The endianness of an OBIDMS is now stored in an informations file that

is read when opening the OBIDMS.

python/obitools3/obidms/_obidms.pyx

@@ -66,12 +66,12 @@ cdef class OBIDMS :
 
 
     cpdef close(self) :
-        #TODO close all columns
+        #TODO close all columns (needs to be discussed)
         if (obi_close_dms(self.pointer)) < 0 :
             raise Exception("Problem closing an OBIDMS")
 
 
-    cpdef dict list(self):
+    cpdef dict list(self):  # TDODO This is a temporary function that will be rewritten
     
         # Declarations
         cdef object p
@@ -100,13 +100,12 @@ cdef class OBIDMS :
                 data_type = bytes2str(name_data_type(header.data_type))
                 line_count = header.line_count
                 creation_date = bytes2str(obi_column_format_date(header.creation_date))
-                obi_unmap_header(header)    # TODO check if error? but C will already warn and there's nothing to do
+                obi_unmap_header(header)
                 latest_version = obi_column_get_latest_version_from_name(self.pointer, column_name_b)
                 dms[column_name]['data_type'] = data_type
                 dms[column_name]['latest_version'] = latest_version
                 dms[column_name]['line_count'] = line_count
                 dms[column_name]['creation_date'] = creation_date
-                # TODO : actually get all the informations in the header
                 print("{:<30} {:<12} {:<25} {:<30} {:<40}".format(column_name, data_type, latest_version, line_count, creation_date))
 
         return dms

python/obitools3/obidms/capi/obidmscolumn.pxd

@@ -15,7 +15,6 @@ from ..capi.obitypes cimport const_char_p, \
 cdef extern from "obidmscolumn.h" nogil:
     
     struct OBIDMS_column_header_t:
-        bint            little_endian
         size_t          header_size
         size_t          data_size
         index_t         line_count

src/obidms.c

@@ -23,6 +23,7 @@
 #include "obidebug.h"
 #include "obidmscolumn.h"
 #include "private_at_functions.h"
+#include "obilittlebigman.h"
 
 
 #define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
@@ -54,6 +55,44 @@
 static char* build_directory_name(const char* dms_name);
 
 
+/**
+ * Internal function building the informations file name from an OBIDMS name.
+ *
+ * The function builds the file name for the informations file of an OBIDMS.
+ *
+ * @warning The returned pointer has to be freed by the caller.
+ *
+ * @param dms_name The name of the OBIDMS.
+ *
+ * @returns A pointer to the file name.
+ * @retval NULL if an error occurred.
+ *
+ * @since November 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+static char* build_infos_file_name(const char* dms_name);
+
+
+/**
+ * Internal function creating the file containing basic informations on the OBIDMS.
+ *
+ * This file contains:
+ * 		- The endianness of the platform
+ *
+ * @warning The returned pointer has to be freed by the caller.
+ *
+ * @param dms_file_descriptor The file descriptor for the OBIDMS directory.
+ * @param dms_name The name of the OBIDMS.
+ *
+ * @retval 0 if the operation was successfully completed.
+ * @retval -1 if an error occurred.
+ *
+ * @since November 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int create_dms_infos_file(int dms_file_descriptor, const char* dms_name);
+
+
 /************************************************************************
  *
  * 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
@@ -85,6 +124,74 @@ static char* build_directory_name(const char* dms_name)
 }
 
 
+static char* build_infos_file_name(const char* dms_name)
+{
+	char* file_name;
+
+	// Build file name
+	if (asprintf(&file_name, "%s_infos", dms_name) < 0)
+	{
+		obi_set_errno(OBIDMS_MEMORY_ERROR);
+		obidebug(1, "\nProblem building an informations file name");
+		return NULL;
+	}
+
+	return file_name;
+}
+
+
+int create_dms_infos_file(int dms_file_descriptor, const char* dms_name)
+{
+	char* 	file_name;
+	int 	infos_file_descriptor;
+	off_t 	file_size;
+	bool	little_endian;
+
+	file_size = sizeof(bool);
+
+	// Create file name
+	file_name = build_infos_file_name(dms_name);
+	if (file_name == NULL)
+		return -1;
+
+    // Create file
+	infos_file_descriptor = openat(dms_file_descriptor, file_name, O_RDWR | O_CREAT | O_EXCL, 0777);
+	if (infos_file_descriptor < 0)
+	{
+		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
+		obidebug(1, "\nError creating an informations file");
+		free(file_name);
+		return -1;
+	}
+
+	free(file_name);
+
+	// Truncate the infos file to the right size
+	if (ftruncate(infos_file_descriptor, file_size) < 0)
+	{
+		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
+		obidebug(1, "\nError truncating an informations file");
+		close(infos_file_descriptor);
+		return -1;
+	}
+
+	// Write endianness
+	little_endian = obi_is_little_endian();
+	if (write(infos_file_descriptor, &little_endian, sizeof(bool)) < ((ssize_t) sizeof(bool)))
+	{
+		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
+		obidebug(1, "\nError writing the endianness in an informations file");
+		close(infos_file_descriptor);
+		return -1;
+	}
+
+	// Close file
+	close(infos_file_descriptor);
+
+	return 0;
+}
+
+
 /**********************************************************************
  *
  * 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
@@ -116,8 +223,8 @@ int obi_dms_exists(const char* dms_name)
 OBIDMS_p obi_create_dms(const char* dms_name)
 {
 	char* directory_name;
-	DIR* dms_dir;
-	int dms_file_descriptor;
+	DIR*  dms_dir;
+	int   dms_file_descriptor;
 
 	// Build and check the directory name
 	directory_name = build_directory_name(dms_name);
@@ -160,13 +267,17 @@ OBIDMS_p obi_create_dms(const char* dms_name)
 	}
 
 	// Create the arrays directory
-	if (mkdirat(dms_file_descriptor, ARRAY_DIR_NAME, 00777) < 0)
+	if (mkdirat(dms_file_descriptor, ARRAYS_DIR_NAME, 00777) < 0)
 	{
 		obi_set_errno(OBI_ARRAY_ERROR);
 		obidebug(1, "\nProblem creating an arrays directory");
 		return NULL;
 	}
 
+	// Create the informations file
+	if (create_dms_infos_file(dms_file_descriptor, dms_name) < 0)
+		return NULL;
+
 	return obi_open_dms(dms_name);
 }
 
@@ -175,6 +286,10 @@ OBIDMS_p obi_open_dms(const char* dms_name)
 {
 	OBIDMS_p	dms;
 	char*	 	directory_name;
+	char* 		infos_file_name;
+	int			infos_file_descriptor;
+	bool		little_endian_dms;
+	bool 		little_endian_platform;
 
 	dms = NULL;
 
@@ -224,7 +339,7 @@ OBIDMS_p obi_open_dms(const char* dms_name)
 		return NULL;
 	}
 
-	// Get file descriptor of DMS directory to open the arrays directory
+	// Get and store file descriptor of DMS directory to open the informations file
 	dms->dir_fd = dirfd(dms->directory);
 	if (dms->dir_fd < 0)
 	{
@@ -235,8 +350,45 @@ OBIDMS_p obi_open_dms(const char* dms_name)
 		return NULL;
 	}
 
+	// Open informations file to check endianness
+	infos_file_name = build_infos_file_name(dms_name);
+	infos_file_descriptor = openat(dms->dir_fd, infos_file_name, O_RDONLY, 0777);
+	if (infos_file_descriptor < 0)
+	{
+		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
+		obidebug(1, "\nError opening an informations file");
+		closedir(dms->directory);
+		free(dms);
+		return NULL;
+	}
+
+	free(infos_file_name);
+
+	// Check endianness of the platform and DMS
+	little_endian_platform = obi_is_little_endian();
+	if (read(infos_file_descriptor, &little_endian_dms, sizeof(bool)) < ((ssize_t) sizeof(bool)))
+	{
+		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
+		obidebug(1, "\nError reading the endianness in an informations file");
+		close(infos_file_descriptor);
+		closedir(dms->directory);
+		free(dms);
+		return NULL;
+	}
+	if (little_endian_platform != little_endian_dms)
+	{
+		obi_set_errno(OBIDMS_BAD_ENDIAN_ERROR);
+		obidebug(1, "\nError: The DMS and the platform have different endianness");
+		close(infos_file_descriptor);
+		closedir(dms->directory);
+		free(dms);
+		return NULL;
+	}
+
+	close(infos_file_descriptor);
+
 	// Open the arrays directory
-	dms->array_directory = private_opendirat(dms->dir_fd, ARRAY_DIR_NAME);
+	dms->array_directory = private_opendirat(dms->dir_fd, ARRAYS_DIR_NAME);
 	if (dms->array_directory == NULL)
 	{
 		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
@@ -251,9 +403,9 @@ OBIDMS_p obi_open_dms(const char* dms_name)
 	if (dms->array_dir_fd < 0)
 	{
 		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
-		obidebug(1, "\nError opening the arrays directory");
-		closedir(dms->directory);
+		obidebug(1, "\nError getting the file descriptor of the arrays directory");
 		closedir(dms->array_directory);
+		closedir(dms->directory);
 		free(dms);
 		return NULL;
 	}

src/obidms.h

@@ -26,7 +26,7 @@
 
 #define OBIDMS_MAX_NAME (2048) 	   /**< The maximum length of an OBIDMS name.
                                 	*/
-#define ARRAY_DIR_NAME "arrays"	   /**< The name of the arrays directory.
+#define ARRAYS_DIR_NAME "arrays"   /**< The name of the arrays directory.
                                 	*/
 
 

src/obidmscolumn.c

@@ -339,7 +339,7 @@ static obiversion_t create_version_file(OBIDMS_column_directory_p column_directo
 		return -1;
 	}
 
-	// Position offset to 0 to prepare for writing
+	// Position offset to 0 to prepare for writing		// TODO Unnecessary?
 	if (lseek(version_file_descriptor, 0, SEEK_SET) != 0)
 	{
 		obi_set_errno(OBICOL_UNKNOWN_ERROR);
@@ -358,7 +358,7 @@ static obiversion_t create_version_file(OBIDMS_column_directory_p column_directo
 	}
 
 	// Prepare for unlocking
-	if (lseek(version_file_descriptor, 0, SEEK_SET) != 0)
+	if (lseek(version_file_descriptor, 0, SEEK_SET) != 0)		// TODO Unnecessary?
 	{
 		obi_set_errno(OBICOL_UNKNOWN_ERROR);
 		obidebug(1, "\nError preparing a version file for unlocking");