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Move compound subset read logic to helper func
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@mattjala
mattjala committed Jan 17, 2024
1 parent 787c2c7 commit 529e47c
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Showing 2 changed files with 94 additions and 71 deletions.
4 changes: 4 additions & 0 deletions src/rest_vol.h
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Original file line number Diff line number Diff line change
Expand Up @@ -786,6 +786,10 @@ herr_t RV_get_compound_subset_info(hid_t src_type_id, hid_t dst_type_id, RV_subs
herr_t RV_get_unused_compound_fields(hid_t mem_type_id, hid_t file_type_id,
RV_compound_info_t *compound_info);

/* Helper function to handle compound type subsetting during reads. */
herr_t RV_handle_compound_subset_read(hid_t src_type_id, hid_t dst_type_id, hid_t dst_space_id,
const void *src_buf, void *dst_buf);

/* Helper function to escape control characters for JSON strings */
herr_t RV_JSON_escape_string(const char *in, char *out, size_t *out_size);

Expand Down
161 changes: 90 additions & 71 deletions src/rest_vol_dataset.c
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Original file line number Diff line number Diff line change
Expand Up @@ -4548,17 +4548,6 @@ rv_dataset_read_cb(hid_t mem_type_id, hid_t mem_space_id, hid_t file_type_id, hi
RV_tconv_reuse_t reuse = RV_TCONV_REUSE_NONE;
hbool_t fill_bkg = FALSE;

int file_nmembs = 0;
RV_compound_info_t compound_info;
compound_info.src_offsets = NULL;
compound_info.dst_offsets = NULL;
compound_info.lengths = NULL;

void *subset_buffer = NULL;

char *dst = NULL;
char *src = NULL;

if (H5T_NO_CLASS == (mem_dtype_class = H5Tget_class(mem_type_id)))
FUNC_GOTO_ERROR(H5E_DATATYPE, H5E_BADVALUE, FAIL, "memory datatype is invalid");

Expand Down Expand Up @@ -4610,54 +4599,10 @@ rv_dataset_read_cb(hid_t mem_type_id, hid_t mem_space_id, hid_t file_type_id, hi
FUNC_GOTO_ERROR(H5E_DATATYPE, H5E_BADVALUE, FAIL,
"error while checking if types are compound subsets");

// TODO - Move this to a helper function
if (subset_info > 0) {
/* Copy unselected fields from user buffer to resp info buffer to avoid overwriting fields that
* weren't selected */

/* Determine which fields to copy */
if ((file_nmembs = H5Tget_nmembers(file_type_id)) < 0)
FUNC_GOTO_ERROR(H5E_DATATYPE, H5E_CANTGET, FAIL,
"can't get number of members in file datatype");

if ((compound_info.lengths = RV_calloc(sizeof(size_t) * (size_t)file_nmembs)) == NULL)
FUNC_GOTO_ERROR(H5E_DATATYPE, H5E_CANTALLOC, FAIL, "can't allocate memory for compound info");

if ((compound_info.src_offsets = RV_calloc(sizeof(size_t) * (size_t)file_nmembs)) == NULL)
FUNC_GOTO_ERROR(H5E_DATATYPE, H5E_CANTALLOC, FAIL, "can't allocate memory for compound info");

if ((compound_info.dst_offsets = RV_calloc(sizeof(size_t) * (size_t)file_nmembs)) == NULL)
FUNC_GOTO_ERROR(H5E_DATATYPE, H5E_CANTALLOC, FAIL, "can't allocate memory for compound info");

compound_info.nmembers = 0;
compound_info.nalloc = file_nmembs;

if (RV_get_unused_compound_fields(mem_type_id, file_type_id, &compound_info) < 0)
FUNC_GOTO_ERROR(H5E_DATATYPE, H5E_CANTGET, FAIL,
"can't get unused fields in compound datatype");

/* Copy those regions of memory from buf to resp_info.buf */
if ((subset_buffer = RV_calloc(mem_data_size)) == NULL)
FUNC_GOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL,
"can't allocate buffer for compound subsetting");

if (H5Dgather(mem_space_id, (const void *)buf, mem_type_id, mem_data_size, subset_buffer, NULL,
NULL) < 0)
FUNC_GOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't gather data from read buffer");

for (size_t i = 0; i < file_select_npoints; i++) {
/* Copy unused field information from subset buffer to response buffer before scattering */
for (size_t j = 0; j < compound_info.nmembers; j++) {
src = (char *)subset_buffer + (i * mem_type_size) + compound_info.src_offsets[j];
dst = (char *)resp_info.buffer + (i * file_type_size) + compound_info.dst_offsets[j];

memcpy(dst, src, compound_info.lengths[j]);
}
}

RV_free(subset_buffer);
subset_buffer = NULL;
}
if (subset_info > 0)
if (RV_handle_compound_subset_read(file_type_id, mem_type_id, file_space_id, (const void *)buf,
resp_info.buffer) < 0)
FUNC_GOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't handle compound subset read");

if ((needs_tconv = RV_need_tconv(file_type_id, mem_type_id)) < 0)
FUNC_GOTO_ERROR(H5E_DATATYPE, H5E_BADVALUE, FAIL, "unable to check if datatypes need conversion");
Expand Down Expand Up @@ -4721,18 +4666,6 @@ rv_dataset_read_cb(hid_t mem_type_id, hid_t mem_space_id, hid_t file_type_id, hi
}

done:
if (compound_info.lengths)
RV_free(compound_info.lengths);

if (compound_info.src_offsets)
RV_free(compound_info.src_offsets);

if (compound_info.dst_offsets)
RV_free(compound_info.dst_offsets);

if (subset_buffer)
RV_free(subset_buffer);

if (obj_ref_buf)
RV_free(obj_ref_buf);

Expand Down Expand Up @@ -5121,3 +5054,89 @@ RV_json_values_to_binary_recursive(yajl_val value_entry, hid_t dtype_id, void *v
done:
return ret_value;
}

/* Helper function to handle compound type subsetting during reads.
* Copies the omitted members from the source buffer to dst buf to
* avoid overwriting them. */
herr_t
RV_handle_compound_subset_read(hid_t src_type_id, hid_t dst_type_id, hid_t dst_space_id, const void *src_buf,
void *dst_buf)
{
herr_t ret_value = SUCCEED;
int src_nmembs = 0;
void *subset_buffer = NULL;
hssize_t npoints = 0;
size_t src_type_size = 0, dst_type_size = 0;
char *src = NULL, *dst = NULL;

RV_compound_info_t compound_info;
compound_info.nalloc = 0;
compound_info.nmembers = 0;
compound_info.dst_offsets = NULL;
compound_info.src_offsets = NULL;
compound_info.lengths = NULL;

/* Copy unselected fields from user buffer to resp info buffer to avoid overwriting fields that
* weren't selected */

/* Determine which fields to copy */
if ((src_nmembs = H5Tget_nmembers(src_type_id)) < 0)
FUNC_GOTO_ERROR(H5E_DATATYPE, H5E_CANTGET, FAIL, "can't get number of members in file datatype");

if ((compound_info.lengths = RV_calloc(sizeof(size_t) * (size_t)src_nmembs)) == NULL)
FUNC_GOTO_ERROR(H5E_DATATYPE, H5E_CANTALLOC, FAIL, "can't allocate memory for compound info");

if ((compound_info.src_offsets = RV_calloc(sizeof(size_t) * (size_t)src_nmembs)) == NULL)
FUNC_GOTO_ERROR(H5E_DATATYPE, H5E_CANTALLOC, FAIL, "can't allocate memory for compound info");

if ((compound_info.dst_offsets = RV_calloc(sizeof(size_t) * (size_t)src_nmembs)) == NULL)
FUNC_GOTO_ERROR(H5E_DATATYPE, H5E_CANTALLOC, FAIL, "can't allocate memory for compound info");

compound_info.nmembers = 0;
compound_info.nalloc = src_nmembs;

if (RV_get_unused_compound_fields(dst_type_id, src_type_id, &compound_info) < 0)
FUNC_GOTO_ERROR(H5E_DATATYPE, H5E_CANTGET, FAIL, "can't get unused fields in compound datatype");

/* Allocate space for gather */
if ((npoints = H5Sget_simple_extent_npoints(dst_space_id)) < 0)
FUNC_GOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get number of points in dst dataspace");

if ((dst_type_size = H5Tget_size(dst_type_id)) == 0)
FUNC_GOTO_ERROR(H5E_DATATYPE, H5E_CANTGET, FAIL, "can't get size of destination datatype");

if ((src_type_size = H5Tget_size(src_type_id)) == 0)
FUNC_GOTO_ERROR(H5E_DATATYPE, H5E_CANTGET, FAIL, "can't get size of source datatype");

if ((subset_buffer = RV_calloc((size_t)npoints * dst_type_size)) == NULL)
FUNC_GOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate buffer for compound subsetting");

/* Gather pre-existing data from src buffer */
if (H5Dgather(dst_space_id, (const void *)src_buf, dst_type_id, (size_t)npoints * dst_type_size,
subset_buffer, NULL, NULL) < 0)
FUNC_GOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't gather data from read buffer");

/* Copy pre-existing data from src buffer to avoid modifying fields that are omitted via
* compound subsetting */
for (size_t i = 0; i < npoints; i++) {
for (size_t j = 0; j < compound_info.nmembers; j++) {
src = (char *)subset_buffer + (i * dst_type_size) + compound_info.src_offsets[j];
dst = (char *)dst_buf + (i * src_type_size) + compound_info.dst_offsets[j];

memcpy(dst, src, compound_info.lengths[j]);
}
}

done:
if (subset_buffer)
RV_free(subset_buffer);

if (compound_info.nalloc > 0) {
if (compound_info.src_offsets)
RV_free(compound_info.src_offsets);
if (compound_info.dst_offsets)
RV_free(compound_info.dst_offsets);
if (compound_info.lengths)
RV_free(compound_info.lengths);
}
}

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