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HDFFV-10282 refactor out assert calls in tools

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This commit is contained in:
Allen Byrne 2017-08-23 16:12:40 -05:00
parent 1b647b18fe
commit b82ba32275
18 changed files with 776 additions and 830 deletions
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13
tools/lib/h5diff_dset.c
View File

@ -358,7 +358,6 @@ hsize_t diff_datasetid( hid_t did1,
nelmts2 *= dims2[i];
h5diffdebug3("nelmts: %ld - %ld\n", nelmts1, nelmts2);
HDassert(nelmts1 == nelmts2);
if(tclass != H5T_ARRAY) {
/*-----------------------------------------------------------------
@ -459,7 +458,7 @@ hsize_t diff_datasetid( hid_t did1,
size = 1;
sm_size[i - 1] = MIN(dadims[i - 1], size);
sm_nbytes *= sm_size[i - 1];
HDassert(sm_nbytes > 0);
h5diffdebug2("sm_nbytes: %ld\n", sm_nbytes);
} /* end for */
/* malloc return code should be verified.
@ -469,10 +468,10 @@ hsize_t diff_datasetid( hid_t did1,
* that fails to address freeing other objects created here.
* E.g., sm_space.
*/
sm_buf1 = HDmalloc((size_t)sm_nbytes);
HDassert(sm_buf1);
sm_buf2 = HDmalloc((size_t)sm_nbytes);
HDassert(sm_buf2);
if((sm_buf1 = HDmalloc((size_t)sm_nbytes)) == NULL)
goto error;
if((sm_buf2 = HDmalloc((size_t)sm_nbytes)) == NULL)
goto error;
sm_nelmts = sm_nbytes / p_type_nbytes;
sm_space = H5Screate_simple(1, &sm_nelmts, NULL);
@ -682,7 +681,6 @@ int diff_can_type( hid_t f_tid1, /* file data type */
* check for non supported classes
*-------------------------------------------------------------------------
*/
HDassert(tclass1 == tclass2);
switch (tclass1) {
case H5T_TIME:
if((options->m_verbose || options->m_list_not_cmp) && obj1_name && obj2_name) {
@ -754,7 +752,6 @@ int diff_can_type( hid_t f_tid1, /* file data type */
* check for different dimensions
*-------------------------------------------------------------------------
*/
HDassert(rank1 == rank2);
for(i = 0; i<rank1; i++) {
if(maxdim1 && maxdim2) {
if(maxdim1[i] != maxdim2[i])

7
tools/lib/h5diff_util.c
View File

@ -283,7 +283,6 @@ get_sign(H5T_sign_t sign)
return "H5T_NSGN";
default:
HDassert(0);
return "unknown sign value";
} /* end switch */
}
@ -340,7 +339,6 @@ get_class(H5T_class_t tclass)
case H5T_NO_CLASS:
case H5T_NCLASSES:
default:
HDassert(0);
return("Invalid class");
} /* end switch */
} /* end get_class() */
@ -395,7 +393,10 @@ herr_t match_up_memsize (hid_t f_tid1_id, hid_t f_tid2_id,
*m_size2 = H5Tget_size(*m_tid2);
} /* end else */
} /* end if */
HDassert((*m_size1) == (*m_size2));
if((*m_size1) != (*m_size2)) {
ret = FAIL;
goto out;
}
out:
return ret;

33
tools/lib/h5tools.c
View File

@ -1283,13 +1283,13 @@ init_acc_pos(h5tools_context_t *ctx, hsize_t *dims)
int i;
unsigned j;
HDassert(ctx->ndims);
ctx->acc[ctx->ndims - 1] = 1;
for (i = ((int)ctx->ndims - 2); i >= 0; i--)
ctx->acc[i] = ctx->acc[i + 1] * dims[i + 1];
for (j = 0; j < ctx->ndims; j++)
ctx->pos[j] = 0;
if(ctx->ndims > 0) {
ctx->acc[ctx->ndims - 1] = 1;
for (i = ((int)ctx->ndims - 2); i >= 0; i--)
ctx->acc[i] = ctx->acc[i + 1] * dims[i + 1];
for (j = 0; j < ctx->ndims; j++)
ctx->pos[j] = 0;
}
}
/*-------------------------------------------------------------------------
@ -1410,13 +1410,17 @@ render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem, hsize_t
memb = H5Tget_super(tid);
ndims = H5Tget_array_ndims(tid);
H5Tget_array_dims2(tid, dims);
HDassert(ndims >= 1 && ndims <= H5S_MAX_RANK);
/* calculate the number of array elements */
for (k = 0, nelmts = 1; k < ndims; k++) {
temp_nelmts = nelmts;
temp_nelmts *= dims[k];
nelmts = (size_t) temp_nelmts;
if(ndims >= 1 && ndims <= H5S_MAX_RANK) {
/* calculate the number of array elements */
for (k = 0, nelmts = 1; k < ndims; k++) {
temp_nelmts = nelmts;
temp_nelmts *= dims[k];
nelmts = (size_t) temp_nelmts;
}
}
else {
H5Tclose(memb);
H5E_THROW(FAIL, H5E_tools_min_id_g, "calculate the number of array elements failed");
}
for (block_index = 0; block_index < block_nelmts; block_index++) {
@ -1641,7 +1645,6 @@ render_bin_output_region_blocks(hid_t region_space, hid_t region_id,
ndims = (unsigned)sndims;
alloc_size = nblocks * ndims * 2 * sizeof(ptdata[0]);
HDassert(alloc_size == (hsize_t) ((size_t) alloc_size)); /*check for overflow*/
if((ptdata = (hsize_t*) HDmalloc((size_t) alloc_size)) == NULL)
HGOTO_ERROR(FALSE, H5E_tools_min_id_g, "Could not allocate buffer for ptdata");

41
tools/lib/h5tools_ref.c
View File

@ -107,19 +107,21 @@ static int
init_ref_path_table(void)
{
/* Sanity check */
HDassert(thefile > 0);
if(thefile > 0) {
/* Create skip list to store reference path information */
if((ref_path_table = H5SL_create(H5SL_TYPE_HADDR, NULL))==NULL)
return (-1);
/* Create skip list to store reference path information */
if((ref_path_table = H5SL_create(H5SL_TYPE_HADDR, NULL))==NULL)
/* Iterate over objects in this file */
if(h5trav_visit(thefile, "/", TRUE, TRUE, init_ref_path_cb, NULL, NULL) < 0) {
error_msg("unable to construct reference path table\n");
h5tools_setstatus(EXIT_FAILURE);
} /* end if */
return(0);
}
else
return (-1);
/* Iterate over objects in this file */
if(h5trav_visit(thefile, "/", TRUE, TRUE, init_ref_path_cb, NULL, NULL) < 0) {
error_msg("unable to construct reference path table\n");
h5tools_setstatus(EXIT_FAILURE);
} /* end if */
return(0);
}
/*-------------------------------------------------------------------------
@ -212,16 +214,17 @@ ref_path_table_put(const char *path, haddr_t objno)
{
ref_path_node_t *new_node;
HDassert(ref_path_table);
HDassert(path);
if(ref_path_table && path) {
if((new_node = (ref_path_node_t *)HDmalloc(sizeof(ref_path_node_t))) == NULL)
return(-1);
if((new_node = (ref_path_node_t *)HDmalloc(sizeof(ref_path_node_t))) == NULL)
return(-1);
new_node->objno = objno;
new_node->path = HDstrdup(path);
new_node->objno = objno;
new_node->path = HDstrdup(path);
return(H5SL_insert(ref_path_table, new_node, &(new_node->objno)));
return(H5SL_insert(ref_path_table, new_node, &(new_node->objno)));
}
else
return (-1);
}
/*

2
tools/lib/h5tools_type.c
View File

@ -92,7 +92,6 @@ h5tools_get_little_endian_type(hid_t tid)
case H5T_NO_CLASS:
case H5T_NCLASSES:
default:
HDassert(0);
break;
} /* end switch */
@ -179,7 +178,6 @@ h5tools_get_big_endian_type(hid_t tid)
case H5T_NO_CLASS:
case H5T_NCLASSES:
default:
HDassert(0);
break;
} /* end switch */

8
tools/lib/h5tools_utils.c
View File

@ -608,7 +608,6 @@ find_objs_cb(const char *name, const H5O_info_t *oinfo, const char *already_seen
case H5O_TYPE_UNKNOWN:
case H5O_TYPE_NTYPES:
default:
HDassert(0);
break;
} /* end switch */
@ -777,8 +776,11 @@ H5tools_get_symlink_info(hid_t file_id, const char * linkpath, h5tool_link_info_
} /* end if */
/* trg_path must be freed out of this function when finished using */
link_info->trg_path = (char*)HDcalloc(link_info->linfo.u.val_size, sizeof(char));
HDassert(link_info->trg_path);
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);
goto out;
} /* 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) {

32
tools/lib/h5trav.c
View File

@ -557,7 +557,7 @@ trav_info_free(trav_info_t *info)
if(info) {
/* Free visited symbolic links path and file (if alloc) */
for(u=0; u < info->symlink_visited.nused; u++)
for(u=0; u < info->symlink_visited.nused; u++)
{
if (info->symlink_visited.objs[u].file)
HDfree(info->symlink_visited.objs[u].file);
@ -789,8 +789,6 @@ trav_table_addlink(trav_table_t *table, haddr_t objno, const char *path)
return;
} /* end for */
} /* end for */
HDassert(0 && "object not in table?!?");
}
@ -1017,7 +1015,7 @@ trav_print_visit_obj(const char *path, const H5O_info_t *oinfo,
/* Finish printing line about object */
printf("\n");
if(trav_verbosity > 0)
H5Aiterate_by_name(print_udata->fid, path, trav_index_by, trav_index_order,
H5Aiterate_by_name(print_udata->fid, path, trav_index_by, trav_index_order,
NULL, trav_attr, &op_data, H5P_DEFAULT);
}
else
@ -1051,12 +1049,12 @@ trav_print_visit_lnk(const char *path, const H5L_info_t *linfo, void *udata)
case H5L_TYPE_SOFT:
if(linfo->u.val_size > 0) {
char *targbuf = (char*)HDmalloc(linfo->u.val_size + 1);
HDassert(targbuf);
if(H5Lget_val(print_udata->fid, path, targbuf, linfo->u.val_size + 1, H5P_DEFAULT) < 0)
targbuf[0] = 0;
printf(" %-10s %s -> %s\n", "link", path, targbuf);
HDfree(targbuf);
if(targbuf) {
if(H5Lget_val(print_udata->fid, path, targbuf, linfo->u.val_size + 1, H5P_DEFAULT) < 0)
targbuf[0] = 0;
printf(" %-10s %s -> %s\n", "link", path, targbuf);
HDfree(targbuf);
}
} /* end if */
else
printf(" %-10s %s ->\n", "link", path);
@ -1069,13 +1067,13 @@ trav_print_visit_lnk(const char *path, const H5L_info_t *linfo, void *udata)
const char *objname = NULL;
targbuf = (char*)HDmalloc(linfo->u.val_size + 1);
HDassert(targbuf);
if(H5Lget_val(print_udata->fid, path, targbuf, linfo->u.val_size + 1, H5P_DEFAULT) < 0)
targbuf[0] = 0;
if(H5Lunpack_elink_val(targbuf, linfo->u.val_size, NULL, &filename, &objname) >= 0)
printf(" %-10s %s -> %s %s\n", "ext link", path, filename, objname);
HDfree(targbuf);
if(targbuf) {
if(H5Lget_val(print_udata->fid, path, targbuf, linfo->u.val_size + 1, H5P_DEFAULT) < 0)
targbuf[0] = 0;
if(H5Lunpack_elink_val(targbuf, linfo->u.val_size, NULL, &filename, &objname) >= 0)
printf(" %-10s %s -> %s %s\n", "ext link", path, filename, objname);
HDfree(targbuf);
}
} /* end if */
else
printf(" %-10s %s ->\n", "ext link", path);

96
tools/src/h5copy/h5copy.c
View File

@ -159,36 +159,28 @@ static int parse_flag(const char* s_flag, unsigned *flag)
{
unsigned fla=0;
if (HDstrcmp(s_flag,"shallow")==0)
{
if (HDstrcmp(s_flag, "shallow") == 0) {
fla = H5O_COPY_SHALLOW_HIERARCHY_FLAG;
}
else if (HDstrcmp(s_flag,"soft")==0)
{
else if (HDstrcmp(s_flag, "soft") == 0) {
fla = H5O_COPY_EXPAND_SOFT_LINK_FLAG;
}
else if (HDstrcmp(s_flag,"ext")==0)
{
else if (HDstrcmp(s_flag, "ext") == 0) {
fla = H5O_COPY_EXPAND_EXT_LINK_FLAG;
}
else if (HDstrcmp(s_flag,"ref")==0)
{
else if (HDstrcmp(s_flag, "ref") == 0) {
fla = H5O_COPY_EXPAND_REFERENCE_FLAG;
}
else if (HDstrcmp(s_flag,"noattr")==0)
{
else if (HDstrcmp(s_flag, "noattr") == 0) {
fla = H5O_COPY_WITHOUT_ATTR_FLAG;
}
else if (HDstrcmp(s_flag,"allflags")==0)
{
else if (HDstrcmp(s_flag, "allflags") == 0) {
fla = H5O_COPY_ALL;
}
else if (HDstrcmp(s_flag,"nullmsg")==0)
{
else if (HDstrcmp(s_flag, "nullmsg") == 0) {
fla = H5O_COPY_PRESERVE_NULL_FLAG;
}
else
{
else {
error_msg("Error in input flag\n");
return -1;
}
@ -247,25 +239,21 @@ main (int argc, const char *argv[])
HDmemset(&linkinfo, 0, sizeof(h5tool_link_info_t));
/* Check for no command line parameters */
if(argc == 1)
{
if(argc == 1) {
usage();
leave(EXIT_FAILURE);
} /* end if */
/* parse command line options */
while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF)
{
switch ((char)opt)
{
while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
switch ((char)opt) {
case 'd':
oname_dst = HDstrdup(opt_arg);
break;
case 'f':
/* validate flag */
if (parse_flag(opt_arg,&flag)<0)
{
if (parse_flag(opt_arg, &flag) < 0) {
usage();
leave(EXIT_FAILURE);
}
@ -316,29 +304,25 @@ main (int argc, const char *argv[])
* check for missing file/object names
*-------------------------------------------------------------------------*/
if (fname_src==NULL)
{
if (fname_src==NULL) {
error_msg("Input file name missing\n");
usage();
leave(EXIT_FAILURE);
}
if (fname_dst==NULL)
{
if (fname_dst==NULL) {
error_msg("Output file name missing\n");
usage();
leave(EXIT_FAILURE);
}
if (oname_src==NULL)
{
if (oname_src==NULL) {
error_msg("Source object name missing\n");
usage();
leave(EXIT_FAILURE);
}
if (oname_dst==NULL)
{
if (oname_dst==NULL) {
error_msg("Destination object name missing\n");
usage();
leave(EXIT_FAILURE);
@ -367,8 +351,7 @@ main (int argc, const char *argv[])
/*-------------------------------------------------------------------------
* test for error in opening input file
*-------------------------------------------------------------------------*/
if (fid_src==-1)
{
if (fid_src==-1) {
error_msg("Could not open input file <%s>...Exiting\n", fname_src);
leave(EXIT_FAILURE);
}
@ -386,8 +369,7 @@ main (int argc, const char *argv[])
/*-------------------------------------------------------------------------
* test for error in opening output file
*-------------------------------------------------------------------------*/
if (fid_dst==-1)
{
if (fid_dst==-1) {
error_msg("Could not open output file <%s>...Exiting\n", fname_dst);
leave(EXIT_FAILURE);
}
@ -396,12 +378,10 @@ main (int argc, const char *argv[])
* print some info
*-------------------------------------------------------------------------*/
if (verbose)
{
if (verbose) {
printf("Copying file <%s> and object <%s> to file <%s> and object <%s>\n",
fname_src, oname_src, fname_dst, oname_dst);
if (flag) {
HDassert(str_flag);
printf("Using %s flag\n", str_flag);
}
}
@ -416,8 +396,7 @@ main (int argc, const char *argv[])
HGOTO_ERROR(EXIT_FAILURE, H5E_tools_min_id_g, "H5Pcreate failed");
/* set options for object copy */
if (flag)
{
if (flag) {
if ( H5Pset_copy_object(ocpl_id, flag) < 0)
HGOTO_ERROR(EXIT_FAILURE, H5E_tools_min_id_g, "H5Pset_copy_object failed");
}
@ -440,24 +419,21 @@ main (int argc, const char *argv[])
if(verbose)
printf("%s: Creating parent groups\n", h5tools_getprogname());
} /* end if */
else /* error, if parent groups doesn't already exist in destination file */
{
else {
/* error, if parent groups doesn't already exist in destination file */
size_t i, len;
len = HDstrlen(oname_dst);
/* check if all the parents groups exist. skip root group */
for (i = 1; i < len; i++)
{
if ('/'==oname_dst[i])
{
for (i = 1; i < len; i++) {
if ('/'==oname_dst[i]) {
char *str_ptr;
str_ptr = (char *)HDcalloc(i + 1, sizeof(char));
HDstrncpy(str_ptr, oname_dst, i);
str_ptr[i]='\0';
if (H5Lexists(fid_dst, str_ptr, H5P_DEFAULT) <= 0)
{
if (H5Lexists(fid_dst, str_ptr, H5P_DEFAULT) <= 0) {
error_msg("group <%s> doesn't exist. Use -p to create parent groups.\n", str_ptr);
HDfree(str_ptr);
HGOTO_ERROR(EXIT_FAILURE, H5E_tools_min_id_g, "H5Lexists failed");
@ -475,15 +451,15 @@ main (int argc, const char *argv[])
linkinfo.opt.msg_mode = 1;
li_ret = H5tools_get_symlink_info(fid_src, oname_src, &linkinfo, 1);
if (li_ret == 0) /* dangling link */
{
if (li_ret == 0) {
/* dangling link */
if(H5Lcopy(fid_src, oname_src,
fid_dst, oname_dst,
H5P_DEFAULT, H5P_DEFAULT) < 0)
HGOTO_ERROR(EXIT_FAILURE, H5E_tools_min_id_g, "H5Lcopy failed");
}
else /* valid link */
{
else {
/* valid link */
if (H5Ocopy(fid_src, /* Source file or group identifier */
oname_src, /* Name of the source object to be copied */
fid_dst, /* Destination file or group identifier */
@ -518,13 +494,13 @@ done:
if (linkinfo.trg_path)
HDfree(linkinfo.trg_path);
H5E_BEGIN_TRY {
H5Pclose(ocpl_id);
H5Pclose(lcpl_id);
H5Fclose(fid_src);
H5Fclose(fid_dst);
} H5E_END_TRY;
H5E_BEGIN_TRY {
H5Pclose(ocpl_id);
H5Pclose(lcpl_id);
H5Fclose(fid_src);
H5Fclose(fid_dst);
} H5E_END_TRY;
leave(ret_value);
leave(ret_value);
}

192
tools/src/h5dump/h5dump.c
View File

@ -721,93 +721,100 @@ parse_mask_list(const char *h_list)
const char *ptr = NULL;
/* sanity check */
HDassert(h_list);
if(h_list) {
HDmemset(packed_mask,0,sizeof(packed_mask));
HDmemset(packed_mask,0,sizeof(packed_mask));
packed_bits_num = 0;
/* scan in pair of offset,length separated by commas. */
ptr = h_list;
while (*ptr) {
/* scan for an offset which is an unsigned int */
if (!HDisdigit(*ptr)) {
error_msg("Bad mask list(%s)\n", h_list);
return FAIL;
}
soffset_value = HDatoi(ptr);
offset_value = (unsigned)soffset_value;
if (soffset_value < 0 || offset_value >= PACKED_BITS_SIZE_MAX) {
error_msg("Packed Bit offset value(%d) must be between 0 and %u\n",
soffset_value, (unsigned)(PACKED_BITS_SIZE_MAX - 1));
return FAIL;
}
/* skip to end of integer */
while (HDisdigit(*++ptr))
;
/* Look for the common separator */
if (*ptr++ != ',') {
error_msg("Bad mask list(%s), missing expected comma separator.\n", h_list);
return FAIL;
}
/* scan for a length which is a positive int */
if (!HDisdigit(*ptr)) {
error_msg("Bad mask list(%s)\n", h_list);
return FAIL;
}
slength_value = HDatoi(ptr);
if (slength_value <= 0) {
error_msg("Packed Bit length value(%d) must be positive.\n", slength_value);
return FAIL;
}
length_value = (unsigned)slength_value;
if ((offset_value + length_value) > PACKED_BITS_SIZE_MAX) {
error_msg("Packed Bit offset+length value(%u) too large. Max is %u\n",
offset_value+length_value, (unsigned)PACKED_BITS_SIZE_MAX);
return FAIL;
}
/* skip to end of int */
while (HDisdigit(*++ptr))
;
/* store the offset,length pair */
if (packed_bits_num >= PACKED_BITS_MAX) {
/* too many requests */
error_msg("Too many masks requested (max. %d). Mask list(%s)\n", PACKED_BITS_MAX, h_list);
return FAIL;
}
packed_offset[packed_bits_num] = offset_value;
packed_length[packed_bits_num] = length_value;
/* create the bit mask by left shift 1's by length, then negate it. */
/* After packed_mask is calculated, packed_length is not needed but */
/* keep it for debug purpose. */
temp_mask = ~0ULL;
if(length_value < (int)(8 *sizeof(unsigned long long))) {
temp_mask = temp_mask << length_value;
packed_mask[packed_bits_num] = ~temp_mask;
}
else
packed_mask[packed_bits_num] = temp_mask;
packed_bits_num++;
/* skip a possible comma separator */
if (*ptr == ',') {
if (!(*++ptr)) {
/* unexpected end of string */
error_msg("Bad mask list(%s), unexpected end of string.\n", h_list);
packed_bits_num = 0;
/* scan in pair of offset,length separated by commas. */
ptr = h_list;
while (*ptr) {
/* scan for an offset which is an unsigned int */
if (!HDisdigit(*ptr)) {
error_msg("Bad mask list(%s)\n", h_list);
return FAIL;
}
soffset_value = HDatoi(ptr);
offset_value = (unsigned)soffset_value;
if (soffset_value < 0 || offset_value >= PACKED_BITS_SIZE_MAX) {
error_msg("Packed Bit offset value(%d) must be between 0 and %u\n",
soffset_value, (unsigned)(PACKED_BITS_SIZE_MAX - 1));
return FAIL;
}
/* skip to end of integer */
while (HDisdigit(*++ptr))
;
/* Look for the common separator */
if (*ptr++ != ',') {
error_msg("Bad mask list(%s), missing expected comma separator.\n", h_list);
return FAIL;
}
/* scan for a length which is a positive int */
if (!HDisdigit(*ptr)) {
error_msg("Bad mask list(%s)\n", h_list);
return FAIL;
}
slength_value = HDatoi(ptr);
if (slength_value <= 0) {
error_msg("Packed Bit length value(%d) must be positive.\n", slength_value);
return FAIL;
}
length_value = (unsigned)slength_value;
if ((offset_value + length_value) > PACKED_BITS_SIZE_MAX) {
error_msg("Packed Bit offset+length value(%u) too large. Max is %u\n",
offset_value+length_value, (unsigned)PACKED_BITS_SIZE_MAX);
return FAIL;
}
/* skip to end of int */
while (HDisdigit(*++ptr))
;
/* store the offset,length pair */
if (packed_bits_num >= PACKED_BITS_MAX) {
/* too many requests */
error_msg("Too many masks requested (max. %d). Mask list(%s)\n", PACKED_BITS_MAX, h_list);
return FAIL;
}
packed_offset[packed_bits_num] = offset_value;
packed_length[packed_bits_num] = length_value;
/* create the bit mask by left shift 1's by length, then negate it. */
/* After packed_mask is calculated, packed_length is not needed but */
/* keep it for debug purpose. */
temp_mask = ~0ULL;
if(length_value < (int)(8 *sizeof(unsigned long long))) {
temp_mask = temp_mask << length_value;
packed_mask[packed_bits_num] = ~temp_mask;
}
else
packed_mask[packed_bits_num] = temp_mask;
packed_bits_num++;
/* skip a possible comma separator */
if (*ptr == ',') {
if (!(*++ptr)) {
/* unexpected end of string */
error_msg("Bad mask list(%s), unexpected end of string.\n", h_list);
return FAIL;
}
}
}
if(packed_bits_num > PACKED_BITS_MAX) {
error_msg("Maximum number of packed bits exceeded\n");
return FAIL;
}
if (packed_bits_num == 0) {
/* got no masks! */
error_msg("Bad mask list(%s)\n", h_list);
return FAIL;
}
return SUCCEED;
}
HDassert(packed_bits_num <= PACKED_BITS_MAX);
if (packed_bits_num == 0) {
/* got no masks! */
error_msg("Bad mask list(%s)\n", h_list);
else {
error_msg("Bad mask list argument\n");
return FAIL;
}
return SUCCEED;
}
@ -1708,13 +1715,18 @@ h5_fileaccess(void)
HDmemset(memb_name, 0, sizeof memb_name);
HDmemset(memb_addr, 0, sizeof memb_addr);
HDassert(HDstrlen(multi_letters)==H5FD_MEM_NTYPES);
for (mt=H5FD_MEM_DEFAULT; mt<H5FD_MEM_NTYPES; H5_INC_ENUM(H5FD_mem_t,mt)) {
memb_fapl[mt] = H5P_DEFAULT;
memb_map[mt] = mt;
sprintf(sv[mt], "%%s-%c.h5", multi_letters[mt]);
memb_name[mt] = sv[mt];
memb_addr[mt] = (haddr_t)MAX(mt - 1, 0) * (HADDR_MAX / 10);
if(HDstrlen(multi_letters)==H5FD_MEM_NTYPES) {
for (mt=H5FD_MEM_DEFAULT; mt<H5FD_MEM_NTYPES; H5_INC_ENUM(H5FD_mem_t,mt)) {
memb_fapl[mt] = H5P_DEFAULT;
memb_map[mt] = mt;
sprintf(sv[mt], "%%s-%c.h5", multi_letters[mt]);
memb_name[mt] = sv[mt];
memb_addr[mt] = (haddr_t)MAX(mt - 1, 0) * (HADDR_MAX / 10);
}
}
else {
error_msg("Bad multi_letters list\n");
return FAIL;
}
if (H5Pset_fapl_multi(fapl, memb_map, memb_fapl, memb_name, memb_addr, FALSE) < 0)
@ -1767,8 +1779,10 @@ h5_fileaccess(void)
static void
init_prefix(char **prfx, size_t prfx_len)
{
HDassert(prfx_len > 0);
*prfx = (char *)HDcalloc(prfx_len, 1);
if(prfx_len > 0)
*prfx = (char *)HDcalloc(prfx_len, 1);
else
error_msg("unable to allocate prefix buffer\n");
}

216
tools/src/h5dump/h5dump_ddl.c
View File

@ -248,17 +248,19 @@ dump_all_cb(hid_t group, const char *name, const H5L_info_t *linfo, void H5_ATTR
/* Keep copy of prefix before iterating into group */
old_prefix = HDstrdup(prefix);
HDassert(old_prefix);
if (old_prefix) {
/* Append group name to prefix */
add_prefix(&prefix, &prefix_len, name);
/* Append group name to prefix */
add_prefix(&prefix, &prefix_len, name);
/* Iterate into group */
dump_function_table->dump_group_function(obj, name);
/* Iterate into group */
dump_function_table->dump_group_function(obj, name);
/* Restore old prefix name */
HDstrcpy(prefix, old_prefix);
HDfree(old_prefix);
/* Restore old prefix name */
HDstrcpy(prefix, old_prefix);
HDfree(old_prefix);
}
else
error_msg("warning: null prefix\n");
/* Close group */
H5Gclose(obj);
@ -408,131 +410,137 @@ dump_all_cb(hid_t group, const char *name, const H5L_info_t *linfo, void H5_ATTR
switch(linfo->type) {
case H5L_TYPE_SOFT:
targbuf = (char *)HDmalloc(linfo->u.val_size);
HDassert(targbuf);
ctx.need_prefix = TRUE;
/* Render the element */
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "%s \"%s\" %s",
h5tools_dump_header_format->softlinkbegin, name,
h5tools_dump_header_format->softlinkblockbegin);
h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0);
ctx.indent_level++;
if(H5Lget_val(group, name, targbuf, linfo->u.val_size, H5P_DEFAULT) < 0) {
error_msg("unable to get link value\n");
if((targbuf = (char *)HDmalloc(linfo->u.val_size)) == NULL) {
error_msg("unable to allocate buffer\n");
h5tools_setstatus(EXIT_FAILURE);
ret = FAIL;
}
else {
/* print the value of a soft link */
/* Standard DDL: no modification */
ctx.need_prefix = TRUE;
/* Render the element */
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "%s \"%s\" %s",
h5tools_dump_header_format->softlinkbegin, name,
h5tools_dump_header_format->softlinkblockbegin);
h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0);
ctx.indent_level++;
if(H5Lget_val(group, name, targbuf, linfo->u.val_size, H5P_DEFAULT) < 0) {
error_msg("unable to get link value\n");
h5tools_setstatus(EXIT_FAILURE);
ret = FAIL;
}
else {
/* print the value of a soft link */
/* Standard DDL: no modification */
ctx.need_prefix = TRUE;
h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0);
/* Render the element */
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "LINKTARGET \"%s\"", targbuf);
h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0);
}
ctx.indent_level--;
ctx.need_prefix = TRUE;
h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0);
/* Render the element */
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "LINKTARGET \"%s\"", targbuf);
h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0);
}
ctx.indent_level--;
ctx.need_prefix = TRUE;
h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0);
/* Render the element */
h5tools_str_reset(&buffer);
if(HDstrlen(h5tools_dump_header_format->softlinkblockend)) {
h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->softlinkblockend);
if(HDstrlen(h5tools_dump_header_format->softlinkblockend)) {
h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->softlinkblockend);
if(HDstrlen(h5tools_dump_header_format->softlinkend))
h5tools_str_append(&buffer, " ");
}
if(HDstrlen(h5tools_dump_header_format->softlinkend))
h5tools_str_append(&buffer, " ");
}
if(HDstrlen(h5tools_dump_header_format->softlinkend))
h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->softlinkend);
h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0);
h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->softlinkend);
h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0);
HDfree(targbuf);
HDfree(targbuf);
}
break;
case H5L_TYPE_EXTERNAL:
targbuf = (char *)HDmalloc(linfo->u.val_size);
HDassert(targbuf);
ctx.need_prefix = TRUE;
h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0);
/* Render the element */
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "%s \"%s\" %s",
h5tools_dump_header_format->extlinkbegin, name,
h5tools_dump_header_format->extlinkblockbegin);
h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0);
if(H5Lget_val(group, name, targbuf, linfo->u.val_size, H5P_DEFAULT) < 0) {
indentation(dump_indent);
error_msg("unable to get external link value\n");
if((targbuf = (char *)HDmalloc(linfo->u.val_size)) == NULL) {
error_msg("unable to allocate buffer\n");
h5tools_setstatus(EXIT_FAILURE);
ret = FAIL;
} /* end if */
}
else {
const char *filename;
const char *targname;
ctx.need_prefix = TRUE;
h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0);
if(H5Lunpack_elink_val(targbuf, linfo->u.val_size, NULL, &filename, &targname) < 0) {
/* Render the element */
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "%s \"%s\" %s",
h5tools_dump_header_format->extlinkbegin, name,
h5tools_dump_header_format->extlinkblockbegin);
h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0);
if(H5Lget_val(group, name, targbuf, linfo->u.val_size, H5P_DEFAULT) < 0) {
indentation(dump_indent);
error_msg("unable to unpack external link value\n");
error_msg("unable to get external link value\n");
h5tools_setstatus(EXIT_FAILURE);
ret = FAIL;
} /* end if */
else {
ctx.indent_level++;
const char *filename;
const char *targname;
ctx.need_prefix = TRUE;
h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0);
if(H5Lunpack_elink_val(targbuf, linfo->u.val_size, NULL, &filename, &targname) < 0) {
indentation(dump_indent);
error_msg("unable to unpack external link value\n");
h5tools_setstatus(EXIT_FAILURE);
ret = FAIL;
} /* end if */
else {
ctx.indent_level++;
/* Render the element */
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "TARGETFILE \"%s\"", filename);
h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0);
ctx.need_prefix = TRUE;
h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0);
ctx.need_prefix = TRUE;
h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0);
/* Render the element */
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "TARGETFILE \"%s\"", filename);
h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0);
/* Render the element */
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "TARGETPATH \"%s\"", targname);
h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0);
ctx.need_prefix = TRUE;
h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0);
/* dump the external link */
dump_extlink(group, name, targname);
ctx.indent_level--;
/* Render the element */
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "TARGETPATH \"%s\"", targname);
h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0);
/* dump the external link */
dump_extlink(group, name, targname);
ctx.indent_level--;
} /* end else */
} /* end else */
} /* end else */
ctx.need_prefix = TRUE;
h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0);
ctx.need_prefix = TRUE;
h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0);
/* Render the element */
h5tools_str_reset(&buffer);
if(HDstrlen(h5tools_dump_header_format->extlinkblockend)) {
h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->extlinkblockend);
/* Render the element */
h5tools_str_reset(&buffer);
if(HDstrlen(h5tools_dump_header_format->extlinkblockend)) {
h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->extlinkblockend);
if(HDstrlen(h5tools_dump_header_format->extlinkend))
h5tools_str_append(&buffer, " ");
}
if(HDstrlen(h5tools_dump_header_format->extlinkend))
h5tools_str_append(&buffer, " ");
}
if(HDstrlen(h5tools_dump_header_format->extlinkend))
h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->extlinkend);
h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0);
h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->extlinkend);
h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0);
HDfree(targbuf);
HDfree(targbuf);
}
break;
case H5L_TYPE_ERROR:
case H5L_TYPE_MAX:
HDassert(0);
/* fall through */
case H5L_TYPE_HARD:
default:
ctx.need_prefix = TRUE;
@ -1082,7 +1090,7 @@ dump_dataset(hid_t did, const char *name, struct subset_t *sset)
case H5T_NO_CLASS:
case H5T_NCLASSES:
default:
HDassert(0);
error_msg("invalid H5TCLASS type\n");
break;
} /* end switch */
} /* for(u=0; u<data_loop; u++) */
@ -1183,10 +1191,10 @@ dump_fcpl(hid_t fid)
size_t off_size; /* size of offsets in the file */
size_t len_size; /* size of lengths in the file */
H5F_fspace_strategy_t fs_strategy; /* file space strategy */
hbool_t fs_persist; /* Persisting free-space or not */
hsize_t fs_threshold; /* free-space section threshold */
hsize_t fsp_size; /* file space page size */
H5F_info2_t finfo; /* file information */
hbool_t fs_persist; /* Persisting free-space or not */
hsize_t fs_threshold; /* free-space section threshold */
hsize_t fsp_size; /* file space page size */
H5F_info2_t finfo; /* file information */
#ifdef SHOW_FILE_DRIVER
hid_t fapl; /* file access property list ID */
hid_t fdriver; /* file driver */
@ -1980,8 +1988,6 @@ handle_links(hid_t fid, const char *links, void H5_ATTR_UNUSED * data, int H5_AT
case H5L_TYPE_ERROR:
case H5L_TYPE_MAX:
HDassert(0);
/* fall through */
case H5L_TYPE_HARD:
default:
begin_obj(h5tools_dump_header_format->udlinkbegin, links, h5tools_dump_header_format->udlinkblockbegin);

493
tools/src/h5dump/h5dump_xml.c
View File

@ -198,18 +198,22 @@ xml_dump_all_cb(hid_t group, const char *name, const H5L_info_t *linfo, void H5_
char *old_prefix; /* Pointer to previous prefix */
/* Keep copy of prefix before iterating into group */
old_prefix = HDstrdup(prefix);
HDassert(old_prefix);
if((old_prefix = HDstrdup(prefix)) == NULL) {
error_msg("unable to allocate buffer\n");
h5tools_setstatus(EXIT_FAILURE);
ret = FAIL;
}
else {
/* Append group name to prefix */
add_prefix(&prefix, &prefix_len, name);
/* Append group name to prefix */
add_prefix(&prefix, &prefix_len, name);
/* Iterate into group */
dump_function_table->dump_group_function(obj, name);
/* Iterate into group */
dump_function_table->dump_group_function(obj, name);
/* Restore old prefix name */
HDstrcpy(prefix, old_prefix);
HDfree(old_prefix);
/* Restore old prefix name */
HDstrcpy(prefix, old_prefix);
HDfree(old_prefix);
}
/* Close group */
H5Gclose(obj);
@ -360,161 +364,167 @@ xml_dump_all_cb(hid_t group, const char *name, const H5L_info_t *linfo, void H5_
switch(linfo->type) {
case H5L_TYPE_SOFT:
targbuf = (char *)HDmalloc(linfo->u.val_size);
HDassert(targbuf);
if(H5Lget_val(group, name, targbuf, linfo->u.val_size, H5P_DEFAULT) < 0) {
error_msg("unable to get link value\n");
if((targbuf = (char *)HDmalloc(linfo->u.val_size)) == NULL) {
error_msg("unable to allocate buffer\n");
h5tools_setstatus(EXIT_FAILURE);
ret = FAIL;
}
else {
/* print the value of a soft link */
/* XML */
char linkxid[100];
char parentxid[100];
char targetxid[100];
char *t_prefix = xml_escape_the_name(HDstrcmp(prefix,"") ? prefix : "/");
char *t_name = xml_escape_the_name(name);
char *t_targbuf = xml_escape_the_name(targbuf);
char *t_obj_path = xml_escape_the_name(obj_path);
char *t_link_path;
int res;
t_link_path = (char *)HDmalloc(HDstrlen(prefix) + linfo->u.val_size + 1);
if(targbuf[0] == '/')
HDstrcpy(t_link_path, targbuf);
else {
HDstrcpy(t_link_path, prefix);
HDstrcat(HDstrcat(t_link_path, "/"), targbuf);
} /* end else */
/* Create OBJ-XIDs for the parent and object */
xml_name_to_XID(t_obj_path, linkxid, (int)sizeof(linkxid), 1);
xml_name_to_XID(prefix, parentxid, (int)sizeof(parentxid), 1);
/* Try to create an OBJ-XID for the object pointed to */
res = xml_name_to_XID(t_link_path, targetxid, (int)sizeof(targetxid), 0);
if (res == 0) {
/* target obj found */
ctx.need_prefix = TRUE;
h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0);
/* Render the element */
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "<%sSoftLink LinkName=\"%s\" "
"OBJ-XID=\"%s\" "
"H5SourcePath=\"%s\" "
"TargetPath=\"%s\" TargetObj=\"%s\" "
"Parents=\"%s\" H5ParentPaths=\"%s\" />",
xmlnsprefix,
t_name, /* LinkName */
linkxid, /* OBJ-XID */
t_obj_path, /* H5SourcePath */
t_targbuf, /* TargetPath */
targetxid, /* TargetObj */
parentxid, /* Parents */
t_prefix); /* H5ParentPaths */
h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0);
}
else {
/* dangling link -- omit from xml attributes */
ctx.need_prefix = TRUE;
h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0);
/* Render the element */
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "<%sSoftLink LinkName=\"%s\" "
"OBJ-XID=\"%s\" "
"H5SourcePath=\"%s\" "
"TargetPath=\"%s\" "
"Parents=\"%s\" H5ParentPaths=\"%s\" />",
xmlnsprefix,
t_name, /* LinkName */
linkxid, /* OBJ-XID */
t_obj_path, /* H5SourcePath */
t_targbuf, /* TargetPath */
parentxid, /* Parents */
t_prefix); /* H5ParentPaths */
h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0);
}
HDfree(t_prefix);
HDfree(t_name);
HDfree(t_targbuf);
HDfree(t_obj_path);
HDfree(t_link_path);
}
HDfree(targbuf);
break;
case H5L_TYPE_EXTERNAL:
targbuf = (char *)HDmalloc(linfo->u.val_size);
HDassert(targbuf);
if(H5Lget_val(group, name, targbuf, linfo->u.val_size, H5P_DEFAULT) < 0) {
error_msg("unable to get external link value\n");
h5tools_setstatus(EXIT_FAILURE);
ret = FAIL;
} /* end if */
else {
const char *filename;
const char *targname;
if(H5Lunpack_elink_val(targbuf, linfo->u.val_size, NULL, &filename, &targname) < 0) {
error_msg("unable to unpack external link value\n");
if(H5Lget_val(group, name, targbuf, linfo->u.val_size, H5P_DEFAULT) < 0) {
error_msg("unable to get link value\n");
h5tools_setstatus(EXIT_FAILURE);
ret = FAIL;
} /* end if */
}
else {
/* print the value of a soft link */
/* XML */
char linkxid[100];
char parentxid[100];
char *t_name = xml_escape_the_name(name);
char targetxid[100];
char *t_prefix = xml_escape_the_name(HDstrcmp(prefix,"") ? prefix : "/");
char *t_name = xml_escape_the_name(name);
char *t_targbuf = xml_escape_the_name(targbuf);
char *t_obj_path = xml_escape_the_name(obj_path);
char *t_filename = xml_escape_the_name(filename);
char *t_targname = xml_escape_the_name(targname);
char *t_link_path;
int res;
t_link_path = (char *)HDmalloc(HDstrlen(prefix) + linfo->u.val_size + 1);
if(targbuf[0] == '/')
HDstrcpy(t_link_path, targbuf);
else {
HDstrcpy(t_link_path, prefix);
HDstrcat(HDstrcat(t_link_path, "/"), targbuf);
} /* end else */
/* Create OBJ-XIDs for the parent and object */
xml_name_to_XID(t_obj_path, linkxid, (int)sizeof(linkxid), 1);
xml_name_to_XID(prefix, parentxid, (int)sizeof(parentxid), 1);
ctx.need_prefix = TRUE;
h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0);
/* Try to create an OBJ-XID for the object pointed to */
res = xml_name_to_XID(t_link_path, targetxid, (int)sizeof(targetxid), 0);
if (res == 0) {
/* target obj found */
ctx.need_prefix = TRUE;
h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0);
/* Render the element */
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "<%sExternalLink LinkName=\"%s\" "
"OBJ-XID=\"%s\" "
"H5SourcePath=\"%s\" "
"TargetFilename=\"%s\" "
"TargetPath=\"%s\" "
"Parents=\"%s\" H5ParentPaths=\"%s\" />",
xmlnsprefix,
t_name, /* LinkName */
linkxid, /* OBJ-XID */
t_obj_path, /* H5SourcePath */
filename, /* TargetFilename */
targname, /* TargetPath*/
parentxid, /* Parents */
t_prefix); /* H5ParentPaths */
h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0);
/* Render the element */
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "<%sSoftLink LinkName=\"%s\" "
"OBJ-XID=\"%s\" "
"H5SourcePath=\"%s\" "
"TargetPath=\"%s\" TargetObj=\"%s\" "
"Parents=\"%s\" H5ParentPaths=\"%s\" />",
xmlnsprefix,
t_name, /* LinkName */
linkxid, /* OBJ-XID */
t_obj_path, /* H5SourcePath */
t_targbuf, /* TargetPath */
targetxid, /* TargetObj */
parentxid, /* Parents */
t_prefix); /* H5ParentPaths */
h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0);
}
else {
/* dangling link -- omit from xml attributes */
ctx.need_prefix = TRUE;
h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0);
/* Render the element */
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "<%sSoftLink LinkName=\"%s\" "
"OBJ-XID=\"%s\" "
"H5SourcePath=\"%s\" "
"TargetPath=\"%s\" "
"Parents=\"%s\" H5ParentPaths=\"%s\" />",
xmlnsprefix,
t_name, /* LinkName */
linkxid, /* OBJ-XID */
t_obj_path, /* H5SourcePath */
t_targbuf, /* TargetPath */
parentxid, /* Parents */
t_prefix); /* H5ParentPaths */
h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0);
}
HDfree(t_prefix);
HDfree(t_name);
HDfree(t_filename);
HDfree(t_targname);
HDfree(t_targbuf);
HDfree(t_obj_path);
HDfree(t_link_path);
}
HDfree(targbuf);
}
break;
case H5L_TYPE_EXTERNAL:
if((targbuf = (char *)HDmalloc(linfo->u.val_size)) == NULL) {
error_msg("unable to allocate buffer\n");
h5tools_setstatus(EXIT_FAILURE);
ret = FAIL;
}
else {
if(H5Lget_val(group, name, targbuf, linfo->u.val_size, H5P_DEFAULT) < 0) {
error_msg("unable to get external link value\n");
h5tools_setstatus(EXIT_FAILURE);
ret = FAIL;
} /* end if */
else {
const char *filename;
const char *targname;
if(H5Lunpack_elink_val(targbuf, linfo->u.val_size, NULL, &filename, &targname) < 0) {
error_msg("unable to unpack external link value\n");
h5tools_setstatus(EXIT_FAILURE);
ret = FAIL;
} /* end if */
else {
char linkxid[100];
char parentxid[100];
char *t_name = xml_escape_the_name(name);
char *t_prefix = xml_escape_the_name(HDstrcmp(prefix,"") ? prefix : "/");
char *t_obj_path = xml_escape_the_name(obj_path);
char *t_filename = xml_escape_the_name(filename);
char *t_targname = xml_escape_the_name(targname);
/* Create OBJ-XIDs for the parent and object */
xml_name_to_XID(t_obj_path, linkxid, (int)sizeof(linkxid), 1);
xml_name_to_XID(prefix, parentxid, (int)sizeof(parentxid), 1);
ctx.need_prefix = TRUE;
h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0);
/* Render the element */
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "<%sExternalLink LinkName=\"%s\" "
"OBJ-XID=\"%s\" "
"H5SourcePath=\"%s\" "
"TargetFilename=\"%s\" "
"TargetPath=\"%s\" "
"Parents=\"%s\" H5ParentPaths=\"%s\" />",
xmlnsprefix,
t_name, /* LinkName */
linkxid, /* OBJ-XID */
t_obj_path, /* H5SourcePath */
filename, /* TargetFilename */
targname, /* TargetPath*/
parentxid, /* Parents */
t_prefix); /* H5ParentPaths */
h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0);
HDfree(t_prefix);
HDfree(t_name);
HDfree(t_filename);
HDfree(t_targname);
HDfree(t_obj_path);
} /* end else */
} /* end else */
} /* end else */
HDfree(targbuf);
HDfree(targbuf);
}
break;
case H5L_TYPE_ERROR:
case H5L_TYPE_MAX:
HDassert(0);
/* fall through */
case H5L_TYPE_HARD:
default:
{
@ -674,7 +684,6 @@ xml_escape_the_name(const char *str)
for (i = 0; i < len; i++) {
size_t esc_len;
HDassert(ncp_len);
if (*cp == '\'') {
HDstrncpy(ncp, apos, ncp_len);
esc_len = HDstrlen(apos);
@ -768,7 +777,6 @@ xml_escape_the_string(const char *str, int slen)
for (i = 0; i < len; i++) {
size_t esc_len;
HDassert(ncp_len);
if (*cp == '\\') {
*ncp++ = '\\';
*ncp = *cp;
@ -1514,8 +1522,6 @@ xml_print_datatype(hid_t type, unsigned in_group)
case H5T_NO_CLASS:
case H5T_NCLASSES:
HDassert(0);
/* fall through */
default:
ctx.need_prefix = TRUE;
h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0);
@ -1968,22 +1974,26 @@ xml_dump_data(hid_t obj_id, int obj_data, struct subset_t H5_ATTR_UNUSED * sset,
for (i = 0; i < ndims; i++)
nelmts *= size[i];
buf = HDmalloc((size_t)(nelmts * MAX(H5Tget_size(type), H5Tget_size(p_type))));
HDassert(buf);
if (H5Aread(obj_id, p_type, buf) >= 0) {
h5tools_context_t datactx;
HDmemset(&datactx, 0, sizeof(datactx));
datactx.need_prefix = TRUE;
datactx.indent_level = ctx.indent_level;
datactx.cur_column = ctx.cur_column;
status = h5tools_dump_mem(rawoutstream, outputformat, &datactx, obj_id, p_type, space, buf);
if((buf = HDmalloc((size_t)(nelmts * MAX(H5Tget_size(type), H5Tget_size(p_type))))) == NULL) {
error_msg("unable to allocate buffer\n");
h5tools_setstatus(EXIT_FAILURE);
status = FAIL;
}
/* Reclaim any VL memory, if necessary */
if (vl_data)
H5Dvlen_reclaim(p_type, space, H5P_DEFAULT, buf);
else {
if (H5Aread(obj_id, p_type, buf) >= 0) {
h5tools_context_t datactx;
HDmemset(&datactx, 0, sizeof(datactx));
datactx.need_prefix = TRUE;
datactx.indent_level = ctx.indent_level;
datactx.cur_column = ctx.cur_column;
status = h5tools_dump_mem(rawoutstream, outputformat, &datactx, obj_id, p_type, space, buf);
}
/* Reclaim any VL memory, if necessary */
if (vl_data)
H5Dvlen_reclaim(p_type, space, H5P_DEFAULT, buf);
HDfree(buf);
HDfree(buf);
}
}
H5Tclose(p_type);
H5Sclose(space);
@ -2239,8 +2249,6 @@ xml_dump_attr(hid_t attr, const char *attr_name, const H5A_info_t H5_ATTR_UNUSED
break;
case H5T_NO_CLASS:
case H5T_NCLASSES:
HDassert(0);
/* fall through */
default:
ctx.need_prefix = TRUE;
h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0);
@ -3672,8 +3680,6 @@ xml_dump_fill_value(hid_t dcpl, hid_t type)
break;
case H5T_NO_CLASS:
case H5T_NCLASSES:
HDassert(0);
/* fall through */
case H5T_STRING:
case H5T_REFERENCE:
default:
@ -3812,91 +3818,95 @@ xml_dump_dataset(hid_t did, const char *name, struct subset_t H5_ATTR_UNUSED * s
/* Print information about storage layout */
if (H5D_CHUNKED == H5Pget_layout(dcpl)) {
maxdims = H5Sget_simple_extent_ndims(space);
HDassert(maxdims >= 0);
chsize = (hsize_t *)HDmalloc((size_t)maxdims * sizeof(hsize_t));
ctx.indent_level++;
dump_indent += COL;
ctx.need_prefix = TRUE;
h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0);
/* Render the element */
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "<%sStorageLayout>", xmlnsprefix);
h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0);
ctx.indent_level++;
dump_indent += COL;
ctx.need_prefix = TRUE;
h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0);
/* Render the element */
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "<%sChunkedLayout ", xmlnsprefix);
ndims = H5Pget_chunk(dcpl, maxdims, chsize);
h5tools_str_append(&buffer, "Ndims=\"%d\">", ndims);
h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0);
ctx.indent_level++;
dump_indent += COL;
for (i = 0; i < ndims; i++) {
if((maxdims = H5Sget_simple_extent_ndims(space)) < 0) {
error_msg("unable to get maxdims\n");
h5tools_setstatus(EXIT_FAILURE);
}
else {
chsize = (hsize_t *)HDmalloc((size_t)maxdims * sizeof(hsize_t));
ctx.indent_level++;
dump_indent += COL;
ctx.need_prefix = TRUE;
h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0);
/* Render the element */
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "<%sChunkDimension DimSize=\"%" H5_PRINTF_LL_WIDTH "u\" />", xmlnsprefix, chsize[i]);
h5tools_str_append(&buffer, "<%sStorageLayout>", xmlnsprefix);
h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0);
ctx.indent_level++;
dump_indent += COL;
ctx.need_prefix = TRUE;
h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0);
/* Render the element */
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "<%sChunkedLayout ", xmlnsprefix);
ndims = H5Pget_chunk(dcpl, maxdims, chsize);
h5tools_str_append(&buffer, "Ndims=\"%d\">", ndims);
h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0);
ctx.indent_level++;
dump_indent += COL;
for (i = 0; i < ndims; i++) {
ctx.need_prefix = TRUE;
h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0);
/* Render the element */
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "<%sChunkDimension DimSize=\"%" H5_PRINTF_LL_WIDTH "u\" />", xmlnsprefix, chsize[i]);
h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0);
}
ctx.need_prefix = TRUE;
h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0);
/* Render the element */
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "<%sRequiredFilter>", xmlnsprefix);
h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0);
ctx.indent_level++;
dump_indent += COL;
check_filters(dcpl);
ctx.indent_level--;
dump_indent -= COL;
ctx.need_prefix = TRUE;
h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0);
/* Render the element */
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "</%sRequiredFilter>", xmlnsprefix);
h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0);
ctx.indent_level--;
dump_indent -= COL;
ctx.need_prefix = TRUE;
h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0);
/* Render the element */
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "</%sChunkedLayout>", xmlnsprefix);
h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0);
ctx.indent_level--;
dump_indent -= COL;
ctx.need_prefix = TRUE;
h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0);
/* Render the element */
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "</%sStorageLayout>", xmlnsprefix);
h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0);
ctx.indent_level--;
dump_indent -= COL;
HDfree(chsize);
}
ctx.need_prefix = TRUE;
h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0);
/* Render the element */
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "<%sRequiredFilter>", xmlnsprefix);
h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0);
ctx.indent_level++;
dump_indent += COL;
check_filters(dcpl);
ctx.indent_level--;
dump_indent -= COL;
ctx.need_prefix = TRUE;
h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0);
/* Render the element */
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "</%sRequiredFilter>", xmlnsprefix);
h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0);
ctx.indent_level--;
dump_indent -= COL;
ctx.need_prefix = TRUE;
h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0);
/* Render the element */
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "</%sChunkedLayout>", xmlnsprefix);
h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0);
ctx.indent_level--;
dump_indent -= COL;
ctx.need_prefix = TRUE;
h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0);
/* Render the element */
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "</%sStorageLayout>", xmlnsprefix);
h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0);
ctx.indent_level--;
dump_indent -= COL;
HDfree(chsize);
}
else if (H5D_CONTIGUOUS == H5Pget_layout(dcpl)) {
ctx.indent_level++;
@ -3984,8 +3994,6 @@ xml_dump_dataset(hid_t did, const char *name, struct subset_t H5_ATTR_UNUSED * s
h5tools_str_append(&buffer, "FillIfSet");
break;
case H5D_FILL_TIME_ERROR:
HDassert(0);
/* fall through */
default:
h5tools_str_append(&buffer, "?");
break;
@ -4005,8 +4013,6 @@ xml_dump_dataset(hid_t did, const char *name, struct subset_t H5_ATTR_UNUSED * s
break;
case H5D_ALLOC_TIME_DEFAULT:
case H5D_ALLOC_TIME_ERROR:
HDassert(0);
/* fall through */
default:
h5tools_str_append(&buffer, "?");
break;
@ -4233,9 +4239,6 @@ xml_dump_dataset(hid_t did, const char *name, struct subset_t H5_ATTR_UNUSED * s
break;
case H5T_NO_CLASS:
case H5T_NCLASSES:
HDassert(0);
/* fall through */
default:
ctx.need_prefix = TRUE;
h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0);

13
tools/src/h5jam/h5jam.c
View File

@ -73,13 +73,13 @@ usage (const char *prog)
HDfprintf (stdout,
"Adds user block to front of an HDF5 file and creates a new concatenated file.\n");
HDfprintf (stdout, "\n");
HDfprintf (stdout,
HDfprintf (stdout,
"OPTIONS\n");
HDfprintf (stdout,
HDfprintf (stdout,
" -i in_file.h5 Specifies the input HDF5 file.\n");
HDfprintf (stdout,
HDfprintf (stdout,
" -u in_user_file Specifies the file to be inserted into the user block.\n");
HDfprintf (stdout,
HDfprintf (stdout,
" Can be any file format except an HDF5 format.\n");
HDfprintf (stdout,
" -o out_file.h5 Specifies the output HDF5 file.\n");
@ -392,7 +392,7 @@ main (int argc, const char *argv[])
HDfree (input_file);
if(output_file)
HDfree (output_file);
if(ufid >= 0)
HDclose (ufid);
if(h5fid >= 0)
@ -548,7 +548,8 @@ write_pad(int ofile, hsize_t old_where, hsize_t *new_where)
char buf[1];
hsize_t psize;
HDassert(new_where);
if(new_where == NULL)
return FAIL;
buf[0] = '\0';

54
tools/src/h5jam/h5unjam.c
View File

@ -133,28 +133,28 @@ static int
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);
if (output_file)
h5tools_set_data_output_file(output_file, 1);
break;
if (output_file)
h5tools_set_data_output_file(output_file, 1);
break;
case 'i':
input_file = HDstrdup(opt_arg);
if (input_file)
h5tools_set_input_file(input_file, 1);
break;;
if (input_file)
h5tools_set_input_file(input_file, 1);
break;;
case 'u':
ub_file = HDstrdup(opt_arg);
if (ub_file)
h5tools_set_output_file(ub_file, 1);
else
rawoutstream = stdout;
if (ub_file)
h5tools_set_output_file(ub_file, 1);
else
rawoutstream = stdout;
break;
case 'd':
@ -180,7 +180,7 @@ parse_command_line(int argc, const char *argv[])
}
return EXIT_SUCCESS;
done:
if(input_file)
HDfree(input_file);
@ -240,7 +240,7 @@ main(int argc, const char *argv[])
h5tools_setstatus(EXIT_FAILURE);
goto done;
}
testval = H5Fis_hdf5(input_file);
if (testval <= 0) {
@ -272,10 +272,8 @@ main(int argc, const char *argv[])
goto done;
}
status = H5Pclose(plist);
HDassert(status >= 0);
status = H5Fclose(ifile);
HDassert(status >= 0);
H5Pclose(plist);
H5Fclose(ifile);
if (usize == 0) {
/* no user block to remove: message? */
@ -303,7 +301,7 @@ main(int argc, const char *argv[])
error_msg("unable to open output HDF5 file \"%s\"\n", input_file);
h5tools_setstatus(EXIT_FAILURE);
goto done;
}
}
/* copy from 0 to 'usize - 1' into ufid */
if (!do_delete) {
@ -321,18 +319,18 @@ main(int argc, const char *argv[])
h5tools_setstatus(EXIT_FAILURE);
goto done;
}
done:
if(input_file)
HDfree(input_file);
if(output_file)
HDfree(output_file);
if(ub_file) {
HDfree(ub_file);
}
h5tools_close();
return h5tools_getstatus();
@ -374,7 +372,7 @@ copy_to_file( FILE *infid, FILE *ofid, ssize_t _where, ssize_t show_much )
else
bytes_in = how_much;
/* Seek to correct position in input file */
/* Seek to correct position in input file */
HDfseek(infid, from, SEEK_SET);
/* Read data to buffer */
@ -396,11 +394,11 @@ copy_to_file( FILE *infid, FILE *ofid, ssize_t _where, ssize_t show_much )
to += (off_t)bytes_read;
/* Write nchars bytes to output file */
bytes_wrote = HDfwrite(buf, (size_t)1, bytes_read, ofid);
if(bytes_wrote != bytes_read || (0 == bytes_wrote && HDferror(ofid))) { /* error */
ret_value = -1;
goto done;
} /* end if */
bytes_wrote = HDfwrite(buf, (size_t)1, bytes_read, ofid);
if(bytes_wrote != bytes_read || (0 == bytes_wrote && HDferror(ofid))) { /* error */
ret_value = -1;
goto done;
} /* end if */
} /* end while */
done:

35
tools/src/h5ls/h5ls.c
View File

@ -1619,9 +1619,9 @@ list_attr(hid_t obj, const char *attr_name, const H5A_info_t H5_ATTR_UNUSED *ain
if(space_type != H5S_NULL && space_type != H5S_NO_CLASS) {
if(hexdump_g)
p_type = H5Tcopy(type);
p_type = H5Tcopy(type);
else
p_type = H5Tget_native_type(type, H5T_DIR_DEFAULT);
p_type = H5Tget_native_type(type, H5T_DIR_DEFAULT);
if(p_type >= 0) {
/* VL data special information */
@ -1631,23 +1631,22 @@ list_attr(hid_t obj, const char *attr_name, const H5A_info_t H5_ATTR_UNUSED *ain
if (h5tools_detect_vlen(p_type) == TRUE)
vl_data = TRUE;
temp_need= nelmts * MAX(H5Tget_size(type), H5Tget_size(p_type));
HDassert(temp_need == (hsize_t)((size_t)temp_need));
temp_need = nelmts * MAX(H5Tget_size(type), H5Tget_size(p_type));
need = (size_t)temp_need;
buf = HDmalloc(need);
HDassert(buf);
if(H5Aread(attr, p_type, buf) >= 0) {
ctx.need_prefix = TRUE;
ctx.indent_level = 2;
ctx.cur_column = (size_t)curr_pos;
h5tools_dump_mem(rawoutstream, info, &ctx, attr, p_type, space, buf);
if((buf = HDmalloc(need)) != NULL) {
if(H5Aread(attr, p_type, buf) >= 0) {
ctx.need_prefix = TRUE;
ctx.indent_level = 2;
ctx.cur_column = (size_t)curr_pos;
h5tools_dump_mem(rawoutstream, info, &ctx, attr, p_type, space, buf);
}
/* Reclaim any VL memory, if necessary */
if (vl_data)
H5Dvlen_reclaim(p_type, space, H5P_DEFAULT, buf);
HDfree(buf);
}
/* Reclaim any VL memory, if necessary */
if (vl_data)
H5Dvlen_reclaim(p_type, space, H5P_DEFAULT, buf);
HDfree(buf);
H5Tclose(p_type);
} /* end if */
}
@ -1875,7 +1874,7 @@ dataset_list2(hid_t dset, const char H5_ATTR_UNUSED *name)
case H5D_LAYOUT_ERROR:
case H5D_NLAYOUTS:
default:
HDassert(0);
h5tools_str_append(&buffer, "layout information not available");
break;
}
/* Print total raw storage size */

1
tools/src/h5repack/h5repack.c
View File

@ -262,7 +262,6 @@ hid_t copy_named_datatype(hid_t type_in, hid_t fidout,
/* Check if this type is the one requested */
if (oinfo.addr == dt->addr_in) {
HDassert(!dt_ret);
dt_ret = dt;
} /* end if */
} /* end if */

2
tools/src/h5repack/h5repack_copy.c
View File

@ -782,7 +782,6 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
switch (travt->objs[i].type) {
case H5TRAV_TYPE_UNKNOWN:
HDassert(0);
break;
/*-------------------------------------------------------------------------
@ -1486,7 +1485,6 @@ static int copy_user_block(const char *infile, const char *outfile, hsize_t size
int infid = -1, outfid = -1; /* File descriptors */
/* User block must be any power of 2 equal to 512 or greater (512, 1024, 2048, etc.) */
HDassert(size > 0);
/* Open files */
if ((infid = HDopen(infile, O_RDONLY)) < 0)

360
tools/src/h5repack/h5repack_filters.c
View File

@ -32,38 +32,33 @@
*
*-------------------------------------------------------------------------
*/
static int
aux_find_obj(const char* name, /* object name from traverse list */
pack_opt_t *options, /* repack options */
pack_info_t *obj /*OUT*/) /* info about object to filter */
static int aux_find_obj(const char* name, /* object name from traverse list */
pack_opt_t *options, /* repack options */
pack_info_t *obj /*OUT*/) /* info about object to filter */
{
char *pdest;
int result;
unsigned int i;
char *pdest;
int result;
unsigned int i;
for ( i=0; i<options->op_tbl->nelems; i++)
{
if (HDstrcmp(options->op_tbl->objs[i].path,name)==0)
{
*obj = options->op_tbl->objs[i];
return (int)i;
}
for (i = 0; i < options->op_tbl->nelems; i++) {
if (HDstrcmp(options->op_tbl->objs[i].path,name) == 0) {
*obj = options->op_tbl->objs[i];
return (int) i;
}
pdest = HDstrstr(name,options->op_tbl->objs[i].path);
result = (int)(pdest - name);
pdest = HDstrstr(name, options->op_tbl->objs[i].path);
result = (int) (pdest - name);
/* found at position 1, meaning without '/' */
if( pdest != NULL && result==1 )
{
*obj = options->op_tbl->objs[i];
return (int)i;
}
}/*i*/
/* found at position 1, meaning without '/' */
if (pdest != NULL && result == 1) {
*obj = options->op_tbl->objs[i];
return (int) i;
}
}/*i*/
return -1;
return -1;
}
/*-------------------------------------------------------------------------
* Function: aux_assign_obj
*
@ -74,35 +69,31 @@ aux_find_obj(const char* name, /* object name from traverse list */
*
*-------------------------------------------------------------------------
*/
static int
aux_assign_obj(const char* name, /* object name from traverse list */
pack_opt_t *options, /* repack options */
pack_info_t *obj /*OUT*/) /* info about object to filter */
static int aux_assign_obj(const char* name, /* object name from traverse list */
pack_opt_t *options, /* repack options */
pack_info_t *obj /*OUT*/) /* info about object to filter */
{
int idx, i;
int idx, i;
pack_info_t tmp;
init_packobject(&tmp);
idx = aux_find_obj(name,options,&tmp);
idx = aux_find_obj(name, options, &tmp);
/* name was on input */
if (idx>=0)
{
if (idx >= 0) {
/* applying to all objects */
if (options->all_layout)
{
if (options->all_layout) {
/* assign the global layout info to the OBJ info */
tmp.layout=options->layout_g;
switch (options->layout_g)
{
tmp.layout = options->layout_g;
switch (options->layout_g) {
case H5D_CHUNKED:
tmp.chunk.rank=options->chunk_g.rank;
for ( i=0; i<tmp.chunk.rank; i++)
tmp.chunk.chunk_lengths[i]=options->chunk_g.chunk_lengths[i];
tmp.chunk.rank = options->chunk_g.rank;
for (i = 0; i < tmp.chunk.rank; i++)
tmp.chunk.chunk_lengths[i] =
options->chunk_g.chunk_lengths[i];
break;
case H5D_LAYOUT_ERROR:
case H5D_COMPACT:
@ -114,15 +105,14 @@ aux_assign_obj(const char* name, /* object name from traverse list */
break;
}/*switch*/
}
else
{
else {
tmp.layout = options->op_tbl->objs[idx].layout;
switch (tmp.layout)
{
switch (tmp.layout) {
case H5D_CHUNKED:
tmp.chunk.rank = options->op_tbl->objs[idx].chunk.rank;
for ( i=0; i<tmp.chunk.rank; i++)
tmp.chunk.chunk_lengths[i]=options->op_tbl->objs[idx].chunk.chunk_lengths[i];
for (i = 0; i < tmp.chunk.rank; i++)
tmp.chunk.chunk_lengths[i] =
options->op_tbl->objs[idx].chunk.chunk_lengths[i];
break;
case H5D_LAYOUT_ERROR:
case H5D_COMPACT:
@ -137,49 +127,37 @@ aux_assign_obj(const char* name, /* object name from traverse list */
}
/* applying to all objects */
if (options->all_filter)
{
if (options->all_filter) {
/* assign the global filter */
tmp.nfilters=1;
tmp.filter[0]=options->filter_g[0];
tmp.nfilters = 1;
tmp.filter[0] = options->filter_g[0];
} /* if all */
else
{
tmp.nfilters=options->op_tbl->objs[idx].nfilters;
for ( i=0; i<tmp.nfilters; i++)
{
else {
tmp.nfilters = options->op_tbl->objs[idx].nfilters;
for (i = 0; i < tmp.nfilters; i++) {
tmp.filter[i] = options->op_tbl->objs[idx].filter[i];
}
}
} /* if idx */
/* no input name */
else
{
if (options->all_filter)
{
else {
if (options->all_filter) {
int k;
/* assign the global filters */
tmp.nfilters=options->n_filter_g;
for ( k = 0; k < options->n_filter_g; k++)
tmp.filter[k]=options->filter_g[k];
tmp.nfilters = options->n_filter_g;
for (k = 0; k < options->n_filter_g; k++)
tmp.filter[k] = options->filter_g[k];
}
if (options->all_layout)
{
if (options->all_layout) {
/* assign the global layout info to the OBJ info */
tmp.layout=options->layout_g;
switch (options->layout_g)
{
tmp.layout = options->layout_g;
switch (options->layout_g) {
case H5D_CHUNKED:
tmp.chunk.rank=options->chunk_g.rank;
for ( i=0; i<tmp.chunk.rank; i++)
tmp.chunk.chunk_lengths[i]=options->chunk_g.chunk_lengths[i];
tmp.chunk.rank = options->chunk_g.rank;
for (i = 0; i < tmp.chunk.rank; i++)
tmp.chunk.chunk_lengths[i] =
options->chunk_g.chunk_lengths[i];
break;
case H5D_LAYOUT_ERROR:
case H5D_COMPACT:
@ -195,10 +173,8 @@ aux_assign_obj(const char* name, /* object name from traverse list */
*obj = tmp;
return 1;
}
/*-------------------------------------------------------------------------
* Function: apply_filters
*
@ -215,74 +191,69 @@ aux_assign_obj(const char* name, /* object name from traverse list */
*-------------------------------------------------------------------------
*/
int apply_filters(const char* name, /* object name from traverse list */
int rank, /* rank of dataset */
hsize_t *dims, /* dimensions of dataset */
size_t msize, /* size of type */
hid_t dcpl_id, /* dataset creation property list */
pack_opt_t *options, /* repack options */
int *has_filter) /* (OUT) object NAME has a filter */
int apply_filters(const char* name, /* object name from traverse list */
int rank, /* rank of dataset */
hsize_t *dims, /* dimensions of dataset */
size_t msize, /* size of type */
hid_t dcpl_id, /* dataset creation property list */
pack_opt_t *options, /* repack options */
int *has_filter) /* (OUT) object NAME has a filter */
{
int nfilters; /* number of filters in DCPL */
hsize_t chsize[64]; /* chunk size in elements */
int nfilters; /* number of filters in DCPL */
hsize_t chsize[64]; /* chunk size in elements */
H5D_layout_t layout;
int i;
pack_info_t obj;
int i;
pack_info_t obj;
*has_filter = 0;
if (rank==0) /* scalar dataset, do not apply */
if (rank == 0) /* scalar dataset, do not apply */
return 0;
/*-------------------------------------------------------------------------
/*-------------------------------------------------------------------------
* initialize the assigment object
*-------------------------------------------------------------------------
*/
init_packobject(&obj);
/*-------------------------------------------------------------------------
/*-------------------------------------------------------------------------
* find options
*-------------------------------------------------------------------------
*/
if (aux_assign_obj(name,options,&obj)==0)
if (aux_assign_obj(name, options, &obj) == 0)
return 0;
/* get information about input filters */
if ((nfilters = H5Pget_nfilters(dcpl_id))<0)
if ((nfilters = H5Pget_nfilters(dcpl_id)) < 0)
return -1;
/*-------------------------------------------------------------------------
/*-------------------------------------------------------------------------
* check if we have filters in the pipeline
* we want to replace them with the input filters
* only remove if we are inserting new ones
*-------------------------------------------------------------------------
*/
if (nfilters && obj.nfilters )
{
if (nfilters && obj.nfilters) {
*has_filter = 1;
if (H5Premove_filter(dcpl_id,H5Z_FILTER_ALL)<0)
if (H5Premove_filter(dcpl_id, H5Z_FILTER_ALL) < 0)
return -1;
}
/*-------------------------------------------------------------------------
/*-------------------------------------------------------------------------
* check if there is an existent chunk
* read it only if there is not a requested layout
*-------------------------------------------------------------------------
*/
if (obj.layout == -1 )
{
if ((layout = H5Pget_layout(dcpl_id))<0)
if (obj.layout == -1) {
if ((layout = H5Pget_layout(dcpl_id)) < 0)
return -1;
if (layout == H5D_CHUNKED)
{
if ((rank = H5Pget_chunk(dcpl_id,NELMTS(chsize),chsize/*out*/))<0)
if (layout == H5D_CHUNKED) {
if ((rank = H5Pget_chunk(dcpl_id, NELMTS(chsize), chsize/*out*/)) < 0)
return -1;
obj.layout = H5D_CHUNKED;
obj.chunk.rank = rank;
for ( i = 0; i < rank; i++)
for (i = 0; i < rank; i++)
obj.chunk.chunk_lengths[i] = chsize[i];
}
}
@ -300,19 +271,15 @@ int apply_filters(const char* name, /* object name from traverse list */
*-------------------------------------------------------------------------
*/
if (obj.nfilters)
{
/*-------------------------------------------------------------------------
* filters require CHUNK layout; if we do not have one define a default
*-------------------------------------------------------------------------
*/
if (obj.layout==-1)
{
if (obj.nfilters) {
/*-------------------------------------------------------------------------
* filters require CHUNK layout; if we do not have one define a default
*-------------------------------------------------------------------------
*/
if (obj.layout == -1) {
/* stripmine info */
hsize_t sm_size[H5S_MAX_RANK]; /*stripmine size */
hsize_t sm_nbytes; /*bytes per stripmine */
hsize_t sm_nbytes; /*bytes per stripmine */
obj.chunk.rank = rank;
@ -321,138 +288,129 @@ int apply_filters(const char* name, /* object name from traverse list */
* a hyperslab whose size is manageable.
*/
sm_nbytes = msize;
for ( i = rank; i > 0; --i)
{
for (i = rank; i > 0; --i) {
hsize_t size = H5TOOLS_BUFSIZE / sm_nbytes;
if ( size == 0) /* datum size > H5TOOLS_BUFSIZE */
if (size == 0) /* datum size > H5TOOLS_BUFSIZE */
size = 1;
sm_size[i - 1] = MIN(dims[i - 1], size);
sm_nbytes *= sm_size[i - 1];
HDassert(sm_nbytes > 0);
}
for ( i = 0; i < rank; i++)
{
for (i = 0; i < rank; i++) {
obj.chunk.chunk_lengths[i] = sm_size[i];
}
}
for ( i=0; i<obj.nfilters; i++)
{
switch (obj.filter[i].filtn)
{
for (i = 0; i < obj.nfilters; i++) {
switch (obj.filter[i].filtn) {
/*-------------------------------------------------------------------------
* H5Z_FILTER_NONE 0 , uncompress if compressed
*-------------------------------------------------------------------------
*/
case H5Z_FILTER_NONE:
break;
/*-------------------------------------------------------------------------
* H5Z_FILTER_DEFLATE 1 , deflation like gzip
* H5Z_FILTER_NONE 0 , uncompress if compressed
*-------------------------------------------------------------------------
*/
case H5Z_FILTER_NONE:
break;
/*-------------------------------------------------------------------------
* H5Z_FILTER_DEFLATE 1 , deflation like gzip
*-------------------------------------------------------------------------
*/
case H5Z_FILTER_DEFLATE:
{
unsigned aggression; /* the deflate level */
unsigned aggression; /* the deflate level */
aggression = obj.filter[i].cd_values[0];
/* set up for deflated data */
if(H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths)<0)
if (H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths) < 0)
return -1;
if(H5Pset_deflate(dcpl_id,aggression)<0)
if (H5Pset_deflate(dcpl_id, aggression) < 0)
return -1;
}
break;
/*-------------------------------------------------------------------------
* H5Z_FILTER_SZIP 4 , szip compression
*-------------------------------------------------------------------------
*/
/*-------------------------------------------------------------------------
* H5Z_FILTER_SZIP 4 , szip compression
*-------------------------------------------------------------------------
*/
case H5Z_FILTER_SZIP:
{
unsigned options_mask;
unsigned pixels_per_block;
unsigned options_mask;
unsigned pixels_per_block;
options_mask = obj.filter[i].cd_values[0];
options_mask = obj.filter[i].cd_values[0];
pixels_per_block = obj.filter[i].cd_values[1];
/* set up for szip data */
if(H5Pset_chunk(dcpl_id,obj.chunk.rank,obj.chunk.chunk_lengths)<0)
if (H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths) < 0)
return -1;
if (H5Pset_szip(dcpl_id,options_mask,pixels_per_block)<0)
if (H5Pset_szip(dcpl_id, options_mask, pixels_per_block) < 0)
return -1;
}
break;
/*-------------------------------------------------------------------------
* H5Z_FILTER_SHUFFLE 2 , shuffle the data
*-------------------------------------------------------------------------
*/
/*-------------------------------------------------------------------------
* H5Z_FILTER_SHUFFLE 2 , shuffle the data
*-------------------------------------------------------------------------
*/
case H5Z_FILTER_SHUFFLE:
if(H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths)<0)
if (H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths) < 0)
return -1;
if (H5Pset_shuffle(dcpl_id)<0)
if (H5Pset_shuffle(dcpl_id) < 0)
return -1;
break;
/*-------------------------------------------------------------------------
* H5Z_FILTER_FLETCHER32 3 , fletcher32 checksum of EDC
*-------------------------------------------------------------------------
*/
/*-------------------------------------------------------------------------
* H5Z_FILTER_FLETCHER32 3 , fletcher32 checksum of EDC
*-------------------------------------------------------------------------
*/
case H5Z_FILTER_FLETCHER32:
if(H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths)<0)
if (H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths) < 0)
return -1;
if (H5Pset_fletcher32(dcpl_id)<0)
if (H5Pset_fletcher32(dcpl_id) < 0)
return -1;
break;
/*----------- -------------------------------------------------------------
* H5Z_FILTER_NBIT , NBIT compression
*-------------------------------------------------------------------------
*/
/*----------- -------------------------------------------------------------
* H5Z_FILTER_NBIT , NBIT compression
*-------------------------------------------------------------------------
*/
case H5Z_FILTER_NBIT:
if(H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths)<0)
if (H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths) < 0)
return -1;
if (H5Pset_nbit(dcpl_id)<0)
if (H5Pset_nbit(dcpl_id) < 0)
return -1;
break;
/*----------- -------------------------------------------------------------
* H5Z_FILTER_SCALEOFFSET , scale+offset compression
*-------------------------------------------------------------------------
*/
/*----------- -------------------------------------------------------------
* H5Z_FILTER_SCALEOFFSET , scale+offset compression
*-------------------------------------------------------------------------
*/
case H5Z_FILTER_SCALEOFFSET:
{
H5Z_SO_scale_type_t scale_type;
int scale_factor;
int scale_factor;
scale_type = (H5Z_SO_scale_type_t)obj.filter[i].cd_values[0];
scale_factor = (int)obj.filter[i].cd_values[1];
scale_type = (H5Z_SO_scale_type_t) obj.filter[i].cd_values[0];
scale_factor = (int) obj.filter[i].cd_values[1];
if(H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths)<0)
if (H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths) < 0)
return -1;
if (H5Pset_scaleoffset(dcpl_id,scale_type,scale_factor)<0)
if (H5Pset_scaleoffset(dcpl_id, scale_type, scale_factor) < 0)
return -1;
}
break;
default:
{
if (H5Pset_filter (dcpl_id, obj.filter[i].filtn, H5Z_FLAG_MANDATORY, obj.filter[i].cd_nelmts, obj.filter[i].cd_values)<0)
return -1;
if(H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths)<0)
return -1;
}
{
if (H5Pset_filter(dcpl_id, obj.filter[i].filtn,
H5Z_FLAG_MANDATORY, obj.filter[i].cd_nelmts,
obj.filter[i].cd_values) < 0)
return -1;
if (H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths) < 0)
return -1;
}
break;
} /* switch */
}/*i*/
}
/*obj.nfilters*/
@ -461,31 +419,27 @@ int apply_filters(const char* name, /* object name from traverse list */
*-------------------------------------------------------------------------
*/
if (obj.layout>=0)
{
if (obj.layout >= 0) {
/* a layout was defined */
if (H5Pset_layout(dcpl_id, obj.layout)<0)
if (H5Pset_layout(dcpl_id, obj.layout) < 0)
return -1;
if (H5D_CHUNKED == obj.layout)
{
if(H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths)<0)
if (H5D_CHUNKED == obj.layout) {
if (H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths) < 0)
return -1;
}
else if (H5D_COMPACT == obj.layout)
{
if (H5Pset_alloc_time(dcpl_id, H5D_ALLOC_TIME_EARLY)<0)
else if (H5D_COMPACT == obj.layout) {
if (H5Pset_alloc_time(dcpl_id, H5D_ALLOC_TIME_EARLY) < 0)
return -1;
}
/* remove filters for the H5D_CONTIGUOUS case */
else if (H5D_CONTIGUOUS == obj.layout)
{
if (H5Premove_filter(dcpl_id,H5Z_FILTER_ALL)<0)
else if (H5D_CONTIGUOUS == obj.layout) {
if (H5Premove_filter(dcpl_id, H5Z_FILTER_ALL) < 0)
return -1;
}
}
return 0;
return 0;
}

8
tools/src/h5repack/h5repack_refs.c
View File

@ -189,8 +189,7 @@ int do_copy_refobjs(hid_t fidin,
/* create the reference, -1 parameter for objects */
if(H5Rcreate(&refbuf[u], fidout, refname, H5R_OBJECT, (hid_t)-1) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Rcreate failed");
if(options->verbose)
{
if(options->verbose) {
printf(FORMAT_OBJ,"dset",travt->objs[i].name );
printf("object <%s> object reference created to <%s>\n",
travt->objs[i].name,
@ -278,8 +277,7 @@ int do_copy_refobjs(hid_t fidin,
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Rcreate failed");
if(H5Sclose(region_id) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed");
if(options->verbose)
{
if(options->verbose) {
printf(FORMAT_OBJ,"dset",travt->objs[i].name );
printf("object <%s> region reference created to <%s>\n",
travt->objs[i].name,
@ -320,8 +318,6 @@ int do_copy_refobjs(hid_t fidin,
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed");
} /* end else */
HDassert(dset_out != FAIL);
/*-------------------------------------------------------------------------
* copy referenced objects in attributes
*-------------------------------------------------------------------------