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-rw-r--r--tools/h5dump/h5dump.c244
-rw-r--r--tools/h5dump/testh5dump.sh.in11
2 files changed, 133 insertions, 122 deletions
diff --git a/tools/h5dump/h5dump.c b/tools/h5dump/h5dump.c
index 4abc0b0..261fe15 100644
--- a/tools/h5dump/h5dump.c
+++ b/tools/h5dump/h5dump.c
@@ -1607,8 +1607,7 @@ dump_all_cb(hid_t group, const char *name, const H5L_info_t *linfo, void UNUSED
begin_obj(dump_header_format->datasetbegin, name,
dump_header_format->datasetblockbegin);
indentation(indent + COL);
- error_msg(h5tools_getprogname(),
- "internal error (file %s:line %d)\n",
+ error_msg("internal error (file %s:line %d)\n",
__FILE__, __LINE__);
indentation(indent);
end_obj(dump_header_format->datasetend,
@@ -2116,8 +2115,7 @@ dump_group(hid_t gid, const char *name)
if (found_obj == NULL) {
indentation(indent);
- error_msg("internal error (file %s:line %d)\n",
- __FILE__, __LINE__);
+ error_msg("internal error (file %s:line %d)\n", __FILE__, __LINE__);
h5tools_setstatus(EXIT_FAILURE);
}
else if (found_obj->displayed) {
@@ -2354,14 +2352,14 @@ dump_subsetting_header(struct subset_t *sset, int dims)
indentation(indent);
printf("%s %s ", dump_header_format->startbegin,
dump_header_format->startblockbegin);
- dump_dims((hsize_t *)sset->start, dims);
+ dump_dims(sset->start.data, dims);
printf("%s %s\n", dump_header_format->startend,
dump_header_format->startblockend);
indentation(indent);
printf("%s %s ", dump_header_format->stridebegin,
dump_header_format->strideblockbegin);
- dump_dims(sset->stride, dims);
+ dump_dims(sset->stride.data, dims);
printf("%s %s\n", dump_header_format->strideend,
dump_header_format->strideblockend);
@@ -2369,8 +2367,8 @@ dump_subsetting_header(struct subset_t *sset, int dims)
printf("%s %s ", dump_header_format->countbegin,
dump_header_format->countblockbegin);
- if (sset->count)
- dump_dims(sset->count, dims);
+ if(sset->count.data)
+ dump_dims(sset->count.data, dims);
else
printf("DEFAULT");
@@ -2381,8 +2379,8 @@ dump_subsetting_header(struct subset_t *sset, int dims)
printf("%s %s ", dump_header_format->blockbegin,
dump_header_format->blockblockbegin);
- if (sset->block)
- dump_dims(sset->block, dims);
+ if(sset->block.data)
+ dump_dims(sset->block.data, dims);
else
printf("DEFAULT");
@@ -3418,25 +3416,22 @@ handle_attributes(hid_t fid, const char *attr, void UNUSED * data, int UNUSED pe
* semicolons (;). The lists themselves can be separated by
* either commas (,) or white spaces.
*
- * Return: Success: hsize_t array. NULL is a valid return type if
- * there aren't any elements in the array.
+ * Return: <none>
*
* Programmer: Bill Wendling
* Tuesday, 6. February 2001
*
- * Modifications:
- *
*-------------------------------------------------------------------------
*/
-static hsize_t *
-parse_hsize_list(const char *h_list)
+static void
+parse_hsize_list(const char *h_list, subset_d *d)
{
hsize_t *p_list;
const char *ptr;
unsigned int size_count = 0, i = 0, last_digit = 0;
if (!h_list || !*h_list || *h_list == ';')
- return NULL;
+ return;
/* count how many integers do we have */
for (ptr = h_list; ptr && *ptr && *ptr != ';' && *ptr != ']'; ptr++)
@@ -3452,10 +3447,10 @@ parse_hsize_list(const char *h_list)
if (size_count == 0)
/* there aren't any integers to read */
- return NULL;
+ return;
/* allocate an array for the integers in the list */
- p_list = calloc(size_count, sizeof(hsize_t));
+ p_list = (hsize_t *)calloc(size_count, sizeof(hsize_t));
for (ptr = h_list; i < size_count && ptr && *ptr && *ptr != ';' && *ptr != ']'; ptr++)
if(isdigit(*ptr)) {
@@ -3466,8 +3461,10 @@ parse_hsize_list(const char *h_list)
/* scroll to end of integer */
ptr++;
}
-
- return p_list;
+ d->data = p_list;
+ d->len = size_count;
+
+ return;
}
/*-------------------------------------------------------------------------
@@ -3499,8 +3496,8 @@ parse_subset_params(char *dset)
if (brace > slash) {
*brace++ = '\0';
- s = calloc(1, sizeof(struct subset_t));
- s->start = parse_hsize_list(brace);
+ s = (struct subset_t *)calloc(1, sizeof(struct subset_t));
+ parse_hsize_list(brace, &s->start);
while (*brace && *brace != ';')
brace++;
@@ -3508,7 +3505,7 @@ parse_subset_params(char *dset)
if (*brace)
brace++;
- s->stride = parse_hsize_list(brace);
+ parse_hsize_list(brace, &s->stride);
while (*brace && *brace != ';')
brace++;
@@ -3516,7 +3513,7 @@ parse_subset_params(char *dset)
if (*brace)
brace++;
- s->count = parse_hsize_list(brace);
+ parse_hsize_list(brace, &s->count);
while (*brace && *brace != ';')
brace++;
@@ -3524,7 +3521,7 @@ parse_subset_params(char *dset)
if (*brace)
brace++;
- s->block = parse_hsize_list(brace);
+ parse_hsize_list(brace, &s->block);
}
}
@@ -3576,79 +3573,83 @@ handle_datasets(hid_t fid, const char *dset, void *data, int pe, const char *dis
} /* end if */
if(sset) {
- if(!sset->start || !sset->stride || !sset->count || !sset->block) {
+ unsigned int i;
+ hid_t sid = H5Dget_space(dsetid);
+ unsigned int ndims = H5Sget_simple_extent_ndims(sid);
+
+ H5Sclose(sid);
+
+ if(!sset->start.data || !sset->stride.data || !sset->count.data || !sset->block.data) {
/* they didn't specify a ``stride'' or ``block''. default to 1 in all
* dimensions */
- hid_t sid = H5Dget_space(dsetid);
- unsigned int ndims = H5Sget_simple_extent_ndims(sid);
-
- if(!sset->start)
+ if(!sset->start.data) {
/* default to (0, 0, ...) for the start coord */
- sset->start = calloc(ndims, sizeof(hsize_t));
-
- if(!sset->stride) {
- unsigned int i;
-
- sset->stride = calloc(ndims, sizeof(hsize_t));
+ sset->start.data = (hsize_t *)calloc(ndims, sizeof(hsize_t));
+ sset->start.len = ndims;
+ }
+ if(!sset->stride.data) {
+ sset->stride.data = (hsize_t *)calloc(ndims, sizeof(hsize_t));
+ sset->stride.len = ndims;
for (i = 0; i < ndims; i++)
- sset->stride[i] = 1;
+ sset->stride.data[i] = 1;
}
- if (!sset->count) {
- unsigned int i;
-
-
- sset->count = calloc(ndims, sizeof(hsize_t));
-
+ if(!sset->count.data) {
+ sset->count.data = (hsize_t *)calloc(ndims, sizeof(hsize_t));
+ sset->count.len = ndims;
for (i = 0; i < ndims; i++)
- sset->count[i] = 1;
+ sset->count.data[i] = 1;
}
- if (!sset->block) {
- unsigned int i;
-
- sset->block = calloc(ndims, sizeof(hsize_t));
-
+ if(!sset->block.data) {
+ sset->block.data = (hsize_t *)calloc(ndims, sizeof(hsize_t));
+ sset->block.len = ndims;
for (i = 0; i < ndims; i++)
- sset->block[i] = 1;
+ sset->block.data[i] = 1;
}
-
- H5Sclose(sid);
}
- }
-
-
- /*-------------------------------------------------------------------------
- * check for block overlap
- *-------------------------------------------------------------------------
- */
-
- if(sset)
- {
- hid_t sid = H5Dget_space(dsetid);
- unsigned int ndims = H5Sget_simple_extent_ndims(sid);
- unsigned int i;
- for ( i = 0; i < ndims; i++)
- {
- if ( sset->count[i] > 1 )
- {
-
- if ( sset->stride[i] < sset->block[i] )
- {
+ /*-------------------------------------------------------------------------
+ * check for dimension overflow
+ *-------------------------------------------------------------------------
+ */
+ if(sset->start.len > ndims) {
+ error_msg("number of start dims (%u) exceed dataset dims (%u)\n", sset->start.len, ndims);
+ h5tools_setstatus(EXIT_FAILURE);
+ return;
+ }
+ if(sset->stride.len > ndims) {
+ error_msg("number of stride dims (%u) exceed dataset dims (%u)\n", sset->stride.len, ndims);
+ h5tools_setstatus(EXIT_FAILURE);
+ return;
+ }
+ if(sset->count.len > ndims) {
+ error_msg("number of count dims (%u) exceed dataset dims (%u)\n", sset->count.len, ndims);
+ h5tools_setstatus(EXIT_FAILURE);
+ return;
+ }
+ if(sset->block.len > ndims) {
+ error_msg("number of block dims (%u) exceed dataset dims (%u)\n", sset->block.len, ndims);
+ h5tools_setstatus(EXIT_FAILURE);
+ return;
+ }
+
+ /*-------------------------------------------------------------------------
+ * check for block overlap
+ *-------------------------------------------------------------------------
+ */
+ for(i = 0; i < ndims; i++) {
+ if(sset->count.data[i] > 1) {
+ if(sset->stride.data[i] < sset->block.data[i]) {
error_msg("wrong subset selection; blocks overlap\n");
h5tools_setstatus(EXIT_FAILURE);
return;
+ } /* end if */
+ } /* end if */
+ } /* end for */
+ } /* end if */
- }
-
- }
-
- }
- H5Sclose(sid);
-
- }
H5Oget_info(dsetid, &oinfo);
if(oinfo.rc > 1 || hit_elink) {
@@ -3726,7 +3727,7 @@ handle_groups(hid_t fid, const char *group, void UNUSED * data, int pe, const ch
if(prefix_len <= new_len)
{
prefix_len = new_len;
- prefix = HDrealloc(prefix, prefix_len);
+ prefix = (char *)HDrealloc(prefix, prefix_len);
} /* end if */
HDstrcpy(prefix, group);
@@ -3764,7 +3765,7 @@ handle_links(hid_t fid, const char *links, void UNUSED * data, int UNUSED pe, co
error_msg("\"%s\" is a hard link\n", links);
h5tools_setstatus(EXIT_FAILURE);
} else {
- char *buf = HDmalloc(linfo.u.val_size);
+ char *buf = (char *)HDmalloc(linfo.u.val_size);
switch(linfo.type) {
case H5L_TYPE_SOFT: /* Soft link */
@@ -3938,7 +3939,7 @@ parse_command_line(int argc, const char *argv[])
}
/* this will be plenty big enough to hold the info */
- hand = calloc((size_t)argc, sizeof(struct handler_t));
+ hand = (struct handler_t *)calloc((size_t)argc, sizeof(struct handler_t));
/* parse command line options */
while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
@@ -4010,7 +4011,7 @@ parse_start:
hand[i].func = handle_datasets;
hand[i].obj = HDstrdup(opt_arg);
hand[i].subset_info = parse_subset_params(hand[i].obj);
- last_dset = hand;
+ last_dset = &hand[i];
break;
}
@@ -4163,8 +4164,7 @@ parse_start:
struct subset_t *s;
if (!last_was_dset) {
- error_msg(h5tools_getprogname(),
- "option `-%c' can only be used after --dataset option\n",
+ error_msg("option `-%c' can only be used after --dataset option\n",
opt);
leave(EXIT_FAILURE);
}
@@ -4176,7 +4176,7 @@ parse_start:
*/
s = last_dset->subset_info;
} else {
- last_dset->subset_info = s = calloc(1, sizeof(struct subset_t));
+ last_dset->subset_info = s = (struct subset_t *)calloc(1, sizeof(struct subset_t));
}
/*
@@ -4192,10 +4192,10 @@ parse_start:
*/
do {
switch ((char)opt) {
- case 's': free(s->start); s->start = parse_hsize_list(opt_arg); break;
- case 'S': free(s->stride); s->stride = parse_hsize_list(opt_arg); break;
- case 'c': free(s->count); s->count = parse_hsize_list(opt_arg); break;
- case 'k': free(s->block); s->block = parse_hsize_list(opt_arg); break;
+ case 's': free(s->start.data); parse_hsize_list(opt_arg, &s->start); break;
+ case 'S': free(s->stride.data); parse_hsize_list(opt_arg, &s->stride); break;
+ case 'c': free(s->count.data); parse_hsize_list(opt_arg, &s->count); break;
+ case 'k': free(s->block.data); parse_hsize_list(opt_arg, &s->block); break;
default: goto end_collect;
}
} while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF);
@@ -4256,10 +4256,10 @@ free_handler(struct handler_t *hand, int len)
free(hand[i].obj);
if (hand[i].subset_info) {
- free(hand[i].subset_info->start);
- free(hand[i].subset_info->stride);
- free(hand[i].subset_info->count);
- free(hand[i].subset_info->block);
+ free(hand[i].subset_info->start.data);
+ free(hand[i].subset_info->stride.data);
+ free(hand[i].subset_info->count.data);
+ free(hand[i].subset_info->block.data);
free(hand[i].subset_info);
}
}
@@ -4588,8 +4588,8 @@ print_enum(hid_t type)
dst_size = H5Tget_size(type);
/* Get the names and raw values of all members */
- name = calloc(nmembs, sizeof(char *));
- value = calloc(nmembs, MAX(H5Tget_size(type), dst_size));
+ name = (char **)calloc(nmembs, sizeof(char *));
+ value = (unsigned char *)calloc(nmembs, MAX(H5Tget_size(type), dst_size));
for (i = 0; i < nmembs; i++) {
name[i] = H5Tget_member_name(type, i);
@@ -4749,7 +4749,7 @@ xml_escape_the_name(const char *str)
return HDstrdup(str);
cp = str;
- rcp = ncp = HDmalloc(len + extra + 1);
+ rcp = ncp = (char *)HDmalloc(len + extra + 1);
if (!ncp)
return NULL; /* ?? */
@@ -4838,7 +4838,7 @@ xml_escape_the_string(const char *str, int slen)
}
cp = str;
- rcp = ncp = calloc((len + extra + 1), sizeof(char));
+ rcp = ncp = (char *)calloc((len + extra + 1), sizeof(char));
if (ncp == NULL)
return NULL; /* ?? */
@@ -4930,7 +4930,7 @@ xml_print_datatype(hid_t type, unsigned in_group)
/* This should be defined somewhere else */
/* These 2 cases are handled the same right now, but
probably will have something different eventually */
- char * dtxid = malloc(100);
+ char * dtxid = (char *)malloc(100);
xml_name_to_XID(found_obj->objname, dtxid, 100, 1);
if (!found_obj->recorded) {
@@ -5290,7 +5290,7 @@ xml_dump_datatype(hid_t type)
if(found_obj) {
/* Shared datatype, must be entered as an object */
/* These 2 cases are the same now, but may change */
- char * dtxid = malloc(100);
+ char * dtxid = (char *)malloc(100);
xml_name_to_XID(found_obj->objname, dtxid, 100, 1);
if (!found_obj->recorded) {
@@ -5669,14 +5669,14 @@ xml_dump_named_datatype(hid_t type, const char *name)
char *t_prefix;
char *t_name;
- tmp = HDmalloc(HDstrlen(prefix) + HDstrlen(name) + 2);
+ tmp = (char *)HDmalloc(HDstrlen(prefix) + HDstrlen(name) + 2);
HDstrcpy(tmp, prefix);
HDstrcat(tmp, "/");
HDstrcat(tmp, name);
indentation(indent);
- dtxid = HDmalloc(100);
- parentxid = HDmalloc(100);
+ dtxid = (char *)HDmalloc(100);
+ parentxid = (char *)HDmalloc(100);
t_tmp = xml_escape_the_name(tmp);
t_prefix = xml_escape_the_name(prefix);
t_name = xml_escape_the_name(name);
@@ -5824,7 +5824,7 @@ xml_dump_group(hid_t gid, const char *name)
isRoot = 1;
tmp = HDstrdup("/");
} else {
- tmp = HDmalloc(HDstrlen(prefix) + HDstrlen(name) + 2);
+ tmp = (char *)HDmalloc(HDstrlen(prefix) + HDstrlen(name) + 2);
HDstrcpy(tmp, prefix);
par = HDstrdup(tmp);
cp = HDstrrchr(par, '/');
@@ -5854,11 +5854,11 @@ xml_dump_group(hid_t gid, const char *name)
h5tools_setstatus(EXIT_FAILURE);
} else {
char *t_name = xml_escape_the_name(name);
- char *grpxid = malloc(100);
- char *parentxid = malloc(100);
+ char *grpxid = (char *)malloc(100);
+ char *parentxid = (char *)malloc(100);
if(found_obj->displayed) {
- char *ptrstr = malloc(100);
+ char *ptrstr = (char *)malloc(100);
/* already seen: enter a groupptr */
if(isRoot) {
@@ -5960,8 +5960,8 @@ xml_dump_group(hid_t gid, const char *name)
/* only link -- must be first time! */
char *t_name = xml_escape_the_name(name);
- char *grpxid = malloc(100);
- char *parentxid = malloc(100);
+ char *grpxid = (char *)malloc(100);
+ char *parentxid = (char *)malloc(100);
if(isRoot) {
xml_name_to_XID("/", grpxid, 100, 1);
@@ -6078,7 +6078,7 @@ xml_print_refs(hid_t did, int source)
ssiz = H5Sget_simple_extent_npoints(space);
ssiz *= H5Tget_size(type);
- buf = calloc((size_t)ssiz, sizeof(char));
+ buf = (char *)calloc((size_t)ssiz, sizeof(char));
if(buf == NULL)
return FAIL;
e = H5Dread(did, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
@@ -6092,7 +6092,7 @@ xml_print_refs(hid_t did, int source)
ssiz = H5Sget_simple_extent_npoints(space);
ssiz *= H5Tget_size(type);
- buf = calloc((size_t)ssiz, sizeof(char));
+ buf = (char *)calloc((size_t)ssiz, sizeof(char));
if (buf == NULL) {
free(buf);
return FAIL;
@@ -6213,7 +6213,7 @@ xml_print_strs(hid_t did, int source)
tsiz = H5Tget_size(type);
bp = (char*)buf;
if(!is_vlstr)
- onestring = (char *) calloc(tsiz, sizeof(char));
+ onestring = (char *)calloc(tsiz, sizeof(char));
for (i = 0; i < ssiz; i++) {
if(is_vlstr) {
@@ -6486,10 +6486,10 @@ xml_dump_dataset(hid_t did, const char *name, struct subset_t UNUSED * sset)
char *tmp;
char *t_name, *t_tmp, *t_prefix;
unsigned attr_crt_order_flags;
- char *rstr = HDmalloc(100);
- char *pstr = HDmalloc(100);
+ char *rstr = (char *)HDmalloc(100);
+ char *pstr = (char *)HDmalloc(100);
- tmp = HDmalloc(HDstrlen(prefix) + HDstrlen(name) + 2);
+ tmp = (char *)HDmalloc(HDstrlen(prefix) + HDstrlen(name) + 2);
HDstrcpy(tmp, prefix);
HDstrcat(tmp, "/");
HDstrcat(tmp, name);
@@ -6521,7 +6521,7 @@ xml_dump_dataset(hid_t did, const char *name, struct subset_t UNUSED * sset)
/* Print information about storage layout */
if(H5D_CHUNKED == H5Pget_layout(dcpl)) {
maxdims = H5Sget_simple_extent_ndims(space);
- chsize = (hsize_t *) malloc(maxdims * sizeof(hsize_t));
+ chsize = (hsize_t *)malloc(maxdims * sizeof(hsize_t));
indent += COL;
indentation(indent);
printf("<%sStorageLayout>\n",xmlnsprefix);
@@ -6804,8 +6804,8 @@ xml_print_enum(hid_t type)
}
/* Get the names and raw values of all members */
- name = calloc(nmembs, sizeof(char *));
- value = calloc(nmembs, MAX(H5Tget_size(type), dst_size));
+ name = (char **)calloc(nmembs, sizeof(char *));
+ value = (unsigned char *)calloc(nmembs, MAX(H5Tget_size(type), dst_size));
for (i = 0; i < nmembs; i++) {
name[i] = H5Tget_member_name(type, i);
@@ -6989,7 +6989,7 @@ static void
init_prefix(char **prfx, size_t prfx_len)
{
HDassert(prfx_len > 0);
- *prfx = HDcalloc(prfx_len, 1);
+ *prfx = (char *)HDcalloc(prfx_len, 1);
}
@@ -7010,7 +7010,7 @@ add_prefix(char **prfx, size_t *prfx_len, const char *name)
/* Check if we need more space */
if(*prfx_len <= new_len) {
*prfx_len = new_len + 1;
- *prfx = HDrealloc(*prfx, *prfx_len);
+ *prfx = (char *)HDrealloc(*prfx, *prfx_len);
}
/* Append object name to prefix */
diff --git a/tools/h5dump/testh5dump.sh.in b/tools/h5dump/testh5dump.sh.in
index 78b7757..9c28ed9 100644
--- a/tools/h5dump/testh5dump.sh.in
+++ b/tools/h5dump/testh5dump.sh.in
@@ -421,6 +421,12 @@ TOOLTEST tindicessub3.ddl -d 3d -s 0,1,2 -S 1,3,3 -c 2,2,2 -k 1,2,2 taindices.
# 4D case
TOOLTEST tindicessub4.ddl -d 4d -s 0,0,1,2 -c 2,2,3,2 -S 1,1,3,3 -k 1,1,2,2 taindices.h5
+#Exceed the dimensions for subsetting
+TOOLTEST1 texceedsubstart.ddl -d 1d -s 1,3 taindices.h5
+TOOLTEST1 texceedsubcount.ddl -d 1d -c 1,3 taindices.h5
+TOOLTEST1 texceedsubstride.ddl -d 1d -S 1,3 taindices.h5
+TOOLTEST1 texceedsubblock.ddl -d 1d -k 1,3 taindices.h5
+
# tests for filters
# SZIP
@@ -528,6 +534,11 @@ TOOLTEST tattrregR.ddl -R tattrreg.h5
TOOLTEST2 tbinregR.exp -d /Dataset1 -s 0 -y -o $TESTDIR/tbinregR.txt tdatareg.h5
+# Clean up text output files
+if test -z "$HDF5_NOCLEANUP"; then
+ rm -f $TESTDIR/tbinregR.txt
+fi
+
# tests for group creation order
# "1" tracked, "2" name, root tracked
TOOLTEST tordergr1.ddl --group=1 --sort_by=creation_order --sort_order=ascending tordergr.h5