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Implement fill values #45

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merged 2 commits into from
Sep 6, 2023
Merged

Implement fill values #45

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58c2506
Implement support for fill values
mattjala Aug 2, 2023
50f2d90
Committing clang-format changes
github-actions[bot] Aug 2, 2023
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5 changes: 4 additions & 1 deletion src/rest_vol.h
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Original file line number Diff line number Diff line change
Expand Up @@ -312,7 +312,7 @@
H5VL_CAP_FLAG_OBJECT_MORE | H5VL_CAP_FLAG_CREATION_ORDER | H5VL_CAP_FLAG_ITERATE | \
H5VL_CAP_FLAG_BY_IDX | H5VL_CAP_FLAG_GET_PLIST | H5VL_CAP_FLAG_EXTERNAL_LINKS | \
H5VL_CAP_FLAG_HARD_LINKS | H5VL_CAP_FLAG_SOFT_LINKS | H5VL_CAP_FLAG_TRACK_TIMES | \
H5VL_CAP_FLAG_FILTERS
H5VL_CAP_FLAG_FILTERS | H5VL_CAP_FLAG_FILL_VALUES
/**********************************
* *
* Global Variables *
Expand Down Expand Up @@ -632,6 +632,9 @@ void RV_free_visited_link_hash_table_key(rv_hash_table_key_t value);
(version.major > major_needed) || (version.major == major_needed && version.minor > minor_needed) || \
(version.major == major_needed && version.minor == minor_needed && version.patch >= patch_needed)

#define SERVER_VERISON_SUPPORTS_FILL_VALUE_ENCODING(version) \
(SERVER_VERSION_MATCHES_OR_EXCEEDS(version, 0, 8, 1))

#ifdef __cplusplus
}
#endif
Expand Down
96 changes: 89 additions & 7 deletions src/rest_vol_dataset.c
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Original file line number Diff line number Diff line change
Expand Up @@ -26,8 +26,10 @@ static herr_t RV_setup_dataset_create_request_body(void *parent_obj, const char
hid_t space_id, hid_t lcpl_id, hid_t dcpl,
char **create_request_body,
size_t *create_request_body_len);

static herr_t RV_convert_dataset_creation_properties_to_JSON(hid_t dcpl_id, char **creation_properties_body,
size_t *creation_properties_body_len);
size_t *creation_properties_body_len,
hid_t type_id, server_api_version version);

/* Helper function to convert a selection within an HDF5 Dataspace into a JSON-format string */
static herr_t RV_convert_dataspace_selection_to_string(hid_t space_id, char **selection_string,
Expand Down Expand Up @@ -1837,7 +1839,8 @@ RV_parse_dataset_creation_properties_callback(char *HTTP_response, void *callbac
*/
static herr_t
RV_convert_dataset_creation_properties_to_JSON(hid_t dcpl, char **creation_properties_body,
size_t *creation_properties_body_len)
size_t *creation_properties_body_len, hid_t type_id,
server_api_version version)
{
const char *const leading_string = "\"creationProperties\": {";
H5D_alloc_time_t alloc_time;
Expand All @@ -1849,8 +1852,11 @@ RV_convert_dataset_creation_properties_to_JSON(hid_t dcpl, char **creation_prope
char *out_string = NULL;
char *out_string_curr_pos; /* The "current position" pointer used to print to the appropriate place
in the buffer and not overwrite important leading data */
int bytes_printed = 0;
herr_t ret_value = SUCCEED;
int bytes_printed = 0;
void *fill_value = NULL;
char *encode_buf_out = NULL;
char *fill_value_str = NULL;
herr_t ret_value = SUCCEED;

#ifdef RV_CONNECTOR_DEBUG
printf("-> Converting dataset creation properties from DCPL to JSON\n\n");
Expand Down Expand Up @@ -2082,6 +2088,8 @@ RV_convert_dataset_creation_properties_to_JSON(hid_t dcpl, char **creation_prope
******************************************************************/
{
H5D_fill_value_t fill_status;
size_t fill_value_size = 0;
size_t encode_buf_out_size = 0;

if (H5Pfill_value_defined(dcpl, &fill_status) < 0)
FUNC_GOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve the \"fill value defined\" status");
Expand All @@ -2105,9 +2113,73 @@ RV_convert_dataset_creation_properties_to_JSON(hid_t dcpl, char **creation_prope

strncat(out_string_curr_pos, null_value, null_value_len);
out_string_curr_pos += null_value_len;
} /* end if */
}
else if (H5D_FILL_VALUE_USER_DEFINED == fill_status) {
if (!(SERVER_VERISON_SUPPORTS_FILL_VALUE_ENCODING(version)))
FUNC_GOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL,
"server API version %zu.%zu.%zu does not support fill value encoding\n",
version.major, version.minor, version.patch);

if ((fill_value_size = H5Tget_size(type_id)) == 0)
FUNC_GOTO_ERROR(H5E_DATATYPE, H5E_CANTGET, FAIL, "can't get the size of fill value type");

if ((fill_value = RV_malloc(fill_value_size)) == NULL)
FUNC_GOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "can't allocate space for fill value");

if (H5Pget_fill_value(dcpl, type_id, fill_value) < 0)
FUNC_GOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL,
"can't get fill value from creation properties");

if (RV_base64_encode(fill_value, fill_value_size, &encode_buf_out, &encode_buf_out_size) < 0)
FUNC_GOTO_ERROR(H5E_DATASET, H5E_CANTENCODE, FAIL, "can't base64-encode fill value");

/* Add encoded fill value to request body */
size_t fill_value_str_len =
strlen(", \"fillValue\": ") + strlen("\"") + strlen(encode_buf_out) + strlen("\"");

if ((fill_value_str = RV_calloc(fill_value_str_len + 1)) == NULL)
FUNC_GOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL,
"can't allocate space for fill value string in request body");

snprintf(fill_value_str, fill_value_str_len + 1, "%s%s%s%s", ", \"fillValue\": ", "\"",
encode_buf_out, "\"");

/* Check whether the buffer needs to be grown */
bytes_to_print = fill_value_str_len + 1;

buf_ptrdiff = out_string_curr_pos - out_string;

if (buf_ptrdiff < 0)
FUNC_GOTO_ERROR(H5E_INTERNAL, H5E_BADVALUE, FAIL,
"unsafe cast: dataset creation properties buffer pointer difference was "
"negative - this should not happen!");

CHECKED_REALLOC(out_string, out_string_len, (size_t)buf_ptrdiff + bytes_to_print,
out_string_curr_pos, H5E_DATASET, FAIL);

strncat(out_string, fill_value_str, fill_value_str_len);
out_string_curr_pos += fill_value_str_len;

/* Write the encoding used to the request body */
const char *encoding_property = ", \"fillValue_encoding\": \"base64\"";

bytes_to_print = strlen(encoding_property);

buf_ptrdiff = out_string_curr_pos - out_string;
if (buf_ptrdiff < 0)
FUNC_GOTO_ERROR(H5E_INTERNAL, H5E_BADVALUE, FAIL,
"unsafe cast: dataset creation properties buffer pointer difference was "
"negative - this should not happen!");

CHECKED_REALLOC(out_string, out_string_len, (size_t)buf_ptrdiff + bytes_to_print,
out_string_curr_pos, H5E_DATASET, FAIL);

strncat(out_string, encoding_property, strlen(encoding_property));
out_string_curr_pos += strlen(encoding_property);
}
else {
FUNC_GOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "dataset fill values are unsupported");
FUNC_GOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL,
"can't retrieve the \"fill value defined\" status");
} /* end else */
} /* end if */
}
Expand Down Expand Up @@ -2865,6 +2937,15 @@ RV_convert_dataset_creation_properties_to_JSON(hid_t dcpl, char **creation_prope
if (chunk_dims_string)
RV_free(chunk_dims_string);

if (fill_value)
RV_free(fill_value);

if (encode_buf_out)
RV_free(encode_buf_out);

if (fill_value_str)
RV_free(fill_value_str);

return ret_value;
} /* end RV_convert_dataset_creation_properties_to_JSON() */

Expand Down Expand Up @@ -2936,7 +3017,8 @@ RV_setup_dataset_create_request_body(void *parent_obj, const char *name, hid_t t
"layout H5D_CONTIGUOUS is unsupported for server versions before 0.8.0");

if (RV_convert_dataset_creation_properties_to_JSON(dcpl, &creation_properties_body,
&creation_properties_body_len) < 0)
&creation_properties_body_len, type_id,
pobj->domain->u.file.server_version) < 0)
FUNC_GOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, FAIL,
"can't convert Dataset Creation Properties to JSON representation");
}
Expand Down