All DMS opened by a program are now listed and closed with atexit system

python/obitools3/dms/capi/obidms.pxd

@@ -17,6 +17,7 @@ cdef extern from "obidms.h" nogil:
     int obi_close_dms(OBIDMS_p dms)
     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()
+    
     obiversion_t obi_import_column(const char* dms_path_1, const char* dms_path_2, const char* column_name, obiversion_t version_number)
     int obi_import_view(const char* dms_path_1, const char* dms_path_2, const char* view_name_1, const char* view_name_2)

python/obitools3/dms/dms.pyx

@@ -1,14 +1,15 @@
 #cython: language_level=3
 
 
-from libc.stdlib  cimport free
+from libc.stdlib  cimport free, atexit
 from cpython.list cimport PyList_Size
 
 from .capi.obidms cimport obi_open_dms, \
                           obi_create_dms, \
                           obi_close_dms, \
                           obi_dms_exists, \
-                          obi_dms_get_full_path
+                          obi_dms_get_full_path, \
+                          obi_close_atexit
                                                       
 from .capi.obitypes cimport const_char_p
                             
@@ -30,6 +31,10 @@ cdef class DMS(OBIWrapper):
     cdef inline OBIDMS_p pointer(self):
         return <OBIDMS_p>(self._pointer)
     
+    @staticmethod
+    def obi_atexit():
+        atexit(obi_close_atexit)
+    
     @staticmethod
     def open_or_new(object dms_name) :
         cdef OBIDMS_p pointer

src/obidms.c

@@ -34,6 +34,10 @@
 #define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
 
 
+// Initialize global list of opened DMS
+OBIDMS_p global_opened_dms_list[MAX_NB_OPENED_DMS+1] = { 0 };
+
+
 /**************************************************************************
  *
  * D E C L A R A T I O N   O F   T H E   P R I V A T E   F U N C T I O N S
@@ -98,6 +102,31 @@ static char* build_infos_file_name(const char* dms_name);
 int create_dms_infos_file(int dms_file_descriptor, const char* dms_name);
 
 
+/**
+ * Internal function adding a DMS in the global list of DMS opened by a program.
+ *
+ * @param dms A pointer on the DMS to add.
+ *
+ * @retval 0 if the operation was successfully completed.
+ * @retval -1 if an error occurred.
+ *
+ * @since October 2017
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+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.
+ *
+ * @since October 2017
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+static void unlist_dms(OBIDMS_p dms);
+
+
 /************************************************************************
  *
  * D E F I N I T I O N   O F   T H E   P R I V A T E   F U N C T I O N S
@@ -202,11 +231,39 @@ int create_dms_infos_file(int dms_file_descriptor, const char* dms_name)
 		return -1;
 	}
 
-
 	return 0;
 }
 
 
+static int list_dms(OBIDMS_p dms)
+{
+	int i = 0;
+	while (global_opened_dms_list[i] != NULL)
+		i++;
+	if (i == (MAX_NB_OPENED_DMS-1))
+	{
+		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
+		obidebug(1, "\nError opening a DMS: maximum number of DMS opened by a program reached");
+		return -1;
+	}
+	global_opened_dms_list[i] = dms;
+	return 0;
+}
+
+
+static void unlist_dms(OBIDMS_p dms)
+{
+	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];
+		i++;
+	}
+}
+
+
 /**********************************************************************
  *
  * D E F I N I T I O N   O F   T H E   P U B L I C   F U N C T I O N S
@@ -538,6 +595,9 @@ OBIDMS_p obi_open_dms(const char* dms_path)
 	dms->opened_indexers = (Opened_indexers_list_p) malloc(sizeof(Opened_indexers_list_t));
 	(dms->opened_indexers)->nb_opened_indexers = 0;
 
+	// Add in the global list of opened DMS
+	list_dms(dms);
+
 	return dms;
 }
 
@@ -617,6 +677,10 @@ int obi_close_dms(OBIDMS_p dms)
 			free(dms);
 			return -1;
 		}
+
+		// Remove DMS from global list of opened DMS
+		unlist_dms(dms);
+
 		free(dms);
 	}
 
@@ -1085,5 +1149,14 @@ int obi_import_view(const char* dms_path_1, const char* dms_path_2, const char*
 }
 
 
+void obi_close_atexit()
+{
+	int i=0;
 
+	while (global_opened_dms_list[i] != NULL)
+	{
+        obi_close_dms(global_opened_dms_list[i]);
+		i++;
+	}
+}
 

src/obidms.h

@@ -36,6 +36,8 @@
                                 	 	 	 	 */
 #define MAX_NB_OPENED_COLUMNS (1000) 			/**< The maximum number of columns open at the same time.
                                 	 	 	 	 */
+#define MAX_NB_OPENED_DMS (1000) 			    /**< The maximum number of DMS open at the same time for a given program.
+                                	 	 	 	 */
 #define MAX_NB_OPENED_INDEXERS (1000) 			/**< The maximum number of indexers open at the same time.
                                 	 	 	 	 */
 #define MAX_PATH_LEN (1024)						/**< Maximum length for the character string defining a
@@ -121,6 +123,12 @@ typedef struct OBIDMS {
 } OBIDMS_t, *OBIDMS_p;
 
 
+/**
+ * @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];
+
+
 /**
  * @brief Checks if an OBIDMS exists.
  *
@@ -403,4 +411,14 @@ obiversion_t obi_import_column(const char* dms_path_1, const char* dms_path_2, c
 int obi_import_view(const char* dms_path_1, const char* dms_path_2, const char* view_name_1, const char* view_name_2);
 
 
+/**
+ * @brief Closes all DMS in the global list of opened DMS.
+ *        To be executed 'at exit' of programs.
+ *
+ * @since October 2017
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+void obi_close_atexit();
+
+
 #endif /* OBIDMS_H_ */