The endianness of an OBIDMS is now stored in an informations file that
is read when opening the OBIDMS.
This commit is contained in:
Celine Mercier
166
src/obidms.c
166
src/obidms.c
@ -23,6 +23,7 @@
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#include "obidebug.h"
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#include "obidmscolumn.h"
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#include "private_at_functions.h"
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#include "obilittlebigman.h"
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#define DEBUG_LEVEL 0 // TODO has to be defined somewhere else (cython compil flag?)
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@ -54,6 +55,44 @@
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static char* build_directory_name(const char* dms_name);
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/**
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* Internal function building the informations file name from an OBIDMS name.
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*
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* The function builds the file name for the informations file of an OBIDMS.
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*
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* @warning The returned pointer has to be freed by the caller.
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*
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* @param dms_name The name of the OBIDMS.
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*
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* @returns A pointer to the file name.
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* @retval NULL if an error occurred.
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*
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* @since November 2015
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* @author Celine Mercier (celine.mercier@metabarcoding.org)
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*/
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static char* build_infos_file_name(const char* dms_name);
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/**
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* Internal function creating the file containing basic informations on the OBIDMS.
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*
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* This file contains:
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* - The endianness of the platform
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*
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* @warning The returned pointer has to be freed by the caller.
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*
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* @param dms_file_descriptor The file descriptor for the OBIDMS directory.
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* @param dms_name The name of the OBIDMS.
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*
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* @retval 0 if the operation was successfully completed.
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* @retval -1 if an error occurred.
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*
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* @since November 2015
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* @author Celine Mercier (celine.mercier@metabarcoding.org)
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*/
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int create_dms_infos_file(int dms_file_descriptor, const char* dms_name);
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/************************************************************************
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*
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* 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
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@ -85,6 +124,74 @@ static char* build_directory_name(const char* dms_name)
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}
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static char* build_infos_file_name(const char* dms_name)
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{
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char* file_name;
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// Build file name
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if (asprintf(&file_name, "%s_infos", dms_name) < 0)
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{
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obi_set_errno(OBIDMS_MEMORY_ERROR);
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obidebug(1, "\nProblem building an informations file name");
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return NULL;
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}
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return file_name;
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}
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int create_dms_infos_file(int dms_file_descriptor, const char* dms_name)
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{
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char* file_name;
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int infos_file_descriptor;
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off_t file_size;
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bool little_endian;
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file_size = sizeof(bool);
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// Create file name
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file_name = build_infos_file_name(dms_name);
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if (file_name == NULL)
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return -1;
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// Create file
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infos_file_descriptor = openat(dms_file_descriptor, file_name, O_RDWR | O_CREAT | O_EXCL, 0777);
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if (infos_file_descriptor < 0)
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{
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obi_set_errno(OBIDMS_UNKNOWN_ERROR);
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obidebug(1, "\nError creating an informations file");
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free(file_name);
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return -1;
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}
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free(file_name);
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// Truncate the infos file to the right size
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if (ftruncate(infos_file_descriptor, file_size) < 0)
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{
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obi_set_errno(OBIDMS_UNKNOWN_ERROR);
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obidebug(1, "\nError truncating an informations file");
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close(infos_file_descriptor);
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return -1;
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}
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// Write endianness
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little_endian = obi_is_little_endian();
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if (write(infos_file_descriptor, &little_endian, sizeof(bool)) < ((ssize_t) sizeof(bool)))
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{
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obi_set_errno(OBIDMS_UNKNOWN_ERROR);
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obidebug(1, "\nError writing the endianness in an informations file");
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close(infos_file_descriptor);
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return -1;
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}
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// Close file
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close(infos_file_descriptor);
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return 0;
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}
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/**********************************************************************
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*
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* 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
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@ -116,8 +223,8 @@ int obi_dms_exists(const char* dms_name)
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OBIDMS_p obi_create_dms(const char* dms_name)
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{
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char* directory_name;
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DIR* dms_dir;
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int dms_file_descriptor;
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DIR* dms_dir;
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int dms_file_descriptor;
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// Build and check the directory name
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directory_name = build_directory_name(dms_name);
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@ -160,13 +267,17 @@ OBIDMS_p obi_create_dms(const char* dms_name)
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}
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// Create the arrays directory
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if (mkdirat(dms_file_descriptor, ARRAY_DIR_NAME, 00777) < 0)
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if (mkdirat(dms_file_descriptor, ARRAYS_DIR_NAME, 00777) < 0)
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{
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obi_set_errno(OBI_ARRAY_ERROR);
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obidebug(1, "\nProblem creating an arrays directory");
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return NULL;
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}
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// Create the informations file
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if (create_dms_infos_file(dms_file_descriptor, dms_name) < 0)
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return NULL;
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return obi_open_dms(dms_name);
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}
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@ -175,6 +286,10 @@ OBIDMS_p obi_open_dms(const char* dms_name)
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{
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OBIDMS_p dms;
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char* directory_name;
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char* infos_file_name;
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int infos_file_descriptor;
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bool little_endian_dms;
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bool little_endian_platform;
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dms = NULL;
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@ -224,7 +339,7 @@ OBIDMS_p obi_open_dms(const char* dms_name)
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return NULL;
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}
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// Get file descriptor of DMS directory to open the arrays directory
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// Get and store file descriptor of DMS directory to open the informations file
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dms->dir_fd = dirfd(dms->directory);
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if (dms->dir_fd < 0)
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{
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@ -235,8 +350,45 @@ OBIDMS_p obi_open_dms(const char* dms_name)
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return NULL;
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}
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// Open informations file to check endianness
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infos_file_name = build_infos_file_name(dms_name);
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infos_file_descriptor = openat(dms->dir_fd, infos_file_name, O_RDONLY, 0777);
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if (infos_file_descriptor < 0)
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{
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obi_set_errno(OBIDMS_UNKNOWN_ERROR);
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obidebug(1, "\nError opening an informations file");
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closedir(dms->directory);
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free(dms);
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return NULL;
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}
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free(infos_file_name);
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// Check endianness of the platform and DMS
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little_endian_platform = obi_is_little_endian();
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if (read(infos_file_descriptor, &little_endian_dms, sizeof(bool)) < ((ssize_t) sizeof(bool)))
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{
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obi_set_errno(OBIDMS_UNKNOWN_ERROR);
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obidebug(1, "\nError reading the endianness in an informations file");
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close(infos_file_descriptor);
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closedir(dms->directory);
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free(dms);
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return NULL;
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}
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if (little_endian_platform != little_endian_dms)
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{
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obi_set_errno(OBIDMS_BAD_ENDIAN_ERROR);
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obidebug(1, "\nError: The DMS and the platform have different endianness");
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close(infos_file_descriptor);
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closedir(dms->directory);
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free(dms);
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return NULL;
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}
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close(infos_file_descriptor);
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// Open the arrays directory
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dms->array_directory = private_opendirat(dms->dir_fd, ARRAY_DIR_NAME);
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dms->array_directory = private_opendirat(dms->dir_fd, ARRAYS_DIR_NAME);
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if (dms->array_directory == NULL)
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{
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obi_set_errno(OBIDMS_UNKNOWN_ERROR);
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@ -251,9 +403,9 @@ OBIDMS_p obi_open_dms(const char* dms_name)
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if (dms->array_dir_fd < 0)
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{
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obi_set_errno(OBIDMS_UNKNOWN_ERROR);
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obidebug(1, "\nError opening the arrays directory");
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closedir(dms->directory);
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obidebug(1, "\nError getting the file descriptor of the arrays directory");
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closedir(dms->array_directory);
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closedir(dms->directory);
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free(dms);
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return NULL;
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}
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