src/lib/osunix.c 1.44
1.44 2009/11/22 00:18:04 kent
Adding simplifyPathToDir
Index: src/lib/osunix.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/lib/osunix.c,v
retrieving revision 1.43
retrieving revision 1.44
diff -b -B -U 1000000 -r1.43 -r1.44
--- src/lib/osunix.c 10 Jul 2009 01:52:27 -0000 1.43
+++ src/lib/osunix.c 22 Nov 2009 00:18:04 -0000 1.44
@@ -1,473 +1,613 @@
/* 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>
#include <regex.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 slName *listDirRegEx(char *dir, char *regEx, int flags)
/* Return an alphabetized list of all files that match
* the regular expression pattern in directory.
* See REGCOMP(3) for flags (e.g. REG_ICASE) */
{
struct slName *list = NULL, *name;
struct dirent *de;
DIR *d;
regex_t re;
int err = regcomp(&re, regEx, flags | REG_NOSUB);
if(err)
errAbort("regcomp failed; err: %d", err);
if ((d = opendir(dir)) == NULL)
return NULL;
while ((de = readdir(d)) != NULL)
{
char *fileName = de->d_name;
if (differentString(fileName, ".") && differentString(fileName, ".."))
{
if (!regexec(&re, fileName, 0, NULL, 0))
{
name = newSlName(fileName);
slAddHead(&list, name);
}
}
}
closedir(d);
regfree(&re);
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;
}
+static void eatSlashSlashInPath(char *path)
+/* Convert multiple // to single // */
+{
+char *s, *d;
+s = d = path;
+char c, lastC = 0;
+while ((c = *s++) != 0)
+ {
+ if (c == '/' && lastC == c)
+ continue;
+ *d++ = c;
+ lastC = c;
+ }
+*d = 0;
+}
+
+static void eatExcessDotDotInPath(char *path)
+/* If there's a /.. in path take it out. Turns
+ * 'this/long/../dir/file' to 'this/dir/file
+ * and
+ * 'this/../file' to 'file'
+ *
+ * and
+ * 'this/long/..' to 'this'
+ * and
+ * 'this/..' to ''
+ * and
+ * /this/..' to '/' */
+{
+/* Take out each /../ individually */
+for (;;)
+ {
+ /* Find first bit that needs to be taken out. */
+ char *excess= strstr(path, "/../");
+ char *excessEnd = excess+4;
+ if (excess == NULL || excess == path)
+ break;
+
+ /* Look for a '/' before this */
+ char *excessStart = matchingCharBeforeInLimits(path, excess, '/');
+ if (excessStart == NULL) /* Preceding '/' not found */
+ excessStart = path;
+ else
+ excessStart += 1;
+ strcpy(excessStart, excessEnd);
+ }
+
+/* Take out final /.. if any */
+if (endsWith(path, "/.."))
+ {
+ if (!sameString(path, "/..")) /* We don't want to turn this to blank. */
+ {
+ int len = strlen(path);
+ char *excessStart = matchingCharBeforeInLimits(path, path+len-3, '/');
+ if (excessStart == NULL) /* Preceding '/' not found */
+ excessStart = path;
+ else
+ excessStart += 1;
+ *excessStart = 0;
+ }
+ }
+}
+
+char *simplifyPathToDir(char *path)
+/* Return path with ~ and .. taken out. Also any // or trailing /.
+ * freeMem result when done. */
+{
+/* Expand ~ if any with result in newPath */
+char newPath[PATH_LEN];
+int newLen = 0;
+char *s = path;
+if (*s == '~')
+ {
+ char *homeDir = getenv("HOME");
+ if (homeDir == NULL)
+ errAbort("No HOME environment var defined after ~ in simplifyPathToDir");
+ ++s;
+ if (*s == '/') /* ~/something */
+ {
+ ++s;
+ safef(newPath, sizeof(newPath), "%s/", homeDir);
+ }
+ else /* ~something */
+ {
+ safef(newPath, sizeof(newPath), "%s/../", homeDir);
+ }
+ newLen = strlen(newPath);
+ }
+int remainingLen = strlen(s);
+if (newLen + remainingLen >= sizeof(newPath))
+ errAbort("path too big in simplifyPathToDir");
+strcpy(newPath+newLen, s);
+
+/* Remove //, .. and trailing / */
+eatSlashSlashInPath(newPath);
+eatExcessDotDotInPath(newPath);
+int lastPos = strlen(newPath)-1;
+if (lastPos > 0 && newPath[lastPos] == '/')
+ newPath[lastPos] = 0;
+
+return cloneString(newPath);
+}
+
+#ifdef DEBUG
+void simplifyPathToDirSelfTest()
+{
+/* First test some cases which should remain the same. */
+assert(sameString(simplifyPathToDir(""),""));
+assert(sameString(simplifyPathToDir("a"),"a"));
+assert(sameString(simplifyPathToDir("a/b"),"a/b"));
+assert(sameString(simplifyPathToDir("/"),"/"));
+assert(sameString(simplifyPathToDir("/.."),"/.."));
+assert(sameString(simplifyPathToDir("/../a"),"/../a"));
+
+/* Now test removing trailing slash. */
+assert(sameString(simplifyPathToDir("a/"),"a"));
+assert(sameString(simplifyPathToDir("a/b/"),"a/b"));
+
+/* Test .. removal. */
+assert(sameString(simplifyPathToDir("a/.."),""));
+assert(sameString(simplifyPathToDir("a/../"),""));
+assert(sameString(simplifyPathToDir("a/../b"),"b"));
+assert(sameString(simplifyPathToDir("/a/.."),"/"));
+assert(sameString(simplifyPathToDir("/a/../"),"/"));
+assert(sameString(simplifyPathToDir("/a/../b"),"/b"));
+assert(sameString(simplifyPathToDir("a/b/.."),"a"));
+assert(sameString(simplifyPathToDir("a/b/../"),"a"));
+assert(sameString(simplifyPathToDir("a/b/../c"),"a/c"));
+assert(sameString(simplifyPathToDir("a/../b/../c"),"c"));
+assert(sameString(simplifyPathToDir("a/../b/../c/.."),""));
+assert(sameString(simplifyPathToDir("/a/../b/../c/.."),"/"));
+
+/* Test // removal */
+assert(sameString(simplifyPathToDir("//"),"/"));
+assert(sameString(simplifyPathToDir("//../"),"/.."));
+assert(sameString(simplifyPathToDir("a//b///c"),"a/b/c"));
+assert(sameString(simplifyPathToDir("a/b///"),"a/b"));
+}
+#endif /* DEBUG */
+
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;
fflush(stdout); // clear buffer before forking
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");
else
{
if (WIFEXITED(wstat))
{
if (WEXITSTATUS(wstat) != 0)
fprintf(stderr, "pstack failed\n");
}
else if (WIFSIGNALED(wstat))
fprintf(stderr, "pstack signaled %d\n", WTERMSIG(wstat));
}
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);
}