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[svn-r15886] Purpose: Close bug 1332

Browse Source 
Description: Improved external link traversal of h5dump.  h5dump will now
    properly avoid all cycles, even those spanning multiple files.  Improvement
    to the output of committed datatypes.  Committed datatypes are now checked
    for uniqueness (like other objects).  Tests added for these cases.

Tested: kagiso, linew, smirom (h5committest)
This commit is contained in:
Neil Fortner 2008-10-15 22:52:16 -05:00
parent 273f31211e
commit ad28fa5b0c
24 changed files with 539 additions and 105 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

3
MANIFEST
View File

@ -1154,6 +1154,9 @@
./tools/testfiles/textlink.h5
./tools/testfiles/textlink.h5.xml
./tools/testfiles/textlink-1.ls
./tools/testfiles/textlinkfar.ddl
./tools/testfiles/textlinkfar.h5
./tools/testfiles/textlinksrc.ddl
./tools/testfiles/textlinksrc.h5
./tools/testfiles/textlinksrc-1.ls
./tools/testfiles/textlinksrc-2.ls

4
release_docs/RELEASE.txt
View File

@ -175,6 +175,10 @@ Bug Fixes since HDF5-1.8.0 release
Tools
-----
- h5dump now checks for uniqueness of committed datatypes.
(NAF - 2008/10/15)
- Fixed unnecessary indentation of committed datatypes in h5dump.
(NAF - 2008/10/15)
- Fixed bugs in h5stat:segmemtation fault when printing groups and
print warning message when traversal of objects is unsuccessful.
(see bug #1253) (VC- 2008/10/13)

394
tools/h5dump/h5dump.c
View File

@ -55,9 +55,24 @@ const char *progname = "h5dump";
#define H5_SZIP_MSB_OPTION_MASK 16
#define H5_SZIP_RAW_OPTION_MASK 128
/* List of table structures. There is one table structure for each file */
typedef struct h5dump_table_list_t {
size_t nalloc;
size_t nused;
struct {
unsigned long fileno; /* File number that these tables refer to */
hid_t oid; /* ID of an object in this file, held open so fileno is consistent */
table_t *group_table; /* Table of groups */
table_t *dset_table; /* Table of datasets */
table_t *type_table; /* Table of datatypes */
} *tables;
} h5dump_table_list_t;
int d_status = EXIT_SUCCESS;
static int unamedtype = 0; /* shared datatype with no name */
static h5dump_table_list_t table_list = {0, 0, NULL};
static table_t *group_table = NULL, *dset_table = NULL, *type_table = NULL;
static hbool_t hit_elink = FALSE; /* whether we have traversed an external link */
static size_t prefix_len = 1024;
static char *prefix;
static const char *driver = NULL; /* The driver to open the file with. */
@ -106,7 +121,7 @@ static void init_prefix(char **prfx, size_t prfx_len);
static void add_prefix(char **prfx, size_t *prfx_len, const char *name);
/* callback function used by H5Literate() */
static herr_t dump_all_cb(hid_t group, const char *name, const H5L_info_t *linfo, void *op_data);
static int dump_extlink(const char *filename, const char *targname);
static int dump_extlink(hid_t group, const char *linkname, const char *objname);
static h5tool_format_t dataformat = {
@ -359,7 +374,7 @@ static char *xml_escape_the_name(const char *);
/* a structure for handling the order command-line parameters come in */
struct handler_t {
void (*func)(hid_t, const char *, void *, int);
void (*func)(hid_t, const char *, void *, int, const char *);
char *obj;
struct subset_t *subset_info;
};
@ -690,6 +705,126 @@ usage(const char *prog)
fprintf(stdout, "\n");
}
/*-------------------------------------------------------------------------
* Function: table_list_add
*
* Purpose: Add a new set of tables
*
* Return: index of added table on success, -1 on failure
*
* Programmer: Neil Fortner, nfortne2@hdfgroup.org
* Adapted from trav_addr_add in h5trav.c by Quincey Koziol
*
* Date: October 13, 2008
*
*-------------------------------------------------------------------------
*/
static ssize_t
table_list_add(hid_t oid, unsigned long file_no)
{
size_t idx; /* Index of table to use */
find_objs_t info;
void *tmp_ptr;
/* Allocate space if necessary */
if(table_list.nused == table_list.nalloc) {
table_list.nalloc = MAX(1, table_list.nalloc * 2);
if(NULL == (tmp_ptr = HDrealloc(table_list.tables, table_list.nalloc * sizeof(table_list.tables[0]))))
return -1;
table_list.tables = tmp_ptr;
} /* end if */
/* Append it */
idx = table_list.nused++;
table_list.tables[idx].fileno = file_no;
table_list.tables[idx].oid = oid;
if(H5Iinc_ref(oid) < 0) {
table_list.nused--;
return -1;
}
if(init_objs(oid, &info, &table_list.tables[idx].group_table,
&table_list.tables[idx].dset_table, &table_list.tables[idx].type_table) < 0) {
H5Idec_ref(oid);
table_list.nused--;
return -1;
}
#ifdef H5DUMP_DEBUG
dump_tables(&info);
#endif /* H5DUMP_DEBUG */
return((ssize_t) idx);
} /* end table_list_add() */
/*-------------------------------------------------------------------------
* Function: table_list_visited
*
* Purpose: Check if a table already exists for the specified fileno
*
* Return: The index of the matching table, or -1 if no matches found
*
* Programmer: Neil Fortner, nfortne2@hdfgroup.org
* Adapted from trav_addr_visited in h5trav.c by Quincey Koziol
*
* Date: October 13, 2008
*
*-------------------------------------------------------------------------
*/
static ssize_t
table_list_visited(unsigned long file_no)
{
size_t u; /* Local index variable */
/* Look for table */
for(u = 0; u < table_list.nused; u++)
/* Check for fileno value already in array */
if(table_list.tables[u].fileno == file_no)
return((ssize_t) u);
/* Didn't find table */
return(-1);
} /* end table_list_visited() */
/*-------------------------------------------------------------------------
* Function: table_list_free
*
* Purpose: Frees the table list
*
* Return: void
*
* Programmer: Neil Fortner, nfortne2@hdfgroup.org
*
* Date: October 13, 2008
*
*-------------------------------------------------------------------------
*/
static void
table_list_free(void)
{
size_t u; /* Local index variable */
/* Iterate over tables */
for(u = 0; u < table_list.nused; u++) {
/* Release object id */
if(H5Idec_ref(table_list.tables[u].oid) < 0)
d_status = EXIT_FAILURE;
/* Free each table */
free_table(table_list.tables[u].group_table);
free_table(table_list.tables[u].dset_table);
free_table(table_list.tables[u].type_table);
}
/* Free the table list */
HDfree(table_list.tables);
table_list.tables = NULL;
table_list.nalloc = table_list.nused = 0;
} /* end table_list_free() */
/*-------------------------------------------------------------------------
* Function: print_datatype
*
@ -1443,7 +1578,7 @@ dump_all_cb(hid_t group, const char *name, const H5L_info_t *linfo, void UNUSED
case H5O_TYPE_DATASET:
if((obj = H5Dopen2(group, name, H5P_DEFAULT)) >= 0) {
if(oinfo.rc > 1) {
if(oinfo.rc > 1 || hit_elink) {
obj_t *found_obj; /* Found object */
found_obj = search_obj(dset_table, oinfo.addr);
@ -1479,6 +1614,7 @@ dump_all_cb(hid_t group, const char *name, const H5L_info_t *linfo, void UNUSED
char *t_obj_path = xml_escape_the_name(obj_path);
char *t_prefix = xml_escape_the_name(HDstrcmp(prefix,"") ? prefix : "/");
char *t_name = xml_escape_the_name(name);
char *t_objname = xml_escape_the_name(found_obj->objname);
char dsetxid[100];
char parentxid[100];
char pointerxid[100];
@ -1501,13 +1637,14 @@ dump_all_cb(hid_t group, const char *name, const H5L_info_t *linfo, void UNUSED
xml_name_to_XID(found_obj->objname, pointerxid, sizeof(pointerxid), 1);
printf("<%sDatasetPtr OBJ-XID=\"%s\" H5Path=\"%s\"/>\n",
xmlnsprefix,
pointerxid,t_obj_path);
pointerxid,t_objname);
indentation(indent);
printf("</%sDataset>\n", xmlnsprefix);
HDfree(t_name);
HDfree(t_obj_path);
HDfree(t_prefix);
HDfree(t_objname);
}
H5Dclose(obj);
@ -1672,7 +1809,7 @@ dump_all_cb(hid_t group, const char *name, const H5L_info_t *linfo, void UNUSED
/* dump the external link */
dump_extlink(filename,targname);
dump_extlink(group, name, targname);
} /* end if */
@ -1786,7 +1923,7 @@ done:
static void
dump_named_datatype(hid_t tid, const char *name)
{
H5O_info_t oinfo;
unsigned attr_crt_order_flags;
hid_t tcpl_id; /* datatype creation property list ID */
@ -1814,13 +1951,33 @@ dump_named_datatype(hid_t tid, const char *name)
printf("%s \"%s\" %s", dump_header_format->datatypebegin, name,
dump_header_format->datatypeblockbegin);
if(H5Tget_class(tid) == H5T_COMPOUND)
print_datatype(tid, 1);
else {
indentation(indent + COL);
print_datatype(tid, 1);
H5Oget_info(tid, &oinfo);
/* Must check for uniqueness of all objects if we've traversed an elink,
* otherwise only check if the reference count > 1.
*/
if(oinfo.rc > 1 || hit_elink) {
obj_t *found_obj; /* Found object */
found_obj = search_obj(type_table, oinfo.addr);
if (found_obj == NULL) {
error_msg(progname, "internal error (file %s:line %d)\n",
__FILE__, __LINE__);
d_status = EXIT_FAILURE;
goto done;
}
else if (found_obj->displayed) {
printf("%s \"%s\"\n", HARDLINK, found_obj->objname);
goto done;
}
else
found_obj->displayed = TRUE;
} /* end if */
print_datatype(tid, 1);
if(H5Tget_class(tid) != H5T_COMPOUND)
printf(";\n");
} /* end else */
/* print attributes */
indent += COL;
@ -1834,6 +1991,8 @@ dump_named_datatype(hid_t tid, const char *name)
H5Aiterate2(tid, H5_INDEX_NAME, sort_order, NULL, dump_attr_cb, NULL);
indent -= COL;
done:
end_obj(dump_header_format->datatypeend,
dump_header_format->datatypeblockend);
}
@ -1921,7 +2080,10 @@ dump_group(hid_t gid, const char *name)
H5Oget_info(gid, &oinfo);
if(oinfo.rc > 1) {
/* Must check for uniqueness of all objects if we've traversed an elink,
* otherwise only check if the reference count > 1.
*/
if(oinfo.rc > 1 || hit_elink) {
obj_t *found_obj; /* Found object */
found_obj = search_obj(group_table, oinfo.addr);
@ -3149,7 +3311,7 @@ set_sort_order(const char *form)
*-------------------------------------------------------------------------
*/
static void
handle_attributes(hid_t fid, const char *attr, void UNUSED * data, int pe)
handle_attributes(hid_t fid, const char *attr, void UNUSED * data, int UNUSED pe, const char UNUSED *display_name)
{
dump_selected_attr(fid, attr);
}
@ -3301,20 +3463,21 @@ parse_subset_params(char *dset)
*-------------------------------------------------------------------------
*/
static void
handle_datasets(hid_t fid, const char *dset, void *data, int pe)
handle_datasets(hid_t fid, const char *dset, void *data, int pe, const char *display_name)
{
H5O_info_t oinfo;
hid_t dsetid;
struct subset_t *sset = (struct subset_t *)data;
const char *real_name = display_name ? display_name : dset;
if((dsetid = H5Dopen2(fid, dset, H5P_DEFAULT)) < 0)
{
if (pe)
{
begin_obj(dump_header_format->datasetbegin, dset,
begin_obj(dump_header_format->datasetbegin, real_name,
dump_header_format->datasetblockbegin);
indentation(COL);
error_msg(progname, "unable to open dataset \"%s\"\n", dset);
error_msg(progname, "unable to open dataset \"%s\"\n", real_name);
end_obj(dump_header_format->datasetend,
dump_header_format->datasetblockend);
d_status = EXIT_FAILURE;
@ -3407,14 +3570,15 @@ handle_datasets(hid_t fid, const char *dset, void *data, int pe)
}
H5Oget_info(dsetid, &oinfo);
if(oinfo.rc > 1) {
if(oinfo.rc > 1 || hit_elink) {
obj_t *found_obj; /* Found object */
found_obj = search_obj(dset_table, oinfo.addr);
if(found_obj) {
if (found_obj->displayed) {
begin_obj(dump_header_format->datasetbegin, dset,
indentation(indent);
begin_obj(dump_header_format->datasetbegin, real_name,
dump_header_format->datasetblockbegin);
indentation(indent + COL);
printf("%s \"%s\"\n", HARDLINK, found_obj->objname);
@ -3423,14 +3587,14 @@ handle_datasets(hid_t fid, const char *dset, void *data, int pe)
dump_header_format->datasetblockend);
} else {
found_obj->displayed = TRUE;
dump_dataset(dsetid, dset, sset);
dump_dataset(dsetid, real_name, sset);
}
}
else
d_status = EXIT_FAILURE;
}
else
dump_dataset(dsetid, dset, sset);
dump_dataset(dsetid, real_name, sset);
if(H5Dclose(dsetid) < 0)
d_status = EXIT_FAILURE;
@ -3459,18 +3623,19 @@ handle_datasets(hid_t fid, const char *dset, void *data, int pe)
*-------------------------------------------------------------------------
*/
static void
handle_groups(hid_t fid, const char *group, void UNUSED * data, int pe)
handle_groups(hid_t fid, const char *group, void UNUSED * data, int pe, const char * display_name)
{
hid_t gid;
hid_t gid;
const char *real_name = display_name ? display_name : group;
if((gid = H5Gopen2(fid, group, H5P_DEFAULT)) < 0)
{
if ( pe )
{
begin_obj(dump_header_format->groupbegin, group, dump_header_format->groupblockbegin);
begin_obj(dump_header_format->groupbegin, real_name, dump_header_format->groupblockbegin);
indentation(COL);
error_msg(progname, "unable to open group \"%s\"\n", group);
error_msg(progname, "unable to open group \"%s\"\n", real_name);
end_obj(dump_header_format->groupend, dump_header_format->groupblockend);
d_status = EXIT_FAILURE;
}
@ -3488,7 +3653,7 @@ handle_groups(hid_t fid, const char *group, void UNUSED * data, int pe)
HDstrcpy(prefix, group);
dump_group(gid, group);
dump_group(gid, real_name);
if(H5Gclose(gid) < 0)
d_status = EXIT_FAILURE;
@ -3510,7 +3675,7 @@ handle_groups(hid_t fid, const char *group, void UNUSED * data, int pe)
*-------------------------------------------------------------------------
*/
static void
handle_links(hid_t fid, const char *links, void UNUSED * data, int pe)
handle_links(hid_t fid, const char *links, void UNUSED * data, int UNUSED pe, const char UNUSED *display_name)
{
H5L_info_t linfo;
@ -3602,9 +3767,10 @@ handle_links(hid_t fid, const char *links, void UNUSED * data, int pe)
*-------------------------------------------------------------------------
*/
static void
handle_datatypes(hid_t fid, const char *type, void UNUSED * data, int pe)
handle_datatypes(hid_t fid, const char *type, void UNUSED * data, int pe, const char *display_name)
{
hid_t type_id;
const char *real_name = display_name ? display_name : type;
if((type_id = H5Topen2(fid, type, H5P_DEFAULT)) < 0)
{
@ -3619,7 +3785,7 @@ handle_datatypes(hid_t fid, const char *type, void UNUSED * data, int pe)
/* unamed datatype */
sprintf(name, "/#"H5_PRINTF_HADDR_FMT, type_table->objs[idx].objno);
if(!HDstrcmp(name, type))
if(!HDstrcmp(name, real_name))
break;
} /* end if */
@ -3631,10 +3797,10 @@ handle_datatypes(hid_t fid, const char *type, void UNUSED * data, int pe)
if ( pe )
{
/* unknown type */
begin_obj(dump_header_format->datatypebegin, type,
begin_obj(dump_header_format->datatypebegin, real_name,
dump_header_format->datatypeblockbegin);
indentation(COL);
error_msg(progname, "unable to open datatype \"%s\"\n", type);
error_msg(progname, "unable to open datatype \"%s\"\n", real_name);
end_obj(dump_header_format->datatypeend,
dump_header_format->datatypeblockend);
d_status = EXIT_FAILURE;
@ -3645,14 +3811,14 @@ handle_datatypes(hid_t fid, const char *type, void UNUSED * data, int pe)
{
hid_t dsetid = H5Dopen2(fid, type_table->objs[idx].objname, H5P_DEFAULT);
type_id = H5Dget_type(dsetid);
dump_named_datatype(type_id, type);
dump_named_datatype(type_id, real_name);
H5Tclose(type_id);
H5Dclose(dsetid);
}
}
else
{
dump_named_datatype(type_id, type);
dump_named_datatype(type_id, real_name);
if(H5Tclose(type_id) < 0)
d_status = EXIT_FAILURE;
@ -4073,7 +4239,7 @@ main(int argc, const char *argv[])
char *fname = NULL;
void *edata;
H5E_auto2_t func;
find_objs_t info;
H5O_info_t oi;
struct handler_t *hand;
int i;
unsigned u;
@ -4162,12 +4328,22 @@ main(int argc, const char *argv[])
}
/* find all shared objects */
if(init_objs(fid, &info, &group_table, &dset_table, &type_table) < 0) {
/* Get object info for root group */
if(H5Oget_info_by_name(fid, "/", &oi, H5P_DEFAULT) < 0) {
error_msg(progname, "internal error (file %s:line %d)\n", __FILE__, __LINE__);
d_status = EXIT_FAILURE;
goto done;
}
/* Initialize object tables */
if(table_list_add(fid, oi.fileno) < 0) {
error_msg(progname, "internal error (file %s:line %d)\n", __FILE__, __LINE__);
d_status = EXIT_FAILURE;
goto done;
}
group_table = table_list.tables[0].group_table;
dset_table = table_list.tables[0].dset_table;
type_table = table_list.tables[0].type_table;
/* does there exist unamed committed datatype */
for (u = 0; u < type_table->nobjs; u++)
@ -4176,10 +4352,6 @@ main(int argc, const char *argv[])
break;
} /* end if */
#ifdef H5DUMP_DEBUG
dump_tables(&info);
#endif /* H5DUMP_DEBUG */
/* start to dump - display file header information */
if (!doxml) {
begin_obj(dump_header_format->filebegin, fname,
@ -4257,7 +4429,7 @@ main(int argc, const char *argv[])
for(i = 0; i < argc; i++)
if(hand[i].func)
hand[i].func(fid, hand[i].obj, hand[i].subset_info, 1);
hand[i].func(fid, hand[i].obj, hand[i].subset_info, 1, NULL);
}
if (!doxml) {
@ -4267,16 +4439,14 @@ main(int argc, const char *argv[])
}
done:
/* Free tables for objects */
table_list_free();
if (H5Fclose(fid) < 0)
d_status = EXIT_FAILURE;
free_handler(hand, argc);
/* Free tables for objects */
free_table(group_table);
free_table(dset_table);
free_table(type_table);
HDfree(prefix);
HDfree(fname);
@ -5435,20 +5605,49 @@ xml_dump_named_datatype(hid_t type, const char *name)
"Parents=\"%s\" H5ParentPaths=\"%s\">\n",
xmlnsprefix,
name, dtxid,
parentxid,(HDstrcmp(prefix, "") ? t_prefix : "/"));
parentxid, HDstrcmp(prefix,"") ? t_prefix : "/");
} else {
H5O_info_t oinfo; /* Object info */
printf("<%sNamedDataType Name=\"%s\" OBJ-XID=\"%s\" "
"H5Path=\"%s\" Parents=\"%s\" H5ParentPaths=\"%s\">\n",
xmlnsprefix,
t_name, dtxid,
t_tmp, parentxid, (HDstrcmp(prefix, "") ? t_prefix : "/"));
/* Check uniqueness of named datatype */
H5Oget_info(type, &oinfo);
if(oinfo.rc > 1) {
obj_t *found_obj; /* Found object */
/* Group with more than one link to it... */
found_obj = search_obj(type_table, oinfo.addr);
if (found_obj == NULL) {
indentation(indent);
error_msg(progname, "internal error (file %s:line %d)\n",
__FILE__, __LINE__);
d_status = EXIT_FAILURE;
goto done;
} else if(found_obj->displayed) {
/* We have already printed this named datatype, print it as a
* NamedDatatypePtr
*/
char pointerxid[100];
char *t_objname = xml_escape_the_name(found_obj->objname);
indentation(indent + COL);
xml_name_to_XID(found_obj->objname, pointerxid, sizeof(pointerxid), 1);
printf("<%sNamedDatatypePtr OBJ-XID=\"%s\" H5Path=\"%s\"/>\n",
xmlnsprefix, pointerxid, t_objname);
indentation(indent);
printf("</%sNamedDataType>\n", xmlnsprefix);
HDfree(t_objname);
goto done;
} else
found_obj->displayed = TRUE;
}
}
HDfree(dtxid);
HDfree(parentxid);
HDfree(t_tmp);
HDfree(t_prefix);
HDfree(t_name);
HDfree(tmp);
indent += COL;
indentation(indent);
@ -5464,6 +5663,14 @@ xml_dump_named_datatype(hid_t type, const char *name)
indent -= COL;
indentation(indent);
printf("</%sNamedDataType>\n",xmlnsprefix);
done:
HDfree(dtxid);
HDfree(parentxid);
HDfree(t_tmp);
HDfree(t_prefix);
HDfree(t_name);
HDfree(tmp);
}
/*-------------------------------------------------------------------------
@ -5581,7 +5788,7 @@ xml_dump_group(hid_t gid, const char *name)
indentation(indent + COL);
ptrstr = malloc(100);
t_objname = xml_escape_the_name(found_obj->objname);
t_objname = xml_escape_the_name(found_obj->objname);/* point to the NDT by name */
par_name = xml_escape_the_name(par);
xml_name_to_XID(found_obj->objname, ptrstr, 100, 1);
xml_name_to_XID(par, parentxid, 100, 1);
@ -6704,32 +6911,87 @@ add_prefix(char **prfx, size_t *prfx_len, const char *name)
* basis, attempting to dump as a dataset, as a group and as a named datatype
* Error messages are supressed
*
* Modifications:
* Neil Fortner
* 13 October 2008
* Function basically rewritten. No longer directly opens the target file,
* now initializes a new set of tables for the external file. No longer
* dumps on a trial and error basis, but errors are still suppressed.
*
*-------------------------------------------------------------------------
*/
static int dump_extlink(const char *filename, const char *targname)
static int dump_extlink(hid_t group, const char *linkname, const char *objname)
{
hid_t fid;
hid_t oid;
H5O_info_t oi;
table_t *old_group_table = group_table;
table_t *old_dset_table = dset_table;
table_t *old_type_table = type_table;
hbool_t old_hit_elink;
ssize_t idx;
fid = h5tools_fopen(filename, H5F_ACC_RDONLY, H5P_DEFAULT, driver, NULL, 0);
/* Open target object */
if ((oid = H5Oopen(group, linkname, H5P_DEFAULT)) < 0)
goto fail;
if (fid < 0)
{
/* Get object info */
if (H5Oget_info(oid, &oi) < 0) {
H5Oclose(oid);
goto fail;
}
/* add some indentation to distinguish that these objects are external */
indent += 2*COL;
/* Check if we have visited this file already */
if ((idx = table_list_visited(oi.fileno)) < 0) {
/* We have not visited this file, build object tables */
if ((idx = table_list_add(oid, oi.fileno)) < 0) {
H5Oclose(oid);
goto fail;
}
}
handle_datasets(fid, targname, NULL, 0);
handle_groups(fid, targname, NULL, 0);
handle_datatypes(fid, targname, NULL, 0);
/* Do not recurse through an external link into the original file (idx=0) */
if (idx) {
/* Update table pointers */
group_table = table_list.tables[idx].group_table;
dset_table = table_list.tables[idx].dset_table;
type_table = table_list.tables[idx].type_table;
indent -= 2*COL;
/* We will now traverse the external link, set this global to indicate this */
old_hit_elink = hit_elink;
hit_elink = TRUE;
/* add some indentation to distinguish that these objects are external */
indent += 2*COL;
if (H5Fclose(fid) < 0)
/* Recurse into the external file */
switch (oi.type) {
case H5O_TYPE_GROUP:
handle_groups(group, linkname, NULL, 0, objname);
break;
case H5O_TYPE_DATASET:
handle_datasets(group, linkname, NULL, 0, objname);
break;
case H5O_TYPE_NAMED_DATATYPE:
handle_datatypes(group, linkname, NULL, 0, objname);
break;
default:
d_status = EXIT_FAILURE;
}
indent -= 2*COL;
/* Reset table pointers */
group_table = old_group_table;
dset_table = old_dset_table;
type_table = old_type_table;
/* Reset hit_elink */
hit_elink = old_hit_elink;
} /* end if */
if (H5Idec_ref(oid) < 0)
d_status = EXIT_FAILURE;

31
tools/h5dump/h5dumpgentest.c
View File

@ -90,6 +90,7 @@
#define FILE60 "tfpformat.h5"
#define FILE61 "textlinksrc.h5"
#define FILE62 "textlinktar.h5"
#define FILE63 "textlinkfar.h5"
@ -225,6 +226,7 @@ typedef struct s1_t {
#define F42_DSETNAME "Dataset"
#define F42_TYPENAME "Datatype"
#define F42_ATTRNAME "Attribute"
#define F42_LINKNAME "Link_to_Datatype"
/* "File 43" macros */
/* Name of dataset to create in datafile */
@ -4417,6 +4419,10 @@ static void gent_named_dtype_attr(void)
ret = H5Tcommit2(fid, F42_TYPENAME, tid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
assert(ret >= 0);
/* Create a hard link to the datatype */
ret = H5Lcreate_hard(fid, F42_TYPENAME, fid, F42_LINKNAME, H5P_DEFAULT, H5P_DEFAULT);
assert(ret >= 0);
/* Create a scalar dataspace used for all objects */
sid = H5Screate(H5S_SCALAR);
assert(sid > 0);
@ -6179,27 +6185,28 @@ gent_fpformat(void)
/*-------------------------------------------------------------------------
* Function: gent_extlinks
*
* Purpose: Generate 2 files to be used in the external links test
* External links point from one HDF5 file to an object (Group, Dataset, or
* committed Datatype) in another file.
* Purpose: Generate 3 files to be used in the external links test
* External links point from one HDF5 file to an object (Group, Dataset,
* or committed Datatype) in another file. Try to create cycles.
*
*-------------------------------------------------------------------------
*/
static void
gent_extlinks(void)
{
hid_t source_fid, target_fid, sid, did, gid, tid;
hid_t source_fid, target_fid, far_fid, sid, did, gid, gid2, tid;
hsize_t dims[1] = {6};
int buf[6] = {1, 2, 3, 4, 5, 6};
/* create two files, a source and a target */
source_fid = H5Fcreate(FILE61, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
target_fid = H5Fcreate(FILE62, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
far_fid = H5Fcreate(FILE63, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/*-------------------------------------------------------------------------
* create Groups, a Dataset, a committed Datatype, and external links in
* the target
* create Groups, a Dataset, a committed Datatype, external links, and a
* cycle in the target
*-------------------------------------------------------------------------
*/
@ -6210,8 +6217,13 @@ gent_extlinks(void)
H5Dwrite(did, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
H5Lcreate_external(FILE61, "/", gid, "elink_t1", H5P_DEFAULT, H5P_DEFAULT);
H5Lcreate_external(FILE61, "/ext_link4", gid, "elink_t2", H5P_DEFAULT, H5P_DEFAULT);
gid2 = H5Gcreate2(gid, "subgroup", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Lcreate_hard(target_fid, "/group", gid2, "link_to_group", H5P_DEFAULT, H5P_DEFAULT);
H5Dclose(did);
H5Sclose(sid);
H5Gclose(gid2);
H5Gclose(gid);
@ -6236,9 +6248,16 @@ gent_extlinks(void)
H5Lcreate_external(FILE62, "group/elink_t2", source_fid, "ext_link4", H5P_DEFAULT, H5P_DEFAULT);
H5Lcreate_external(FILE62, "empty_group", source_fid, "ext_link5", H5P_DEFAULT, H5P_DEFAULT);
/*-------------------------------------------------------------------------
* create external link in the "far" file pointing to the source file
*-------------------------------------------------------------------------
*/
H5Lcreate_external(FILE61, "/", far_fid, "src_file", H5P_DEFAULT, H5P_DEFAULT);
/* close */
H5Fclose(source_fid);
H5Fclose(target_fid);
H5Fclose(far_fid);
}

4
tools/h5dump/testh5dump.sh.in
View File

@ -499,6 +499,10 @@ TOOLTEST torderattr4.ddl -H --sort_by=creation_order --sort_order=descending tor
# tests for floating point user defined printf format
TOOLTEST tfpformat.ddl -m %.7f tfpformat.h5
# tests for traversal of external links
TOOLTEST textlinksrc.ddl textlinksrc.h5
TOOLTEST textlinkfar.ddl textlinkfar.h5
if test $nerrors -eq 0 ; then

2
tools/h5ls/h5ls.c
View File

@ -1845,8 +1845,8 @@ elink_trav_visited(elink_trav_t *visited, const char *file, const char *path)
/* Didn't find elink */
return(FALSE);
} /* end elink_trav_visited() */
/*-------------------------------------------------------------------------
* Function: list_lnk
*

24
tools/lib/h5tools_utils.c
View File

@ -485,21 +485,21 @@ find_objs_cb(const char *name, const H5O_info_t *oinfo, const char *already_seen
break;
case H5O_TYPE_NAMED_DATATYPE:
{
obj_t *found_obj;
if(NULL == already_seen) {
obj_t *found_obj;
if((found_obj = search_obj(info->type_table, oinfo->addr)) == NULL)
add_obj(info->type_table, oinfo->addr, name, TRUE);
else {
/* Use latest version of name */
HDfree(found_obj->objname);
found_obj->objname = HDstrdup(name);
if((found_obj = search_obj(info->type_table, oinfo->addr)) == NULL)
add_obj(info->type_table, oinfo->addr, name, TRUE);
else {
/* Use latest version of name */
HDfree(found_obj->objname);
found_obj->objname = HDstrdup(name);
/* Mark named datatype as having valid name */
found_obj->recorded = TRUE;
} /* end else */
/* Mark named datatype as having valid name */
found_obj->recorded = TRUE;
} /* end else */
} /* end if */
break;
}
default:
break;

69
tools/testfiles/textlinkfar.ddl Normal file
View File

@ -0,0 +1,69 @@
#############################
Expected output for 'h5dump textlinkfar.h5'
#############################
HDF5 "textlinkfar.h5" {
GROUP "/" {
EXTERNAL_LINK "src_file" {
TARGETFILE "textlinksrc.h5"
TARGETPATH "/"
GROUP "/" {
EXTERNAL_LINK "ext_link1" {
TARGETFILE "textlinktar.h5"
TARGETPATH "group"
GROUP "group" {
DATASET "dset" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 6 ) / ( 6 ) }
DATA {
(0): 1, 2, 3, 4, 5, 6
}
}
EXTERNAL_LINK "elink_t1" {
TARGETFILE "textlinksrc.h5"
TARGETPATH "/"
GROUP "/" {
HARDLINK "/"
}
}
EXTERNAL_LINK "elink_t2" {
TARGETFILE "textlinksrc.h5"
TARGETPATH "/ext_link4"
}
GROUP "subgroup" {
GROUP "link_to_group" {
HARDLINK "/group"
}
}
}
}
EXTERNAL_LINK "ext_link2" {
TARGETFILE "textlinktar.h5"
TARGETPATH "dset"
DATASET "dset" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 6 ) / ( 6 ) }
DATA {
(0): 1, 2, 3, 4, 5, 6
}
}
}
EXTERNAL_LINK "ext_link3" {
TARGETFILE "textlinktar.h5"
TARGETPATH "type"
DATATYPE "type" H5T_STD_I32LE;
}
EXTERNAL_LINK "ext_link4" {
TARGETFILE "textlinktar.h5"
TARGETPATH "group/elink_t2"
}
EXTERNAL_LINK "ext_link5" {
TARGETFILE "textlinktar.h5"
TARGETPATH "empty_group"
GROUP "empty_group" {
}
}
}
}
}
}

BIN
tools/testfiles/textlinkfar.h5 Normal file
View File

Binary file not shown.

2
tools/testfiles/textlinksrc-1.ls
View File

@ -11,6 +11,8 @@
/ext_link1/elink_t1/ext_link4 External Link {textlinktar.h5//group/elink_t2} {**NOT FOUND**}
/ext_link1/elink_t1/ext_link5 External Link {textlinktar.h5//empty_group} {Group}
/ext_link1/elink_t2 External Link {textlinksrc.h5//ext_link4} {**NOT FOUND**}
/ext_link1/subgroup Group
/ext_link1/subgroup/link_to_group Group, same as /ext_link1
/ext_link2 External Link {textlinktar.h5//dset} {Already Visited}
/ext_link3 External Link {textlinktar.h5//type} {Already Visited}
/ext_link4 External Link {textlinktar.h5//group/elink_t2} {Already Visited}

2
tools/testfiles/textlinksrc-3.ls
View File

@ -10,3 +10,5 @@ ext_link1 External Link {textlinktar.h5//group} {Group}
/elink_t1/ext_link4 External Link {textlinktar.h5//group/elink_t2} {**NOT FOUND**}
/elink_t1/ext_link5 External Link {textlinktar.h5//empty_group} {Group}
/elink_t2 External Link {textlinksrc.h5//ext_link4} {**NOT FOUND**}
/subgroup Group
/subgroup/link_to_group Group, same as /ext_link1

60
tools/testfiles/textlinksrc.ddl Normal file
View File

@ -0,0 +1,60 @@
#############################
Expected output for 'h5dump textlinksrc.h5'
#############################
HDF5 "textlinksrc.h5" {
GROUP "/" {
EXTERNAL_LINK "ext_link1" {
TARGETFILE "textlinktar.h5"
TARGETPATH "group"
GROUP "group" {
DATASET "dset" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 6 ) / ( 6 ) }
DATA {
(0): 1, 2, 3, 4, 5, 6
}
}
EXTERNAL_LINK "elink_t1" {
TARGETFILE "textlinksrc.h5"
TARGETPATH "/"
}
EXTERNAL_LINK "elink_t2" {
TARGETFILE "textlinksrc.h5"
TARGETPATH "/ext_link4"
}
GROUP "subgroup" {
GROUP "link_to_group" {
HARDLINK "/group"
}
}
}
}
EXTERNAL_LINK "ext_link2" {
TARGETFILE "textlinktar.h5"
TARGETPATH "dset"
DATASET "dset" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 6 ) / ( 6 ) }
DATA {
(0): 1, 2, 3, 4, 5, 6
}
}
}
EXTERNAL_LINK "ext_link3" {
TARGETFILE "textlinktar.h5"
TARGETPATH "type"
DATATYPE "type" H5T_STD_I32LE;
}
EXTERNAL_LINK "ext_link4" {
TARGETFILE "textlinktar.h5"
TARGETPATH "group/elink_t2"
}
EXTERNAL_LINK "ext_link5" {
TARGETFILE "textlinktar.h5"
TARGETPATH "empty_group"
GROUP "empty_group" {
}
}
}
}

BIN
tools/testfiles/textlinktar.h5
View File

Binary file not shown.

4
tools/testfiles/thlink.h5.xml
View File

@ -31,11 +31,11 @@ Expected output for 'h5dump --xml thlink.h5'
</hdf5:Dataset>
<hdf5:Group Name="g1" OBJ-XID="xid_1408" H5Path="/g1" Parents="xid_96" H5ParentPaths="/" >
<hdf5:Dataset Name="dset2" OBJ-XID="xid_808-1" H5Path="/g1/dset2" Parents="xid_1408" H5ParentPaths="/g1">
<hdf5:DatasetPtr OBJ-XID="xid_808" H5Path="/g1/dset2"/>
<hdf5:DatasetPtr OBJ-XID="xid_808" H5Path="/dset1"/>
</hdf5:Dataset>
<hdf5:Group Name="g1.1" OBJ-XID="xid_2000" H5Path="/g1/g1.1" Parents="xid_1408" H5ParentPaths="/g1" >
<hdf5:Dataset Name="dset3" OBJ-XID="xid_808-2" H5Path="/g1/g1.1/dset3" Parents="xid_2000" H5ParentPaths="/g1/g1.1">
<hdf5:DatasetPtr OBJ-XID="xid_808" H5Path="/g1/g1.1/dset3"/>
<hdf5:DatasetPtr OBJ-XID="xid_808" H5Path="/dset1"/>
</hdf5:Dataset>
</hdf5:Group>
</hdf5:Group>

4
tools/testfiles/tmany.h5.xml
View File

@ -267,7 +267,7 @@ Expected output for 'h5dump --xml tmany.h5'
</hdf5:Group>
<hdf5:Group Name="g1.2" OBJ-XID="xid_5968" H5Path="/g1/g1.2" Parents="xid_800" H5ParentPaths="/g1" >
<hdf5:Dataset Name="link1" OBJ-XID="xid_2864-1" H5Path="/g1/g1.2/link1" Parents="xid_5968" H5ParentPaths="/g1/g1.2">
<hdf5:DatasetPtr OBJ-XID="xid_2864" H5Path="/g1/g1.2/link1"/>
<hdf5:DatasetPtr OBJ-XID="xid_2864" H5Path="/g1/g1.1/dset1"/>
</hdf5:Dataset>
</hdf5:Group>
</hdf5:Group>
@ -313,7 +313,7 @@ Expected output for 'h5dump --xml tmany.h5'
</hdf5:Group>
<hdf5:Group Name="g4" OBJ-XID="xid_10784" H5Path="/g4" Parents="xid_96" H5ParentPaths="/" >
<hdf5:Dataset Name="dset2" OBJ-XID="xid_11488-2" H5Path="/g4/dset2" Parents="xid_10784" H5ParentPaths="/g4">
<hdf5:DatasetPtr OBJ-XID="xid_11488" H5Path="/g4/dset2"/>
<hdf5:DatasetPtr OBJ-XID="xid_11488" H5Path="/g3/link3"/>
</hdf5:Dataset>
</hdf5:Group>
<hdf5:Group Name="g5" OBJ-XID="xid_8416" H5Path="/g5" Parents="xid_96" H5ParentPaths="/" >

4
tools/testfiles/tnamed_dtype_attr.ddl
View File

@ -17,7 +17,7 @@ GROUP "/" {
}
}
}
DATATYPE "Datatype" H5T_STD_I32LE;
DATATYPE "Datatype" H5T_STD_I32LE;
ATTRIBUTE "Attribute" {
DATATYPE H5T_STD_I32LE
DATASPACE SCALAR
@ -26,6 +26,8 @@ GROUP "/" {
}
}
DATATYPE "Link_to_Datatype" HARDLINK "/Datatype"
GROUP "g1" {
ATTRIBUTE "Attribute" {
DATATYPE "/Datatype"

BIN
tools/testfiles/tnamed_dtype_attr.h5
View File

Binary file not shown.

15
tools/testfiles/tnamed_dtype_attr.h5.xml
View File

@ -4,7 +4,7 @@ Expected output for 'h5dump --xml tnamed_dtype_attr.h5'
<?xml version="1.0" encoding="UTF-8"?>
<hdf5:HDF5-File xmlns:hdf5="http://hdfgroup.org/DTDs/HDF5-File" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://hdfgroup.org/DTDs/HDF5File http://hdfgroup.org/DTDs/HDF5-File.xsd">
<hdf5:RootGroup OBJ-XID="xid_96" H5Path="/">
<hdf5:Dataset Name="Dataset" OBJ-XID="xid_1264" H5Path= "/Dataset" Parents="xid_96" H5ParentPaths="/">
<hdf5:Dataset Name="Dataset" OBJ-XID="xid_1256" H5Path= "/Dataset" Parents="xid_96" H5ParentPaths="/">
<hdf5:StorageLayout>
<hdf5:ContiguousLayout/>
</hdf5:StorageLayout>
@ -16,12 +16,12 @@ Expected output for 'h5dump --xml tnamed_dtype_attr.h5'
<hdf5:Dataspace>
<hdf5:ScalarDataspace />
</hdf5:Dataspace>
<hdf5:NamedDataTypePtr OBJ-XID="xid_792" H5Path="/Datatype" />
<hdf5:NamedDataTypePtr OBJ-XID="xid_800" H5Path="/Datatype" />
<hdf5:Attribute Name="Attribute">
<hdf5:Dataspace>
<hdf5:ScalarDataspace />
</hdf5:Dataspace>
<hdf5:NamedDataTypePtr OBJ-XID="xid_792" H5Path="/Datatype" />
<hdf5:NamedDataTypePtr OBJ-XID="xid_800" H5Path="/Datatype" />
<hdf5:Data>
<hdf5:DataFromFile>
8
@ -32,19 +32,22 @@ Expected output for 'h5dump --xml tnamed_dtype_attr.h5'
<hdf5:NoData/>
</hdf5:Data>
</hdf5:Dataset>
<hdf5:NamedDataType Name="Datatype" OBJ-XID="xid_792" H5Path="/Datatype" Parents="xid_96" H5ParentPaths="/">
<hdf5:NamedDataType Name="Datatype" OBJ-XID="xid_800" H5Path="/Datatype" Parents="xid_96" H5ParentPaths="/">
<hdf5:DataType>
<hdf5:AtomicType>
<hdf5:IntegerType ByteOrder="LE" Sign="true" Size="4" />
</hdf5:AtomicType>
</hdf5:DataType>
</hdf5:NamedDataType>
<hdf5:Group Name="g1" OBJ-XID="xid_1536" H5Path="/g1" Parents="xid_96" H5ParentPaths="/" >
<hdf5:NamedDataType Name="Link_to_Datatype" OBJ-XID="xid_800" H5Path="/Link_to_Datatype" Parents="xid_96" H5ParentPaths="/">
<hdf5:NamedDatatypePtr OBJ-XID="xid_800" H5Path="/Datatype"/>
</hdf5:NamedDataType>
<hdf5:Group Name="g1" OBJ-XID="xid_1528" H5Path="/g1" Parents="xid_96" H5ParentPaths="/" >
<hdf5:Attribute Name="Attribute">
<hdf5:Dataspace>
<hdf5:ScalarDataspace />
</hdf5:Dataspace>
<hdf5:NamedDataTypePtr OBJ-XID="xid_792" H5Path="/Datatype" />
<hdf5:NamedDataTypePtr OBJ-XID="xid_800" H5Path="/Datatype" />
<hdf5:Data>
<hdf5:DataFromFile>
8

4
tools/testfiles/torderattr1.ddl
View File

@ -75,7 +75,7 @@ GROUP "/" {
DATASPACE SCALAR
}
}
DATATYPE "t" H5T_STD_I32LE;
DATATYPE "t" H5T_STD_I32LE;
ATTRIBUTE "a" {
DATATYPE H5T_STD_U8LE
DATASPACE SCALAR
@ -89,7 +89,7 @@ GROUP "/" {
DATASPACE SCALAR
}
DATATYPE "tt" H5T_STD_I32LE;
DATATYPE "tt" H5T_STD_I32LE;
ATTRIBUTE "a" {
DATATYPE H5T_STD_U8LE
DATASPACE SCALAR

4
tools/testfiles/torderattr2.ddl
View File

@ -15,7 +15,7 @@ GROUP "/" {
DATATYPE H5T_STD_U8LE
DATASPACE SCALAR
}
DATATYPE "tt" H5T_STD_I32LE;
DATATYPE "tt" H5T_STD_I32LE;
ATTRIBUTE "c" {
DATATYPE H5T_STD_U8LE
DATASPACE SCALAR
@ -29,7 +29,7 @@ GROUP "/" {
DATASPACE SCALAR
}
DATATYPE "t" H5T_STD_I32LE;
DATATYPE "t" H5T_STD_I32LE;
ATTRIBUTE "c" {
DATATYPE H5T_STD_U8LE
DATASPACE SCALAR

4
tools/testfiles/torderattr3.ddl
View File

@ -75,7 +75,7 @@ GROUP "/" {
DATASPACE SCALAR
}
}
DATATYPE "t" H5T_STD_I32LE;
DATATYPE "t" H5T_STD_I32LE;
ATTRIBUTE "a" {
DATATYPE H5T_STD_U8LE
DATASPACE SCALAR
@ -89,7 +89,7 @@ GROUP "/" {
DATASPACE SCALAR
}
DATATYPE "tt" H5T_STD_I32LE;
DATATYPE "tt" H5T_STD_I32LE;
ATTRIBUTE "c" {
DATATYPE H5T_STD_U8LE
DATASPACE SCALAR

4
tools/testfiles/torderattr4.ddl
View File

@ -15,7 +15,7 @@ GROUP "/" {
DATATYPE H5T_STD_U8LE
DATASPACE SCALAR
}
DATATYPE "tt" H5T_STD_I32LE;
DATATYPE "tt" H5T_STD_I32LE;
ATTRIBUTE "a" {
DATATYPE H5T_STD_U8LE
DATASPACE SCALAR
@ -29,7 +29,7 @@ GROUP "/" {
DATASPACE SCALAR
}
DATATYPE "t" H5T_STD_I32LE;
DATATYPE "t" H5T_STD_I32LE;
ATTRIBUTE "c" {
DATATYPE H5T_STD_U8LE
DATASPACE SCALAR

2
tools/testfiles/tvlstr.ddl
View File

@ -24,7 +24,7 @@ GROUP "/" {
(2): "", NULL
}
}
DATATYPE "vl_string_type" H5T_STRING {
DATATYPE "vl_string_type" H5T_STRING {
STRSIZE H5T_VARIABLE;
STRPAD H5T_STR_NULLPAD;
CSET H5T_CSET_ASCII;

4
windows/tools/h5dump/testh5dump.bat
View File

@ -594,6 +594,10 @@ rem ############################################################################
rem Note: Make sure to use PERCENT rather than "%", because Windows needs
rem to handle it specially. --SJW 5/12/08
call :tooltest tfpformat.ddl -m PERCENT.7f tfpformat.h5
rem tests for traversal of external links
call :tooltest textlinksrc.ddl textlinksrc.h5
call :tooltest textlinkfar.ddl textlinkfar.h5