j - p);
+          scp[j - p] = '\0';
+          printf ("%s\n%*s", scp, BORDER + 2, "");
+          free (scp);
+          p = j + 1;
+          slen = BORDER + 2;
+          goto OUTER;
+        }
+      }
+      /* could not find space to break line */
+      scp = malloc (78 - slen + 1);
+      memcpy (scp, &trans[p], 78 - slen);
+      scp[78 - slen] = '\0';
+      printf ("%s\n%*s", scp, BORDER + 2, "");
+      free (scp);
+      slen = BORDER + 2;
+      p = p + 78 - slen;
+    }
+    /* print rest */
+    if (p < ml)
+      printf ("%s\n", &trans[p]);
+    if (strlen (trans) == 0)
+      printf ("\n");
+    i++;
+  }
+  printf ("Report bugs to address@hidden"
+          "GNUnet home page: http://www.gnu.org/software/gnunet/\n";
+          "General help using GNU software: http://www.gnu.org/gethelp/\n";);
+  return GNUNET_SYSERR;
+}
+
+
+/**
+ * Set an option of type 'unsigned int' from the command line. Each
+ * time the option flag is given, the value is incremented by one.
+ * A pointer to this function should be passed as part of the
+ * 'struct GNUNET_GETOPT_CommandLineOption' array to initialize options
+ * of this type.  It should be followed by a pointer to a value of
+ * type 'int'.
+ *
+ * @param ctx command line processing context
+ * @param scls additional closure (will point to the 'int')
+ * @param option name of the option
+ * @param value not used (NULL)
+ * @return GNUNET_OK
+ */
+int
+GNUNET_GETOPT_increment_value (struct GNUNET_GETOPT_CommandLineProcessorContext
+                               *ctx, void *scls, const char *option,
+                               const char *value)
+{
+  int *val = scls;
+
+  (*val)++;
+  return GNUNET_OK;
+}
+
+
+/**
+ * Set an option of type 'int' from the command line to 1 if the
+ * given option is present.
+ * A pointer to this function should be passed as part of the
+ * 'struct GNUNET_GETOPT_CommandLineOption' array to initialize options
+ * of this type.  It should be followed by a pointer to a value of
+ * type 'int'.
+ *
+ * @param ctx command line processing context
+ * @param scls additional closure (will point to the 'int')
+ * @param option name of the option
+ * @param value not used (NULL)
+ * @return GNUNET_OK
+ */
+int
+GNUNET_GETOPT_set_one (struct GNUNET_GETOPT_CommandLineProcessorContext *ctx,
+                       void *scls, const char *option, const char *value)
+{
+  int *val = scls;
+
+  *val = 1;
+  return GNUNET_OK;
+}
+
+
+/**
+ * Set an option of type 'char *' from the command line.
+ * A pointer to this function should be passed as part of the
+ * 'struct GNUNET_GETOPT_CommandLineOption' array to initialize options
+ * of this type.  It should be followed by a pointer to a value of
+ * type 'char *'.
+ *
+ * @param ctx command line processing context
+ * @param scls additional closure (will point to the 'char *',
+ *             which will be allocated)
+ * @param option name of the option
+ * @param value actual value of the option (a string)
+ * @return GNUNET_OK
+ */
+int
+GNUNET_GETOPT_set_string (struct GNUNET_GETOPT_CommandLineProcessorContext 
*ctx,
+                          void *scls, const char *option, const char *value)
+{
+  char **val = scls;
+
+//  GNUNET_assert (value != NULL);
+//  GNUNET_free_non_null (*val);
+  if(*val != NULL) free(*val);
+  *val = strdup (value);
+  return GNUNET_OK;
+}
+
+
+/**
+ * Set an option of type 'unsigned long long' from the command line.
+ * A pointer to this function should be passed as part of the
+ * 'struct GNUNET_GETOPT_CommandLineOption' array to initialize options
+ * of this type.  It should be followed by a pointer to a value of
+ * type 'unsigned long long'.
+ *
+ * @param ctx command line processing context
+ * @param scls additional closure (will point to the 'unsigned long long')
+ * @param option name of the option
+ * @param value actual value of the option as a string.
+ * @return GNUNET_OK if parsing the value worked
+ */
+int
+GNUNET_GETOPT_set_ulong (struct GNUNET_GETOPT_CommandLineProcessorContext *ctx,
+                         void *scls, const char *option, const char *value)
+{
+  unsigned long long *val = scls;
+
+  if (1 != SSCANF (value, "%llu", val))
+  {
+    FPRINTF (stderr, "You must pass a number to the `%s' option.\n", option);
+    return GNUNET_SYSERR;
+  }
+  return GNUNET_OK;
+}
+
+
+/**
+ * Set an option of type 'unsigned int' from the command line.
+ * A pointer to this function should be passed as part of the
+ * 'struct GNUNET_GETOPT_CommandLineOption' array to initialize options
+ * of this type.  It should be followed by a pointer to a value of
+ * type 'unsigned int'.
+ *
+ * @param ctx command line processing context
+ * @param scls additional closure (will point to the 'unsigned int')
+ * @param option name of the option
+ * @param value actual value of the option as a string.
+ * @return GNUNET_OK if parsing the value worked
+ */
+int
+GNUNET_GETOPT_set_uint (struct GNUNET_GETOPT_CommandLineProcessorContext *ctx,
+                        void *scls, const char *option, const char *value)
+{
+  unsigned int *val = scls;
+
+  if (1 != SSCANF (value, "%u", val))
+  {
+    FPRINTF (stderr, "You must pass a number to the `%s' option.\n", option);
+    return GNUNET_SYSERR;
+  }
+  return GNUNET_OK;
+}
+
+
+/* end of getopt_helpers.c */




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