src/lib/osunix.c 1.41
1.41 2009/06/07 07:11:55 markd
make sure dumpStack does end up being recusivel called due to an error
Index: src/lib/osunix.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/lib/osunix.c,v
retrieving revision 1.40
retrieving revision 1.41
diff -b -B -U 1000000 -r1.40 -r1.41
--- src/lib/osunix.c 3 Jun 2009 00:34:11 -0000 1.40
+++ src/lib/osunix.c 7 Jun 2009 07:11:55 -0000 1.41
@@ -1,437 +1,437 @@
/* Some wrappers around operating-system specific stuff.
*
* This file is copyright 2002 Jim Kent, but license is hereby
* granted for all use - public, private or commercial. */
#include "common.h"
#include <dirent.h>
#include <sys/utsname.h>
#include <sys/time.h>
#include <pwd.h>
#include <termios.h>
#include "portable.h"
#include "portimpl.h"
#include <sys/wait.h>
static char const rcsid[] = "$Id$";
off_t fileSize(char *pathname)
/* get file size for pathname. return -1 if not found */
{
struct stat mystat;
ZeroVar(&mystat);
if (stat(pathname,&mystat)==-1)
{
return -1;
}
return mystat.st_size;
}
long clock1000()
/* A millisecond clock. */
{
struct timeval tv;
static long origSec;
gettimeofday(&tv, NULL);
if (origSec == 0)
origSec = tv.tv_sec;
return (tv.tv_sec-origSec)*1000 + tv.tv_usec / 1000;
}
void sleep1000(int milli)
/* Sleep for given number of 1000ths of second */
{
if (milli > 0)
{
struct timeval tv;
tv.tv_sec = milli/1000;
tv.tv_usec = (milli%1000)*1000;
select(0, NULL, NULL, NULL, &tv);
}
}
long clock1()
/* A seconds clock. */
{
struct timeval tv;
gettimeofday(&tv, NULL);
return tv.tv_sec;
}
void uglyfBreak()
/* Go into debugger. */
{
static char *nullPt = NULL;
nullPt[0] = 0;
}
char *getCurrentDir()
/* Return current directory. Abort if it fails. */
{
static char dir[PATH_LEN];
if (getcwd( dir, sizeof(dir) ) == NULL )
errnoAbort("can't get current directory");
return dir;
}
void setCurrentDir(char *newDir)
/* Set current directory. Abort if it fails. */
{
if (chdir(newDir) != 0)
errnoAbort("can't to set current directory: %s", newDir);
}
boolean maybeSetCurrentDir(char *newDir)
/* Change directory, return FALSE (and set errno) if fail. */
{
return chdir(newDir) == 0;
}
struct slName *listDir(char *dir, char *pattern)
/* Return an alphabetized list of all files that match
* the wildcard pattern in directory. */
{
struct slName *list = NULL, *name;
struct dirent *de;
DIR *d;
if ((d = opendir(dir)) == NULL)
return NULL;
while ((de = readdir(d)) != NULL)
{
char *fileName = de->d_name;
if (differentString(fileName, ".") && differentString(fileName, ".."))
{
if (pattern == NULL || wildMatch(pattern, fileName))
{
name = newSlName(fileName);
slAddHead(&list, name);
}
}
}
closedir(d);
slNameSort(&list);
return list;
}
struct fileInfo *newFileInfo(char *name, off_t size, bool isDir, int statErrno,
time_t lastAccess)
/* Return a new fileInfo. */
{
int len = strlen(name);
struct fileInfo *fi = needMem(sizeof(*fi) + len);
fi->size = size;
fi->isDir = isDir;
fi->statErrno = statErrno;
fi->lastAccess = lastAccess;
strcpy(fi->name, name);
return fi;
}
int cmpFileInfo(const void *va, const void *vb)
/* Compare two fileInfo. */
{
const struct fileInfo *a = *((struct fileInfo **)va);
const struct fileInfo *b = *((struct fileInfo **)vb);
return strcmp(a->name, b->name);
}
boolean makeDir(char *dirName)
/* Make dir. Returns TRUE on success. Returns FALSE
* if failed because directory exists. Prints error
* message and aborts on other error. */
{
int err;
if ((err = mkdir(dirName, 0777)) < 0)
{
if (errno != EEXIST)
{
perror("");
errAbort("Couldn't make directory %s", dirName);
}
return FALSE;
}
return TRUE;
}
struct fileInfo *listDirXExt(char *dir, char *pattern, boolean fullPath, boolean ignoreStatFailures)
/* Return list of files matching wildcard pattern with
* extra info. If full path is true then the path will be
* included in the name of each file. */
{
struct fileInfo *list = NULL, *el;
struct dirent *de;
DIR *d;
int dirNameSize = strlen(dir);
int fileNameOffset = dirNameSize+1;
char pathName[512];
if ((d = opendir(dir)) == NULL)
return NULL;
memcpy(pathName, dir, dirNameSize);
pathName[dirNameSize] = '/';
while ((de = readdir(d)) != NULL)
{
char *fileName = de->d_name;
if (differentString(fileName, ".") && differentString(fileName, ".."))
{
if (pattern == NULL || wildMatch(pattern, fileName))
{
struct stat st;
bool isDir = FALSE;
int statErrno = 0;
strcpy(pathName+fileNameOffset, fileName);
if (stat(pathName, &st) < 0)
{
if (ignoreStatFailures)
statErrno = errno;
else
errAbort("stat failed in listDirX");
}
if (S_ISDIR(st.st_mode))
isDir = TRUE;
if (fullPath)
fileName = pathName;
el = newFileInfo(fileName, st.st_size, isDir, statErrno, st.st_atime);
slAddHead(&list, el);
}
}
}
closedir(d);
slSort(&list, cmpFileInfo);
return list;
}
struct fileInfo *listDirX(char *dir, char *pattern, boolean fullPath)
/* Return list of files matching wildcard pattern with
* extra info. If full path is true then the path will be
* included in the name of each file. */
{
return listDirXExt(dir, pattern, fullPath, FALSE);
}
unsigned long fileModTime(char *pathName)
/* Return file last modification time. The units of
* these may vary from OS to OS, but you can depend on
* later files having a larger time. */
{
struct stat st;
if (stat(pathName, &st) < 0)
errAbort("stat failed in fileModTime: %s", pathName);
return st.st_mtime;
}
char *getHost()
/* Return host name. */
{
static char *hostName = NULL;
static char buf[128];
if (hostName == NULL)
{
hostName = getenv("HTTP_HOST");
if (hostName == NULL)
{
hostName = getenv("HOST");
if (hostName == NULL)
{
if (hostName == NULL)
{
static struct utsname unamebuf;
if (uname(&unamebuf) >= 0)
hostName = unamebuf.nodename;
else
hostName = "unknown";
}
}
}
strncpy(buf, hostName, sizeof(buf));
chopSuffix(buf);
hostName = buf;
}
return hostName;
}
char *mysqlHost()
/* Return host computer on network for mySQL database. */
{
boolean gotIt = FALSE;
static char *host = NULL;
if (!gotIt)
{
static char hostBuf[128];
gotIt = TRUE;
if (fileExists("mysqlHost"))
{
return (host = firstWordInFile("mysqlHost", hostBuf, sizeof(hostBuf)));
}
else
return (host = getenv("MYSQLHOST"));
}
return host;
}
char *semiUniqName(char *base)
/* Figure out a name likely to be unique.
* Name will have no periods. Returns a static
* buffer, so best to clone result unless using
* immediately. */
{
int pid = getpid();
int num = time(NULL)&0xFFFFF;
char host[512];
strcpy(host, getHost());
char *s = strchr(host, '.');
if (s != NULL)
*s = 0;
subChar(host, '-', '_');
static char name[PATH_LEN];
safef(name, sizeof(name), "%s_%s_%x_%x",
base, host, pid, num);
return name;
}
char *rTempName(char *dir, char *base, char *suffix)
/* Make a temp name that's almost certainly unique. */
{
char *x;
static char fileName[PATH_LEN];
int i;
for (i=0;;++i)
{
x = semiUniqName(base);
safef(fileName, sizeof(fileName), "%s/%s%d%s",
dir, x, i, suffix);
if (!fileExists(fileName))
break;
}
return fileName;
}
char *getUser()
/* Get user name */
{
uid_t uid = geteuid();
struct passwd *pw = getpwuid(uid);
if (pw == NULL)
errnoAbort("can't get user name for uid %d", (int)uid);
return pw->pw_name;
}
int mustFork()
/* Fork or abort. */
{
int childId = fork();
if (childId == -1)
errnoAbort("Unable to fork");
return childId;
}
int rawKeyIn()
/* Read in an unbuffered, unechoed character from keyboard. */
{
struct termios attr;
tcflag_t old;
char c;
/* Set terminal to non-echoing non-buffered state. */
if (tcgetattr(STDIN_FILENO, &attr) != 0)
errAbort("Couldn't do tcgetattr");
old = attr.c_lflag;
attr.c_lflag &= ~ICANON;
attr.c_lflag &= ~ECHO;
if (tcsetattr(STDIN_FILENO, TCSANOW, &attr) == -1)
errAbort("Couldn't do tcsetattr");
/* Read one byte */
if (read(STDIN_FILENO,&c,1) != 1)
errnoAbort("I/O error");
/* Put back terminal to how it was. */
attr.c_lflag = old;
if (tcsetattr(STDIN_FILENO, TCSANOW, &attr) == -1)
errAbort("Couldn't do tcsetattr2");
return c;
}
boolean isPipe(int fd)
/* determine in an open file is a pipe */
{
struct stat buf;
if (fstat(fd, &buf) < 0)
errnoAbort("fstat failed");
return S_ISFIFO(buf.st_mode);
}
static void execPStack(pid_t ppid)
/* exec pstack on the specified pid */
{
char *cmd[3], pidStr[32];
safef(pidStr, sizeof(pidStr), "%ld", (long)ppid);
cmd[0] = "pstack";
cmd[1] = pidStr;
cmd[2] = NULL;
// redirect stdout to stderr
if (dup2(2, 1) < 0)
errAbort("dup2 failed");
execvp(cmd[0], cmd);
errAbort("exec failed: %s", cmd[0]);
}
void vaDumpStack(char *format, va_list args)
/* debugging function to run the pstack program on the current process. In
* prints a message, following by a new line, and then the stack track. Just
* prints errors to stderr rather than aborts. For debugging purposes
* only. */
{
+static boolean inDumpStack = FALSE; // don't allow re-entry if called from error handler
+if (inDumpStack)
+ return;
+inDumpStack = TRUE;
+
vfprintf(stderr, format, args);
fputc('\n', stderr);
fflush(stderr);
pid_t ppid = getpid();
pid_t pid = fork();
if (pid < 0)
{
perror("can't fork pstack");
return;
}
if (pid == 0)
execPStack(ppid);
int wstat;
if (waitpid(pid, &wstat, 0) < 0)
- {
perror("waitpid on pstack failed");
- return;
- }
-if (WIFEXITED(wstat))
+else
{
- if (WEXITSTATUS(wstat) != 0)
+ if (WIFEXITED(wstat))
{
+ if (WEXITSTATUS(wstat) != 0)
fprintf(stderr, "pstack failed\n");
- return;
- }
}
-else if (WIFSIGNALED(wstat))
- {
+ else if (WIFSIGNALED(wstat))
fprintf(stderr, "pstack signaled %d\n", WTERMSIG(wstat));
- return;
}
+inDumpStack = FALSE;
}
void dumpStack(char *format, ...)
/* debugging function to run the pstack program on the current process. In
* prints a message, following by a new line, and then the stack track. Just
* prints errors to stderr rather than aborts. For debugging purposes
* only. */
{
va_list args;
va_start(args, format);
vaDumpStack(format, args);
va_end(args);
}