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
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
1011
1012
1013
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
1025
1026
1027
1028
1029
1030
1031
1032
1033
1034
1035
1036
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
1055
1056
1057
1058
1059
1060
1061
1062
1063
1064
1065
1066
1067
1068
1069
1070
1071
1072
1073
1074
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
1088
1089
1090
1091
1092
1093
1094
1095
1096
1097
1098
1099
1100
1101
1102
1103
1104
1105
1106
1107
1108
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125
1126
1127
1128
1129
1130
1131
1132
1133
1134
1135
1136
1137
1138
1139
1140
1141
1142
1143
1144
1145
1146
1147
1148
1149
1150
1151
1152
1153
1154
1155
1156
1157
1158
1159
1160
1161
1162
1163
1164
1165
1166
1167
1168
1169
1170
1171
1172
1173
1174
1175
1176
1177
1178
|
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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://www.hdfgroup.org/licenses. *
* If you do not have access to either file, you may request a copy from *
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*
* Portions of this work are derived from _Obfuscated C and Other Mysteries_,
* by Don Libes, copyright (c) 1993 by John Wiley & Sons, Inc.
*/
#include "h5tools.h"
#include "h5tools_utils.h"
#include "H5private.h"
#include "h5trav.h"
#ifdef H5_HAVE_ROS3_VFD
#include "H5FDros3.h"
#endif
/* Global variables */
unsigned h5tools_nCols = 80;
static int h5tools_d_status = 0;
static const char *h5tools_progname = "h5tools";
/*
* The output functions need a temporary buffer to hold a piece of the
* dataset while it's being printed. This constant sets the limit on the
* size of that temporary buffer in bytes. For efficiency's sake, choose the
* largest value suitable for your machine (for testing use a small value).
*/
/* Maximum size used in a call to malloc for a dataset */
hsize_t H5TOOLS_MALLOCSIZE = (256 * 1024 * 1024); /* 256 MB */
/* size of hyperslab buffer when a dataset is bigger than H5TOOLS_MALLOCSIZE */
hsize_t H5TOOLS_BUFSIZE = (32 * 1024 * 1024); /* 32 MB */
/* ``parallel_print'' variables */
unsigned char g_Parallel = 0; /*0 for serial, 1 for parallel */
char outBuff[OUTBUFF_SIZE];
unsigned outBuffOffset;
FILE * overflow_file = NULL;
/* local functions */
static void init_table(hid_t fid, table_t **tbl);
#ifdef H5DUMP_DEBUG
static void dump_table(hid_t fid, char *tablename, table_t *table);
#endif /* H5DUMP_DEBUG */
static void add_obj(table_t *table, const H5O_token_t *obj_token, const char *objname, hbool_t recorded);
/*-------------------------------------------------------------------------
* Function: parallel_print
*
* Purpose: wrapper for printf for use in parallel mode.
*-------------------------------------------------------------------------
*/
void
parallel_print(const char *format, ...)
{
int bytes_written;
va_list ap;
HDva_start(ap, format);
if (!g_Parallel)
HDvprintf(format, ap);
else {
if (overflow_file == NULL) /*no overflow has occurred yet */ {
bytes_written = HDvsnprintf(outBuff + outBuffOffset, OUTBUFF_SIZE - outBuffOffset, format, ap);
HDva_end(ap);
HDva_start(ap, format);
if ((bytes_written < 0) || ((unsigned)bytes_written >= (OUTBUFF_SIZE - outBuffOffset))) {
/* Terminate the outbuff at the end of the previous output */
outBuff[outBuffOffset] = '\0';
overflow_file = HDtmpfile();
if (overflow_file == NULL)
HDfprintf(rawerrorstream,
"warning: could not create overflow file. Output may be truncated.\n");
else
bytes_written = HDvfprintf(overflow_file, format, ap);
}
else
outBuffOffset += (unsigned)bytes_written;
}
else
bytes_written = HDvfprintf(overflow_file, format, ap);
}
HDva_end(ap);
}
/*-------------------------------------------------------------------------
* Function: error_msg
*
* Purpose: Print a nicely formatted error message to stderr flushing the
* stdout stream first.
*
* Return: Nothing
*-------------------------------------------------------------------------
*/
void
error_msg(const char *fmt, ...)
{
va_list ap;
HDva_start(ap, fmt);
FLUSHSTREAM(rawattrstream);
FLUSHSTREAM(rawdatastream);
FLUSHSTREAM(rawoutstream);
HDfprintf(rawerrorstream, "%s error: ", h5tools_getprogname());
HDvfprintf(rawerrorstream, fmt, ap);
HDva_end(ap);
}
/*-------------------------------------------------------------------------
* Function: warn_msg
*
* Purpose: Print a nicely formatted warning message to stderr flushing
* the stdout stream first.
*
* Return: Nothing
*-------------------------------------------------------------------------
*/
void
warn_msg(const char *fmt, ...)
{
va_list ap;
HDva_start(ap, fmt);
FLUSHSTREAM(rawattrstream);
FLUSHSTREAM(rawdatastream);
FLUSHSTREAM(rawoutstream);
HDfprintf(rawerrorstream, "%s warning: ", h5tools_getprogname());
HDvfprintf(rawerrorstream, fmt, ap);
HDva_end(ap);
}
/*-------------------------------------------------------------------------
* Function: help_ref_msg
*
* Purpose: Print a message to refer help page
*
* Return: Nothing
*-------------------------------------------------------------------------
*/
void
help_ref_msg(FILE *output)
{
HDfprintf(output, "Try '-h' or '--help' for more information or ");
HDfprintf(output, "see the <%s> entry in the 'HDF5 Reference Manual'.\n", h5tools_getprogname());
}
/*****************************************************************************
*
* Function: parse_tuple()
*
* Purpose:
*
* Create array of pointers to strings, identified as elements in a tuple
* of arbitrary length separated by provided character.
* ("tuple" because "nple" looks strange)
*
* * Receives pointer to start of tuple sequence string, '('.
* * Attempts to separate elements by token-character `sep`.
* * If the separator character is preceded by a backslash '\',
* the backslash is deleted and the separator is included in the
* element string as any other character.
* * To end an element with a backslash, escape the backslash, e.g.
* "(myelem\\,otherelem) -> {"myelem\", "otherelem"}
* * In all other cases, a backslash appearing not as part of "\\" or
* "\<sep>" digraph will be included berbatim.
* * Last two characters in the string MUST be ")\0".
*
* * Generates a copy of the input string `start`, (src..")\0"), replacing
* separators and close-paren with null charaters.
* * This string is allocated at runtime and should be freed when done.
* * Generates array of char pointers, and directs start of each element
* (each pointer) into this copy.
* * Each tuple element points to the start of its string (substring)
* and ends with a null terminator.
* * This array is allocated at runtime and should be freed when done.
* * Reallocates and expands elements array during parsing.
* * Initially allocated for 2 (plus one null entry), and grows by
* powers of 2.
* * The final 'slot' in the element array (elements[nelements], e.g.)
* always points to NULL.
* * The number of elements found and stored are passed out through pointer
* to unsigned, `nelems`.
*
* Return:
*
* FAIL If malformed--does not look like a tuple "(...)"
* or major error was encountered while parsing.
* or
* SUCCEED String looks properly formed "(...)" and no major errors.
*
* Stores number of elements through pointer `nelems`.
* Stores list of pointers to char (first char in each element
* string) through pointer `ptrs_out`.
* NOTE: `ptrs_out[nelems] == NULL` should be true.
* NOTE: list is malloc'd by function, and should be freed
* when done.
* Stores "source string" for element pointers through `cpy_out`.
* NOTE: Each element substring is null-terminated.
* NOTE: There may be extra characters after the last element
* (past its null terminator), but is guaranteed to
* be null-terminated.
* NOTE: `cpy_out` string is malloc'd by function,
* and should be freed when done.
*
* Programmer: Jacob Smith
* 2017-11-10
*
*****************************************************************************
*/
herr_t
parse_tuple(const char *start, int sep, char **cpy_out, unsigned *nelems, char ***ptrs_out)
{
char * elem_ptr = NULL;
char * dest_ptr = NULL;
unsigned elems_count = 0;
char ** elems = NULL; /* more like *elems[], but complier... */
char ** elems_re = NULL; /* temporary pointer, for realloc */
char * cpy = NULL;
herr_t ret_value = SUCCEED;
unsigned init_slots = 2;
/*****************
* SANITY-CHECKS *
*****************/
/* must start with "("
*/
if (start[0] != '(') {
ret_value = FAIL;
goto done;
}
/* must end with ")"
*/
while (start[elems_count] != '\0') {
elems_count++;
}
if (start[elems_count - 1] != ')') {
ret_value = FAIL;
goto done;
}
elems_count = 0;
/***********
* PREPARE *
***********/
/* create list
*/
elems = (char **)HDmalloc(sizeof(char *) * (init_slots + 1));
if (elems == NULL) {
ret_value = FAIL;
goto done;
} /* CANTALLOC */
/* create destination string
*/
start++; /* advance past opening paren '(' */
cpy = (char *)HDmalloc(sizeof(char) * (HDstrlen(start))); /* no +1; less '(' */
if (cpy == NULL) {
ret_value = FAIL;
goto done;
} /* CANTALLOC */
/* set pointers
*/
dest_ptr = cpy; /* start writing copy here */
elem_ptr = cpy; /* first element starts here */
elems[elems_count++] = elem_ptr; /* set first element pointer into list */
/*********
* PARSE *
*********/
while (*start != '\0') {
/* For each character in the source string...
*/
if (*start == '\\') {
/* Possibly an escape digraph.
*/
if ((*(start + 1) == '\\') || (*(start + 1) == sep)) {
/* Valid escape digraph of "\\" or "\<sep>".
*/
start++; /* advance past escape char '\' */
*(dest_ptr++) = *(start++); /* Copy subsequent char */
/* and advance pointers. */
}
else {
/* Not an accepted escape digraph.
* Copy backslash character.
*/
*(dest_ptr++) = *(start++);
}
}
else if (*start == sep) {
/* Non-escaped separator.
* Terminate elements substring in copy, record element, advance.
* Expand elements list if appropriate.
*/
*(dest_ptr++) = 0; /* Null-terminate elem substring in copy */
/* and advance pointer. */
start++; /* Advance src pointer past separator. */
elem_ptr = dest_ptr; /* Element pointer points to start of first */
/* character after null sep in copy. */
elems[elems_count++] = elem_ptr; /* Set elem pointer in list */
/* and increment count. */
/* Expand elements list, if necessary.
*/
if (elems_count == init_slots) {
init_slots *= 2;
elems_re = (char **)realloc(elems, sizeof(char *) * (init_slots + 1));
if (elems_re == NULL) {
/* CANTREALLOC */
ret_value = FAIL;
goto done;
}
elems = elems_re;
}
}
else if (*start == ')' && *(start + 1) == '\0') {
/* Found terminal, non-escaped close-paren. Last element.
* Write null terminator to copy.
* Advance source pointer to gently break from loop.
* Requred to prevent ")" from always being added to last element.
*/
start++;
}
else {
/* Copy character into destination. Advance pointers.
*/
*(dest_ptr++) = *(start++);
}
}
*dest_ptr = '\0'; /* Null-terminate destination string. */
elems[elems_count] = NULL; /* Null-terminate elements list. */
/********************
* PASS BACK VALUES *
********************/
*ptrs_out = elems;
*nelems = elems_count;
*cpy_out = cpy;
done:
if (ret_value == FAIL) {
/* CLEANUP */
if (cpy)
free(cpy);
if (elems)
free(elems);
}
return ret_value;
} /* parse_tuple */
/*-------------------------------------------------------------------------
* Function: indentation
*
* Purpose: Print spaces for indentation
*
* Return: void
*-------------------------------------------------------------------------
*/
void
indentation(unsigned x)
{
if (x < h5tools_nCols) {
while (x-- > 0)
PRINTVALSTREAM(rawoutstream, " ");
}
else {
HDfprintf(rawerrorstream, "error: the indentation exceeds the number of cols.\n");
HDexit(1);
}
}
/*-------------------------------------------------------------------------
* Function: print_version
*
* Purpose: Print the program name and the version information which is
* defined the same as the HDF5 library version.
*
* Return: void
*-------------------------------------------------------------------------
*/
void
print_version(const char *progname)
{
PRINTSTREAM(rawoutstream, "%s: Version %u.%u.%u%s%s\n", progname, H5_VERS_MAJOR, H5_VERS_MINOR,
H5_VERS_RELEASE, ((const char *)H5_VERS_SUBRELEASE)[0] ? "-" : "", H5_VERS_SUBRELEASE);
}
/*-------------------------------------------------------------------------
* Function: init_table
*
* Purpose: allocate and initialize tables for shared groups, datasets,
* and committed types
*
* Return: void
*-------------------------------------------------------------------------
*/
static void
init_table(hid_t fid, table_t **tbl)
{
table_t *table = (table_t *)HDmalloc(sizeof(table_t));
table->fid = fid;
table->size = 20;
table->nobjs = 0;
table->objs = (obj_t *)HDmalloc(table->size * sizeof(obj_t));
*tbl = table;
}
/*-------------------------------------------------------------------------
* Function: free_table
*
* Purpose: free tables for shared groups, datasets,
* and committed types
*
* Return: void
*-------------------------------------------------------------------------
*/
void
free_table(table_t *table)
{
unsigned u; /* Local index value */
/* Free the names for the objects in the table */
for (u = 0; u < table->nobjs; u++)
if (table->objs[u].objname)
HDfree(table->objs[u].objname);
HDfree(table->objs);
}
#ifdef H5DUMP_DEBUG
/*-------------------------------------------------------------------------
* Function: dump_table
*
* Purpose: display the contents of tables for debugging purposes
*
* Return: void
*-------------------------------------------------------------------------
*/
static void
dump_table(hid_t fid, char *tablename, table_t *table)
{
unsigned u;
char * obj_tok_str = NULL;
PRINTSTREAM(rawoutstream, "%s: # of entries = %d\n", tablename, table->nobjs);
for (u = 0; u < table->nobjs; u++) {
H5VLconnector_token_to_str(fid, table->objs[u].obj_token, &obj_tok_str);
PRINTSTREAM(rawoutstream, "%s %s %d %d\n", obj_tok_str, table->objs[u].objname,
table->objs[u].displayed, table->objs[u].recorded);
H5VLfree_token_str(fid, obj_tok_str);
}
}
/*-------------------------------------------------------------------------
* Function: dump_tables
*
* Purpose: display the contents of tables for debugging purposes
*
* Return: void
*-------------------------------------------------------------------------
*/
void
dump_tables(find_objs_t *info)
{
dump_table(info->fid, "group_table", info->group_table);
dump_table(info->fid, "dset_table", info->dset_table);
dump_table(info->fid, "type_table", info->type_table);
}
#endif /* H5DUMP_DEBUG */
/*-------------------------------------------------------------------------
* Function: search_obj
*
* Purpose: search the object specified by objno in the table
*
* Return: Success: an integer, the location of the object
*
* Failure: FAIL if object is not found
*-------------------------------------------------------------------------
*/
H5_ATTR_PURE obj_t *
search_obj(table_t *table, const H5O_token_t *obj_token)
{
unsigned u;
int token_cmp;
for (u = 0; u < table->nobjs; u++) {
if (H5Otoken_cmp(table->fid, &table->objs[u].obj_token, obj_token, &token_cmp) < 0)
return NULL;
if (!token_cmp)
return &(table->objs[u]);
}
return NULL;
}
/*-------------------------------------------------------------------------
* Function: find_objs_cb
*
* Purpose: Callback to find objects, committed types and store them in tables
*
* Return: Success: SUCCEED
*
* Failure: FAIL
*-------------------------------------------------------------------------
*/
static herr_t
find_objs_cb(const char *name, const H5O_info2_t *oinfo, const char *already_seen, void *op_data)
{
find_objs_t *info = (find_objs_t *)op_data;
herr_t ret_value = 0;
switch (oinfo->type) {
case H5O_TYPE_GROUP:
if (NULL == already_seen)
add_obj(info->group_table, &oinfo->token, name, TRUE);
break;
case H5O_TYPE_DATASET:
if (NULL == already_seen) {
hid_t dset = H5I_INVALID_HID;
/* Add the dataset to the list of objects */
add_obj(info->dset_table, &oinfo->token, name, TRUE);
/* Check for a dataset that uses a named datatype */
if ((dset = H5Dopen2(info->fid, name, H5P_DEFAULT)) >= 0) {
hid_t type = H5Dget_type(dset);
if (H5Tcommitted(type) > 0) {
H5O_info2_t type_oinfo;
H5Oget_info3(type, &type_oinfo, H5O_INFO_BASIC);
if (search_obj(info->type_table, &type_oinfo.token) == NULL)
add_obj(info->type_table, &type_oinfo.token, name, FALSE);
} /* end if */
H5Tclose(type);
H5Dclose(dset);
} /* end if */
else
ret_value = FAIL;
} /* end if */
break;
case H5O_TYPE_NAMED_DATATYPE:
if (NULL == already_seen) {
obj_t *found_obj;
if ((found_obj = search_obj(info->type_table, &oinfo->token)) == NULL)
add_obj(info->type_table, &oinfo->token, name, TRUE);
else {
/* Use latest version of name */
HDfree(found_obj->objname);
found_obj->objname = HDstrdup(name);
/* Mark named datatype as having valid name */
found_obj->recorded = TRUE;
} /* end else */
} /* end if */
break;
case H5O_TYPE_MAP:
case H5O_TYPE_UNKNOWN:
case H5O_TYPE_NTYPES:
default:
break;
} /* end switch */
return ret_value;
}
/*-------------------------------------------------------------------------
* Function: init_objs
*
* Purpose: Initialize tables for groups, datasets & named datatypes
*
* Return: Success: SUCCEED
*
* Failure: FAIL
*-------------------------------------------------------------------------
*/
herr_t
init_objs(hid_t fid, find_objs_t *info, table_t **group_table, table_t **dset_table, table_t **type_table)
{
herr_t ret_value = SUCCEED;
/* Initialize the tables */
init_table(fid, group_table);
init_table(fid, dset_table);
init_table(fid, type_table);
/* Init the find_objs_t */
info->fid = fid;
info->group_table = *group_table;
info->type_table = *type_table;
info->dset_table = *dset_table;
/* Find all shared objects */
if ((ret_value = h5trav_visit(fid, "/", TRUE, TRUE, find_objs_cb, NULL, info, H5O_INFO_BASIC)) < 0)
H5TOOLS_GOTO_ERROR(FAIL, "finding shared objects failed");
done:
/* Release resources */
if (ret_value < 0) {
free_table(*group_table);
info->group_table = NULL;
free_table(*type_table);
info->type_table = NULL;
free_table(*dset_table);
info->dset_table = NULL;
}
return ret_value;
}
/*-------------------------------------------------------------------------
* Function: add_obj
*
* Purpose: add a shared object to the table
* realloc the table if necessary
*
* Return: void
*-------------------------------------------------------------------------
*/
static void
add_obj(table_t *table, const H5O_token_t *obj_token, const char *objname, hbool_t record)
{
size_t u;
/* See if we need to make table larger */
if (table->nobjs == table->size) {
table->size *= 2;
table->objs = (struct obj_t *)HDrealloc(table->objs, table->size * sizeof(table->objs[0]));
} /* end if */
/* Increment number of objects in table */
u = table->nobjs++;
/* Set information about object */
HDmemcpy(&table->objs[u].obj_token, obj_token, sizeof(H5O_token_t));
table->objs[u].objname = HDstrdup(objname);
table->objs[u].recorded = record;
table->objs[u].displayed = 0;
}
#ifndef H5_HAVE_TMPFILE
/*-------------------------------------------------------------------------
* Function: tmpfile
*
* Purpose: provide tmpfile() function when it is not supported by the
* system. Always return NULL for now.
*
* Return: a stream description when succeeds.
* NULL if fails.
*-------------------------------------------------------------------------
*/
FILE *
tmpfile(void)
{
return NULL;
}
#endif
/*-------------------------------------------------------------------------
* Function: H5tools_get_symlink_info
*
* Purpose: Get symbolic link (soft, external) info and its target object type
(dataset, group, named datatype) and path, if exist
*
* Patameters:
* - [IN] fileid : link file id
* - [IN] linkpath : link path
* - [OUT] link_info: returning target object info (h5tool_link_info_t)
*
* Return:
* 2 : given pathname is object
* 1 : Succeed to get link info.
* 0 : Detected as a dangling link
* -1 : H5 API failed.
*
* NOTE:
* link_info->trg_path must be freed out of this function
*-------------------------------------------------------------------------*/
int
H5tools_get_symlink_info(hid_t file_id, const char *linkpath, h5tool_link_info_t *link_info,
hbool_t get_obj_type)
{
htri_t l_ret;
H5O_info2_t trg_oinfo;
hid_t fapl = H5P_DEFAULT;
hid_t lapl = H5P_DEFAULT;
int ret_value = -1; /* init to fail */
/* init */
link_info->trg_type = H5O_TYPE_UNKNOWN;
/* if path is root, return group type */
if (!HDstrcmp(linkpath, "/")) {
link_info->trg_type = H5O_TYPE_GROUP;
H5TOOLS_GOTO_DONE(2);
}
/* check if link itself exist */
if (H5Lexists(file_id, linkpath, H5P_DEFAULT) <= 0) {
if (link_info->opt.msg_mode == 1)
parallel_print("Warning: link <%s> doesn't exist \n", linkpath);
H5TOOLS_GOTO_DONE(FAIL);
} /* end if */
/* get info from link */
if (H5Lget_info2(file_id, linkpath, &(link_info->linfo), H5P_DEFAULT) < 0) {
if (link_info->opt.msg_mode == 1)
parallel_print("Warning: unable to get link info from <%s>\n", linkpath);
H5TOOLS_GOTO_DONE(FAIL);
} /* end if */
/* given path is hard link (object) */
if (link_info->linfo.type == H5L_TYPE_HARD)
H5TOOLS_GOTO_DONE(2);
/* trg_path must be freed out of this function when finished using */
if ((link_info->trg_path = (char *)HDcalloc(link_info->linfo.u.val_size, sizeof(char))) == NULL) {
if (link_info->opt.msg_mode == 1)
parallel_print("Warning: unable to allocate buffer for <%s>\n", linkpath);
H5TOOLS_GOTO_DONE(FAIL);
} /* end if */
/* get link value */
if (H5Lget_val(file_id, linkpath, (void *)link_info->trg_path, link_info->linfo.u.val_size, H5P_DEFAULT) <
0) {
if (link_info->opt.msg_mode == 1)
parallel_print("Warning: unable to get link value from <%s>\n", linkpath);
H5TOOLS_GOTO_DONE(FAIL);
} /* end if */
/*-----------------------------------------------------
* if link type is external link use different lapl to
* follow object in other file
*/
if (link_info->linfo.type == H5L_TYPE_EXTERNAL) {
if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
H5TOOLS_GOTO_DONE(FAIL);
if (H5Pset_fapl_sec2(fapl) < 0)
H5TOOLS_GOTO_DONE(FAIL);
if ((lapl = H5Pcreate(H5P_LINK_ACCESS)) < 0)
H5TOOLS_GOTO_DONE(FAIL);
if (H5Pset_elink_fapl(lapl, fapl) < 0)
H5TOOLS_GOTO_DONE(FAIL);
} /* end if */
/* Check for retrieving object info */
if (get_obj_type) {
/*--------------------------------------------------------------
* if link's target object exist, get type
*/
/* check if target object exist */
l_ret = H5Oexists_by_name(file_id, linkpath, lapl);
/* detect dangling link */
if (l_ret == FALSE) {
H5TOOLS_GOTO_DONE(0);
}
else if (l_ret < 0) { /* function failed */
H5TOOLS_GOTO_DONE(FAIL);
}
/* get target object info */
if (H5Oget_info_by_name3(file_id, linkpath, &trg_oinfo, H5O_INFO_BASIC, lapl) < 0) {
if (link_info->opt.msg_mode == 1)
parallel_print("Warning: unable to get object information for <%s>\n", linkpath);
H5TOOLS_GOTO_DONE(FAIL);
} /* end if */
/* check unknown type */
if (trg_oinfo.type < H5O_TYPE_GROUP || trg_oinfo.type >= H5O_TYPE_NTYPES) {
if (link_info->opt.msg_mode == 1)
parallel_print("Warning: target object of <%s> is unknown type\n", linkpath);
H5TOOLS_GOTO_DONE(FAIL);
} /* end if */
/* set target obj type to return */
HDmemcpy(&link_info->obj_token, &trg_oinfo.token, sizeof(H5O_token_t));
link_info->trg_type = trg_oinfo.type;
link_info->fileno = trg_oinfo.fileno;
} /* end if */
else
link_info->trg_type = H5O_TYPE_UNKNOWN;
/* succeed */
ret_value = 1;
done:
if (fapl != H5P_DEFAULT)
H5Pclose(fapl);
if (lapl != H5P_DEFAULT)
H5Pclose(lapl);
return ret_value;
} /* end H5tools_get_symlink_info() */
/*-------------------------------------------------------------------------
* Audience: Public
*
* Purpose: Initialize the name and operation status of the H5 Tools library
*
* Description:
* These are utility functions to set/get the program name and operation status.
*-------------------------------------------------------------------------
*/
void
h5tools_setprogname(const char *Progname)
{
h5tools_progname = Progname;
}
void
h5tools_setstatus(int D_status)
{
h5tools_d_status = D_status;
}
H5_ATTR_PURE const char *
h5tools_getprogname(void)
{
return h5tools_progname;
}
H5_ATTR_PURE int
h5tools_getstatus(void)
{
return h5tools_d_status;
}
/*-----------------------------------------------------------
* PURPOSE :
* if environment variable H5TOOLS_BUFSIZE is set,
* update H5TOOLS_BUFSIZE and H5TOOLS_MALLOCSIZE from the env
* This can be called from each tools main() as part of initial act.
* Note: this is more of debugging purpose for now.
*/
int
h5tools_getenv_update_hyperslab_bufsize(void)
{
const char *env_str = NULL;
long hyperslab_bufsize_mb;
int ret_value = 1;
/* check if environment variable is set for the hyperslab buffer size */
if (NULL != (env_str = HDgetenv("H5TOOLS_BUFSIZE"))) {
errno = 0;
hyperslab_bufsize_mb = HDstrtol(env_str, (char **)NULL, 10);
if (errno != 0 || hyperslab_bufsize_mb <= 0)
H5TOOLS_GOTO_ERROR(FAIL, "hyperslab buffer size failed");
/* convert MB to byte */
H5TOOLS_BUFSIZE = (hsize_t)hyperslab_bufsize_mb * 1024 * 1024;
H5TOOLS_MALLOCSIZE = MAX(H5TOOLS_BUFSIZE, H5TOOLS_MALLOCSIZE);
}
done:
return ret_value;
}
#ifdef H5_HAVE_ROS3_VFD
/*----------------------------------------------------------------------------
*
* Function: h5tools_parse_ros3_fapl_tuple
*
* Purpose: A convenience function that parses a string containing a tuple
* of S3 VFD credential information and then passes the result to
* `h5tools_populate_ros3_fapl()` in order to setup a valid
* configuration for the S3 VFD.
*
* Return: SUCCEED/FAIL
*
*----------------------------------------------------------------------------
*/
herr_t
h5tools_parse_ros3_fapl_tuple(const char *tuple_str, int delim, H5FD_ros3_fapl_t *fapl_config_out)
{
const char *ccred[3];
unsigned nelems = 0;
char * s3cred_src = NULL;
char ** s3cred = NULL;
herr_t ret_value = SUCCEED;
/* Attempt to parse S3 credentials tuple */
if (parse_tuple(tuple_str, delim, &s3cred_src, &nelems, &s3cred) < 0)
H5TOOLS_GOTO_ERROR(FAIL, "failed to parse S3 VFD info tuple");
/* Sanity-check tuple count */
if (nelems != 3)
H5TOOLS_GOTO_ERROR(FAIL, "invalid S3 VFD credentials");
ccred[0] = (const char *)s3cred[0];
ccred[1] = (const char *)s3cred[1];
ccred[2] = (const char *)s3cred[2];
if (0 == h5tools_populate_ros3_fapl(fapl_config_out, ccred))
H5TOOLS_GOTO_ERROR(FAIL, "failed to populate S3 VFD FAPL config");
done:
if (s3cred)
HDfree(s3cred);
if (s3cred_src)
HDfree(s3cred_src);
return ret_value;
}
/*----------------------------------------------------------------------------
*
* Function: h5tools_populate_ros3_fapl()
*
* Purpose:
*
* Set the values of a ROS3 fapl configuration object.
*
* If the values pointer is NULL, sets fapl target `fa` to a default
* (valid, current-version, non-authenticating) fapl config.
*
* If `values` pointer is _not_ NULL, expects `values` to contain at least
* three non-null pointers to null-terminated strings, corresponding to:
* { aws_region,
* secret_id,
* secret_key,
* }
* If all three strings are empty (""), the default fapl will be default.
* Both aws_region and secret_id values must be both empty or both
* populated. If
* Only secret_key is allowed to be empty (the empty string, "").
* All values are checked against overflow as defined in the ros3 vfd
* header file; if a value overruns the permitted space, FAIL is returned
* and the function aborts without resetting the fapl to values initially
* present.
*
* Return:
*
* 0 (failure) if...
* * Read-Only S3 VFD is not enabled.
* * NULL fapl pointer: (NULL, {...} )
* * Warning: In all cases below, fapl will be set as "default"
* before error occurs.
* * NULL value strings: (&fa, {NULL?, NULL? NULL?, ...})
* * Incomplete fapl info:
* * empty region, non-empty id, key either way
* * (&fa, {"", "...", "?"})
* * empty id, non-empty region, key either way
* * (&fa, {"...", "", "?"})
* * "non-empty key and either id or region empty
* * (&fa, {"", "", "...")
* * (&fa, {"", "...", "...")
* * (&fa, {"...", "", "...")
* * Any string would overflow allowed space in fapl definition.
* or
* 1 (success)
* * Sets components in fapl_t pointer, copying strings as appropriate.
* * "Default" fapl (valid version, authenticate->False, empty strings)
* * `values` pointer is NULL
* * (&fa, NULL)
* * first three strings in `values` are empty ("")
* * (&fa, {"", "", "", ...}
* * Authenticating fapl
* * region, id, and optional key provided
* * (&fa, {"...", "...", ""})
* * (&fa, {"...", "...", "..."})
*
* Programmer: Jacob Smith
* 2017-11-13
*
*----------------------------------------------------------------------------
*/
int
h5tools_populate_ros3_fapl(H5FD_ros3_fapl_t *fa, const char **values)
{
int show_progress = 0; /* set to 1 for debugging */
int ret_value = 1; /* 1 for success, 0 for failure */
/* e.g.? if (!populate()) { then failed } */
if (show_progress) {
HDprintf("called h5tools_populate_ros3_fapl\n");
}
if (fa == NULL) {
if (show_progress) {
HDprintf(" ERROR: null pointer to fapl_t\n");
}
ret_value = 0;
goto done;
}
if (show_progress) {
HDprintf(" preset fapl with default values\n");
}
fa->version = H5FD_CURR_ROS3_FAPL_T_VERSION;
fa->authenticate = FALSE;
*(fa->aws_region) = '\0';
*(fa->secret_id) = '\0';
*(fa->secret_key) = '\0';
/* sanity-check supplied values
*/
if (values != NULL) {
if (values[0] == NULL) {
if (show_progress) {
HDprintf(" ERROR: aws_region value cannot be NULL\n");
}
ret_value = 0;
goto done;
}
if (values[1] == NULL) {
if (show_progress) {
HDprintf(" ERROR: secret_id value cannot be NULL\n");
}
ret_value = 0;
goto done;
}
if (values[2] == NULL) {
if (show_progress) {
HDprintf(" ERROR: secret_key value cannot be NULL\n");
}
ret_value = 0;
goto done;
}
/* if region and ID are supplied (key optional), write to fapl...
* fail if value would overflow
*/
if (*values[0] != '\0' && *values[1] != '\0') {
if (HDstrlen(values[0]) > H5FD_ROS3_MAX_REGION_LEN) {
if (show_progress) {
HDprintf(" ERROR: aws_region value too long\n");
}
ret_value = 0;
goto done;
}
HDmemcpy(fa->aws_region, values[0], (HDstrlen(values[0]) + 1));
if (show_progress) {
HDprintf(" aws_region set\n");
}
if (HDstrlen(values[1]) > H5FD_ROS3_MAX_SECRET_ID_LEN) {
if (show_progress) {
HDprintf(" ERROR: secret_id value too long\n");
}
ret_value = 0;
goto done;
}
HDmemcpy(fa->secret_id, values[1], (HDstrlen(values[1]) + 1));
if (show_progress) {
HDprintf(" secret_id set\n");
}
if (HDstrlen(values[2]) > H5FD_ROS3_MAX_SECRET_KEY_LEN) {
if (show_progress) {
HDprintf(" ERROR: secret_key value too long\n");
}
ret_value = 0;
goto done;
}
HDmemcpy(fa->secret_key, values[2], (HDstrlen(values[2]) + 1));
if (show_progress) {
HDprintf(" secret_key set\n");
}
fa->authenticate = TRUE;
if (show_progress) {
HDprintf(" set to authenticate\n");
}
}
else if (*values[0] != '\0' || *values[1] != '\0' || *values[2] != '\0') {
if (show_progress) {
HDprintf(" ERROR: invalid assortment of empty/non-empty values\n");
}
ret_value = 0;
goto done;
}
} /* values != NULL */
done:
return ret_value;
} /* h5tools_populate_ros3_fapl */
#endif /* H5_HAVE_ROS3_VFD */
#ifdef H5_HAVE_LIBHDFS
/*----------------------------------------------------------------------------
*
* Function: h5tools_parse_hdfs_fapl_tuple
*
* Purpose: A convenience function that parses a string containing a tuple
* of HDFS VFD configuration information.
*
* Return: SUCCEED/FAIL
*
*----------------------------------------------------------------------------
*/
herr_t
h5tools_parse_hdfs_fapl_tuple(const char *tuple_str, int delim, H5FD_hdfs_fapl_t *fapl_config_out)
{
unsigned long k = 0;
unsigned nelems = 0;
char * props_src = NULL;
char ** props = NULL;
herr_t ret_value = SUCCEED;
/* Attempt to parse HDFS configuration tuple */
if (parse_tuple(tuple_str, delim, &props_src, &nelems, &props) < 0)
H5TOOLS_GOTO_ERROR(FAIL, "failed to parse HDFS VFD configuration tuple");
/* Sanity-check tuple count */
if (nelems != 5)
H5TOOLS_GOTO_ERROR(FAIL, "invalid HDFS VFD configuration");
/* Populate fapl configuration structure with given properties.
* WARNING: No error-checking is done on length of input strings...
* Silent overflow is possible, albeit unlikely.
*/
if (HDstrncmp(props[0], "", 1)) {
HDstrncpy(fapl_config_out->namenode_name, (const char *)props[0], HDstrlen(props[0]));
}
if (HDstrncmp(props[1], "", 1)) {
k = strtoul((const char *)props[1], NULL, 0);
if (errno == ERANGE)
H5TOOLS_GOTO_ERROR(FAIL, "supposed port number wasn't");
fapl_config_out->namenode_port = (int32_t)k;
}
if (HDstrncmp(props[2], "", 1)) {
HDstrncpy(fapl_config_out->kerberos_ticket_cache, (const char *)props[2], HDstrlen(props[2]));
}
if (HDstrncmp(props[3], "", 1)) {
HDstrncpy(fapl_config_out->user_name, (const char *)props[3], HDstrlen(props[3]));
}
if (HDstrncmp(props[4], "", 1)) {
k = HDstrtoul((const char *)props[4], NULL, 0);
if (errno == ERANGE)
H5TOOLS_GOTO_ERROR(FAIL, "supposed buffersize number wasn't");
fapl_config_out->stream_buffer_size = (int32_t)k;
}
done:
if (props)
HDfree(props);
if (props_src)
HDfree(props_src);
return ret_value;
}
#endif /* H5_HAVE_LIBHDFS */
|