/******************************************************************** * OBIDMS functions * ********************************************************************/ /** * @file obidms.c * @author Eric Coissac (eric.coissac@metabarcoding.org) * @date 23 May 2015 * @brief OBIDMS functions. */ #include #include #include #include #include #include #include #include "obidms.h" #include "obierrno.h" #include "obidebug.h" #include "obidmscolumn.h" #include "private_at_functions.h" #define DEBUG_LEVEL 0 // TODO has to be defined somewhere else (cython compil flag?) /************************************************************************** * * 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 * **************************************************************************/ /** * Internal function building the OBIDMS directory name from an OBIDMS name. * * The function builds the directory name corresponding to an OBIDMS. * It also checks that the name is not too long. * * @warning The returned pointer has to be freed by the caller. * * @param dms_name The name of the OBIDMS. * * @returns A pointer to the directory name. * @retval NULL if an error occurred. * * @since May 2015 * @author Eric Coissac (eric.coissac@metabarcoding.org) */ static char* build_directory_name(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 * ************************************************************************/ static char* build_directory_name(const char* dms_name) { char* directory_name; // Build the database directory name if (asprintf(&directory_name, "%s.obidms", dms_name) < 0) { obi_set_errno(OBIDMS_MEMORY_ERROR); obidebug(1, "\nProblem building an OBIDMS directory name"); return NULL; } // Test if the database name is not too long if (strlen(directory_name) >= OBIDMS_MAX_NAME) { obi_set_errno(OBIDMS_LONG_NAME_ERROR); obidebug(1, "\nProblem building an OBIDMS directory name"); free(directory_name); return NULL; } return directory_name; } /********************************************************************** * * 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 * **********************************************************************/ int obi_dms_exists(const char* dms_name) { struct stat buffer; char *directory_name; int check_dir; // Build and check the directory name directory_name = build_directory_name(dms_name); if (directory_name == NULL) return -1; check_dir = stat(directory_name, &buffer); free(directory_name); if (check_dir == 0) return 1; else return 0; } OBIDMS_p obi_create_dms(const char* dms_name) { char* directory_name; DIR* dms_dir; int dms_file_descriptor; // Build and check the directory name directory_name = build_directory_name(dms_name); if (directory_name == NULL) return NULL; // Try to create the directory if (mkdir(directory_name, 00777) < 0) { if (errno == EEXIST) obi_set_errno(OBIDMS_EXIST_ERROR); else obi_set_errno(OBIDMS_UNKNOWN_ERROR); obidebug(1, "\nProblem creating an OBIDMS directory"); free(directory_name); return NULL; } // Get file descriptor of DMS directory to create the arrays directory dms_dir = opendir(directory_name); if (dms_dir == NULL) { obi_set_errno(OBIDMS_UNKNOWN_ERROR); obidebug(1, "\nProblem opening a newly created OBIDMS directory"); free(directory_name); return NULL; } free(directory_name); dms_file_descriptor = dirfd(dms_dir); if (dms_file_descriptor < 0) { obi_set_errno(OBIDMS_UNKNOWN_ERROR); obidebug(1, "\nProblem getting the file descriptor of a newly created OBIDMS directory"); return NULL; } // Create the arrays directory if (mkdirat(dms_file_descriptor, ARRAY_DIR_NAME, 00777) < 0) { obi_set_errno(OBI_ARRAY_ERROR); obidebug(1, "\nProblem creating an arrays directory"); return NULL; } return obi_open_dms(dms_name); } OBIDMS_p obi_open_dms(const char* dms_name) { OBIDMS_p dms; char* directory_name; dms = NULL; // Allocate the data structure dms = (OBIDMS_p) malloc(sizeof(OBIDMS_t)); if (dms == NULL) { obi_set_errno(OBIDMS_MEMORY_ERROR); obidebug(1, "\nError allocating the memory for the OBIDMS structure"); return NULL; } // Build and check the directory name directory_name = build_directory_name(dms_name); if (directory_name == NULL) { free(dms); return NULL; } strncpy(dms->directory_name, directory_name, OBIDMS_MAX_NAME); free(directory_name); // Try to open the directory dms->directory = opendir(dms->directory_name); if (dms->directory == NULL) { switch (errno) { case ENOENT: obi_set_errno(OBIDMS_NOT_EXIST_ERROR); break; case EACCES: obi_set_errno(OBIDMS_ACCESS_ERROR); break; case ENOMEM: obi_set_errno(OBIDMS_MEMORY_ERROR); break; default: obi_set_errno(OBIDMS_UNKNOWN_ERROR); } obidebug(1, "\nCan't open OBIDMS directory"); free(dms); return NULL; } // Get file descriptor of DMS directory to open the arrays directory dms->dir_fd = dirfd(dms->directory); if (dms->dir_fd < 0) { obi_set_errno(OBIDMS_UNKNOWN_ERROR); obidebug(1, "\nError getting the file descriptor for a newly created OBIDMS directory"); closedir(dms->directory); free(dms); return NULL; } // Open the arrays directory dms->array_directory = private_opendirat(dms->dir_fd, ARRAY_DIR_NAME); if (dms->array_directory == NULL) { obi_set_errno(OBIDMS_UNKNOWN_ERROR); obidebug(1, "\nError opening the arrays directory"); closedir(dms->directory); free(dms); return NULL; } // Store the array directory's file descriptor dms->array_dir_fd = dirfd(dms->array_directory); if (dms->array_dir_fd < 0) { obi_set_errno(OBIDMS_UNKNOWN_ERROR); obidebug(1, "\nError opening the arrays directory"); closedir(dms->directory); closedir(dms->array_directory); free(dms); return NULL; } return dms; } OBIDMS_p obi_dms(const char* dms_name) { int exists; exists = obi_dms_exists(dms_name); switch (exists) { case 0: return obi_create_dms(dms_name); case 1: return obi_open_dms(dms_name); }; obidebug(1, "\nError checking if an OBIDMS directory exists"); return NULL; } int obi_close_dms(OBIDMS_p dms) { if (dms != NULL) { if (closedir(dms->directory) < 0) { obi_set_errno(OBIDMS_MEMORY_ERROR); obidebug(1, "\nError closing an OBIDMS directory"); free(dms); return -1; } if (closedir(dms->array_directory) < 0) { obi_set_errno(OBI_ARRAY_ERROR); obidebug(1, "\nError closing an array directory"); free(dms); return -1; } free(dms); } return 0; }