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lib/hdf5-db: Store attribute data in database (#99)
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@michaelkuhn
michaelkuhn committed Mar 16, 2021
1 parent 3051d7d commit c8807f4
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Showing 3 changed files with 84 additions and 57 deletions.
129 changes: 84 additions & 45 deletions lib/hdf5-db/jhdf5-db-attr.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -112,6 +112,11 @@ H5VL_julea_db_attr_init(hid_t vipl_id)
j_goto_error();
}

if (!j_db_schema_add_field(julea_db_schema_attr, "data", J_DB_TYPE_BLOB, &error))
{
j_goto_error();
}

{
const gchar* index[] = {
"file",
Expand Down Expand Up @@ -238,10 +243,10 @@ H5VL_julea_db_attr_create(void* obj, const H5VL_loc_params_t* loc_params, const
g_autoptr(GError) error = NULL;
g_autoptr(JBatch) batch = NULL;
g_autoptr(JDBEntry) entry = NULL;
g_autofree char* hex_buf = NULL;
JHDF5Object_t* object = NULL;
JHDF5Object_t* parent = obj;
JHDF5Object_t* file;
gchar dummy[1];

(void)loc_params;
(void)acpl_id;
Expand Down Expand Up @@ -324,39 +329,22 @@ H5VL_julea_db_attr_create(void* obj, const H5VL_loc_params_t* loc_params, const
j_goto_error();
}

if (!j_db_entry_insert(entry, batch, &error))
{
j_goto_error();
}

if (!j_batch_execute(batch))
if (!j_db_entry_set_field(entry, "data", dummy, 0, &error))
{
j_goto_error();
}

if (!j_db_entry_get_id(entry, &object->backend_id, &object->backend_id_len, &error))
{
j_goto_error();
}

if (!(object->attr.distribution = j_distribution_new(J_DISTRIBUTION_ROUND_ROBIN)))
{
j_goto_error();
}

if (!(hex_buf = H5VL_julea_db_buf_to_hex("attr", object->backend_id, object->backend_id_len)))
if (!j_db_entry_insert(entry, batch, &error))
{
j_goto_error();
}

if (!(object->attr.object = j_distributed_object_new(JULEA_HDF5_DB_NAMESPACE, hex_buf, object->attr.distribution)))
if (!j_batch_execute(batch))
{
j_goto_error();
}

j_distributed_object_create(object->attr.object, batch);

if (!j_batch_execute(batch))
if (!j_db_entry_get_id(entry, &object->backend_id, &object->backend_id_len, &error))
{
j_goto_error();
}
Expand Down Expand Up @@ -384,7 +372,6 @@ H5VL_julea_db_attr_open(void* obj, const H5VL_loc_params_t* loc_params, const ch
g_autoptr(JBatch) batch = NULL;
g_autoptr(JDBIterator) iterator = NULL;
g_autoptr(JDBSelector) selector = NULL;
g_autofree char* hex_buf = NULL;
g_autofree void* space_id_buf = NULL;
g_autofree void* datatype_id_buf = NULL;
JHDF5Object_t* object = NULL;
Expand Down Expand Up @@ -491,21 +478,6 @@ H5VL_julea_db_attr_open(void* obj, const H5VL_loc_params_t* loc_params, const ch

g_assert(!j_db_iterator_next(iterator, NULL));

if (!(object->attr.distribution = j_distribution_new(J_DISTRIBUTION_ROUND_ROBIN)))
{
j_goto_error();
}

if (!(hex_buf = H5VL_julea_db_buf_to_hex("attr", object->backend_id, object->backend_id_len)))
{
j_goto_error();
}

if (!(object->attr.object = j_distributed_object_new(JULEA_HDF5_DB_NAMESPACE, hex_buf, object->attr.distribution)))
{
j_goto_error();
}

return object;

_error:
Expand All @@ -521,10 +493,14 @@ H5VL_julea_db_attr_read(void* obj, hid_t mem_type_id, void* buf, hid_t dxpl_id,
{
J_TRACE_FUNCTION(NULL);

g_autoptr(JBatch) batch = NULL;
g_autoptr(GError) error = NULL;
g_autoptr(JDBIterator) iterator = NULL;
g_autoptr(JDBSelector) selector = NULL;
guint64 bytes_read;
gsize data_size;
g_autofree gpointer tmp = NULL;
JHDF5Object_t* object = obj;
JDBType type;

(void)mem_type_id;
(void)dxpl_id;
Expand All @@ -533,17 +509,40 @@ H5VL_julea_db_attr_read(void* obj, hid_t mem_type_id, void* buf, hid_t dxpl_id,
g_return_val_if_fail(buf != NULL, 1);
g_return_val_if_fail(object->type == J_HDF5_OBJECT_TYPE_ATTR, 1);

batch = j_batch_new_for_template(J_SEMANTICS_TEMPLATE_DEFAULT);
bytes_read = 0;
data_size = object->dataset.datatype->datatype.type_total_size;
data_size *= object->attr.space->space.dim_total_count;
j_distributed_object_read(object->attr.object, buf, data_size, 0, &bytes_read, batch);

if (!j_batch_execute(batch))
if (!(selector = j_db_selector_new(julea_db_schema_attr, J_DB_SELECTOR_MODE_AND, &error)))
{
j_goto_error();
}

if (!j_db_selector_add_field(selector, "_id", J_DB_SELECTOR_OPERATOR_EQ, object->backend_id, object->backend_id_len, &error))
{
j_goto_error();
}

if (!(iterator = j_db_iterator_new(julea_db_schema_attr, selector, &error)))
{
j_goto_error();
}

if (!j_db_iterator_next(iterator, &error))
{
j_goto_error();
}

if (!j_db_iterator_get_field(iterator, "data", &type, &tmp, &bytes_read, &error))
{
j_goto_error();
}

g_assert(!j_db_iterator_next(iterator, NULL));
g_assert_cmpuint(data_size, ==, bytes_read);

memcpy(buf, tmp, bytes_read);

return 0;

_error:
Expand All @@ -555,8 +554,10 @@ H5VL_julea_db_attr_write(void* obj, hid_t mem_type_id, const void* buf, hid_t dx
{
J_TRACE_FUNCTION(NULL);

g_autoptr(GError) error = NULL;
g_autoptr(JBatch) batch = NULL;
guint64 bytes_written;
g_autoptr(JDBEntry) entry = NULL;
g_autoptr(JDBSelector) selector = NULL;
gsize data_size;
JHDF5Object_t* object = obj;

Expand All @@ -568,10 +569,48 @@ H5VL_julea_db_attr_write(void* obj, hid_t mem_type_id, const void* buf, hid_t dx
g_return_val_if_fail(object->type == J_HDF5_OBJECT_TYPE_ATTR, 1);

batch = j_batch_new_for_template(J_SEMANTICS_TEMPLATE_DEFAULT);
bytes_written = 0;
data_size = object->dataset.datatype->datatype.type_total_size;
data_size *= object->attr.space->space.dim_total_count;
j_distributed_object_write(object->attr.object, buf, data_size, 0, &bytes_written, batch);

if (!(selector = j_db_selector_new(julea_db_schema_attr, J_DB_SELECTOR_MODE_AND, &error)))
{
j_goto_error();
}

if (!j_db_selector_add_field(selector, "_id", J_DB_SELECTOR_OPERATOR_EQ, object->backend_id, object->backend_id_len, &error))
{
j_goto_error();
}

if (!(entry = j_db_entry_new(julea_db_schema_attr, &error)))
{
j_goto_error();
}

if (!j_db_entry_set_field(entry, "file", object->attr.file->backend_id, object->attr.file->backend_id_len, &error))
{
j_goto_error();
}

if (!j_db_entry_set_field(entry, "datatype", object->attr.datatype->backend_id, object->attr.datatype->backend_id_len, &error))
{
j_goto_error();
}

if (!j_db_entry_set_field(entry, "space", object->attr.space->backend_id, object->attr.space->backend_id_len, &error))
{
j_goto_error();
}

if (!j_db_entry_set_field(entry, "data", buf, data_size, &error))
{
j_goto_error();
}

if (!j_db_entry_update(entry, selector, batch, &error))
{
j_goto_error();
}

if (!j_batch_execute(batch))
{
Expand Down
10 changes: 0 additions & 10 deletions lib/hdf5-db/jhdf5-db-shared.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -146,16 +146,6 @@ H5VL_julea_db_object_unref(JHDF5Object_t* object)
H5VL_julea_db_object_unref(object->attr.space);
H5VL_julea_db_object_unref(object->attr.datatype);

if (object->attr.distribution)
{
j_distribution_unref(object->attr.distribution);
}

if (object->attr.object)
{
j_distributed_object_unref(object->attr.object);
}

break;
case J_HDF5_OBJECT_TYPE_GROUP:
H5VL_julea_db_object_unref(object->group.file);
Expand Down
2 changes: 0 additions & 2 deletions lib/hdf5-db/jhdf5-db.h
View file
Original file line number Diff line number Diff line change
Expand Up @@ -78,8 +78,6 @@ struct JHDF5Object_t
JHDF5Object_t* file;
JHDF5Object_t* datatype;
JHDF5Object_t* space;
JDistribution* distribution;
JDistributedObject* object;
} attr;
struct
{
Expand Down

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