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The default name of an AVL is now the column name + '_indexer', and when

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an AVL is opened (as opposed to created), it is read-only
This commit is contained in:
Celine Mercier
2016-04-15 12:55:26 +02:00
parent e04ea85d1e
commit 02d67c257f
4 changed files with 34 additions and 14 deletions
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2
python/obitools3/obidms/_obidms.pyx
View File

@ -352,7 +352,7 @@ cdef class OBIView :
index_t nb_lines=0,
index_t nb_elements_per_line=1, # TODO 1?
list elements_names=None,
str indexer_name="default_indexer",
str indexer_name="",
str comments="",
bint create=True # TODO
) :

29
src/obiavl.c
View File

@ -1672,7 +1672,7 @@ OBIDMS_avl_p obi_open_avl(OBIDMS_p dms, const char* avl_name, int avl_idx)
return NULL;
// Open file
avl_data_file_descriptor = openat(avl_dir_file_descriptor, avl_data_file_name, O_RDWR, 0777);
avl_data_file_descriptor = openat(avl_dir_file_descriptor, avl_data_file_name, O_RDONLY, 0777);
if (avl_data_file_descriptor < 0)
{
obi_set_errno(OBI_AVL_ERROR);
@ -1710,7 +1710,7 @@ OBIDMS_avl_p obi_open_avl(OBIDMS_p dms, const char* avl_name, int avl_idx)
// Fill the avl data structure
avl_data->header = mmap(NULL,
header_size,
PROT_READ | PROT_WRITE,
PROT_READ,
MAP_SHARED,
avl_data_file_descriptor,
0
@ -1728,7 +1728,7 @@ OBIDMS_avl_p obi_open_avl(OBIDMS_p dms, const char* avl_name, int avl_idx)
avl_data->data = mmap(NULL,
(avl_data->header)->data_size_max,
PROT_READ | PROT_WRITE,
PROT_READ,
MAP_SHARED,
avl_data_file_descriptor,
header_size
@ -1759,7 +1759,7 @@ OBIDMS_avl_p obi_open_avl(OBIDMS_p dms, const char* avl_name, int avl_idx)
}
// Open file
avl_file_descriptor = openat(avl_dir_file_descriptor, avl_file_name, O_RDWR, 0777);
avl_file_descriptor = openat(avl_dir_file_descriptor, avl_file_name, O_RDONLY, 0777);
if (avl_file_descriptor < 0)
{
obi_set_errno(OBI_AVL_ERROR);
@ -1799,7 +1799,7 @@ OBIDMS_avl_p obi_open_avl(OBIDMS_p dms, const char* avl_name, int avl_idx)
// Fill the avl structure
avl->header = mmap(NULL,
header_size,
PROT_READ | PROT_WRITE,
PROT_READ,
MAP_SHARED,
avl_file_descriptor,
0
@ -1818,7 +1818,7 @@ OBIDMS_avl_p obi_open_avl(OBIDMS_p dms, const char* avl_name, int avl_idx)
avl->tree = mmap(NULL,
(((avl->header)->nb_items_max) * sizeof(AVL_node_t)),
PROT_READ | PROT_WRITE,
PROT_READ,
MAP_SHARED,
avl_file_descriptor,
header_size
@ -1899,6 +1899,9 @@ OBIDMS_avl_group_p obi_create_avl_group(OBIDMS_p dms, const char* avl_name)
// Set counter to 1
avl_group->counter = 1;
// Set as writable
avl_group->writable = true;
return avl_group;
}
@ -1956,6 +1959,9 @@ OBIDMS_avl_group_p obi_open_avl_group(OBIDMS_p dms, const char* avl_name)
// Set counter to 1
avl_group->counter = 1;
// Set as read-only
avl_group->writable = false;
return avl_group;
}
@ -2247,7 +2253,16 @@ index_t obi_avl_group_add(OBIDMS_avl_group_p avl_group, Obi_blob_p value)
}
// Not found in any AVL: add in current
// First, check if make new AVL
// Check if the AVL group is writable
if (!(avl_group->writable))
{
obi_set_errno(OBI_AVL_ERROR);
obidebug(1, "\nTrying to add a value in an AVL group that is read-only.");
return -1;
}
// Check if need to make new AVL
if (((((avl_group->sub_avls)[avl_group->current_avl_idx])->header)->nb_items == MAX_NODE_COUNT_PER_AVL) || (((((avl_group->sub_avls)[avl_group->current_avl_idx])->data)->header)->data_size_used >= MAX_DATA_SIZE_PER_AVL))
{
if (add_new_avl_in_group(avl_group) < 0)

2
src/obiavl.h
View File

@ -167,6 +167,8 @@ typedef struct OBIDMS_avl_group {
*/
OBIDMS_p dms; /**< Pointer to the OBIDMS structure to which the AVL group belongs.
*/
bool writable; /**< Indicates whether the AVL group is read-only or not.
*/
size_t counter; /**< Indicates by how many threads/programs (TODO) the AVL group is used.
*/
} OBIDMS_avl_group_t, *OBIDMS_avl_group_p;

15
src/obidmscolumn.c
View File

@ -535,6 +535,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
index_t minimum_line_count;
OBIType_t returned_data_type;
OBIType_t stored_data_type;
char final_indexer_name[INDEXER_MAX_NAME];
new_column = NULL;
@ -554,11 +555,13 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
obidebug(1, "\nCan't create column because of invalid data type");
return NULL;
}
if (((data_type == OBI_STR) || (data_type == OBI_SEQ)) && (indexer_name == NULL))
{
obidebug(1, "\nCan't create column because of empty indexer name");
return NULL;
if (((data_type == OBI_STR) || (data_type == OBI_SEQ)) && (strcmp(indexer_name, "") == 0))
{ // TODO make function in obiblob_indexer.c and discuss the fact that it's here
strcpy(final_indexer_name, column_name);
strcat(final_indexer_name, "_indexer");
}
else
strcpy(final_indexer_name, indexer_name);
returned_data_type = data_type;
if ((data_type == OBI_STR) || (data_type == OBI_SEQ))
@ -727,7 +730,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
// If the data type is OBI_STR or OBI_SEQ, the associated obi_indexer is opened or created
if ((returned_data_type == OBI_STR) || (returned_data_type == OBI_SEQ))
{
new_column->indexer = obi_indexer(dms, indexer_name);
new_column->indexer = obi_indexer(dms, final_indexer_name);
if (new_column->indexer == NULL)
{
obidebug(1, "\nError opening or creating the indexer associated with a column");
@ -736,7 +739,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
free(new_column);
return NULL;
}
strncpy(header->indexer_name, indexer_name, INDEXER_MAX_NAME);
strncpy(header->indexer_name, final_indexer_name, INDEXER_MAX_NAME);
}
// Fill the data with NA values