1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
|
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have *
* access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#include <stdio.h>
#include <sys/types.h>
#include <fcntl.h>
#include <sys/stat.h>
#ifdef H5_HAVE_UNISTD_H
#include <unistd.h>
#endif
#include "hdf5.h"
#include "H5private.h"
#include "h5tools_utils.h"
#define TRUE 1
#define FALSE 0
hsize_t write_pad( int , hsize_t );
hsize_t compute_pad( hsize_t );
hsize_t copy_to_file( int , int , ssize_t, ssize_t );
const char *progname = "h5unjam";
int d_status = EXIT_SUCCESS;
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";
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)
{
fflush(stdout);
fprintf(stdout, "usage: %s -i h5_file -o user_block_file_out -o h5_file_out [-d | --delete]\n", prog);
fprintf(stdout, " Extract user block from 'h5_file' into 'user_block_file'\n");
fprintf(stdout, " and HDF5 file into 'h5_file_out'\n");
fprintf(stdout, " %s -h\n",prog);
fprintf(stdout, " Print a usage message and exit\n");
}
/*-------------------------------------------------------------------------
* 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 = strdup (opt_arg);
break;
case 'i':
input_file = strdup (opt_arg);
break;
case 'u':
ub_file = strdup (opt_arg);
break;
case 'd':
do_delete = TRUE;
break;
case 'h':
usage(progname);
exit(EXIT_SUCCESS);
case '?':
default:
usage(progname);
exit(EXIT_FAILURE);
}
}
/* check for file name to be processed */
/*
if (argc <= opt_ind+2) {
error_msg(progname, "missing file name\n");
usage(progname);
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;
int ufid;
int h5fid;
void *edata;
H5E_auto_t func;
hid_t ifile;
off_t fsize;
hsize_t usize;
htri_t testval;
herr_t status;
hid_t plist;
int res;
struct stat sbuf;
/* Disable error reporting */
H5Eget_auto(&func, &edata);
H5Eset_auto(NULL, NULL);
parse_command_line(argc, argv);
testval = H5Fis_hdf5(input_file);
if (testval <= 0) {
error_msg(progname, "Input HDF5 file is not HDF \"%s\"\n", input_file);
exit(EXIT_FAILURE);
}
ifile = H5Fopen(input_file, H5F_ACC_RDONLY , H5P_DEFAULT);
if (ifile < 0) {
error_msg(progname, "Can't open input HDF5 file \"%s\"\n", input_file);
exit(EXIT_FAILURE);
}
plist = H5Fget_create_plist(ifile);
if (plist < 0) {
error_msg(progname, "Can't get file creation plist for file \"%s\"\n", input_file);
exit(EXIT_FAILURE);
}
status = H5Pget_userblock(plist, & usize );
if (status < 0) {
error_msg(progname, "Can't get user block for file \"%s\"\n", input_file);
exit(EXIT_FAILURE);
}
if (usize == 0) {
/* no user block to remove: message? */
error_msg(progname, "\"%s\" has no user block: no change to file\n", input_file);
exit(EXIT_SUCCESS);
}
res = stat(input_file, &sbuf);
if (res < 0) {
error_msg(progname, "Can't stat file \"%s\"\n", input_file);
exit(EXIT_FAILURE);
}
fsize = sbuf.st_size;
ifid = HDopen(input_file,O_RDONLY,0);
if (ifid < 0) {
error_msg(progname, "unable to open input HDF5 file \"%s\"\n", input_file);
exit(EXIT_FAILURE);
}
if (do_delete && (ub_file != NULL)) {
error_msg(progname, "??\"%s\"\n", ub_file);
exit(EXIT_FAILURE);
}
if (ub_file == NULL) {
/* write to sdtout */
ufid = dup(1);
} else {
ufid = HDopen(ub_file,O_WRONLY|O_CREAT|O_TRUNC, 0644 );
if (ufid < 0) {
error_msg(progname, "unable to open user block file for output\"%s\"\n", ub_file);
exit(EXIT_FAILURE);
}
}
if (output_file == NULL) {
h5fid = HDopen(input_file,O_WRONLY, 0);
if (h5fid < 0) {
error_msg(progname, "unable to open output HDF5 file \"%s\"\n", input_file);
exit(EXIT_FAILURE);
}
} else {
h5fid = open(output_file,O_WRONLY|O_CREAT|O_TRUNC, 0644 );
if (h5fid < 0) {
error_msg(progname, "unable to open output HDF5 file \"%s\"\n", output_file);
exit(EXIT_FAILURE);
}
}
/* copy from 0 to 'usize - 1' into ufid */
if (!do_delete) {
copy_to_file( ifid, ufid, 0, (ssize_t) usize);
}
/* copy from usize to end of file into h5fid,
* starting at end of user block if present
*/
copy_to_file( ifid, h5fid, (ssize_t) usize, (ssize_t)(fsize - (ssize_t)usize) );
close(ufid);
close(h5fid);
close(ifid);
return d_status;
}
/*
* Copy 'how_much' bytes from the input file to the output file,
* starting at byte 'where' in the input file.
*
* Returns the size of the output file.
*/
hsize_t
copy_to_file( int infid, int ofid, ssize_t where, ssize_t how_much ) {
char buf[1024];
off_t to;
off_t from;
ssize_t nchars = -1;
if (how_much <= 0) {
/* nothing to copy */
return(where);
}
from = where;
to = 0;
while( how_much > 0) {
HDlseek(infid,from,SEEK_SET);
if (how_much > 512) {
nchars = HDread(infid,buf,(unsigned)512);
} else {
nchars = HDread(infid,buf,(unsigned)how_much);
}
HDlseek(ofid,to,SEEK_SET);
HDwrite(ofid,buf,(unsigned)nchars);
how_much -= nchars;
from += nchars;
to += nchars;
}
return (where+how_much);
}
|