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hdf5/tools/h5jam/h5unjam.c
Jonathan Kim e703a6a2a4 [svn-r21236] Purpose: 
Work for:
   HDFFV-7515 - GMQS: h5unjam - incorrect help page and should display when 
   no file is given.
   and
   HDFFV-5941 - h5jam: specifying a user block file with a proper HDF5 magic
   number will result in a corrupted HDF5 file.


Description:
   - Revised command help pages of h5jam and h5unjam. The descriptions
     were not up to date and some were missing. (HDFFV-7515)
   - Fixed h5jam not to allow specifying an HDF5 formatted file as input 
     file for -u (user block file) option, because the original HDF5 file 
     will not be accessible if allows. (HDFFV-5941)

Tested:
    jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Cmake (jam, Wondows)
2011-08-16 15:41:47 -05:00

446 lines
12 KiB
C
Raw Blame History

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the files COPYING and Copyright.html. COPYING can be found at the root *
* of the source code distribution tree; Copyright.html can be found at the *
* root level of an installed copy of the electronic HDF5 document set and *
* is linked from the top-level documents page. It can also be found at *
* http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have *
* access to either file, you may request a copy from help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#include "hdf5.h"
#include "H5private.h"
#include "h5tools_utils.h"
/* Name of tool */
#define PROGRAMNAME "h5unjam"
#define TRUE 1
#define FALSE 0
#define COPY_BUF_SIZE 1024
hsize_t write_pad( int , hsize_t );
hsize_t compute_pad( hsize_t );
herr_t copy_to_file( int , int , ssize_t, ssize_t );
int do_delete = FALSE;
char *output_file = NULL;
char *input_file = NULL;
char *ub_file = NULL;
/*
* Command-line options: The user can specify short or long-named
* parameters. The long-named ones can be partially spelled. When
* adding more, make sure that they don't clash with each other.
*/
static const char *s_opts = "hu:i:o:d:V";
static struct long_options l_opts[] = {
{ "help", no_arg, 'h' },
{ "hel", no_arg, 'h' },
{"i", require_arg, 'i'}, /* input file */
{"u", require_arg, 'u'}, /* user block file */
{"o", require_arg, 'o'}, /* output file */
{"delete", no_arg, 'd'}, /* delete ub */
{"delet", no_arg, 'd'},
{"dele", no_arg, 'd'},
{"del", no_arg, 'd'},
{"de", no_arg, 'd'},
{ NULL, 0, '\0' }
};
/*-------------------------------------------------------------------------
* Function: usage
*
* Purpose: Print the usage message
*
* Return: void
*
* Programmer:
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void
usage(const char *prog)
{
HDfflush(stdout);
HDfprintf(stdout,
"usage: %s -i <in_file.h5> [-o <out_file.h5> ] [-u <out_user_file> | --delete]\n", prog);
HDfprintf(stdout, "\n");
HDfprintf(stdout,
"Splits user file and HDF5 file into two files: user block data and HDF5 data.\n");
HDfprintf(stdout, "\n");
HDfprintf(stdout,
"OPTIONS\n");
HDfprintf(stdout,
" -i in_file.h5 Specifies the HDF5 as input. If the input HDF5 file\n");
HDfprintf(stdout,
" contains no user block, exit with an error message.\n");
HDfprintf(stdout,
" -o out_file.h5 Specifies output HDF5 file without a user block.\n");
HDfprintf(stdout,
" If not specified, the user block will be removed from the\n");
HDfprintf(stdout,
" input HDF5 file.\n");
HDfprintf(stdout,
" -u out_user_file\n");
HDfprintf(stdout,
" Specifies the output file containing the data from the\n");
HDfprintf(stdout,
" user block.\n");
HDfprintf(stdout,
" Cannot be used with --delete option.\n");
HDfprintf(stdout,
" --delete Remove the user block from the input HDF5 file. The content\n");
HDfprintf(stdout,
" of the user block is discarded.\n");
HDfprintf(stdout,
" Cannot be used with the -u option.\n");
HDfprintf(stdout, "\n");
HDfprintf(stdout,
" -h Prints a usage message and exits.\n");
HDfprintf(stdout,
" -V Prints the HDF5 library version and exits.\n");
HDfprintf(stdout, "\n");
HDfprintf(stdout,
" If neither --delete nor -u is specified, the user block from the input file\n");
HDfprintf(stdout,
" will be displayed to stdout.\n");
HDfprintf(stdout, "\n");
HDfprintf(stdout,
"Exit Status:\n");
HDfprintf(stdout,
" 0 Succeeded.\n");
HDfprintf(stdout,
" >0 An error occurred.\n");
}
/*-------------------------------------------------------------------------
* Function: leave
*
* Purpose: Shutdown and call exit()
*
* Return: Does not return
*
*-------------------------------------------------------------------------
*/
static void
leave(int ret)
{
if (ub_file)
HDfree (ub_file);
if (input_file)
HDfree (input_file);
if (output_file)
HDfree (output_file);
h5tools_close();
exit(ret);
}
/*-------------------------------------------------------------------------
* Function: parse_command_line
*
* Purpose: Parse the command line for the h5dumper.
*
* Return: Success:
*
* Failure: Exits program with EXIT_FAILURE value.
*
* Programmer:
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void
parse_command_line(int argc, const char *argv[])
{
int opt = FALSE;
/* parse command line options */
while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
switch ((char) opt) {
case 'o':
output_file = HDstrdup (opt_arg);
break;
case 'i':
input_file = HDstrdup (opt_arg);
break;
case 'u':
ub_file = HDstrdup (opt_arg);
break;
case 'd':
do_delete = TRUE;
break;
case 'h':
usage(h5tools_getprogname());
leave(EXIT_SUCCESS);
case 'V':
print_version(h5tools_getprogname());
leave(EXIT_SUCCESS);
case '?':
default:
usage(h5tools_getprogname());
leave(EXIT_FAILURE);
}
}
/* check for file name to be processed */
/*
if (argc <= opt_ind+2) {
error_msg("missing file name\n");
usage(h5tools_getprogname());
exit(EXIT_FAILURE);
}
*/
}
/*-------------------------------------------------------------------------
* Function: main
*
* Purpose: HDF5 user block unjammer
*
* Return: Success: 0
* Failure: 1
*
* Programmer:
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
int
main(int argc, const char *argv[])
{
int ifid = -1;
int ufid = -1;
int h5fid = -1;
void *edata;
H5E_auto2_t func;
hid_t ifile = -1;
hid_t plist = -1;
off_t fsize;
hsize_t usize;
htri_t testval;
herr_t status;
int res;
h5_stat_t sbuf;
h5tools_setprogname(PROGRAMNAME);
h5tools_setstatus(EXIT_SUCCESS);
/* Disable error reporting */
H5Eget_auto2(H5E_DEFAULT, &func, &edata);
H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
parse_command_line(argc, argv);
if (input_file == NULL) {
/* no user block */
error_msg("missing arguemnt for HDF5 file input.\n");
help_ref_msg(stderr);
leave (EXIT_FAILURE);
}
testval = H5Fis_hdf5(input_file);
if (testval <= 0) {
error_msg("Input HDF5 file \"%s\" is not HDF\n", input_file);
help_ref_msg (stderr);
h5tools_setstatus(EXIT_FAILURE);
goto done;
}
ifile = H5Fopen(input_file, H5F_ACC_RDONLY , H5P_DEFAULT);
if (ifile < 0) {
error_msg("Can't open input HDF5 file \"%s\"\n", input_file);
h5tools_setstatus(EXIT_FAILURE);
goto done;
}
plist = H5Fget_create_plist(ifile);
if (plist < 0) {
error_msg("Can't get file creation plist for file \"%s\"\n", input_file);
h5tools_setstatus(EXIT_FAILURE);
goto done;
}
status = H5Pget_userblock(plist, & usize);
if (status < 0) {
error_msg("Can't get user block for file \"%s\"\n", input_file);
h5tools_setstatus(EXIT_FAILURE);
goto done;
}
H5Pclose(plist);
H5Fclose(ifile);
if (usize == 0) {
/* no user block to remove: message? */
error_msg("\"%s\" has no user block: no change to file\n", input_file);
h5tools_setstatus(EXIT_SUCCESS);
goto done;
}
ifid = HDopen(input_file,O_RDONLY,0);
if(ifid < 0) {
error_msg("unable to open input HDF5 file \"%s\"\n", input_file);
h5tools_setstatus(EXIT_FAILURE);
goto done;
}
res = HDfstat(ifid, &sbuf);
if(res < 0) {
error_msg("Can't stat file \"%s\"\n", input_file);
h5tools_setstatus(EXIT_FAILURE);
goto done;
}
fsize = sbuf.st_size;
if (do_delete && (ub_file != NULL)) {
error_msg("??\"%s\"\n", ub_file);
h5tools_setstatus(EXIT_FAILURE);
goto done;
}
if (ub_file == NULL) {
/* write to sdtout */
ufid = HDdup(1);
}
else {
ufid = HDopen(ub_file,O_WRONLY|O_CREAT|O_TRUNC, 0644 );
if (ufid < 0) {
error_msg("unable to open user block file for output\"%s\"\n", ub_file);
h5tools_setstatus(EXIT_FAILURE);
goto done;
}
}
if (output_file == NULL) {
h5fid = HDopen(input_file,O_WRONLY, 0);
if (h5fid < 0) {
error_msg("unable to open output HDF5 file \"%s\"\n", input_file);
h5tools_setstatus(EXIT_FAILURE);
goto done;
}
}
else {
h5fid = HDopen(output_file,O_WRONLY|O_CREAT|O_TRUNC, 0644 );
if (h5fid < 0) {
error_msg("unable to open output HDF5 file \"%s\"\n", output_file);
h5tools_setstatus(EXIT_FAILURE);
goto done;
}
}
/* copy from 0 to 'usize - 1' into ufid */
if (!do_delete) {
if(copy_to_file(ifid, ufid, 0, (ssize_t) usize) < 0) {
error_msg("unable to copy user block to output file \"%s\"\n", ub_file);
h5tools_setstatus(EXIT_FAILURE);
goto done;
}
}
/* copy from usize to end of file into h5fid,
* starting at end of user block if present
*/
if(copy_to_file(ifid, h5fid, (ssize_t) usize, (ssize_t)(fsize - (ssize_t)usize)) < 0) {
error_msg("unable to copy hdf5 data to output file \"%s\"\n", output_file);
h5tools_setstatus(EXIT_FAILURE);
goto done;
}
done:
if (ub_file) {
HDfree (ub_file);
if (ufid >= 0) HDclose(ufid);
}
if (input_file)
HDfree (input_file);
if (output_file)
HDfree (output_file);
if (h5fid >= 0) HDclose(h5fid);
if (ifid >= 0) HDclose(ifid);
return h5tools_getstatus();
}
/*
* Copy 'how_much' bytes from the input file to the output file,
* starting at byte 'where' in the input file.
*
* Returns 0 on success, -1 on failure.
*/
herr_t
copy_to_file( int infid, int ofid, ssize_t where, ssize_t how_much )
{
static char buf[COPY_BUF_SIZE];
off_t to;
off_t from;
ssize_t nchars = -1;
ssize_t wnchars = -1;
herr_t ret_value = 0;
/* nothing to copy */
if(how_much <= 0)
goto done;
from = where;
to = 0;
while(how_much > 0) {
/* Seek to correct position in input file */
HDlseek(infid,from,SEEK_SET);
/* Read data to buffer */
if (how_much > COPY_BUF_SIZE)
nchars = HDread(infid,buf,(unsigned)COPY_BUF_SIZE);
else
nchars = HDread(infid,buf,(unsigned)how_much);
if(nchars < 0) {
ret_value = -1;
goto done;
} /* end if */
/* Seek to correct position in output file */
HDlseek(ofid,to,SEEK_SET);
/* Update positions/size */
how_much -= nchars;
from += nchars;
to += nchars;
/* Write nchars bytes to output file */
wnchars = nchars;
while(nchars > 0) {
wnchars = HDwrite(ofid,buf,(unsigned)nchars);
if(wnchars < 0) {
ret_value = -1;
goto done;
} /* end if */
nchars -= wnchars;
} /* end while */
} /* end while */
done:
return ret_value;
} /* end copy_to_file */
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