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OBIDMS: Opened DMS now have a counter associated so that DMS are not

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actually opened several times by the same program, which triggers the
cleaning of unfinished views and columns (to discuss)
This commit is contained in:
Celine Mercier
2017-11-24 17:58:47 +01:00
parent ee5d647d0d
commit 9e3ac477eb
4 changed files with 167 additions and 54 deletions
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2
python/obitools3/dms/capi/obidms.pxd
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@ -14,7 +14,7 @@ cdef extern from "obidms.h" nogil:
OBIDMS_p obi_test_open_dms(const_char_p dms_path)
OBIDMS_p obi_create_dms(const_char_p dms_path)
int obi_dms_exists(const char* dms_path)
int obi_close_dms(OBIDMS_p dms)
int obi_close_dms(OBIDMS_p dms, bint force)
char* obi_dms_get_dms_path(OBIDMS_p dms)
char* obi_dms_get_full_path(OBIDMS_p dms, const_char_p path_name)
void obi_close_atexit()

2
python/obitools3/dms/dms.pyx
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@ -92,7 +92,7 @@ cdef class DMS(OBIWrapper):
cdef OBIDMS_p pointer = self.pointer()
if self.active() :
OBIWrapper.close(self)
if (obi_close_dms(pointer)) < 0 :
if (obi_close_dms(pointer, False)) < 0 :
raise Exception("Problem closing an OBIDMS")

207
src/obidms.c
View File

@ -34,8 +34,10 @@
#define DEBUG_LEVEL 0 // TODO has to be defined somewhere else (cython compil flag?)
// Initialize global list of opened DMS
// Initialize global list of opened DMS and their associated counters
OBIDMS_p global_opened_dms_list[MAX_NB_OPENED_DMS+1] = { 0 };
int global_opened_dms_counter_list[MAX_NB_OPENED_DMS+1] = { 0 };
/**************************************************************************
@ -120,11 +122,44 @@ static int list_dms(OBIDMS_p dms);
* Internal function removing a DMS from the global list of DMS opened by a program.
*
* @param dms A pointer on the DMS to remove.
* @param force Whether the DMS should be unlisted even if it is opened more than once.
*
* @retval 0 if the operation was successfully completed.
* @retval -1 if the DMS was not found.
*
* @since October 2017
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
static void unlist_dms(OBIDMS_p dms);
static int unlist_dms(OBIDMS_p dms, bool force);
/**
* Internal function checking if a DMS is already in the global list of DMS opened by the program.
*
* @param full_dms_path The absolute path to the DMS directory.
*
* @returns A pointer on the DMS if it is already opened, or NULL if it was not opened.
*
* @since November 2017
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
static OBIDMS_p check_if_dms_in_list(const char* full_dms_path);
/**
* Internal function returning the count for an opened DMS (how many times the DMS is opened) in the global list of DMS opened by the program.
*
* @param dms A pointer on the DMS.
*
* @returns The count indicating how many times the DMS has been opened by the program.
*
* @retval -1 if the DMS was not found.
*
* @since November 2017
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
static int dms_count_in_list(OBIDMS_p dms);
/************************************************************************
@ -238,7 +273,7 @@ int create_dms_infos_file(int dms_file_descriptor, const char* dms_name)
static int list_dms(OBIDMS_p dms)
{
int i = 0;
while (global_opened_dms_list[i] != NULL)
while ((global_opened_dms_list[i] != NULL) && (global_opened_dms_list[i] != dms))
i++;
if (i == (MAX_NB_OPENED_DMS-1))
{
@ -246,21 +281,63 @@ static int list_dms(OBIDMS_p dms)
obidebug(1, "\nError opening a DMS: maximum number of DMS opened by a program reached");
return -1;
}
global_opened_dms_list[i] = dms;
if (global_opened_dms_list[i] == NULL)
{ // new dms
global_opened_dms_list[i] = dms;
global_opened_dms_counter_list[i] = 0;
}
else
{ // already opened dms
(global_opened_dms_counter_list[i])++;
}
return 0;
}
static void unlist_dms(OBIDMS_p dms)
static int unlist_dms(OBIDMS_p dms, bool force)
{
int i = 0;
while (global_opened_dms_list[i] != dms)
i++;
while (global_opened_dms_list[i] != NULL)
{
global_opened_dms_list[i] = global_opened_dms_list[i+1];
while ((global_opened_dms_list[i] != dms) && (i <= MAX_NB_OPENED_DMS))
i++;
if (i == MAX_NB_OPENED_DMS)
return -1; // DMS not found
// If opened more than once, and the unlisting is not forced, decrement counter
if ((global_opened_dms_counter_list[i] > 1) && (! force))
(global_opened_dms_counter_list[i])--;
else
{ // If opened once or forced unlisting, delete and unlist by shifting the list
while (global_opened_dms_list[i] != NULL)
{
global_opened_dms_list[i] = global_opened_dms_list[i+1];
i++;
}
}
return 0;
}
static OBIDMS_p check_if_dms_in_list(const char* full_dms_path)
{
int i = 0;
while ((i <= MAX_NB_OPENED_DMS) && (global_opened_dms_list[i] != NULL) && (strcmp(global_opened_dms_list[i]->directory_path, full_dms_path) != 0))
i++;
if (i == MAX_NB_OPENED_DMS)
return NULL; // DMS not found
if (global_opened_dms_list[i] != NULL)
return global_opened_dms_list[i];
return NULL;
}
static int dms_count_in_list(OBIDMS_p dms)
{
int i = 0;
while ((i <= MAX_NB_OPENED_DMS) && (global_opened_dms_list[i] != dms))
i++;
if (i == MAX_NB_OPENED_DMS)
return -1; // DMS not found
return global_opened_dms_counter_list[i];
}
@ -384,7 +461,8 @@ OBIDMS_p obi_create_dms(const char* dms_path)
OBIDMS_p obi_open_dms(const char* dms_path)
{
OBIDMS_p dms;
char* complete_dms_path;
char* relative_dms_path;
char* absolute_dms_path;
char* infos_file_name;
int infos_file_descriptor;
bool little_endian_dms;
@ -392,6 +470,32 @@ OBIDMS_p obi_open_dms(const char* dms_path)
dms = NULL;
// Build and check the directory name including the relative path
relative_dms_path = build_directory_name(dms_path);
if (relative_dms_path == NULL)
return NULL;
// Get and store the absolute path to the DMS directory
absolute_dms_path = realpath(relative_dms_path, NULL);
if (absolute_dms_path == NULL)
{
obi_set_errno(OBIDMS_UNKNOWN_ERROR);
obidebug(1, "\nError getting the absolute path to the DMS directory (DMS does not exist)");
free(relative_dms_path);
return NULL;
}
free(relative_dms_path);
// Check if the DMS is already opened
dms = check_if_dms_in_list(absolute_dms_path);
if (dms != NULL)
{
list_dms(dms);
free(absolute_dms_path);
return dms;
}
// Allocate the data structure
dms = (OBIDMS_p) malloc(sizeof(OBIDMS_t));
if (dms == NULL)
@ -401,36 +505,8 @@ OBIDMS_p obi_open_dms(const char* dms_path)
return NULL;
}
/*
// Isolate and store the dms name
j = 0;
for (i=0; i<strlen(dms_path); i++)
{
if (dms_path[i] == '/')
j = i+1;
i++;
}
*/
strcpy(dms->dms_name, basename((char*)dms_path));
// Build and check the directory name including the relative path
complete_dms_path = build_directory_name(dms_path);
if (complete_dms_path == NULL)
{
free(dms);
return NULL;
}
// Get and store the absolute path to the DMS directory
if (realpath(complete_dms_path, dms->directory_path) == NULL)
{
obi_set_errno(OBIDMS_UNKNOWN_ERROR);
obidebug(1, "\nError getting the absolute path to the DMS directory (DMS does not exist)");
free(complete_dms_path);
return NULL;
}
free(complete_dms_path);
strcpy(dms->directory_path, absolute_dms_path);
// Try to open the directory
dms->directory = opendir(dms->directory_path);
@ -620,7 +696,18 @@ OBIDMS_p obi_open_dms(const char* dms_path)
(dms->opened_indexers)->nb_opened_indexers = 0;
// Add in the global list of opened DMS
list_dms(dms);
if (list_dms(dms) < 0)
{
obidebug(1, "\nError cleaning unfinished columns when opening an OBIDMS");
closedir(dms->indexer_directory);
closedir(dms->tax_directory);
closedir(dms->view_directory);
closedir(dms->directory);
free(dms->opened_columns);
free(dms->opened_indexers);
free(dms);
return NULL;
}
return dms;
}
@ -664,8 +751,27 @@ OBIDMS_p obi_dms(const char* dms_name)
}
int obi_close_dms(OBIDMS_p dms)
int obi_close_dms(OBIDMS_p dms, bool force)
{
int dms_counter;
if (!force)
{
dms_counter = dms_count_in_list(dms);
if (dms_counter < 0)
obidebug(1, "\nError checking the counter of an OBIDMS in the global list of opened OBIDMS");
if (dms_counter > 1) // Don't close if the DMS is opened more than once
{
if (unlist_dms(dms, force) < 0)
{
obidebug(1, "\nError decrementing the counter of an OBIDMS in the global list of opened OBIDMS");
return -1;
}
return 0;
}
}
if (dms != NULL)
{
// Close all columns
@ -703,7 +809,12 @@ int obi_close_dms(OBIDMS_p dms)
}
// Remove DMS from global list of opened DMS
unlist_dms(dms);
if (unlist_dms(dms, force) < 0)
{
obidebug(1, "\nError removing an OBIDMS from the global list of opened OBIDMS when closing it");
free(dms);
return -1;
}
free(dms);
}
@ -1060,8 +1171,8 @@ obiversion_t obi_import_column(const char* dms_path_1, const char* dms_path_2, c
// TODO no? because if iterating over all columns in a view etc.... iterate and change associated columns version refs afterwards?
// Close the DMS
obi_close_dms(dms_1);
obi_close_dms(dms_2);
obi_close_dms(dms_1, false);
obi_close_dms(dms_2, false);
return new_version;
}
@ -1167,8 +1278,8 @@ int obi_import_view(const char* dms_path_1, const char* dms_path_2, const char*
}
// Close the DMS
obi_close_dms(dms_1);
obi_close_dms(dms_2);
obi_close_dms(dms_1, false);
obi_close_dms(dms_2, false);
return 0;
}
@ -1180,7 +1291,7 @@ void obi_close_atexit()
while (global_opened_dms_list[i] != NULL)
{
obi_close_dms(global_opened_dms_list[i]);
obi_close_dms(global_opened_dms_list[i], true);
i++;
}
}

10
src/obidms.h
View File

@ -54,7 +54,7 @@ typedef struct OBIDMS_column* OBIDMS_column_p; /**< Declarations to avoid circu
typedef struct Opened_columns_list {
int nb_opened_columns; /**< Number of opened columns.
*/
OBIDMS_column_p columns[MAX_NB_OPENED_COLUMNS]; /**< Array of pointers on the opened columns.
OBIDMS_column_p columns[MAX_NB_OPENED_COLUMNS+1]; /**< Array of pointers on the opened columns.
*/
} Opened_columns_list_t, *Opened_columns_list_p;
@ -70,7 +70,7 @@ typedef OBIDMS_avl_group_p Obi_indexer_p; /**< Declarations to avoid circular
typedef struct Opened_indexers_list {
int nb_opened_indexers; /**< Number of opened indexers.
*/
Obi_indexer_p indexers[MAX_NB_OPENED_INDEXERS]; /**< Array of pointers on the opened indexers.
Obi_indexer_p indexers[MAX_NB_OPENED_INDEXERS+1]; /**< Array of pointers on the opened indexers.
*/
} Opened_indexers_list_t, *Opened_indexers_list_p;
@ -87,7 +87,7 @@ typedef struct OBIDMS {
char directory_name[OBIDMS_MAX_NAME+1]; /**< The name of the directory
* containing the DMS.
*/
char directory_path[MAX_PATH_LEN]; /**< The absolute path of the directory
char directory_path[MAX_PATH_LEN+1]; /**< The absolute path of the directory
* containing the DMS.
*/
DIR* directory; /**< A directory entry usable to
@ -127,6 +127,7 @@ typedef struct OBIDMS {
* @brief Global Array of DMS pointers listing all the DMS opened by a program.
*/
extern OBIDMS_p global_opened_dms_list[MAX_NB_OPENED_DMS+1];
extern int global_opened_dms_counter_list[MAX_NB_OPENED_DMS+1];
/**
@ -223,6 +224,7 @@ OBIDMS_p obi_dms(const char* dms_path);
* @brief Closes an opened OBITools Data Management instance (OBIDMS).
*
* @param dms A pointer as returned by obi_create_dms() or obi_open_dms().
* @param force Whether the DMS should be closed even if it is opened more than once.
*
* @returns An integer value indicating the success of the operation. Even on
* error, the `OBIDMS` structure is freed.
@ -234,7 +236,7 @@ OBIDMS_p obi_dms(const char* dms_path);
* @since May 2015
* @author Eric Coissac (eric.coissac@metabarcoding.org)
*/
int obi_close_dms(OBIDMS_p dms);
int obi_close_dms(OBIDMS_p dms, bool force);
/**