diff options
| -rw-r--r-- | release_docs/RELEASE.txt | 1 | ||||
| -rw-r--r-- | src/H5Aint.c | 536 | ||||
| -rw-r--r-- | src/H5Apkg.h | 9 | ||||
| -rw-r--r-- | src/H5Oainfo.c | 66 | ||||
| -rw-r--r-- | src/H5Oattr.c | 283 | ||||
| -rwxr-xr-x | test/objcopy.c | 189 |
6 files changed, 769 insertions, 315 deletions
diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt index b225ae5..7ca6ecf 100644 --- a/release_docs/RELEASE.txt +++ b/release_docs/RELEASE.txt @@ -51,6 +51,7 @@ New Features Library: -------- + - Added support for dense attributes to H5Ocopy. (XCao/NAF - 2009/01/29) - Added H5Pset_elink_cb and H5Pget_elink_cb functions to support a user-defined callback function for external link traversal. (NAF - 2009/01/08) diff --git a/src/H5Aint.c b/src/H5Aint.c index aadf79c..a93d807 100644 --- a/src/H5Aint.c +++ b/src/H5Aint.c @@ -66,6 +66,17 @@ typedef struct { size_t curr_attr; /* Current attribute to operate on */ } H5A_dense_bt_ud_t; +/* Data exchange structure to use when copying an attribute from _SRC to _DST */ +typedef struct { + H5O_ainfo_t *ainfo; /* dense information */ + H5F_t *file; /* file */ + hbool_t *recompute_size; /* Flag to indicate if size changed */ + H5O_copy_t *cpy_info; /* Information on copying options */ + hid_t dxpl_id; /* DXPL for operation */ + H5O_loc_t *oloc_src; + H5O_loc_t *oloc_dst; +} H5A_dense_file_cp_ud_t; + /********************/ /* Package Typedefs */ @@ -765,3 +776,528 @@ H5A_set_version(const H5F_t *f, H5A_t *attr) FUNC_LEAVE_NOAPI(SUCCEED) } /* end H5A_set_version() */ + +/*------------------------------------------------------------------------- + * Function: H5A_attr_copy_file + * + * Purpose: Copies a message from _MESG to _DEST in file + * + * Return: Success: Ptr to _DEST + * + * Failure: NULL + * + * Programmer: Quincey Koziol + * November 1, 2005 + * + *------------------------------------------------------------------------- + */ +H5A_t * +H5A_attr_copy_file(H5A_t *attr_src, H5F_t *file_dst, hbool_t *recompute_size, + H5O_copy_t *cpy_info, hid_t dxpl_id) +{ + H5A_t *attr_dst = NULL; + + /* for dataype conversion */ + hid_t tid_src = -1; /* Datatype ID for source datatype */ + hid_t tid_dst = -1; /* Datatype ID for destination datatype */ + hid_t tid_mem = -1; /* Datatype ID for memory datatype */ + void *buf = NULL; /* Buffer for copying data */ + void *reclaim_buf = NULL; /* Buffer for reclaiming data */ + hid_t buf_sid = -1; /* ID for buffer dataspace */ + + H5A_t *ret_value; /* Return value */ + + FUNC_ENTER_NOAPI_NOINIT(H5A_attr_copy_file) + + /* check args */ + HDassert(attr_src); + HDassert(file_dst); + HDassert(cpy_info); + HDassert(!cpy_info->copy_without_attr); + + /* Allocate space for the destination message */ + if(NULL == (attr_dst = H5FL_CALLOC(H5A_t))) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") + + /* Copy the top level of the attribute */ + *attr_dst = *attr_src; + + if(NULL == (attr_dst->shared = H5FL_CALLOC(H5A_shared_t))) + HGOTO_ERROR(H5E_FILE, H5E_NOSPACE, NULL, "can't allocate shared attr structure") + + /* Don't have an opened group location for copy */ + H5O_loc_reset(&(attr_dst->shared->oloc)); + H5G_name_reset(&(attr_dst->path)); + attr_dst->obj_opened = FALSE; + + /* Reference count for the header message in the cache */ + attr_dst->shared->nrefs = 1; + + /* Copy attribute's name */ + attr_dst->shared->name = H5MM_strdup(attr_src->shared->name); + HDassert(attr_dst->shared->name); + + /* Copy attribute's datatype */ + /* (Start destination datatype as transient, even if source is named) */ + if(NULL == (attr_dst->shared->dt = H5T_copy(attr_src->shared->dt, H5T_COPY_ALL))) + HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, NULL, "cannot copy datatype") + + /* Set the location of the destination datatype */ + if(H5T_set_loc(attr_dst->shared->dt, file_dst, H5T_LOC_DISK) < 0) + HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, NULL, "cannot mark datatype on disk") + + /* Check for named datatype being copied */ + if(H5T_committed(attr_src->shared->dt)) { + H5O_loc_t *src_oloc; /* Pointer to source datatype's object location */ + H5O_loc_t *dst_oloc; /* Pointer to dest. datatype's object location */ + + /* Get group entries for source & destination */ + src_oloc = H5T_oloc(attr_src->shared->dt); + HDassert(src_oloc); + dst_oloc = H5T_oloc(attr_dst->shared->dt); + HDassert(dst_oloc); + + /* Reset object location for new object */ + H5O_loc_reset(dst_oloc); + dst_oloc->file = file_dst; + + /* Copy the shared object from source to destination */ + if(H5O_copy_header_map(src_oloc, dst_oloc, dxpl_id, cpy_info, FALSE) < 0) + HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, NULL, "unable to copy object") + + /* Update shared message info from named datatype info */ + H5T_update_shared(attr_dst->shared->dt); + } /* end if */ + else { + /* If the datatype is not named, it may have been shared in the + * source file's heap. Un-share it for now. We'll try to shared + * it in the destination file below. + */ + if(H5O_msg_reset_share(H5O_DTYPE_ID, attr_dst->shared->dt) < 0) + HGOTO_ERROR(H5E_OHDR, H5E_CANTINIT, NULL, "unable to reset datatype sharing") + } /* end else */ + + /* Copy the dataspace for the attribute */ + attr_dst->shared->ds = H5S_copy(attr_src->shared->ds, FALSE, FALSE); + HDassert(attr_dst->shared->ds); + + /* Reset the dataspace's sharing in the source file before trying to share + * it in the destination. + */ + if(H5O_msg_reset_share(H5O_SDSPACE_ID, attr_dst->shared->ds) < 0) + HGOTO_ERROR(H5E_OHDR, H5E_CANTINIT, NULL, "unable to reset dataspace sharing") + + + /* Try to share both the datatype and dataset. This does nothing if the + * datatype is committed or sharing is disabled. + */ + if(H5SM_try_share(file_dst, dxpl_id, NULL, H5O_DTYPE_ID, attr_dst->shared->dt, NULL) < 0) + HGOTO_ERROR(H5E_OHDR, H5E_WRITEERROR, NULL, "can't share attribute datatype") + if(H5SM_try_share(file_dst, dxpl_id, NULL, H5O_SDSPACE_ID, attr_dst->shared->ds, NULL) < 0) + HGOTO_ERROR(H5E_OHDR, H5E_WRITEERROR, NULL, "can't share attribute dataspace") + + /* Compute the sizes of the datatype and dataspace. This is their raw + * size unless they're shared. + */ + attr_dst->shared->dt_size = H5O_msg_raw_size(file_dst, H5O_DTYPE_ID, FALSE, attr_dst->shared->dt); + HDassert(attr_dst->shared->dt_size > 0); + attr_dst->shared->ds_size = H5O_msg_raw_size(file_dst, H5O_SDSPACE_ID, FALSE, attr_dst->shared->ds); + HDassert(attr_dst->shared->ds_size > 0); + + /* Check whether to recompute the size of the attribute */ + /* (happens when the datatype or dataspace changes sharing status) */ + if(attr_dst->shared->dt_size != attr_src->shared->dt_size || attr_dst->shared->ds_size != attr_src->shared->ds_size) + *recompute_size = TRUE; + + /* Compute the size of the data */ + H5_ASSIGN_OVERFLOW(attr_dst->shared->data_size, H5S_GET_EXTENT_NPOINTS(attr_dst->shared->ds) * H5T_get_size(attr_dst->shared->dt), hsize_t, size_t); + + /* Copy (& convert) the data, if necessary */ + if(attr_src->shared->data) { + if(NULL == (attr_dst->shared->data = H5FL_BLK_MALLOC(attr_buf, attr_dst->shared->data_size))) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") + + /* Check if we need to convert data */ + if(H5T_detect_class(attr_src->shared->dt, H5T_VLEN) > 0) { + H5T_path_t *tpath_src_mem, *tpath_mem_dst; /* Datatype conversion paths */ + H5T_t *dt_mem; /* Memory datatype */ + size_t src_dt_size; /* Source datatype size */ + size_t tmp_dt_size; /* Temp. datatype size */ + size_t max_dt_size; /* Max atatype size */ + H5S_t *buf_space; /* Dataspace describing buffer */ + hsize_t buf_dim; /* Dimension for buffer */ + size_t nelmts; /* Number of elements in buffer */ + size_t buf_size; /* Size of copy buffer */ + + /* Create datatype ID for src datatype */ + if((tid_src = H5I_register(H5I_DATATYPE, attr_src->shared->dt, FALSE)) < 0) + HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, NULL, "unable to register source file datatype") + + /* create a memory copy of the variable-length datatype */ + if(NULL == (dt_mem = H5T_copy(attr_src->shared->dt, H5T_COPY_TRANSIENT))) + HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, NULL, "unable to copy") + if((tid_mem = H5I_register(H5I_DATATYPE, dt_mem, FALSE)) < 0) + HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, NULL, "unable to register memory datatype") + + /* create variable-length datatype at the destinaton file */ + if((tid_dst = H5I_register(H5I_DATATYPE, attr_dst->shared->dt, FALSE)) < 0) + HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, NULL, "unable to register destination file datatype") + + /* Set up the conversion functions */ + if(NULL == (tpath_src_mem = H5T_path_find(attr_src->shared->dt, dt_mem, NULL, NULL, dxpl_id, FALSE))) + HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, NULL, "unable to convert between src and mem datatypes") + if(NULL == (tpath_mem_dst = H5T_path_find(dt_mem, attr_dst->shared->dt, NULL, NULL, dxpl_id, FALSE))) + HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, NULL, "unable to convert between mem and dst datatypes") + + /* Determine largest datatype size */ + if(0 == (src_dt_size = H5T_get_size(attr_src->shared->dt))) + HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, NULL, "unable to determine datatype size") + if(0 == (tmp_dt_size = H5T_get_size(dt_mem))) + HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, NULL, "unable to determine datatype size") + max_dt_size = MAX(src_dt_size, tmp_dt_size); + if(0 == (tmp_dt_size = H5T_get_size(attr_dst->shared->dt))) + HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, NULL, "unable to determine datatype size") + max_dt_size = MAX(max_dt_size, tmp_dt_size); + + /* Set number of whole elements that fit in buffer */ + if(0 == (nelmts = attr_src->shared->data_size / src_dt_size)) + HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, NULL, "element size too large") + + /* Set up number of bytes to copy, and initial buffer size */ + buf_size = nelmts * max_dt_size; + + /* Create dataspace for number of elements in buffer */ + buf_dim = nelmts; + + /* Create the space and set the initial extent */ + if(NULL == (buf_space = H5S_create_simple((unsigned)1, &buf_dim, NULL))) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, NULL, "can't create simple dataspace") + + /* Atomize */ + if((buf_sid = H5I_register(H5I_DATASPACE, buf_space, FALSE)) < 0) { + H5S_close(buf_space); + HGOTO_ERROR(H5E_ATOM, H5E_CANTREGISTER, NULL, "unable to register dataspace ID") + } /* end if */ + + /* Allocate memory for recclaim buf */ + if(NULL == (reclaim_buf = H5FL_BLK_MALLOC(attr_buf, buf_size))) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation NULLed for raw data chunk") + + /* Allocate memory for copying the chunk */ + if(NULL == (buf = H5FL_BLK_MALLOC(attr_buf, buf_size))) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation NULLed for raw data chunk") + + HDmemcpy(buf, attr_src->shared->data, attr_src->shared->data_size); + + /* Convert from source file to memory */ + if(H5T_convert(tpath_src_mem, tid_src, tid_mem, nelmts, (size_t)0, (size_t)0, buf, NULL, dxpl_id) < 0) + HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, NULL, "datatype conversion NULLed") + + HDmemcpy(reclaim_buf, buf, buf_size); + + /* Convert from memory to destination file */ + if(H5T_convert(tpath_mem_dst, tid_mem, tid_dst, nelmts, (size_t)0, (size_t)0, buf, NULL, dxpl_id) < 0) + HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, NULL, "datatype conversion NULLed") + + HDmemcpy(attr_dst->shared->data, buf, attr_dst->shared->data_size); + + if(H5D_vlen_reclaim(tid_mem, buf_space, H5P_DATASET_XFER_DEFAULT, reclaim_buf) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_BADITER, NULL, "unable to reclaim variable-length data") + } /* end if */ + else { + HDassert(attr_dst->shared->data_size == attr_src->shared->data_size); + HDmemcpy(attr_dst->shared->data, attr_src->shared->data, attr_src->shared->data_size); + } /* end else */ + } /* end if(attr_src->shared->data) */ + + /* Recompute the version to encode the destination attribute */ + if(H5A_set_version(file_dst, attr_dst) < 0) + HGOTO_ERROR(H5E_ATTR, H5E_CANTSET, NULL, "unable to update attribute version") + + /* Indicate that the fill values aren't to be written out */ + attr_dst->shared->initialized = TRUE; + + /* Set return value */ + ret_value = attr_dst; + +done: + if(buf_sid > 0) + if(H5I_dec_ref(buf_sid, FALSE) < 0) + HDONE_ERROR(H5E_ATTR, H5E_CANTFREE, NULL, "Can't decrement temporary dataspace ID") + if(tid_src > 0) + /* Don't decrement ID, we want to keep underlying datatype */ + if(H5I_remove(tid_src) == NULL) + HDONE_ERROR(H5E_ATTR, H5E_CANTFREE, NULL, "Can't decrement temporary datatype ID") + if(tid_dst > 0) + /* Don't decrement ID, we want to keep underlying datatype */ + if(H5I_remove(tid_dst) == NULL) + HDONE_ERROR(H5E_ATTR, H5E_CANTFREE, NULL, "Can't decrement temporary datatype ID") + if(tid_mem > 0) + /* Decrement the memory datatype ID, it's transient */ + if(H5I_dec_ref(tid_mem, FALSE) < 0) + HDONE_ERROR(H5E_ATTR, H5E_CANTFREE, NULL, "Can't decrement temporary datatype ID") + if(buf) + buf = H5FL_BLK_FREE(attr_buf, buf); + if(reclaim_buf) + reclaim_buf = H5FL_BLK_FREE(attr_buf, reclaim_buf); + + /* Release destination attribute information on failure */ + if(!ret_value && attr_dst && H5A_close(attr_dst) < 0) + HDONE_ERROR(H5E_ATTR, H5E_CANTFREE, NULL, "can't close attribute") + + FUNC_LEAVE_NOAPI(ret_value) +} /* H5A_attr_copy_file() */ + + +/*------------------------------------------------------------------------- + * Function: H5A_attr_post_copy_file + * + * Purpose: Finish copying a message from between files. + * We have to copy the values of a reference attribute in the + * post copy because H5O_post_copy_file() fails at the case that + * an object may have a reference attribute that points to the + * object itself. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Peter Cao + * March 6, 2005 + * + *------------------------------------------------------------------------- + */ +herr_t +H5A_attr_post_copy_file(const H5O_loc_t *src_oloc, const H5A_t UNUSED *attr_src, + H5O_loc_t *dst_oloc, H5A_t *attr_dst, hid_t dxpl_id, H5O_copy_t *cpy_info) +{ + H5F_t *file_src = src_oloc->file; + H5F_t *file_dst = dst_oloc->file; + herr_t ret_value = SUCCEED; /* Return value */ + + + FUNC_ENTER_NOAPI_NOINIT(H5A_attr_post_copy_file) + + /* check args */ + HDassert(attr_dst); + HDassert(file_dst); + + + /* Only need to fix reference attribute with real data being copied to + * another file. + */ + if((NULL != attr_dst->shared->data) && (H5T_get_class(attr_dst->shared->dt, FALSE) == H5T_REFERENCE) ) { + + /* copy object pointed by reference. The current implementation does not + * deal with nested reference such as reference in a compound structure + */ + + /* Check for expanding references */ + if(cpy_info->expand_ref) { + size_t ref_count; + + /* Determine # of reference elements to copy */ + ref_count = attr_dst->shared->data_size / H5T_get_size(attr_dst->shared->dt); + + /* Copy objects referenced in source buffer to destination file and set destination elements */ + if(H5O_copy_expand_ref(file_src, attr_dst->shared->data, dxpl_id, + file_dst, attr_dst->shared->data, ref_count, H5T_get_ref_type(attr_dst->shared->dt), cpy_info) < 0) + HGOTO_ERROR(H5E_ATTR, H5E_CANTCOPY, FAIL, "unable to copy reference attribute") + } /* end if */ + else + /* Reset value to zero */ + HDmemset(attr_dst->shared->data, 0, attr_dst->shared->data_size); + } /* end if */ + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* H5A_attr_post_copy_file() */ + + +/*------------------------------------------------------------------------- + * Function: H5A_dense_copy_file_cb + * + * Purpose: Callback routine for copying a dense attribute from SRC to DST. + * + * Return: Success: Non-negative + * Failure: Negative + * + * Programmer: Peter Cao + * xcao@hdfgroup.org + * July 20, 2007 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5A_dense_copy_file_cb(const H5A_t *attr_src, void *_udata) +{ + H5A_dense_file_cp_ud_t *udata = (H5A_dense_file_cp_ud_t *)_udata; + H5A_t *attr_dst = NULL; + herr_t ret_value = H5_ITER_CONT; /* Return value */ + + FUNC_ENTER_NOAPI_NOINIT(H5A_dense_copy_file_cb) + + /* check arguments */ + HDassert(attr_src); + HDassert(udata); + HDassert(udata->ainfo); + HDassert(udata->file); + HDassert(udata->cpy_info); + + if ( NULL == (attr_dst=H5A_attr_copy_file(attr_src, udata->file, + udata->recompute_size, udata->cpy_info, udata->dxpl_id))) + HGOTO_ERROR(H5E_ATTR, H5E_CANTCOPY, H5_ITER_ERROR, "can't copy attribute") + + /* Reset shared location information */ + if(H5O_msg_reset_share(H5O_ATTR_ID, attr_dst) < 0) + HGOTO_ERROR(H5E_OHDR, H5E_CANTINIT, FAIL, "unable to reset attribute sharing") + + /* Insert attribute into dense storage */ + if(H5A_dense_insert(udata->file, udata->dxpl_id, udata->ainfo, attr_dst) < 0) + HGOTO_ERROR(H5E_OHDR, H5E_CANTINSERT, H5_ITER_ERROR, "unable to add to dense storage") + +done: + if (attr_dst) { + (void)H5A_free(attr_dst); + H5FL_FREE(H5A_t, attr_dst); + } + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5A_dense_copy_file_cb() */ + + +/*------------------------------------------------------------------------- + * Function: H5A_dense_copy_file_all + * + * Purpose: Copy all dense attributes from SRC to DST. + * + * Return: Success: Non-negative + * Failure: Negative + * + * Programmer: Peter Cao + * xcao@hdfgroup.org + * July 20, 2007 + * + *------------------------------------------------------------------------- + */ +herr_t +H5A_dense_copy_file_all(H5F_t *file_src, H5O_ainfo_t *ainfo_src, H5F_t *file_dst, + H5O_ainfo_t *ainfo_dst, hbool_t *recompute_size, H5O_copy_t *cpy_info, hid_t dxpl_id) +{ + H5A_dense_file_cp_ud_t udata; /* User data for iteration callback */ + H5A_attr_iter_op_t attr_op; /* Attribute operator */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI_NOINIT(H5A_dense_copy_file_all) + + /* check arguments */ + HDassert(ainfo_src); + HDassert(ainfo_dst); + + udata.ainfo = ainfo_dst; /* Destination dense information */ + udata.file = file_dst; /* Destination file */ + udata.recompute_size = recompute_size; /* Flag to indicate if size changed */ + udata.cpy_info = cpy_info; /* Information on copying options */ + udata.dxpl_id = dxpl_id; /* DXPL for operation */ + + attr_op.op_type = H5A_ATTR_OP_LIB; + attr_op.u.lib_op = H5A_dense_copy_file_cb; + + if(H5A_dense_iterate(file_src, dxpl_id, (hid_t)0, ainfo_src, H5_INDEX_NAME, + H5_ITER_NATIVE, (hsize_t)0, NULL, &attr_op, &udata) < 0) + HGOTO_ERROR(H5E_ATTR, H5E_CANTINIT, FAIL, "error building attribute table") + +done: + FUNC_LEAVE_NOAPI(ret_value) +} + + +/*------------------------------------------------------------------------- + * Function: H5A_dense_post_copy_file_cb + * + * Purpose: Callback routine to perfom post copy for a dense attribute. + * + * Return: Success: Non-negative + * Failure: Negative + * + * Programmer: Peter Cao + * xcao@hdfgroup.org + * July 25, 2007 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5A_dense_post_copy_file_cb(const H5A_t *attr_dst, void *_udata) +{ + H5A_dense_file_cp_ud_t *udata = (H5A_dense_file_cp_ud_t *)_udata; + H5A_t *attr_src = NULL; + herr_t ret_value = H5_ITER_CONT; /* Return value */ + + FUNC_ENTER_NOAPI_NOINIT(H5A_dense_post_copy_file_cb) + + /* check arguments */ + HDassert(attr_dst); + HDassert(udata); + HDassert(udata->ainfo); + HDassert(udata->file); + HDassert(udata->cpy_info); + + if ( H5A_attr_post_copy_file(udata->oloc_src, NULL, + udata->oloc_dst, attr_dst, udata->dxpl_id, udata->cpy_info) < 0) + HGOTO_ERROR(H5E_ATTR, H5E_CANTCOPY, H5_ITER_ERROR, "can't copy attribute") + +done: + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5A_dense_post_copy_file_cb() */ + + +/*------------------------------------------------------------------------- + * Function: H5A_dense_post_copy_file_all + * + * Purpose: Do post copy for all dense attributes. + * + * Return: Success: Non-negative + * Failure: Negative + * + * Programmer: Peter Cao + * xcao@hdfgroup.org + * July 25, 2007 + * + *------------------------------------------------------------------------- + */ +herr_t +H5A_dense_post_copy_file_all(const H5O_loc_t *src_oloc, const H5O_ainfo_t *ainfo_src, + H5O_loc_t *dst_oloc, H5O_ainfo_t *ainfo_dst, hid_t dxpl_id, H5O_copy_t *cpy_info) +{ + H5A_dense_file_cp_ud_t udata; /* User data for iteration callback */ + H5A_attr_iter_op_t attr_op; /* Attribute operator */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI_NOINIT(H5A_dense_post_copy_file_all) + + /* check arguments */ + HDassert(ainfo_src); + HDassert(ainfo_dst); + HDassert(src_oloc); + HDassert(dst_oloc); + HDassert(src_oloc->file); + HDassert(dst_oloc->file); + + udata.ainfo = ainfo_src; + udata.file = src_oloc->file; + udata.cpy_info = cpy_info; /* Information on copying options */ + udata.dxpl_id = dxpl_id; /* DXPL for operation */ + udata.oloc_src = src_oloc; + udata.oloc_dst = dst_oloc; + + attr_op.op_type = H5A_ATTR_OP_LIB; + attr_op.u.lib_op = H5A_dense_post_copy_file_cb; + + if(H5A_dense_iterate(dst_oloc->file, dxpl_id, (hid_t)0, ainfo_dst, H5_INDEX_NAME, + H5_ITER_NATIVE, (hsize_t)0, NULL, &attr_op, &udata) < 0) + HGOTO_ERROR(H5E_ATTR, H5E_CANTINIT, FAIL, "error building attribute table") + +done: + FUNC_LEAVE_NOAPI(ret_value) +} + + diff --git a/src/H5Apkg.h b/src/H5Apkg.h index a1b5e62..f66fa77 100644 --- a/src/H5Apkg.h +++ b/src/H5Apkg.h @@ -279,6 +279,15 @@ H5_DLL htri_t H5O_attr_exists(const H5O_loc_t *loc, const char *name, hid_t dxpl #ifndef H5_NO_DEPRECATED_SYMBOLS H5_DLL int H5O_attr_count(const H5O_loc_t *loc, hid_t dxpl_id); #endif /* H5_NO_DEPRECATED_SYMBOLS */ +H5_DLL H5A_t *H5A_attr_copy_file(H5A_t *attr_src, H5F_t *file_dst, hbool_t *recompute_size, + H5O_copy_t *cpy_info, hid_t dxpl_id); +H5_DLL herr_t H5A_attr_post_copy_file(const H5O_loc_t *src_oloc, const H5A_t *mesg_src, + H5O_loc_t *dst_oloc, H5A_t *mesg_dst, hid_t dxpl_id, H5O_copy_t *cpy_info); +H5_DLL herr_t H5A_dense_copy_file_all(H5F_t *file_src, H5O_ainfo_t *ainfo_src, H5F_t *file_dst, + H5O_ainfo_t *ainfo_dst, hbool_t *recompute_size, H5O_copy_t *cpy_info, hid_t dxpl_id); +H5_DLL herr_t H5A_dense_post_copy_file_all(const H5O_loc_t *src_oloc, const H5O_ainfo_t * ainfo_src, + H5O_loc_t *dst_oloc, H5O_ainfo_t *ainfo_dst, hid_t dxpl_id, H5O_copy_t *cpy_info); + /* Testing functions */ #ifdef H5A_TESTING diff --git a/src/H5Oainfo.c b/src/H5Oainfo.c index 2a9d403..7f6a55d 100644 --- a/src/H5Oainfo.c +++ b/src/H5Oainfo.c @@ -48,6 +48,9 @@ static herr_t H5O_ainfo_pre_copy_file(H5F_t *file_src, const void *mesg_src, static void *H5O_ainfo_copy_file(H5F_t *file_src, void *mesg_src, H5F_t *file_dst, hbool_t *recompute_size, H5O_copy_t *cpy_info, void *udata, hid_t dxpl_id); +static herr_t H5O_ainfo_post_copy_file(const H5O_loc_t *src_oloc, + const void *mesg_src, H5O_loc_t *dst_oloc, void *mesg_dst, hid_t dxpl_id, + H5O_copy_t *cpy_info); static herr_t H5O_ainfo_debug(H5F_t *f, hid_t dxpl_id, const void *_mesg, FILE * stream, int indent, int fwidth); @@ -69,7 +72,7 @@ const H5O_msg_class_t H5O_MSG_AINFO[1] = {{ NULL, /*can share method */ H5O_ainfo_pre_copy_file, /* pre copy native value to file */ H5O_ainfo_copy_file, /* copy native value to file */ - NULL, /* post copy native value to file */ + H5O_ainfo_post_copy_file, /* post copy native value to file */ NULL, /* get creation index */ NULL, /* set creation index */ H5O_ainfo_debug /*debug the message */ @@ -393,15 +396,14 @@ H5O_ainfo_pre_copy_file(H5F_t UNUSED *file_src, const void UNUSED *native_src, * Return: Success: Ptr to _DEST * Failure: NULL * - * Programmer: Quincey Koziol - * March 9, 2007 + * Programmer: Peter Cao + * July 18, 2007 * *------------------------------------------------------------------------- */ static void * -H5O_ainfo_copy_file(H5F_t UNUSED *file_src, void *mesg_src, - H5F_t UNUSED *file_dst, hbool_t UNUSED *recompute_size, - H5O_copy_t UNUSED *cpy_info, void UNUSED *udata, hid_t UNUSED dxpl_id) +H5O_ainfo_copy_file(H5F_t *file_src, void *mesg_src, H5F_t *file_dst, + hbool_t *recompute_size, H5O_copy_t *cpy_info, void *udata, hid_t dxpl_id) { H5O_ainfo_t *ainfo_src = (H5O_ainfo_t *)mesg_src; H5O_ainfo_t *ainfo_dst = NULL; @@ -416,10 +418,6 @@ H5O_ainfo_copy_file(H5F_t UNUSED *file_src, void *mesg_src, HDassert(cpy_info); HDassert(!cpy_info->copy_without_attr); -/* XXX: Bail out for now, if the source object has densely stored attributes */ - if(H5F_addr_defined(ainfo_src->fheap_addr)) - HGOTO_ERROR(H5E_OHDR, H5E_UNSUPPORTED, NULL, "densely stored attributes not supported yet") - /* Allocate space for the destination message */ if(NULL == (ainfo_dst = H5FL_MALLOC(H5O_ainfo_t))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") @@ -427,6 +425,16 @@ H5O_ainfo_copy_file(H5F_t UNUSED *file_src, void *mesg_src, /* Copy the top level of the information */ *ainfo_dst = *ainfo_src; + if(H5F_addr_defined(ainfo_src->fheap_addr)) { + /* copy dense attribute */ + + if(H5A_dense_create(file_dst, dxpl_id, ainfo_dst) < 0) + HGOTO_ERROR(H5E_OHDR, H5E_CANTINIT, NULL, "unable to create dense storage for attributes") + + if ( (H5A_dense_copy_file_all(file_src, ainfo_src, file_dst, ainfo_dst, recompute_size, cpy_info, dxpl_id)) <0) + HGOTO_ERROR(H5E_OHDR, H5E_CANTINIT, NULL, "unable to create dense storage for attributes") + } + /* Set return value */ ret_value = ainfo_dst; @@ -440,6 +448,44 @@ done: /*------------------------------------------------------------------------- + * Function: H5O_ainfo_post_copy_file + * + * Purpose: Finish copying a message from between files. + * We have to copy the values of a reference attribute in the + * post copy because H5O_post_copy_file() fails at the case that + * an object may have a reference attribute that points to the + * object itself. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Peter Cao + * July 25, 2007 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5O_ainfo_post_copy_file(const H5O_loc_t *src_oloc, const void *mesg_src, + H5O_loc_t *dst_oloc, void *mesg_dst, hid_t dxpl_id, H5O_copy_t *cpy_info) +{ + H5O_ainfo_t *ainfo_src = (const H5O_ainfo_t *)mesg_src; + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI_NOINIT(H5O_ainfo_post_copy_file) + + HDassert(ainfo_src); + + if(H5F_addr_defined(ainfo_src->fheap_addr)) { + if ( H5A_dense_post_copy_file_all(src_oloc, ainfo_src, dst_oloc, + (H5O_ainfo_t *)mesg_dst, dxpl_id, cpy_info) < 0) + HGOTO_ERROR(H5E_ATTR, H5E_CANTCOPY, FAIL, "can't copy attribute") + } + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* H5O_ainfo_post_copy_file() */ + + +/*------------------------------------------------------------------------- * Function: H5O_ainfo_debug * * Purpose: Prints debugging info for a message. diff --git a/src/H5Oattr.c b/src/H5Oattr.c index 85b1ef3..db216ad 100644 --- a/src/H5Oattr.c +++ b/src/H5Oattr.c @@ -641,257 +641,20 @@ H5O_attr_copy_file(H5F_t UNUSED *file_src, const H5O_msg_class_t UNUSED *mesg_ty void *native_src, H5F_t *file_dst, hbool_t *recompute_size, H5O_copy_t *cpy_info, void UNUSED *udata, hid_t dxpl_id) { - H5A_t *attr_src = (H5A_t *)native_src; - H5A_t *attr_dst = NULL; - - /* for dataype conversion */ - hid_t tid_src = -1; /* Datatype ID for source datatype */ - hid_t tid_dst = -1; /* Datatype ID for destination datatype */ - hid_t tid_mem = -1; /* Datatype ID for memory datatype */ - void *buf = NULL; /* Buffer for copying data */ - void *reclaim_buf = NULL; /* Buffer for reclaiming data */ - hid_t buf_sid = -1; /* ID for buffer dataspace */ - void *ret_value; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5O_attr_copy_file) /* check args */ - HDassert(attr_src); + HDassert(native_src); HDassert(file_dst); HDassert(cpy_info); HDassert(!cpy_info->copy_without_attr); - /* Allocate space for the destination message */ - if(NULL == (attr_dst = H5FL_CALLOC(H5A_t))) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") - - /* Copy the top level of the attribute */ - *attr_dst = *attr_src; - - if(NULL == (attr_dst->shared = H5FL_CALLOC(H5A_shared_t))) - HGOTO_ERROR(H5E_FILE, H5E_NOSPACE, NULL, "can't allocate shared attr structure") - - /* Don't have an opened group location for copy */ - H5O_loc_reset(&(attr_dst->shared->oloc)); - H5G_name_reset(&(attr_dst->path)); - attr_dst->obj_opened = FALSE; - - /* Reference count for the header message in the cache */ - attr_dst->shared->nrefs = 1; - - /* Copy attribute's name */ - attr_dst->shared->name = H5MM_strdup(attr_src->shared->name); - HDassert(attr_dst->shared->name); - - /* Copy attribute's datatype */ - /* (Start destination datatype as transient, even if source is named) */ - if(NULL == (attr_dst->shared->dt = H5T_copy(attr_src->shared->dt, H5T_COPY_ALL))) - HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, NULL, "cannot copy datatype") - - /* Set the location of the destination datatype */ - if(H5T_set_loc(attr_dst->shared->dt, file_dst, H5T_LOC_DISK) < 0) - HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, NULL, "cannot mark datatype on disk") - - /* Check for named datatype being copied */ - if(H5T_committed(attr_src->shared->dt)) { - H5O_loc_t *src_oloc; /* Pointer to source datatype's object location */ - H5O_loc_t *dst_oloc; /* Pointer to dest. datatype's object location */ - - /* Get group entries for source & destination */ - src_oloc = H5T_oloc(attr_src->shared->dt); - HDassert(src_oloc); - dst_oloc = H5T_oloc(attr_dst->shared->dt); - HDassert(dst_oloc); - - /* Reset object location for new object */ - H5O_loc_reset(dst_oloc); - dst_oloc->file = file_dst; - - /* Copy the shared object from source to destination */ - if(H5O_copy_header_map(src_oloc, dst_oloc, dxpl_id, cpy_info, FALSE) < 0) - HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, NULL, "unable to copy object") - - /* Update shared message info from named datatype info */ - H5T_update_shared(attr_dst->shared->dt); - } /* end if */ - else { - /* If the datatype is not named, it may have been shared in the - * source file's heap. Un-share it for now. We'll try to shared - * it in the destination file below. - */ - if(H5O_msg_reset_share(H5O_DTYPE_ID, attr_dst->shared->dt) < 0) - HGOTO_ERROR(H5E_OHDR, H5E_CANTINIT, NULL, "unable to reset datatype sharing") - } /* end else */ - - /* Copy the dataspace for the attribute */ - attr_dst->shared->ds = H5S_copy(attr_src->shared->ds, FALSE, FALSE); - HDassert(attr_dst->shared->ds); - - /* Reset the dataspace's sharing in the source file before trying to share - * it in the destination. - */ - if(H5O_msg_reset_share(H5O_SDSPACE_ID, attr_dst->shared->ds) < 0) - HGOTO_ERROR(H5E_OHDR, H5E_CANTINIT, NULL, "unable to reset dataspace sharing") - - - /* Try to share both the datatype and dataset. This does nothing if the - * datatype is committed or sharing is disabled. - */ - if(H5SM_try_share(file_dst, dxpl_id, NULL, H5O_DTYPE_ID, attr_dst->shared->dt, NULL) < 0) - HGOTO_ERROR(H5E_OHDR, H5E_WRITEERROR, NULL, "can't share attribute datatype") - if(H5SM_try_share(file_dst, dxpl_id, NULL, H5O_SDSPACE_ID, attr_dst->shared->ds, NULL) < 0) - HGOTO_ERROR(H5E_OHDR, H5E_WRITEERROR, NULL, "can't share attribute dataspace") - - /* Compute the sizes of the datatype and dataspace. This is their raw - * size unless they're shared. - */ - attr_dst->shared->dt_size = H5O_msg_raw_size(file_dst, H5O_DTYPE_ID, FALSE, attr_dst->shared->dt); - HDassert(attr_dst->shared->dt_size > 0); - attr_dst->shared->ds_size = H5O_msg_raw_size(file_dst, H5O_SDSPACE_ID, FALSE, attr_dst->shared->ds); - HDassert(attr_dst->shared->ds_size > 0); - - /* Check whether to recompute the size of the attribute */ - /* (happens when the datatype or dataspace changes sharing status) */ - if(attr_dst->shared->dt_size != attr_src->shared->dt_size || attr_dst->shared->ds_size != attr_src->shared->ds_size) - *recompute_size = TRUE; - - /* Compute the size of the data */ - H5_ASSIGN_OVERFLOW(attr_dst->shared->data_size, H5S_GET_EXTENT_NPOINTS(attr_dst->shared->ds) * H5T_get_size(attr_dst->shared->dt), hsize_t, size_t); - - /* Copy (& convert) the data, if necessary */ - if(attr_src->shared->data) { - if(NULL == (attr_dst->shared->data = H5FL_BLK_MALLOC(attr_buf, attr_dst->shared->data_size))) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") - - /* Check if we need to convert data */ - if(H5T_detect_class(attr_src->shared->dt, H5T_VLEN) > 0) { - H5T_path_t *tpath_src_mem, *tpath_mem_dst; /* Datatype conversion paths */ - H5T_t *dt_mem; /* Memory datatype */ - size_t src_dt_size; /* Source datatype size */ - size_t tmp_dt_size; /* Temp. datatype size */ - size_t max_dt_size; /* Max atatype size */ - H5S_t *buf_space; /* Dataspace describing buffer */ - hsize_t buf_dim; /* Dimension for buffer */ - size_t nelmts; /* Number of elements in buffer */ - size_t buf_size; /* Size of copy buffer */ - - /* Create datatype ID for src datatype */ - if((tid_src = H5I_register(H5I_DATATYPE, attr_src->shared->dt, FALSE)) < 0) - HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, NULL, "unable to register source file datatype") - - /* create a memory copy of the variable-length datatype */ - if(NULL == (dt_mem = H5T_copy(attr_src->shared->dt, H5T_COPY_TRANSIENT))) - HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, NULL, "unable to copy") - if((tid_mem = H5I_register(H5I_DATATYPE, dt_mem, FALSE)) < 0) - HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, NULL, "unable to register memory datatype") - - /* create variable-length datatype at the destinaton file */ - if((tid_dst = H5I_register(H5I_DATATYPE, attr_dst->shared->dt, FALSE)) < 0) - HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, NULL, "unable to register destination file datatype") - - /* Set up the conversion functions */ - if(NULL == (tpath_src_mem = H5T_path_find(attr_src->shared->dt, dt_mem, NULL, NULL, dxpl_id, FALSE))) - HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, NULL, "unable to convert between src and mem datatypes") - if(NULL == (tpath_mem_dst = H5T_path_find(dt_mem, attr_dst->shared->dt, NULL, NULL, dxpl_id, FALSE))) - HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, NULL, "unable to convert between mem and dst datatypes") - - /* Determine largest datatype size */ - if(0 == (src_dt_size = H5T_get_size(attr_src->shared->dt))) - HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, NULL, "unable to determine datatype size") - if(0 == (tmp_dt_size = H5T_get_size(dt_mem))) - HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, NULL, "unable to determine datatype size") - max_dt_size = MAX(src_dt_size, tmp_dt_size); - if(0 == (tmp_dt_size = H5T_get_size(attr_dst->shared->dt))) - HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, NULL, "unable to determine datatype size") - max_dt_size = MAX(max_dt_size, tmp_dt_size); - - /* Set number of whole elements that fit in buffer */ - if(0 == (nelmts = attr_src->shared->data_size / src_dt_size)) - HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, NULL, "element size too large") - - /* Set up number of bytes to copy, and initial buffer size */ - buf_size = nelmts * max_dt_size; - - /* Create dataspace for number of elements in buffer */ - buf_dim = nelmts; - - /* Create the space and set the initial extent */ - if(NULL == (buf_space = H5S_create_simple((unsigned)1, &buf_dim, NULL))) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, NULL, "can't create simple dataspace") - - /* Atomize */ - if((buf_sid = H5I_register(H5I_DATASPACE, buf_space, FALSE)) < 0) { - H5S_close(buf_space); - HGOTO_ERROR(H5E_ATOM, H5E_CANTREGISTER, NULL, "unable to register dataspace ID") - } /* end if */ - - /* Allocate memory for recclaim buf */ - if(NULL == (reclaim_buf = H5FL_BLK_MALLOC(attr_buf, buf_size))) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation NULLed for raw data chunk") - - /* Allocate memory for copying the chunk */ - if(NULL == (buf = H5FL_BLK_MALLOC(attr_buf, buf_size))) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation NULLed for raw data chunk") - - HDmemcpy(buf, attr_src->shared->data, attr_src->shared->data_size); - - /* Convert from source file to memory */ - if(H5T_convert(tpath_src_mem, tid_src, tid_mem, nelmts, (size_t)0, (size_t)0, buf, NULL, dxpl_id) < 0) - HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, NULL, "datatype conversion NULLed") - - HDmemcpy(reclaim_buf, buf, buf_size); - - /* Convert from memory to destination file */ - if(H5T_convert(tpath_mem_dst, tid_mem, tid_dst, nelmts, (size_t)0, (size_t)0, buf, NULL, dxpl_id) < 0) - HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, NULL, "datatype conversion NULLed") - - HDmemcpy(attr_dst->shared->data, buf, attr_dst->shared->data_size); - - if(H5D_vlen_reclaim(tid_mem, buf_space, H5P_DATASET_XFER_DEFAULT, reclaim_buf) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_BADITER, NULL, "unable to reclaim variable-length data") - } /* end if */ - else { - HDassert(attr_dst->shared->data_size == attr_src->shared->data_size); - HDmemcpy(attr_dst->shared->data, attr_src->shared->data, attr_src->shared->data_size); - } /* end else */ - } /* end if(attr_src->shared->data) */ - - /* Recompute the version to encode the destination attribute */ - if(H5A_set_version(file_dst, attr_dst) < 0) - HGOTO_ERROR(H5E_ATTR, H5E_CANTSET, NULL, "unable to update attribute version") - - /* Indicate that the fill values aren't to be written out */ - attr_dst->shared->initialized = TRUE; - - /* Set return value */ - ret_value = attr_dst; + if ( NULL == (ret_value=H5A_attr_copy_file((H5A_t *)native_src, file_dst, recompute_size, cpy_info, dxpl_id))) + HGOTO_ERROR(H5E_ATTR, H5E_CANTCOPY, NULL, "can't copy attribute") done: - if(buf_sid > 0) - if(H5I_dec_ref(buf_sid, FALSE) < 0) - HDONE_ERROR(H5E_ATTR, H5E_CANTFREE, NULL, "Can't decrement temporary dataspace ID") - if(tid_src > 0) - /* Don't decrement ID, we want to keep underlying datatype */ - if(H5I_remove(tid_src) == NULL) - HDONE_ERROR(H5E_ATTR, H5E_CANTFREE, NULL, "Can't decrement temporary datatype ID") - if(tid_dst > 0) - /* Don't decrement ID, we want to keep underlying datatype */ - if(H5I_remove(tid_dst) == NULL) - HDONE_ERROR(H5E_ATTR, H5E_CANTFREE, NULL, "Can't decrement temporary datatype ID") - if(tid_mem > 0) - /* Decrement the memory datatype ID, it's transient */ - if(H5I_dec_ref(tid_mem, FALSE) < 0) - HDONE_ERROR(H5E_ATTR, H5E_CANTFREE, NULL, "Can't decrement temporary datatype ID") - if(buf) - buf = H5FL_BLK_FREE(attr_buf, buf); - if(reclaim_buf) - reclaim_buf = H5FL_BLK_FREE(attr_buf, reclaim_buf); - - /* Release destination attribute information on failure */ - if(!ret_value && attr_dst && H5A_close(attr_dst) < 0) - HDONE_ERROR(H5E_ATTR, H5E_CANTFREE, NULL, "can't close attribute") - FUNC_LEAVE_NOAPI(ret_value) } /* H5O_attr_copy_file() */ @@ -916,48 +679,14 @@ static herr_t H5O_attr_post_copy_file(const H5O_loc_t *src_oloc, const void *mesg_src, H5O_loc_t *dst_oloc, void *mesg_dst, hid_t dxpl_id, H5O_copy_t *cpy_info) { - const H5A_t *attr_src = (const H5A_t *)mesg_src; - H5A_t *attr_dst = (H5A_t *)mesg_dst; - H5F_t *file_src = src_oloc->file; - H5F_t *file_dst = dst_oloc->file; herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5O_attr_post_copy_file) - /* check args */ - HDassert(attr_src); - HDassert(file_src); - HDassert(attr_dst); - HDassert(file_dst); - - /* Only need to fix reference attribute with real data being copied to - * another file. - */ - if((NULL != attr_src->shared->data) && - (H5T_get_class(attr_src->shared->dt, FALSE) == H5T_REFERENCE) && - (file_src != file_dst)) { - - /* copy object pointed by reference. The current implementation does not - * deal with nested reference such as reference in a compound structure - */ - - /* Check for expanding references */ - if(cpy_info->expand_ref) { - size_t ref_count; - - /* Determine # of reference elements to copy */ - ref_count = attr_dst->shared->data_size / H5T_get_size(attr_dst->shared->dt); - - /* Copy objects referenced in source buffer to destination file and set destination elements */ - if(H5O_copy_expand_ref(file_src, attr_src->shared->data, dxpl_id, - file_dst, attr_dst->shared->data, ref_count, H5T_get_ref_type(attr_src->shared->dt), cpy_info) < 0) - HGOTO_ERROR(H5E_ATTR, H5E_CANTCOPY, FAIL, "unable to copy reference attribute") - } /* end if */ - else - /* Reset value to zero */ - HDmemset(attr_dst->shared->data, 0, attr_dst->shared->data_size); - } /* end if */ + if ( H5A_attr_post_copy_file(src_oloc, (const H5A_t *)mesg_src, + dst_oloc, (H5A_t *)mesg_dst, dxpl_id, cpy_info) < 0) + HGOTO_ERROR(H5E_ATTR, H5E_CANTCOPY, FAIL, "can't copy attribute") done: FUNC_LEAVE_NOAPI(ret_value) diff --git a/test/objcopy.c b/test/objcopy.c index aca041f..61963b5 100755 --- a/test/objcopy.c +++ b/test/objcopy.c @@ -55,7 +55,8 @@ const char *FILENAME[] = { #define CONFIG_SHARE_SRC 1 #define CONFIG_SHARE_DST 2 #define CONFIG_NEW_FORMAT 4 -#define MAX_CONFIGURATION 7 +#define CONFIG_DENSE 8 +#define MAX_CONFIGURATION 15 #define FILE_EXT "objcopy_ext.dat" /* The fill_old.h5 is generated from gen_old_fill.c in HDF5 'test' directory @@ -69,6 +70,7 @@ const char *FILENAME[] = { #define NAME_DATATYPE_VL "vlen of int" #define NAME_DATATYPE_VL_VL "vlen of vlen of int" #define NAME_DATASET_SIMPLE "dataset_simple" +#define NAME_DATASET_SIMPLE2 "dataset_simple_copy" #define NAME_DATASET_COMPOUND "dataset_compound" #define NAME_DATASET_CHUNKED "dataset_chunked" #define NAME_DATASET_COMPACT "dataset_compact" @@ -104,7 +106,6 @@ const char *FILENAME[] = { #define NAME_OLD_FORMAT "/dset1" #define NAME_BUF_SIZE 1024 -#define NUM_ATTRIBUTES 4 #define ATTR_NAME_LEN 80 #define DIM_SIZE_1 12 #define DIM_SIZE_2 6 @@ -116,6 +117,8 @@ const char *FILENAME[] = { char src_obj_full_name[215]; /* the full path + name of the object to be copied */ +int num_attributes_g; /* Number of attributes created */ + /* Table containing object id and object name */ /* (Used for detecting duplicate objects when comparing groups */ static struct { @@ -535,7 +538,7 @@ test_copy_attach_attributes(hid_t loc_id, hid_t type_id) if((sid = H5Screate_simple(1, &dim1, NULL)) < 0 ) goto done; - for (i=0; i<NUM_ATTRIBUTES; i++) { + for (i=0; i<num_attributes_g; i++) { sprintf(attr_name, "%d attr", i); /* Set attribute data */ @@ -588,7 +591,7 @@ test_copy_attach_paired_attributes(hid_t loc_id, hid_t loc_id2, hid_t type_id) if((sid = H5Screate_simple(1, &dim1, NULL)) < 0 ) goto done; - for (i=0; i<NUM_ATTRIBUTES; i++) { + for (i=0; i<num_attributes_g; i++) { sprintf(attr_name, "%d attr", i); /* Set attribute data */ @@ -1779,6 +1782,112 @@ error: /*------------------------------------------------------------------------- + * Function: test_copy_dataset_simple_samefile + * + * Purpose: Create a simple dataset in SRC file and copy it to SRC file + * + * Return: Success: 0 + * Failure: number of errors + * + * Programmer: Neil Fortner + * Thursday, January 15, 2009 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +static int +test_copy_dataset_simple_samefile(hid_t fcpl, hid_t fapl, int config) +{ + hid_t fid = -1; /* File ID */ + hid_t sid = -1; /* Dataspace ID */ + hid_t did = -1, did2 = -1; /* Dataset IDs */ + int buf[DIM_SIZE_1][DIM_SIZE_2]; /* Buffer for writing data */ + hsize_t dim2d[2]; /* Dataset dimensions */ + int i, j; /* local index variables */ + char filename[NAME_BUF_SIZE]; + + TESTING("H5Ocopy(): simple dataset within the same file"); + + /* Initialize write buffer */ + for (i=0; i<DIM_SIZE_1; i++) + for (j=0; j<DIM_SIZE_2; j++) + buf[i][j] = 10000 + 100*i+j; + + /* Initialize the filenames */ + h5_fixname(FILENAME[0], fapl, filename, sizeof filename); + + /* Reset file address checking info */ + addr_reset(); + + /* create source file */ + if((fid = H5Fcreate(filename, H5F_ACC_TRUNC, fcpl, fapl)) < 0) TEST_ERROR + + /* Set dataspace dimensions */ + dim2d[0] = DIM_SIZE_1; + dim2d[1] = DIM_SIZE_2; + + /* create 2D dataspace */ + if((sid = H5Screate_simple(2, dim2d, NULL)) < 0) TEST_ERROR + + /* create 2D int dataset at SRC file */ + if((did = H5Dcreate2(fid, NAME_DATASET_SIMPLE, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0) TEST_ERROR + + /* write data into file */ + if(H5Dwrite(did, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0) TEST_ERROR + + /* close dataspace */ + if(H5Sclose(sid) < 0) TEST_ERROR + + /* attach attributes to the dataset */ + if(test_copy_attach_attributes(did, H5T_NATIVE_INT) < 0) TEST_ERROR + + /* close the dataset */ + if(H5Dclose(did) < 0) TEST_ERROR + + /* close the SRC file */ + if(H5Fclose(fid) < 0) TEST_ERROR + + + /* open the source file with read-write */ + if((fid = H5Fopen(filename, H5F_ACC_RDWR, fapl)) < 0) TEST_ERROR + + /* copy the dataset from SRC to DST */ + if(H5Ocopy(fid, NAME_DATASET_SIMPLE, fid, NAME_DATASET_SIMPLE2, H5P_DEFAULT, H5P_DEFAULT) < 0) TEST_ERROR + + /* open the dataset for copy */ + if((did = H5Dopen2(fid, NAME_DATASET_SIMPLE, H5P_DEFAULT)) < 0) TEST_ERROR + + /* open the destination dataset */ + if((did2 = H5Dopen2(fid, NAME_DATASET_SIMPLE2, H5P_DEFAULT)) < 0) TEST_ERROR + + /* Check if the datasets are equal */ + if(compare_datasets(did, did2, H5P_DEFAULT, buf) != TRUE) TEST_ERROR + + /* close the destination dataset */ + if(H5Dclose(did2) < 0) TEST_ERROR + + /* close the source dataset */ + if(H5Dclose(did) < 0) TEST_ERROR + + /* close the SRC file */ + if(H5Fclose(fid) < 0) TEST_ERROR + + PASSED(); + return 0; + +error: + H5E_BEGIN_TRY { + H5Dclose(did2); + H5Dclose(did); + H5Sclose(sid); + H5Fclose(fid); + } H5E_END_TRY; + return 1; +} /* end test_copy_dataset_simple_samefile */ + + +/*------------------------------------------------------------------------- * Function: test_copy_dataset_simple_empty * * Purpose: Create a simple dataset in SRC file and copy it to DST file @@ -7150,7 +7259,8 @@ main(void) { int nerrors = 0; hid_t fapl, fapl2; - hid_t fcpl_shared; + hid_t fcpl_shared, ocpl; + unsigned max_compact, min_dense; int configuration; /* Configuration of tests. */ int ExpressMode; @@ -7173,6 +7283,11 @@ main(void) if(H5Pset_shared_mesg_nindexes(fcpl_shared, 1) < 0) TEST_ERROR if(H5Pset_shared_mesg_index(fcpl_shared, 0, H5O_SHMESG_ALL_FLAG, (size_t) 10) < 0) TEST_ERROR + /* Obtain the default attribute storage phase change values */ + if((ocpl = H5Pcreate(H5P_OBJECT_CREATE)) < 0) TEST_ERROR + if(H5Pget_attr_phase_change(ocpl, &max_compact, &min_dense) < 0) TEST_ERROR + if(H5Pclose(ocpl) < 0) TEST_ERROR + /* Test in all configurations */ for(configuration = 0; configuration <= MAX_CONFIGURATION; configuration++) { hid_t my_fapl; @@ -7207,40 +7322,29 @@ main(void) my_fapl = fapl; } /* end else */ + /* Test with and without dense attributes */ + if(configuration & CONFIG_DENSE) { + puts("Testing with dense attributes:"); + num_attributes_g = max_compact + 1; + } + else { + puts("Testing without dense attributes:"); + num_attributes_g = MAX(min_dense, 2) - 1; + } /* The tests... */ - nerrors += test_copy_named_datatype(fcpl_src, fcpl_dst, my_fapl); - nerrors += test_copy_named_datatype_vl(fcpl_src, fcpl_dst, my_fapl); - nerrors += test_copy_named_datatype_vl_vl(fcpl_src, fcpl_dst, my_fapl); nerrors += test_copy_dataset_simple(fcpl_src, fcpl_dst, my_fapl); + nerrors += test_copy_dataset_simple_samefile(fcpl_src, my_fapl, configuration); nerrors += test_copy_dataset_simple_empty(fcpl_src, fcpl_dst, my_fapl); nerrors += test_copy_dataset_compound(fcpl_src, fcpl_dst, my_fapl); nerrors += test_copy_dataset_chunked(fcpl_src, fcpl_dst, my_fapl); - nerrors += test_copy_dataset_chunked_empty(fcpl_src, fcpl_dst, my_fapl); nerrors += test_copy_dataset_chunked_sparse(fcpl_src, fcpl_dst, my_fapl); nerrors += test_copy_dataset_compressed(fcpl_src, fcpl_dst, my_fapl); nerrors += test_copy_dataset_compact(fcpl_src, fcpl_dst, my_fapl); - nerrors += test_copy_dataset_external(fcpl_src, fcpl_dst, my_fapl); - nerrors += test_copy_dataset_named_dtype(fcpl_src, fcpl_dst, my_fapl); - nerrors += test_copy_dataset_named_dtype_hier(fcpl_src, fcpl_dst, my_fapl); - nerrors += test_copy_dataset_named_dtype_hier_outside(fcpl_src, fcpl_dst, my_fapl); nerrors += test_copy_dataset_multi_ohdr_chunks(fcpl_src, fcpl_dst, my_fapl); nerrors += test_copy_dataset_attr_named_dtype(fcpl_src, fcpl_dst, my_fapl); - nerrors += test_copy_dataset_contig_vl(fcpl_src, fcpl_dst, my_fapl); - nerrors += test_copy_dataset_chunked_vl(fcpl_src, fcpl_dst, my_fapl); - nerrors += test_copy_dataset_compact_vl(fcpl_src, fcpl_dst, my_fapl); - nerrors += test_copy_dataset_compressed_vl(fcpl_src, fcpl_dst, my_fapl); - nerrors += test_copy_attribute_vl(fcpl_src, fcpl_dst, my_fapl); - nerrors += test_copy_dataset_compact_named_vl(fcpl_src, fcpl_dst, my_fapl); - nerrors += test_copy_dataset_contig_named_vl(fcpl_src, fcpl_dst, my_fapl); - nerrors += test_copy_dataset_chunked_named_vl(fcpl_src, fcpl_dst, my_fapl); - nerrors += test_copy_dataset_compressed_named_vl(fcpl_src, fcpl_dst, my_fapl); - nerrors += test_copy_dataset_compact_vl_vl(fcpl_src, fcpl_dst, my_fapl); - nerrors += test_copy_dataset_contig_vl_vl(fcpl_src, fcpl_dst, my_fapl); - nerrors += test_copy_dataset_chunked_vl_vl(fcpl_src, fcpl_dst, my_fapl); - nerrors += test_copy_dataset_compressed_vl_vl(fcpl_src, fcpl_dst, my_fapl); nerrors += test_copy_group_empty(fcpl_src, fcpl_dst, my_fapl); nerrors += test_copy_root_group(fcpl_src, fcpl_dst, my_fapl); nerrors += test_copy_group(fcpl_src, fcpl_dst, my_fapl); @@ -7254,8 +7358,7 @@ main(void) #endif /* H5_CANNOT_OPEN_TWICE */ nerrors += test_copy_exist(fcpl_src, fcpl_dst, my_fapl); nerrors += test_copy_path(fcpl_src, fcpl_dst, my_fapl); - nerrors += test_copy_same_file_named_datatype(fcpl_src, my_fapl); - nerrors += test_copy_old_layout(fcpl_dst, my_fapl); + nerrors += test_copy_option(fcpl_src, fcpl_dst, my_fapl, H5O_COPY_WITHOUT_ATTR_FLAG, FALSE, "H5Ocopy(): without attributes"); nerrors += test_copy_option(fcpl_src, fcpl_dst, my_fapl, 0, TRUE, @@ -7271,6 +7374,36 @@ main(void) nerrors += test_copy_option(fcpl_src, fcpl_dst, my_fapl, H5O_COPY_WITHOUT_ATTR_FLAG | H5O_COPY_PRESERVE_NULL_FLAG, TRUE, "H5Ocopy(): preserve NULL messages"); + /* Tests that do not use attributes and do not need to be tested + * multiple times for different attribute configurations */ + if(configuration < CONFIG_DENSE) { + nerrors += test_copy_named_datatype(fcpl_src, fcpl_dst, my_fapl); + nerrors += test_copy_named_datatype_vl(fcpl_src, fcpl_dst, my_fapl); + nerrors += test_copy_named_datatype_vl_vl(fcpl_src, fcpl_dst, my_fapl); + + nerrors += test_copy_dataset_external(fcpl_src, fcpl_dst, my_fapl); + nerrors += test_copy_dataset_named_dtype(fcpl_src, fcpl_dst, my_fapl); + nerrors += test_copy_dataset_named_dtype_hier(fcpl_src, fcpl_dst, my_fapl); + nerrors += test_copy_dataset_named_dtype_hier_outside(fcpl_src, fcpl_dst, my_fapl); + + nerrors += test_copy_dataset_contig_vl(fcpl_src, fcpl_dst, my_fapl); + nerrors += test_copy_dataset_chunked_vl(fcpl_src, fcpl_dst, my_fapl); + nerrors += test_copy_dataset_compact_vl(fcpl_src, fcpl_dst, my_fapl); + nerrors += test_copy_dataset_compressed_vl(fcpl_src, fcpl_dst, my_fapl); + nerrors += test_copy_attribute_vl(fcpl_src, fcpl_dst, my_fapl); + nerrors += test_copy_dataset_compact_named_vl(fcpl_src, fcpl_dst, my_fapl); + nerrors += test_copy_dataset_contig_named_vl(fcpl_src, fcpl_dst, my_fapl); + nerrors += test_copy_dataset_chunked_named_vl(fcpl_src, fcpl_dst, my_fapl); + nerrors += test_copy_dataset_compressed_named_vl(fcpl_src, fcpl_dst, my_fapl); + nerrors += test_copy_dataset_compact_vl_vl(fcpl_src, fcpl_dst, my_fapl); + nerrors += test_copy_dataset_contig_vl_vl(fcpl_src, fcpl_dst, my_fapl); + nerrors += test_copy_dataset_chunked_vl_vl(fcpl_src, fcpl_dst, my_fapl); + nerrors += test_copy_dataset_compressed_vl_vl(fcpl_src, fcpl_dst, my_fapl); + + nerrors += test_copy_same_file_named_datatype(fcpl_src, my_fapl); + nerrors += test_copy_old_layout(fcpl_dst, my_fapl); + } + /* TODO: not implemented nerrors += test_copy_option(my_fapl, H5O_COPY_EXPAND_EXT_LINK_FLAG, FALSE, "H5Ocopy: expand external link"); nerrors += test_copy_mount(my_fapl); |