diff options
Diffstat (limited to 'tools')
| -rw-r--r-- | tools/h5repack/h5repack.c | 331 | ||||
| -rw-r--r-- | tools/h5repack/h5repack.h | 16 | ||||
| -rwxr-xr-x | tools/h5repack/h5repack.sh.in | 2 | ||||
| -rw-r--r-- | tools/h5repack/h5repack_copy.c | 331 | ||||
| -rw-r--r-- | tools/h5repack/h5repack_refs.c | 24 | ||||
| -rw-r--r-- | tools/h5repack/h5repacktst.c | 400 | ||||
| -rw-r--r-- | tools/h5repack/testfiles/h5repack_refs.h5 | bin | 9280 -> 9472 bytes |
7 files changed, 701 insertions, 403 deletions
diff --git a/tools/h5repack/h5repack.c b/tools/h5repack/h5repack.c index db0b158..96b8369 100644 --- a/tools/h5repack/h5repack.c +++ b/tools/h5repack/h5repack.c @@ -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 diff --git a/tools/h5repack/h5repack.h b/tools/h5repack/h5repack.h index 3c3b9b8..4d601ec 100644 --- a/tools/h5repack/h5repack.h +++ b/tools/h5repack/h5repack.h @@ -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 } diff --git a/tools/h5repack/h5repack.sh.in b/tools/h5repack/h5repack.sh.in index 35fc5fd..6a4f63e 100755 --- a/tools/h5repack/h5repack.sh.in +++ b/tools/h5repack/h5repack.sh.in @@ -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 diff --git a/tools/h5repack/h5repack_copy.c b/tools/h5repack/h5repack_copy.c index f95db63..12fdabc 100644 --- a/tools/h5repack/h5repack_copy.c +++ b/tools/h5repack/h5repack_copy.c @@ -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); @@ -1200,195 +1190,6 @@ 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 * * Purpose: print name, filters, percentage compression of a dataset @@ -1494,138 +1295,6 @@ 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 * * Purpose: copy user block from one file to another diff --git a/tools/h5repack/h5repack_refs.c b/tools/h5repack/h5repack_refs.c index 9945f49..fcdfbd5 100644 --- a/tools/h5repack/h5repack_refs.c +++ b/tools/h5repack/h5repack_refs.c @@ -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; diff --git a/tools/h5repack/h5repacktst.c b/tools/h5repack/h5repacktst.c index 0d6f186..9b17144 100644 --- a/tools/h5repack/h5repacktst.c +++ b/tools/h5repack/h5repacktst.c @@ -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) @@ -5604,29 +5607,173 @@ out: } /* end make_named_dtype() */ /*------------------------------------------------------------------------- - * Function: gen_obj_ref + * Function: add_attr_with_objref * * Purpose: - * Generate object references to objects (dataset,group and named datatype) + * Create attributes with object reference to objects (dset, + * group, datatype). * * Note: - * copied from h5copygentest.c and upate to create named datatype + * this function depends on locally created objects, however can be modified + * to be independent as necessary * - * Programmer: Jonathan Kim (March 18, 2010) + * Programmer: Jonathan Kim (March 23, 2010) *------------------------------------------------------------------------*/ -static herr_t gen_obj_ref(hid_t loc_id) +static herr_t add_attr_with_objref(hid_t file_id, hid_t obj_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 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; - /*-------------- - * add dataset */ + /* 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) { @@ -5635,15 +5782,15 @@ static herr_t gen_obj_ref(hid_t loc_id) goto out; } - oid = H5Dcreate2 (loc_id, NAME_OBJ_DS, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); - if (oid < 0) + 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(oid, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, data); + 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__); @@ -5651,22 +5798,21 @@ static herr_t gen_obj_ref(hid_t loc_id) goto out; } - H5Dclose(oid); - H5Sclose(sid); - /*-------------- - * add group */ - oid = H5Gcreate2 (loc_id, NAME_OBJ_GRP, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); - if (oid < 0) + * 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; } - H5Gclose(oid); /*---------------------- * 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); @@ -5677,12 +5823,87 @@ static herr_t gen_obj_ref(hid_t loc_id) 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 + * + * Purpose: + * Generate object references to objects (dataset,group and named datatype) + * + * Note: + * copied from h5copygentest.c and upate to create named datatype + * + * Programmer: Jonathan Kim (March 18, 2010) + *------------------------------------------------------------------------*/ +static herr_t gen_obj_ref(hid_t loc_id) +{ + int status; + herr_t ret = SUCCEED; + + hid_t sid=0, oid=0; + hsize_t dims_dset_objref[1]={3}; + + /* attr with int type */ + hsize_t dim_attr_int[1]={2}; + int data_attr_int[2] = {10,20}; + + /* 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) - { - 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; - } + /* attr with int type */ + hsize_t dim_attr_int[1]={2}; + int data_attr_int[2] = {10,20}; - /* write values to dataset */ - status = H5Dwrite (oid2, H5T_NATIVE_CHAR, H5S_ALL, H5S_ALL, H5P_DEFAULT, data); - if (status < 0) + sid_trg = H5Screate_simple (2, dims_trg, NULL); + if (sid_trg < 0) { - fprintf(stderr, "Error: %s %d> H5Dwrite failed.\n", FUNC, __LINE__); + fprintf(stderr, "Error: %s %d> H5Screate_simple 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) diff --git a/tools/h5repack/testfiles/h5repack_refs.h5 b/tools/h5repack/testfiles/h5repack_refs.h5 Binary files differindex 23d53e6..525267f 100644 --- a/tools/h5repack/testfiles/h5repack_refs.h5 +++ b/tools/h5repack/testfiles/h5repack_refs.h5 |