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[svn-r18454] Purpose:

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Fix for the bug1726 - NPOESS: h5repack loses attributes for datasets of 
    type H5T_REFERENCE.

Description:
    include test cases.
    also test cases for attribute with object and region reference.

Tested:
    jam, amani, linew
This commit is contained in:
Jonathan Kim 2010-03-25 12:29:51 -05:00
parent 1267cda989
commit 20fd1f47b7
7 changed files with 734 additions and 436 deletions
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331
tools/h5repack/h5repack.c
View File

@ -240,6 +240,337 @@ int h5repack_addlayout(const char* str,
return 0;
}
/* Note: The below copy_named_datatype(), named_datatype_free(), copy_attr()
* were located in h5repack_copy.c as static prior to bugfix1726.
* Made shared functions as copy_attr() was needed in h5repack_refs.c.
* However copy_attr() may be obsoleted when H5Acopy is available and put back
* others to static in h5repack_copy.c.
*/
/*-------------------------------------------------------------------------
* Function: copy_named_datatype
*
* Purpose: Copies the specified datatype anonymously, and returns an open
* id for that datatype in the output file. The first time this
* is called it scans every named datatype in travt into a
* private stack, afterwards it simply scans that stack. The id
* returned must be closed after it is no longer needed.
* named_datatype_free must be called before the program exits
* to free the stack.
*
* Programmer: Neil Fortner
*
* Date: April 14, 2009
*
*-------------------------------------------------------------------------
*/
hid_t copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_head_p, trav_table_t *travt, pack_opt_t *options)
{
named_dt_t *dt = *named_dt_head_p; /* Stack pointer */
named_dt_t *dt_ret = NULL; /* Datatype to return */
H5O_info_t oinfo; /* Object info of input dtype */
hid_t ret_value = -1; /* The identifier of the named dtype in the out file */
if(H5Oget_info(type_in, &oinfo) < 0)
goto error;
if(*named_dt_head_p)
{
/* Stack already exists, search for the datatype */
while(dt && dt->addr_in != oinfo.addr)
dt = dt->next;
dt_ret = dt;
}
else
{
/* Create the stack */
size_t i;
for(i=0; i<travt->nobjs; i++)
if(travt->objs[i].type == H5TRAV_TYPE_NAMED_DATATYPE)
{
/* Push onto the stack */
if(NULL == (dt = (named_dt_t *) HDmalloc(sizeof(named_dt_t))))
goto error;
dt->next = *named_dt_head_p;
*named_dt_head_p = dt;
/* Update the address and id */
dt->addr_in = travt->objs[i].objno;
dt->id_out = -1;
/* Check if this type is the one requested */
if(oinfo.addr == dt->addr_in)
{
HDassert(!dt_ret);
dt_ret = dt;
} /* end if */
} /* end if */
} /* end else */
/* Handle the case that the requested datatype was not found. This is
* possible if the datatype was committed anonymously in the input file. */
if(!dt_ret)
{
/* Push the new datatype onto the stack */
if(NULL == (dt_ret = (named_dt_t *) HDmalloc(sizeof(named_dt_t))))
goto error;
dt_ret->next = *named_dt_head_p;
*named_dt_head_p = dt_ret;
/* Update the address and id */
dt_ret->addr_in = oinfo.addr;
dt_ret->id_out = -1;
} /* end if */
/* If the requested datatype does not yet exist in the output file, copy it
* anonymously */
if(dt_ret->id_out < 0)
{
if (options->use_native==1)
dt_ret->id_out = h5tools_get_native_type(type_in);
else
dt_ret->id_out = H5Tcopy(type_in);
if(dt_ret->id_out < 0)
goto error;
if(H5Tcommit_anon(fidout, dt_ret->id_out, H5P_DEFAULT, H5P_DEFAULT) < 0)
goto error;
} /* end if */
/* Set return value */
ret_value = dt_ret->id_out;
/* Increment the ref count on id_out, because the calling function will try
* to close it */
if(H5Iinc_ref(ret_value) < 0)
goto error;
return(ret_value);
error:
return(-1);
} /* end copy_named_datatype */
/*-------------------------------------------------------------------------
* Function: named_datatype_free
*
* Purpose: Frees the stack of named datatypes.
*
* Programmer: Neil Fortner
*
* Date: April 14, 2009
*
*-------------------------------------------------------------------------
*/
int named_datatype_free(named_dt_t **named_dt_head_p, int ignore_err)
{
named_dt_t *dt = *named_dt_head_p;
while(dt)
{
/* Pop the datatype off the stack and free it */
if(H5Tclose(dt->id_out) < 0 && !ignore_err)
goto error;
dt = dt->next;
HDfree(*named_dt_head_p);
*named_dt_head_p = dt;
} /* end while */
return 0;
error:
return -1;
} /* end named_datatype_free */
/*-------------------------------------------------------------------------
* Function: copy_attr
*
* Purpose: copy attributes located in LOC_IN, which is obtained either from
* loc_id = H5Gopen2( fid, name);
* loc_id = H5Dopen2( fid, name);
* loc_id = H5Topen2( fid, name);
*
* Return: 0, ok, -1 no
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: October, 28, 2003
*
*-------------------------------------------------------------------------
*/
int copy_attr(hid_t loc_in,
hid_t loc_out,
named_dt_t **named_dt_head_p,
trav_table_t *travt,
pack_opt_t *options)
{
hid_t attr_id=-1; /* attr ID */
hid_t attr_out=-1; /* attr ID */
hid_t space_id=-1; /* space ID */
hid_t ftype_id=-1; /* file type ID */
hid_t wtype_id=-1; /* read/write type ID */
size_t msize; /* size of type */
void *buf=NULL; /* data buffer */
hsize_t nelmts; /* number of elements in dataset */
int rank; /* rank of dataset */
htri_t is_named; /* Whether the datatype is named */
hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
char name[255];
H5O_info_t oinfo; /* object info */
int j;
unsigned u;
if(H5Oget_info(loc_in, &oinfo) < 0)
goto error;
/*-------------------------------------------------------------------------
* copy all attributes
*-------------------------------------------------------------------------
*/
for ( u = 0; u < (unsigned)oinfo.num_attrs; u++)
{
buf=NULL;
/* open attribute */
if((attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t)u, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto error;
/* get name */
if (H5Aget_name( attr_id, (size_t)255, name ) < 0)
goto error;
/* get the file datatype */
if ((ftype_id = H5Aget_type( attr_id )) < 0 )
goto error;
/* Check if the datatype is committed */
if((is_named = H5Tcommitted(ftype_id)) < 0)
goto error;
if(is_named)
{
hid_t fidout;
/* Create out file id */
if((fidout = H5Iget_file_id(loc_out)) < 0)
goto error;
/* Copy named dt */
if((wtype_id = copy_named_datatype(ftype_id, fidout, named_dt_head_p,
travt, options)) < 0)
{
H5Fclose(fidout);
goto error;
} /* end if */
if(H5Fclose(fidout) < 0)
goto error;
} /* end if */
/* get the dataspace handle */
if ((space_id = H5Aget_space( attr_id )) < 0 )
goto error;
/* get dimensions */
if ( (rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0 )
goto error;
nelmts=1;
for (j=0; j<rank; j++)
nelmts*=dims[j];
/* wtype_id will have already been set if using a named dtype */
if(!is_named)
{
if (options->use_native==1)
wtype_id = h5tools_get_native_type(ftype_id);
else
wtype_id = H5Tcopy(ftype_id);
} /* end if */
if ((msize=H5Tget_size(wtype_id))==0)
goto error;
/*-------------------------------------------------------------------------
* object references are a special case
* we cannot just copy the buffers, but instead we recreate the reference
* this is done on a second sweep of the file that just copies
* the referenced objects
*-------------------------------------------------------------------------
*/
if (H5T_REFERENCE==H5Tget_class(wtype_id))
{
;
}
else
{
/*-------------------------------------------------------------------------
* read to memory
*-------------------------------------------------------------------------
*/
buf = (void *)HDmalloc((size_t)(nelmts * msize));
if(buf == NULL)
{
error_msg("h5repack", "cannot read into memory\n" );
goto error;
}
if(H5Aread(attr_id, wtype_id, buf) < 0)
goto error;
/*-------------------------------------------------------------------------
* copy
*-------------------------------------------------------------------------
*/
if((attr_out = H5Acreate2(loc_out, name, wtype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto error;
if(H5Awrite(attr_out, wtype_id, buf) < 0)
goto error;
/*close*/
if(H5Aclose(attr_out) < 0)
goto error;
if(buf)
free(buf);
} /*H5T_REFERENCE*/
if(options->verbose)
printf(FORMAT_OBJ_ATTR, "attr", name);
/*-------------------------------------------------------------------------
* close
*-------------------------------------------------------------------------
*/
if (H5Tclose(ftype_id) < 0) goto error;
if (H5Tclose(wtype_id) < 0) goto error;
if (H5Sclose(space_id) < 0) goto error;
if (H5Aclose(attr_id) < 0) goto error;
} /* u */
return 0;
error:
H5E_BEGIN_TRY {
H5Tclose(ftype_id);
H5Tclose(wtype_id);
H5Sclose(space_id);
H5Aclose(attr_id);
H5Aclose(attr_out);
if (buf)
free(buf);
} H5E_END_TRY;
return -1;
}
/*-------------------------------------------------------------------------
* Function: check_options

16
tools/h5repack/h5repack.h
View File

@ -119,6 +119,11 @@ typedef struct {
} pack_opt_t;
typedef struct named_dt_t {
haddr_t addr_in; /* Address of the named dtype in the in file */
hid_t id_out; /* Open identifier for the dtype in the out file */
struct named_dt_t *next; /* Next dtype */
} named_dt_t;
/*-------------------------------------------------------------------------
* public functions
@ -137,6 +142,17 @@ int h5repack_end(pack_opt_t *options);
int h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options);
int h5repack_cmp_pl(const char *fname1, const char *fname2);
/* Note: The below copy_named_datatype(), named_datatype_free(), copy_attr()
* and struct named_dt_t were located in h5repack_copy.c as static prior to
* bugfix1726.
* Made shared functions as copy_attr() was needed in h5repack_refs.c.
* However copy_attr() may be obsoleted when H5Acopy is available and put back
* others to static in h5repack_copy.c.
*/
hid_t copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_head_p, trav_table_t *travt, pack_opt_t *options);
int named_datatype_free(named_dt_t **named_dt_head_p, int ignore_err);
int copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p,
trav_table_t *travt, pack_opt_t *options);
#ifdef __cplusplus
}

2
tools/h5repack/h5repack.sh.in
View File

@ -532,7 +532,7 @@ TOOLTEST $FILE15
# tests family driver (file is located in common testfiles folder, uses TOOLTEST1
TOOLTEST1 $FILE16
# test various references (bug 1814)
# test various references (bug 1814 and 1726)
TOOLTEST $FILE_REF
if test $nerrors -eq 0 ; then

331
tools/h5repack/h5repack_copy.c
View File

@ -25,11 +25,6 @@
* typedefs
*-------------------------------------------------------------------------
*/
typedef struct named_dt_t {
haddr_t addr_in; /* Address of the named dtype in the in file */
hid_t id_out; /* Open identifier for the dtype in the out file */
struct named_dt_t *next; /* Next dtype */
} named_dt_t;
/*-------------------------------------------------------------------------
* globals
@ -49,11 +44,6 @@ extern char *progname;
*/
static void print_dataset_info(hid_t dcpl_id,char *objname,double per, int pr);
static int do_copy_objects(hid_t fidin,hid_t fidout,trav_table_t *travt,pack_opt_t *options);
static int copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p,
trav_table_t *travt, pack_opt_t *options);
static hid_t copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_head_p,
trav_table_t *travt, pack_opt_t *options);
static int named_datatype_free(named_dt_t **named_dt_head_p, int ignore_err);
static int copy_user_block(const char *infile, const char *outfile, hsize_t size);
#if defined (H5REPACK_DEBUG_USER_BLOCK)
static void print_user_block(const char *filename, hid_t fid);
@ -1199,195 +1189,6 @@ error:
}
/*-------------------------------------------------------------------------
* Function: copy_attr
*
* Purpose: copy attributes located in LOC_IN, which is obtained either from
* loc_id = H5Gopen2( fid, name);
* loc_id = H5Dopen2( fid, name);
* loc_id = H5Topen2( fid, name);
*
* Return: 0, ok, -1 no
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: October, 28, 2003
*
*-------------------------------------------------------------------------
*/
int copy_attr(hid_t loc_in,
hid_t loc_out,
named_dt_t **named_dt_head_p,
trav_table_t *travt,
pack_opt_t *options
)
{
hid_t attr_id=-1; /* attr ID */
hid_t attr_out=-1; /* attr ID */
hid_t space_id=-1; /* space ID */
hid_t ftype_id=-1; /* file type ID */
hid_t wtype_id=-1; /* read/write type ID */
size_t msize; /* size of type */
void *buf=NULL; /* data buffer */
hsize_t nelmts; /* number of elements in dataset */
int rank; /* rank of dataset */
htri_t is_named; /* Whether the datatype is named */
hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
char name[255];
H5O_info_t oinfo; /* object info */
int j;
unsigned u;
if(H5Oget_info(loc_in, &oinfo) < 0)
goto error;
/*-------------------------------------------------------------------------
* copy all attributes
*-------------------------------------------------------------------------
*/
for ( u = 0; u < (unsigned)oinfo.num_attrs; u++)
{
buf=NULL;
/* open attribute */
if((attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t)u, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto error;
/* get name */
if (H5Aget_name( attr_id, (size_t)255, name ) < 0)
goto error;
/* get the file datatype */
if ((ftype_id = H5Aget_type( attr_id )) < 0 )
goto error;
/* Check if the datatype is committed */
if((is_named = H5Tcommitted(ftype_id)) < 0)
goto error;
if(is_named) {
hid_t fidout;
/* Create out file id */
if((fidout = H5Iget_file_id(loc_out)) < 0)
goto error;
/* Copy named dt */
if((wtype_id = copy_named_datatype(ftype_id, fidout, named_dt_head_p,
travt, options)) < 0) {
H5Fclose(fidout);
goto error;
} /* end if */
if(H5Fclose(fidout) < 0)
goto error;
} /* end if */
/* get the dataspace handle */
if ((space_id = H5Aget_space( attr_id )) < 0 )
goto error;
/* get dimensions */
if ( (rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0 )
goto error;
nelmts=1;
for (j=0; j<rank; j++)
nelmts*=dims[j];
/* wtype_id will have already been set if using a named dtype */
if(!is_named) {
if (options->use_native==1)
wtype_id = h5tools_get_native_type(ftype_id);
else
wtype_id = H5Tcopy(ftype_id);
} /* end if */
if ((msize=H5Tget_size(wtype_id))==0)
goto error;
/*-------------------------------------------------------------------------
* object references are a special case
* we cannot just copy the buffers, but instead we recreate the reference
* this is done on a second sweep of the file that just copies
* the referenced objects
*-------------------------------------------------------------------------
*/
if (H5T_REFERENCE==H5Tget_class(wtype_id))
{
;
}
else
{
/*-------------------------------------------------------------------------
* read to memory
*-------------------------------------------------------------------------
*/
buf = (void *)HDmalloc((size_t)(nelmts * msize));
if(buf == NULL) {
error_msg(progname, "cannot read into memory\n" );
goto error;
}
if(H5Aread(attr_id, wtype_id, buf) < 0)
goto error;
/*-------------------------------------------------------------------------
* copy
*-------------------------------------------------------------------------
*/
if((attr_out = H5Acreate2(loc_out, name, wtype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto error;
if(H5Awrite(attr_out, wtype_id, buf) < 0)
goto error;
/*close*/
if(H5Aclose(attr_out) < 0)
goto error;
if(buf)
free(buf);
} /*H5T_REFERENCE*/
if(options->verbose)
printf(FORMAT_OBJ_ATTR, "attr", name);
/*-------------------------------------------------------------------------
* close
*-------------------------------------------------------------------------
*/
if (H5Tclose(ftype_id) < 0) goto error;
if (H5Tclose(wtype_id) < 0) goto error;
if (H5Sclose(space_id) < 0) goto error;
if (H5Aclose(attr_id) < 0) goto error;
} /* u */
return 0;
error:
H5E_BEGIN_TRY {
H5Tclose(ftype_id);
H5Tclose(wtype_id);
H5Sclose(space_id);
H5Aclose(attr_id);
H5Aclose(attr_out);
if (buf)
free(buf);
} H5E_END_TRY;
return -1;
}
/*-------------------------------------------------------------------------
* Function: print_dataset_info
*
@ -1493,138 +1294,6 @@ static void print_dataset_info(hid_t dcpl_id,
}
/*-------------------------------------------------------------------------
* Function: copy_named_datatype
*
* Purpose: Copies the specified datatype anonymously, and returns an open
* id for that datatype in the output file. The first time this
* is called it scans every named datatype in travt into a
* private stack, afterwards it simply scans that stack. The id
* returned must be closed after it is no longer needed.
* named_datatype_free must be called before the program exits
* to free the stack.
*
* Programmer: Neil Fortner
*
* Date: April 14, 2009
*
*-------------------------------------------------------------------------
*/
static hid_t
copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_head_p, trav_table_t *travt, pack_opt_t *options)
{
named_dt_t *dt = *named_dt_head_p; /* Stack pointer */
named_dt_t *dt_ret = NULL; /* Datatype to return */
H5O_info_t oinfo; /* Object info of input dtype */
hid_t ret_value = -1; /* The identifier of the named dtype in the out file */
if(H5Oget_info(type_in, &oinfo) < 0)
goto error;
if(*named_dt_head_p) {
/* Stack already exists, search for the datatype */
while(dt && dt->addr_in != oinfo.addr)
dt = dt->next;
dt_ret = dt;
} else {
/* Create the stack */
size_t i;
for(i=0; i<travt->nobjs; i++)
if(travt->objs[i].type == H5TRAV_TYPE_NAMED_DATATYPE) {
/* Push onto the stack */
if(NULL == (dt = (named_dt_t *) HDmalloc(sizeof(named_dt_t))))
goto error;
dt->next = *named_dt_head_p;
*named_dt_head_p = dt;
/* Update the address and id */
dt->addr_in = travt->objs[i].objno;
dt->id_out = -1;
/* Check if this type is the one requested */
if(oinfo.addr == dt->addr_in) {
HDassert(!dt_ret);
dt_ret = dt;
} /* end if */
} /* end if */
} /* end else */
/* Handle the case that the requested datatype was not found. This is
* possible if the datatype was committed anonymously in the input file. */
if(!dt_ret) {
/* Push the new datatype onto the stack */
if(NULL == (dt_ret = (named_dt_t *) HDmalloc(sizeof(named_dt_t))))
goto error;
dt_ret->next = *named_dt_head_p;
*named_dt_head_p = dt_ret;
/* Update the address and id */
dt_ret->addr_in = oinfo.addr;
dt_ret->id_out = -1;
} /* end if */
/* If the requested datatype does not yet exist in the output file, copy it
* anonymously */
if(dt_ret->id_out < 0) {
if (options->use_native==1)
dt_ret->id_out = h5tools_get_native_type(type_in);
else
dt_ret->id_out = H5Tcopy(type_in);
if(dt_ret->id_out < 0)
goto error;
if(H5Tcommit_anon(fidout, dt_ret->id_out, H5P_DEFAULT, H5P_DEFAULT) < 0)
goto error;
} /* end if */
/* Set return value */
ret_value = dt_ret->id_out;
/* Increment the ref count on id_out, because the calling function will try
* to close it */
if(H5Iinc_ref(ret_value) < 0)
goto error;
return(ret_value);
error:
return(-1);
} /* end copy_named_datatype */
/*-------------------------------------------------------------------------
* Function: named_datatype_free
*
* Purpose: Frees the stack of named datatypes.
*
* Programmer: Neil Fortner
*
* Date: April 14, 2009
*
*-------------------------------------------------------------------------
*/
static int
named_datatype_free(named_dt_t **named_dt_head_p, int ignore_err)
{
named_dt_t *dt = *named_dt_head_p;
while(dt) {
/* Pop the datatype off the stack and free it */
if(H5Tclose(dt->id_out) < 0 && !ignore_err)
goto error;
dt = dt->next;
HDfree(*named_dt_head_p);
*named_dt_head_p = dt;
} /* end while */
return 0;
error:
return -1;
} /* end named_datatype_free */
/*-------------------------------------------------------------------------
* Function: copy_user_block
*

24
tools/h5repack/h5repack_refs.c
View File

@ -68,6 +68,8 @@ int do_copy_refobjs(hid_t fidin,
hsize_t dims[H5S_MAX_RANK]; /* dimensions of dataset */
unsigned int i, j;
int k;
named_dt_t *named_dt_head=NULL; /* Pointer to the stack of named datatypes
copied */
/*-------------------------------------------------------------------------
* browse
@ -220,13 +222,20 @@ int do_copy_refobjs(hid_t fidin,
HDfree(buf);
if(refbuf)
HDfree(refbuf);
/*------------------------------------------------------
* copy attrs
*----------------------------------------------------*/
if(copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0)
goto error;
} /*H5T_STD_REF_OBJ*/
/*-------------------------------------------------------------------------
* dataset region references
*-------------------------------------------------------------------------
*/
else if(H5Tequal(mtype_id, H5T_STD_REF_DSETREG)) {
else if(H5Tequal(mtype_id, H5T_STD_REF_DSETREG))
{
hid_t refobj_id;
hdset_reg_ref_t *refbuf = NULL; /* input buffer for region references */
hdset_reg_ref_t *buf = NULL; /* output buffer */
@ -305,6 +314,12 @@ int do_copy_refobjs(hid_t fidin,
HDfree(buf);
if(refbuf)
HDfree(refbuf);
/*-----------------------------------------------------
* copy attrs
*----------------------------------------------------*/
if(copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0)
goto error;
} /* H5T_STD_REF_DSETREG */
/*-------------------------------------------------------------------------
* not references, open previously created object in 1st traversal
@ -380,6 +395,12 @@ int do_copy_refobjs(hid_t fidin,
} /* end switch */
} /* end for */
/* Finalize (link) the stack of named datatypes (if any)
* This function is paired with copy_named_datatype() which is called
* in copy_attr(), so need to free.
*/
named_datatype_free(&named_dt_head, 0);
return 0;
error:
@ -393,6 +414,7 @@ error:
H5Tclose(ftype_id);
H5Tclose(mtype_id);
H5Tclose(type_in);
named_datatype_free(&named_dt_head, 0);
} H5E_END_TRY;
return -1;

466
tools/h5repack/h5repacktst.c
View File

@ -103,11 +103,11 @@ int d_status = EXIT_SUCCESS;
#define USERBLOCK_SIZE 2048
/* obj and region references */
#define NAME_OBJ_DS "Dset1"
#define NAME_OBJ_DS1 "Dset1"
#define NAME_OBJ_GRP "Group"
#define NAME_OBJ_NDTYPE "NamedDatatype"
#define NAME_OBJ_DS2 "Dset2"
#define REG_REF_DS1 "Dset_REGREF"
#define REG_REF_DS2 "Dset2"
/*-------------------------------------------------------------------------
* prototypes
@ -1774,10 +1774,13 @@ int make_testfiles(void)
return -1;
/*-------------------------------------------------------------------------
* create a file with obj and region references
* create obj and region reference type datasets (bug1814)
* add attribute with int type (bug1726)
* add attribute with obj and region reference type (bug1726)
*-------------------------------------------------------------------------*/
if((fid = H5Fcreate(FNAME_REF,H5F_ACC_TRUNC,H5P_DEFAULT,H5P_DEFAULT)) < 0)
return -1;
/* create reference type datasets */
if (make_references(fid) < 0)
goto out;
if(H5Fclose(fid) < 0)
@ -5603,6 +5606,272 @@ out:
return -1;
} /* end make_named_dtype() */
/*-------------------------------------------------------------------------
* Function: add_attr_with_objref
*
* Purpose:
* Create attributes with object reference to objects (dset,
* group, datatype).
*
* Note:
* this function depends on locally created objects, however can be modified
* to be independent as necessary
*
* Programmer: Jonathan Kim (March 23, 2010)
*------------------------------------------------------------------------*/
static herr_t add_attr_with_objref(hid_t file_id, hid_t obj_id)
{
int ret = SUCCEED;
int status;
int data_attr_int[2] = {10,20};
/* attr obj ref */
hsize_t dim_attr_objref[1]={3};
hobj_ref_t data_attr_objref[3];
/* --------------------------------
* add attribute with obj ref type
*/
/* ref to dset */
status = H5Rcreate(&data_attr_objref[0],file_id,NAME_OBJ_DS1,H5R_OBJECT,-1);
if (status < 0)
{
fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
/* ref to group */
status = H5Rcreate(&data_attr_objref[1],file_id,NAME_OBJ_GRP,H5R_OBJECT,-1);
if (status < 0)
{
fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
/* ref to datatype */
status = H5Rcreate(&data_attr_objref[2],file_id,NAME_OBJ_NDTYPE,H5R_OBJECT,-1);
if (status < 0)
{
fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
/* create attr with obj ref type */
status = make_attr(obj_id,1,dim_attr_objref,"Attr_OBJREF",H5T_STD_REF_OBJ,data_attr_objref);
if (status < 0)
{
fprintf(stderr, "Error: %s %d> make_attr failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
out:
return ret;
}
/*-------------------------------------------------------------------------
* Function: add_attr_with_regref
*
* Purpose:
* Create attributes with region reference to dset
*
* Note:
* this function depends on locally created objects, however can be modified
* to be independent as necessary
*
* Programmer: Jonathan Kim (March 23, 2010)
*------------------------------------------------------------------------*/
static herr_t add_attr_with_regref(hid_t file_id, hid_t obj_id)
{
int ret = SUCCEED;
int status;
/* attr region ref */
hid_t sid_regrefed_dset=0;
hsize_t dim_regrefed_dset[2]={3,6};
hsize_t coords_regrefed_dset[3][2] = {{0,1},{1,2},{2,3}};
hsize_t dim_attr_regref[1]= {1}; /* dim of */
hdset_reg_ref_t data_attr_regref[1];
/* -----------------------------------
* add attribute with region ref type
*/
sid_regrefed_dset = H5Screate_simple (2, dim_regrefed_dset, NULL);
if (sid_regrefed_dset < 0)
{
fprintf(stderr, "Error: %s %d> H5Screate_simple failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
/* select elements space for reference */
status = H5Sselect_elements (sid_regrefed_dset, H5S_SELECT_SET, 3, coords_regrefed_dset[0]);
if (status < 0)
{
fprintf(stderr, "Error: %s %d> H5Sselect_elements failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
/* create region reference from elements space */
status = H5Rcreate (&data_attr_regref[0], file_id, NAME_OBJ_DS2, H5R_DATASET_REGION, sid_regrefed_dset);
if (status < 0)
{
fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
/* create attr with region ref type */
status = make_attr(obj_id,1,dim_attr_regref,"Attr_REGREF",H5T_STD_REF_DSETREG,data_attr_regref);
if (status < 0)
{
fprintf(stderr, "Error: %s %d> make_attr failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
out:
if (sid_regrefed_dset > 0)
H5Sclose (sid_regrefed_dset);
return ret;
}
/*-------------------------------------------------------------------------
* Function: gen_refered_objs
*
* Purpose:
* Create objects (dataset, group, datatype) to be referenced
*
* Note:
* This function is to use along with gen_obj_ref() gen_region_ref()
*
* Programmer: Jonathan Kim (March 23, 2010)
*------------------------------------------------------------------------*/
static herr_t gen_refered_objs(hid_t loc_id)
{
int status;
herr_t ret = SUCCEED;
/* objects (dset, group, datatype) */
hid_t sid=0, did1=0, gid=0, tid=0;
hsize_t dims1[1]={3};
int data[3] = {10,20,30};
/* Dset2 */
hid_t sid2=0, did2=0;
hsize_t dims2[2] = {3,16};
char data2[3][16] = {"The quick brown", "fox jumps over ", "the 5 lazy dogs"};
/*-----------------------
* add short dataset
* (define NAME_OBJ_DS1)
*/
sid = H5Screate_simple(1, dims1, NULL);
if (sid < 0)
{
fprintf(stderr, "Error: %s %d> H5Screate_simple failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
did1 = H5Dcreate2 (loc_id, NAME_OBJ_DS1, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (did1 < 0)
{
fprintf(stderr, "Error: %s %d> H5Dcreate2 failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
status = H5Dwrite(did1, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);
if (status < 0)
{
fprintf(stderr, "Error: %s %d> H5Dwrite failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
/*--------------
* add group
* (define NAME_OBJ_GRP)
*/
gid = H5Gcreate2 (loc_id, NAME_OBJ_GRP, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (gid < 0)
{
fprintf(stderr, "Error: %s %d> H5Gcreate2 failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
/*----------------------
* add named datatype
* (define NAME_OBJ_NDTYPE)
*/
tid = H5Tcopy(H5T_NATIVE_INT);
status = H5Tcommit2(loc_id, NAME_OBJ_NDTYPE, tid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (status < 0)
{
fprintf(stderr, "Error: %s %d> H5Tcommit2 failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
/*--------------------------
* create long dataset
* (define NAME_OBJ_DS2)
*/
sid2 = H5Screate_simple (2, dims2, NULL);
if (sid2 < 0)
{
fprintf(stderr, "Error: %s %d> H5Screate_simple failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
/* create normal dataset which is refered */
did2 = H5Dcreate2 (loc_id, NAME_OBJ_DS2, H5T_STD_I8LE, sid2, H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
if (did2 < 0)
{
fprintf(stderr, "Error: %s %d> H5Dcreate2 failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
/* write values to dataset */
status = H5Dwrite (did2, H5T_NATIVE_CHAR, H5S_ALL, H5S_ALL, H5P_DEFAULT, data2);
if (status < 0)
{
fprintf(stderr, "Error: %s %d> H5Dwrite failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
out:
if(did1 > 0)
H5Dclose(did1);
if(gid > 0)
H5Gclose(gid);
if(tid > 0)
H5Tclose(tid);
if(sid > 0)
H5Sclose(sid);
if(did2 > 0)
H5Dclose(did2);
if(sid2 > 0)
H5Sclose(sid2);
return ret;
}
/*-------------------------------------------------------------------------
* Function: gen_obj_ref
*
@ -5616,73 +5885,25 @@ out:
*------------------------------------------------------------------------*/
static herr_t gen_obj_ref(hid_t loc_id)
{
hid_t sid=0, oid=0, tid=0;
hsize_t dims1[1]={3};
hsize_t dims2[1]={3};
int data[3] = {10,20,30};
hobj_ref_t objref_buf[3]; /* write buffer for obj reference */
int status;
herr_t ret = SUCCEED;
/*--------------
* add dataset */
sid = H5Screate_simple(1, dims1, NULL);
if (sid < 0)
{
fprintf(stderr, "Error: %s %d> H5Screate_simple failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
hid_t sid=0, oid=0;
hsize_t dims_dset_objref[1]={3};
oid = H5Dcreate2 (loc_id, NAME_OBJ_DS, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (oid < 0)
{
fprintf(stderr, "Error: %s %d> H5Dcreate2 failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
/* attr with int type */
hsize_t dim_attr_int[1]={2};
int data_attr_int[2] = {10,20};
status = H5Dwrite(oid, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);
if (status < 0)
{
fprintf(stderr, "Error: %s %d> H5Dwrite failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
H5Dclose(oid);
H5Sclose(sid);
/*--------------
* add group */
oid = H5Gcreate2 (loc_id, NAME_OBJ_GRP, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (oid < 0)
{
fprintf(stderr, "Error: %s %d> H5Gcreate2 failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
H5Gclose(oid);
/*----------------------
* add named datatype
*/
tid = H5Tcopy(H5T_NATIVE_INT);
status = H5Tcommit2(loc_id, NAME_OBJ_NDTYPE, tid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (status < 0)
{
fprintf(stderr, "Error: %s %d> H5Tcommit2 failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
/* write buffer for obj reference */
hobj_ref_t objref_buf[3];
/*---------------------------------------------------------
* create obj references to the previously created objects.
* Passing -1 as reference is an object.*/
/* obj ref to dataset */
status = H5Rcreate (&objref_buf[0], loc_id, NAME_OBJ_DS, H5R_OBJECT, -1);
status = H5Rcreate (&objref_buf[0], loc_id, NAME_OBJ_DS1, H5R_OBJECT, -1);
if (status < 0)
{
fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
@ -5711,7 +5932,7 @@ static herr_t gen_obj_ref(hid_t loc_id)
/*---------------------------------------------------------
* create dataset contain references
*/
sid = H5Screate_simple (1, dims2, NULL);
sid = H5Screate_simple (1, dims_dset_objref, NULL);
if (sid < 0)
{
fprintf(stderr, "Error: %s %d> H5Screate_simple failed.\n", FUNC, __LINE__);
@ -5735,11 +5956,31 @@ static herr_t gen_obj_ref(hid_t loc_id)
goto out;
}
/* add attribute with int type */
if (make_attr(oid,1,dim_attr_int,"integer",H5T_NATIVE_INT,data_attr_int) < 0)
goto out;
/* add attribute with obj ref */
status = add_attr_with_objref(loc_id, oid);
if (status < 0)
{
fprintf(stderr, "Error: %s %d> add_attr_with_objref failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
/* add attribute with region ref */
status = add_attr_with_regref(loc_id, oid);
if (status < 0)
{
fprintf(stderr, "Error: %s %d> add_attr_with_regref failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
out:
if(oid > 0)
H5Dclose(oid);
if(tid > 0)
H5Tclose(tid);
if(sid > 0)
H5Sclose(sid);
@ -5759,13 +6000,18 @@ out:
*------------------------------------------------------------------------*/
static herr_t gen_region_ref(hid_t loc_id)
{
hid_t sid=0, oid1=0, oid2=0;
int status;
herr_t ret = SUCCEED;
char data[3][16] = {"The quick brown", "fox jumps over ", "the 5 lazy dogs"};
hsize_t dims2[2] = {3,16};
hsize_t coords[4][2] = { {0,1}, {2,11}, {1,0}, {2,4} };
/* target dataset */
hid_t sid_trg=0;
hsize_t dims_trg[2] = {3,16};
/* dset with region ref type */
hid_t sid_ref=0, oid_ref=0;
/* region ref to target dataset */
hsize_t coords[4][2] = { {0,1}, {2,11}, {1,0}, {2,4} };
hdset_reg_ref_t rr_data[2];
hsize_t start[2] = {0,0};
hsize_t stride[2] = {2,11};
@ -5773,34 +6019,20 @@ static herr_t gen_region_ref(hid_t loc_id)
hsize_t block[2] = {1,3};
hsize_t dims1[1] = {2};
sid = H5Screate_simple (2, dims2, NULL);
if (sid < 0)
/* attr with int type */
hsize_t dim_attr_int[1]={2};
int data_attr_int[2] = {10,20};
sid_trg = H5Screate_simple (2, dims_trg, NULL);
if (sid_trg < 0)
{
fprintf(stderr, "Error: %s %d> H5Screate_simple failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
/* create normal dataset which is refered */
oid2 = H5Dcreate2 (loc_id, REG_REF_DS2, H5T_STD_I8LE, sid, H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
if (oid2 < 0)
{
fprintf(stderr, "Error: %s %d> H5Dcreate2 failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
/* write values to dataset */
status = H5Dwrite (oid2, H5T_NATIVE_CHAR, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);
if (status < 0)
{
fprintf(stderr, "Error: %s %d> H5Dwrite failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
/* select elements space for reference */
status = H5Sselect_elements (sid, H5S_SELECT_SET, 4, coords[0]);
status = H5Sselect_elements (sid_trg, H5S_SELECT_SET, 4, coords[0]);
if (status < 0)
{
fprintf(stderr, "Error: %s %d> H5Sselect_elements failed.\n", FUNC, __LINE__);
@ -5809,7 +6041,7 @@ static herr_t gen_region_ref(hid_t loc_id)
}
/* create region reference from elements space */
status = H5Rcreate (&rr_data[0], loc_id, REG_REF_DS2, H5R_DATASET_REGION, sid);
status = H5Rcreate (&rr_data[0], loc_id, NAME_OBJ_DS2, H5R_DATASET_REGION, sid_trg);
if (status < 0)
{
fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
@ -5818,7 +6050,7 @@ static herr_t gen_region_ref(hid_t loc_id)
}
/* select hyperslab space for reference */
status = H5Sselect_hyperslab (sid, H5S_SELECT_SET, start, stride, count, block);
status = H5Sselect_hyperslab (sid_trg, H5S_SELECT_SET, start, stride, count, block);
if (status < 0)
{
fprintf(stderr, "Error: %s %d> H5Sselect_hyperslab failed.\n", FUNC, __LINE__);
@ -5827,7 +6059,7 @@ static herr_t gen_region_ref(hid_t loc_id)
}
/* create region reference from hyperslab space */
status = H5Rcreate (&rr_data[1], loc_id, REG_REF_DS2, H5R_DATASET_REGION, sid);
status = H5Rcreate (&rr_data[1], loc_id, NAME_OBJ_DS2, H5R_DATASET_REGION, sid_trg);
if (status < 0)
{
fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
@ -5835,11 +6067,9 @@ static herr_t gen_region_ref(hid_t loc_id)
goto out;
}
H5Sclose (sid);
/* Create dataspace. */
sid = H5Screate_simple (1, dims1, NULL);
if (sid < 0)
sid_ref = H5Screate_simple (1, dims1, NULL);
if (sid_ref < 0)
{
fprintf(stderr, "Error: %s %d> H5Screate_simple failed.\n", FUNC, __LINE__);
ret = FAIL;
@ -5847,8 +6077,8 @@ static herr_t gen_region_ref(hid_t loc_id)
}
/* create region reference dataset */
oid1 = H5Dcreate2 (loc_id, REG_REF_DS1, H5T_STD_REF_DSETREG, sid, H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
if (oid1 < 0)
oid_ref = H5Dcreate2 (loc_id, REG_REF_DS1, H5T_STD_REF_DSETREG, sid_ref, H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
if (oid_ref < 0)
{
fprintf(stderr, "Error: %s %d> H5Dcreate2 failed.\n", FUNC, __LINE__);
ret = FAIL;
@ -5856,7 +6086,7 @@ static herr_t gen_region_ref(hid_t loc_id)
}
/* write data as region references */
status = H5Dwrite (oid1, H5T_STD_REF_DSETREG, H5S_ALL, H5S_ALL, H5P_DEFAULT, rr_data);
status = H5Dwrite (oid_ref, H5T_STD_REF_DSETREG, H5S_ALL, H5S_ALL, H5P_DEFAULT, rr_data);
if (status < 0)
{
fprintf(stderr, "Error: %s %d> H5Dwrite failed.\n", FUNC, __LINE__);
@ -5864,13 +6094,35 @@ static herr_t gen_region_ref(hid_t loc_id)
goto out;
}
/* add attribute with int type */
if (make_attr(oid_ref,1,dim_attr_int,"integer",H5T_NATIVE_INT,data_attr_int) < 0)
goto out;
/* add attribute with obj ref */
status = add_attr_with_objref(loc_id, oid_ref);
if (status < 0)
{
fprintf(stderr, "Error: %s %d> add_attr_with_objref failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
/* add attribute with region ref */
status = add_attr_with_regref(loc_id, oid_ref);
if (status < 0)
{
fprintf(stderr, "Error: %s %d> add_attr_with_regref failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
out:
if (oid1 > 0)
H5Dclose (oid1);
if (oid2 > 0)
H5Dclose (oid2);
if (sid > 0)
H5Sclose (sid);
if (oid_ref > 0)
H5Dclose (oid_ref);
if (sid_ref > 0)
H5Sclose (sid_ref);
if (sid_trg > 0)
H5Sclose (sid_trg);
return ret;
}
@ -5888,6 +6140,14 @@ static herr_t make_references(hid_t loc_id)
herr_t ret = SUCCEED;
herr_t status;
/* add target objects */
status = gen_refered_objs(loc_id);
if (status == FAIL)
{
fprintf(stderr, "Failed to generate referenced object.\n");
ret = FAIL;
}
/* add object reference */
status = gen_obj_ref(loc_id);
if (status == FAIL)

BIN
tools/h5repack/testfiles/h5repack_refs.h5
View File

Binary file not shown.