summaryrefslogtreecommitdiffstats
path: root/tools/h5jam/h5jam.c
blob: b15a18f1eb4dff46bd979e7972fcebe8de26e07f (plain)
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
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
 * 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 COPYING file, which can be found at the root of the source code       *
 * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
 * 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.h"
#include "h5tools_utils.h"

/* Name of tool */
#define PROGRAMNAME "h5jam"

#define TRUE 1
#define FALSE 0

hsize_t write_pad (int, hsize_t);
hsize_t compute_user_block_size (hsize_t);
hsize_t copy_some_to_file (int, int, hsize_t, hsize_t, ssize_t);
void parse_command_line (int, const char *[]);

int do_clobber = 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 = "hi:u:o:c:V";  /* add more later ? */
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 */
  {"clobber", no_arg, 'c'},  /* clobber existing UB */
  {"clobbe", no_arg, 'c'},
  {"clobb", no_arg, 'c'},
  {"clob", no_arg, 'c'},
  {"clo", no_arg, 'c'},
  {"cl", no_arg, 'c'},
  {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> -u <in_user_file> [-o <out_file.h5>] [--clobber]\n", prog);
    HDfprintf (stdout, "\n");
    HDfprintf (stdout,
    "Adds user block to front of an HDF5 file and creates a new concatenated file.\n");
    HDfprintf (stdout, "\n");
    HDfprintf (stdout, 
    "OPTIONS\n");
    HDfprintf (stdout, 
    "  -i in_file.h5    Specifies the input HDF5 file.\n");
    HDfprintf (stdout, 
    "  -u in_user_file  Specifies the file to be inserted into the user block.\n");
    HDfprintf (stdout, 
    "                   Can be any file format except an HDF5 format.\n");
    HDfprintf (stdout,
    "  -o out_file.h5   Specifies the output HDF5 file.\n");
    HDfprintf (stdout,
    "                   If not specified, the user block will be concatenated in\n");
    HDfprintf (stdout,
    "                   place to the input HDF5 file.\n");
    HDfprintf (stdout,
    "  --clobber        Wipes out any existing user block before concatenating\n");
    HDfprintf (stdout,
    "                   the given user block.\n");
    HDfprintf (stdout,
    "                   The size of the new user block will be the larger of;\n");
    HDfprintf (stdout,
    "                    - the size of existing user block in the input HDF5 file\n");
    HDfprintf (stdout,
    "                    - the size of user block required by new input user file\n");
    HDfprintf (stdout,
    "                   (size = 512 x 2N,  N is positive integer.)\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,
    "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();

    HDexit(ret);
}

/*-------------------------------------------------------------------------
 * Function:    parse_command_line
 *
 * Purpose:     Parse the command line for the h5dumper.
 *
 * Return:      Success:
 *
 *              Failure:    Exits program with EXIT_FAILURE value.
 *
 * Programmer:
 *
 * Modifications:
 *
 *-------------------------------------------------------------------------
 */

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 'c':
          do_clobber = 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);
      }
    }
}

/*-------------------------------------------------------------------------
 * Function:    main
 *
 * Purpose:     HDF5 user block jammer
 *
 * Return:      Success:    0
 *              Failure:    1
 *
 * Programmer:
 *
 * Modifications:
 *
 *-------------------------------------------------------------------------
 */
int
main (int argc, const char *argv[])
{
    int         ufid = -1;
    int         h5fid = -1;
    int         ofid = -1;
    void       *edata;
    H5E_auto2_t func;
    hid_t       ifile = -1;
    hid_t       plist = -1;
    herr_t      status;
    htri_t      testval;
    hsize_t     usize;
    hsize_t     h5fsize;
    hsize_t     startub;
    hsize_t     where;
    hsize_t     newubsize;
    off_t       fsize;
    h5_stat_t   sbuf;
    h5_stat_t   sbuf2;
    int         res;

    h5tools_setprogname(PROGRAMNAME);
    h5tools_setstatus(EXIT_SUCCESS);

    /* Disable error reporting */
    H5Eget_auto2(H5E_DEFAULT, &func, &edata);
    H5Eset_auto2(H5E_DEFAULT, NULL, NULL);

    /* Initialize h5tools lib */
    h5tools_init();

    parse_command_line (argc, argv);

    if (ub_file == NULL) {
        /* no user block */
        error_msg("missing arguemnt for -u <user_file>.\n");
        help_ref_msg(stderr);
        leave (EXIT_FAILURE);
    }

    testval = H5Fis_hdf5 (ub_file);

    if (testval > 0) {
        error_msg("-u <user_file> cannot be HDF5 file, but it appears to be an HDF5 file.\n");
        help_ref_msg(stderr);
        leave (EXIT_FAILURE);
    }

    if (input_file == NULL) {
        error_msg("missing arguemnt for -i <HDF5 file>.\n");
        help_ref_msg(stderr);
        leave (EXIT_FAILURE);
    }

    testval = H5Fis_hdf5 (input_file);

    if (testval <= 0) {
        error_msg("Input HDF5 file \"%s\" is not HDF5 format.\n", input_file);
        help_ref_msg(stderr);
        leave (EXIT_FAILURE);
    }

    ifile = H5Fopen (input_file, H5F_ACC_RDONLY, H5P_DEFAULT);

    if (ifile < 0) {
        error_msg("Can't open input HDF5 file \"%s\"\n", input_file);
        leave (EXIT_FAILURE);
    }

    plist = H5Fget_create_plist (ifile);
    if (plist < 0) {
        error_msg("Can't get file creation plist for file \"%s\"\n", input_file);
        H5Fclose(ifile);
        leave (EXIT_FAILURE);
    }

    status = H5Pget_userblock (plist, &usize);
    if (status < 0) {
        error_msg("Can't get user block for file \"%s\"\n", input_file);
        H5Pclose(plist);
        H5Fclose(ifile);
        leave (EXIT_FAILURE);
    }

    H5Pclose(plist);
    H5Fclose(ifile);

    ufid = HDopen(ub_file, O_RDONLY, 0);
    if(ufid < 0) {
        error_msg("unable to open user block file \"%s\"\n", ub_file);
        leave (EXIT_FAILURE);
    }

    res = HDfstat(ufid, &sbuf);
    if(res < 0) {
        error_msg("Can't stat file \"%s\"\n", ub_file);
        HDclose (ufid);
        leave (EXIT_FAILURE);
    }

    fsize = (off_t)sbuf.st_size;

    h5fid = HDopen(input_file, O_RDONLY, 0);
    if(h5fid < 0) {
        error_msg("unable to open HDF5 file for read \"%s\"\n", input_file);
        HDclose (ufid);
        leave (EXIT_FAILURE);
    }

    res = HDfstat(h5fid, &sbuf2);
    if(res < 0) {
        error_msg("Can't stat file \"%s\"\n", input_file);
        HDclose (h5fid);
        HDclose (ufid);
        leave (EXIT_FAILURE);
    }

    h5fsize = (hsize_t)sbuf2.st_size;

    if (output_file == NULL) {
        ofid = HDopen (input_file, O_WRONLY, 0);

        if (ofid < 0) {
            error_msg("unable to open output file \"%s\"\n", output_file);
            HDclose (h5fid);
            HDclose (ufid);
            leave (EXIT_FAILURE);
        }
    }
    else {
        ofid = HDopen (output_file, O_WRONLY | O_CREAT | O_TRUNC, 0644);

        if (ofid < 0) {
            error_msg("unable to create output file \"%s\"\n", output_file);
            HDclose (h5fid);
            HDclose (ufid);
            leave (EXIT_FAILURE);
        }
    }

    newubsize = compute_user_block_size ((hsize_t) fsize);

    startub = usize;

    if (usize > 0) {
        if (do_clobber == TRUE) {
            /* where is max of the current size or the new UB */
            if (usize > newubsize) {
                newubsize = usize;
            }
            startub = 0;    /*blast the old */
        }
        else {
            /* add new ub to current ublock, pad to new offset */
            newubsize += usize;
            newubsize = compute_user_block_size ((hsize_t) newubsize);
        }
    }

    /* copy the HDF5 from starting at usize to starting at newubsize:
     *  makes room at 'from' for new ub */
    /* if no current ub, usize is 0 */
    copy_some_to_file (h5fid, ofid, usize, newubsize, (ssize_t) (h5fsize - usize));

    /* copy the old ub to the beginning of the new file */
    if (!do_clobber) {
        where = copy_some_to_file (h5fid, ofid, (hsize_t) 0, (hsize_t) 0, (ssize_t) usize);
    }

    /* copy the new ub to the end of the ub */
    where = copy_some_to_file (ufid, ofid, (hsize_t) 0, startub, (ssize_t) - 1);

    /* pad the ub */
    where = write_pad (ofid, where);

    if(ub_file)
        HDfree (ub_file);
    if(input_file)
        HDfree (input_file);
    if(output_file)
        HDfree (output_file);
    
    if(ufid >= 0)
        HDclose (ufid);
    if(h5fid >= 0)
        HDclose (h5fid);
    if(ofid >= 0)
        HDclose (ofid);

    return h5tools_getstatus();
}

/*-------------------------------------------------------------------------
 * Function:    copy_some_to_file
 *
 * Purpose:     Copy part of the input file to output.
 *      infid: fd of file to read
 *      outfid: fd of file to write
 *      startin: offset of where to read from infid
 *      startout: offset of where to write to outfid
 *      limit: bytes to read/write
 *
 *    If limit is < 0, the entire input file is copied.
 *
 *    Note: this routine can be used to copy within
 *    the same file, i.e., infid and outfid can be the
 *    same file.
 *
 * Return:      Success:    last byte written in the output.
 *              Failure:    Exits program with EXIT_FAILURE value.
 *
 *-------------------------------------------------------------------------
 */
hsize_t
copy_some_to_file(int infid, int outfid, hsize_t startin, hsize_t startout,
       ssize_t limit)
{
    char buf[1024];
    h5_stat_t sbuf;
    int res;
    ssize_t tot = 0;
    ssize_t howmuch = 0;
    ssize_t nchars = -1;
    ssize_t to;
    ssize_t from;
    ssize_t toend;
    ssize_t fromend;

    if(startin > startout) {
        /* this case is prohibited */
        error_msg("copy_some_to_file: panic: startin > startout?\n");
        exit (EXIT_FAILURE);
    } /* end if */

    if(limit < 0) {
        res = HDfstat(infid, &sbuf);
        if(res < 0) {
            error_msg("Can't stat file \n");
            HDexit(EXIT_FAILURE);
        } /* end if */

        howmuch = (ssize_t)sbuf.st_size;
    } else {
        howmuch = limit;
    } /* end if */

    if(0 == howmuch)
        return 0;

    toend = (ssize_t) startout + howmuch;
    fromend = (ssize_t) startin + howmuch;

    if (howmuch > 512) {
        to = toend - 512;
        from = fromend - 512;
    } else {
        to = toend - howmuch;
        from = fromend - howmuch;
    } /* end if */

    while (howmuch > 0) {
        HDlseek(outfid, (off_t) to, SEEK_SET);
        HDlseek(infid, (off_t) from, SEEK_SET);

        if (howmuch > 512) {
            nchars = HDread(infid, buf, (unsigned) 512);
        } else {
            nchars = HDread(infid, buf, (unsigned)howmuch);
        } /* end if */

        if (nchars <= 0) {
            error_msg("Read error \n");
            HDexit(EXIT_FAILURE);
        } /* end if */

        if(HDwrite (outfid, buf, (unsigned) nchars) < 0) {
            error_msg("Write error \n");
            HDexit(EXIT_FAILURE);
        }

        tot += nchars;
        howmuch -= nchars;
        if(howmuch > 512) {
            to -= nchars;
            from -= nchars;
        } else {
            to -= howmuch;
            from -= howmuch;
        } /* end if */
    } /* end while */

    return (hsize_t)tot + (hsize_t)startout;
} /* end copy_some_to_file() */


/*-------------------------------------------------------------------------
 * Function:    compute_user_block_size
 *
 * Purpose:     Find the offset of the HDF5 header after the user block:
 *                 align at 0, 512, 1024, etc.
 *      ublock_size: the size of the user block (bytes).
 *
 * Return:      Success:    the location of the header == the size of the
 *        padded user block.
 *              Failure:    none
 *
 * Return:      Success:    last byte written in the output.
 *              Failure:    Exits program with EXIT_FAILURE value.
 *-------------------------------------------------------------------------
 */
hsize_t
compute_user_block_size (hsize_t ublock_size)
{
    hsize_t where = 512;

    if(0 == ublock_size)
        return 0;

    while(where < ublock_size)
        where *= 2;

    return where;
} /* end compute_user_block_size() */

/*
 *  Write zeroes to fill the file from 'where' to 512, 1024, etc. bytes.
 *
 *  Returns the size of the padded file.
 */
hsize_t
write_pad(int ofile, hsize_t where)
{
    unsigned int i;
    char buf[1];
    hsize_t psize;

    buf[0] = '\0';

    HDlseek(ofile, (off_t) where, SEEK_SET);

    psize = compute_user_block_size (where);
    psize -= where;

    for(i = 0; i < psize; i++)
        HDwrite (ofile, buf, 1);

    return(where + psize);  /* the new size of the file. */
}