diff --git a/python/obitools3/obidms/capidms.cfiles b/python/obitools3/obidms/capidms.cfiles index d4f6611..b16f90e 100644 --- a/python/obitools3/obidms/capidms.cfiles +++ b/python/obitools3/obidms/capidms.cfiles @@ -6,5 +6,5 @@ ../../../src/obilittlebigman.c ../../../src/obitypes.h ../../../src/obitypes.c -../../../src/private_openat.h -../../../src/private_openat.c +../../../src/private_at_functions.h +../../../src/private_at_functions.c diff --git a/python/obitools3/obidms/capidms.pxd b/python/obitools3/obidms/capidms.pxd index 494b2ce..41ff4b7 100644 --- a/python/obitools3/obidms/capidms.pxd +++ b/python/obitools3/obidms/capidms.pxd @@ -16,11 +16,11 @@ cdef extern from "obidms.h" nogil: ctypedef OBIDMS_t* OBIDMS_p - OBIDMS_p obi_create_dms(const_char_p name) + OBIDMS_p obi_create_dms(const_char_p dms_name) - OBIDMS_p obi_open_dms(const_char_p name) + OBIDMS_p obi_open_dms(const_char_p dms_name) - OBIDMS_p obi_dms(const_char_p name) + OBIDMS_p obi_dms(const_char_p dms_name) int obi_close_dms(OBIDMS_p dms) diff --git a/python/obitools3/obidms/obidmscolumn/capidmscolumn.cfiles b/python/obitools3/obidms/obidmscolumn/capidmscolumn.cfiles index f318290..486332a 100644 --- a/python/obitools3/obidms/obidmscolumn/capidmscolumn.cfiles +++ b/python/obitools3/obidms/obidmscolumn/capidmscolumn.cfiles @@ -1,5 +1,7 @@ ../../../../src/obidmscolumn.h ../../../../src/obidmscolumn.c +../../../../src/obidmscolumngroup.h +../../../../src/obidmscolumngroup.c ../../../../src/obidms.h ../../../../src/obidms.c ../../../../src/obierrno.h @@ -8,5 +10,5 @@ ../../../../src/obilittlebigman.c ../../../../src/obitypes.h ../../../../src/obitypes.c -../../../../src/private_openat.h -../../../../src/private_openat.c +../../../../src/private_at_functions.h +../../../../src/private_at_functions.c diff --git a/src/obidms.c b/src/obidms.c index b2d1da1..2b7a966 100644 --- a/src/obidms.c +++ b/src/obidms.c @@ -7,15 +7,20 @@ #include #include +#include +#include +#include +#include #include "obidms.h" +#include "obierrno.h" -/************************************************************************ +/************************************************************************** * - * 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 + * 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 * - ************************************************************************/ + **************************************************************************/ /** @@ -33,7 +38,7 @@ * @retvalue NULL if an error occurs * * ###Error values - * - OBIDMS_MEMORY_ERROR : something wrong occured during memory allocation. + * - OBIDMS_MEMORY_ERROR : something wrong occurred during memory allocation. * - OBIDMS_LONG_NAME_ERROR : the database name exceeds the limit. * * @since May 2015 @@ -42,11 +47,11 @@ 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 + * 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) { @@ -71,31 +76,31 @@ 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 U B L I C F U N C T I O N S + * 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 exists; + int check_dir; // Build and check the directory name directory_name = build_directory_name(dms_name); if (directory_name == NULL) return -1; - exists = stat(directory_name, &buffer); + check_dir = stat(directory_name, &buffer); free(directory_name); - if(exists == 0) + if (check_dir == 0) return 1; - else // -1 - return 0; + else + return 0; } @@ -108,7 +113,6 @@ OBIDMS_p obi_create_dms(const char* dms_name) if (directory_name == NULL) return NULL; - // Try to create the directory if (mkdir(directory_name, 0x777) < 0) { @@ -140,24 +144,26 @@ OBIDMS_p obi_open_dms(const char* dms_name) if (directory_name == NULL) return NULL; - // try to open the directory + // Try to open the directory directory = opendir(directory_name); - if (directory == NULL) { - switch (errno) { - case ENOENT: - obi_set_errno(OBIDMS_NOT_EXIST_ERROR); - break; + if (directory == NULL) + { + switch (errno) + { + case ENOENT: + obi_set_errno(OBIDMS_NOT_EXIST_ERROR); + break; - case EACCES: - obi_set_errno(OBIDMS_ACCESS_ERROR); - break; + case EACCES: + obi_set_errno(OBIDMS_ACCESS_ERROR); + break; - case ENOMEM: - obi_set_errno(OBIDMS_MEMORY_ERROR); - break; + case ENOMEM: + obi_set_errno(OBIDMS_MEMORY_ERROR); + break; - default: - obi_set_errno(OBIDMS_UNKNOWN_ERROR); + default: + obi_set_errno(OBIDMS_UNKNOWN_ERROR); } free(directory_name); return NULL; @@ -165,7 +171,6 @@ OBIDMS_p obi_open_dms(const char* dms_name) // Allocate the data structure dms = (OBIDMS_p) malloc(sizeof(OBIDMS_t)); - if (dms == NULL) { obi_set_errno(OBIDMS_MEMORY_ERROR); @@ -178,15 +183,19 @@ OBIDMS_p obi_open_dms(const char* dms_name) dms->directory = directory; free(directory_name); + return dms; } OBIDMS_p obi_dms(const char* dms_name) { - int exists = obi_dms_exists(dms_name); + int exists; - switch (exists) { + exists = obi_dms_exists(dms_name); + + switch (exists) + { case 0: return obi_create_dms(dms_name); case 1: @@ -194,7 +203,6 @@ OBIDMS_p obi_dms(const char* dms_name) }; return NULL; - } diff --git a/src/obidms.h b/src/obidms.h index 889dde9..aa001df 100644 --- a/src/obidms.h +++ b/src/obidms.h @@ -41,12 +41,12 @@ typedef struct OBIDMS { * * @param dms_name a pointer to a C string containing the name of the database. * The actual directory name used to store the DMS will be - * `.obidms`. + * `.obidms`. * * @return an integer value indicating the status of the database * @retvalue 1 the database exist * @retvalue 0 the database does not exist - * @retvalue -1 an error occured + * @retvalue -1 an error occurred * * @see obi_close_dms() * @since May 2015 @@ -72,7 +72,7 @@ int obi_dms_exists(const char* dms_name); * ###Error values * - OBIDMS_EXIST_ERROR : a database with the same name already exists. * - OBIDMS_LONG_NAME_ERROR : the database name exceeds the limit. - * - OBIDMS_MEMORY_ERROR : something wrong occured during memory allocation. + * - OBIDMS_MEMORY_ERROR : something wrong occurred during memory allocation. * * @see obi_close_dms() * @since May 2015 @@ -92,9 +92,8 @@ OBIDMS_p obi_create_dms(const char *dms_name); * @retval NULL on error and the `obi_errno`variable is set. * * ###Error values - * - OBIDMS_EXIST_ERROR : a database with the same name already exists. * - OBIDMS_LONG_NAME_ERROR : the database name exceeds the limit. - * - OBIDMS_MEMORY_ERROR : something wrong occured during memory allocation. + * - OBIDMS_MEMORY_ERROR : something wrong occurred during memory allocation. * * @see obi_close_dms() * @since May 2015 @@ -118,7 +117,7 @@ OBIDMS_p obi_open_dms(const char *dms_name); * * ###Error values * - OBIDMS_LONG_NAME_ERROR : the database name exceeds the limit. - * - OBIDMS_MEMORY_ERROR : something wrong occured during memory allocation. + * - OBIDMS_MEMORY_ERROR : something wrong occurred during memory allocation. * * @see obi_close_dms() * @since May 2015 diff --git a/src/obidmscolumn.c b/src/obidmscolumn.c index 056a20c..164045c 100644 --- a/src/obidmscolumn.c +++ b/src/obidmscolumn.c @@ -1,5 +1,5 @@ /**************************************************************************** - * OBIDMS_column functions * + * OBIDMS_column functions * ****************************************************************************/ /** @@ -13,22 +13,25 @@ #include #include #include +#include #include #include +#include #include /* mmap() is defined in this header */ #include "obidmscolumn.h" +#include "obidmscolumngroup.h" #include "obidms.h" #include "obitypes.h" #include "obierrno.h" #include "obilittlebigman.h" -#include "private_openat.h" +#include "private_at_functions.h" -/************************************************************************* +/************************************************************************** * * 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 * - *************************************************************************/ + **************************************************************************/ /** @@ -44,7 +47,7 @@ * @retvalue NULL if an error occurs * * ###Error values - * - OBIDMS_MEMORY_ERROR : something wrong occured during memory allocation. + * - OBIDMS_MEMORY_ERROR : something wrong occurred during memory allocation. * * @since May 2015 * @author Eric Coissac (eric.coissac@metabarcoding.org) @@ -90,7 +93,7 @@ static char *build_version_file_name(const char *column_name); * @since May 2015 * @author Eric Coissac (eric.coissac@metabarcoding.org) */ -static obiversion_t obi_get_new_version_number(OBIDMS_p dms, char *column_name, bool block); +static obiversion_t obi_get_new_version_number(OBIDMS_column_group_p column_group, bool block); /** @@ -108,7 +111,7 @@ static obiversion_t obi_get_new_version_number(OBIDMS_p dms, char *column_name, * @since May 2015 * @author Eric Coissac (eric.coissac@metabarcoding.org) */ -static int create_version_file(OBIDMS_p dms, char *column_name); +static int create_version_file(OBIDMS_column_group_p column_group); /************************************************************************ @@ -124,7 +127,7 @@ static char *build_column_file_name(const char *column_name, obiversion_t versio // Build the database directory name if (asprintf(&filename,"%s@%d.odc", column_name, version_number) < 0) { - obi_set_errno(OBIDMS_MEMORY_ERROR); + obi_set_errno(OBICOL_MEMORY_ERROR); return NULL; } @@ -139,7 +142,7 @@ static char *build_version_file_name(const char *column_name) // Build the database directory name if (asprintf(&filename,"%s.odv", column_name) < 0) { - obi_set_errno(OBIDMS_MEMORY_ERROR); + obi_set_errno(OBICOL_MEMORY_ERROR); return NULL; } @@ -147,12 +150,12 @@ static char *build_version_file_name(const char *column_name) } -static obiversion_t obi_get_new_version_number(OBIDMS_p dms, char *column_name, bool block) +static obiversion_t obi_get_new_version_number(OBIDMS_column_group_p column_group, bool block) { off_t loc_size; obiversion_t new_version_number; char* version_file_name; - int directory_file_descriptor; + int column_dir_file_descriptor; int version_file_descriptor; bool little_endian; int lock_mode; @@ -166,34 +169,31 @@ static obiversion_t obi_get_new_version_number(OBIDMS_p dms, char *column_name, else lock_mode=F_TLOCK; - // build the version file name - version_file_name = build_version_file_name(column_name); + // Build the version file name + version_file_name = build_version_file_name(column_group->column_name); if (version_file_name == NULL) return -1; - // Get the file descriptor associated to the database directory - directory_file_descriptor = dirfd(dms->directory); - if (directory_file_descriptor < 0) + // Get the file descriptor associated to the column group directory + column_dir_file_descriptor = dirfd(column_group->directory); + if (column_dir_file_descriptor < 0) { - obi_set_errno(OBIDMS_UNKNOWN_ERROR); + obi_set_errno(OBICOL_UNKNOWN_ERROR); free(version_file_name); return -1; } - //open the version file - version_file_descriptor = private_openat(directory_file_descriptor, version_file_name, O_RDWR); - + // Open the version file + version_file_descriptor = private_openat(column_dir_file_descriptor, version_file_name, O_RDWR); if (version_file_descriptor < 0) { free(version_file_name); - + //close(column_dir_file_descriptor); if (errno == ENOENT) - { - return create_version_file(dms, column_name); - } + return create_version_file(column_group); else { - obi_set_errno(OBIDMS_UNKNOWN_ERROR); + obi_set_errno(OBICOL_UNKNOWN_ERROR); return -1; } } @@ -201,199 +201,223 @@ static obiversion_t obi_get_new_version_number(OBIDMS_p dms, char *column_name, // Test if the version file size is ok if (lseek(version_file_descriptor, 0, SEEK_END) < loc_size) { + obi_set_errno(OBICOL_UNKNOWN_ERROR); close(version_file_descriptor); - obi_set_errno(OBIDMS_UNKNOWN_ERROR); + close(column_dir_file_descriptor); free(version_file_name); return -1; } - // prepare the file for locking + // Prepare the file for locking if (lseek(version_file_descriptor, 0, SEEK_SET) != 0) { + obi_set_errno(OBICOL_UNKNOWN_ERROR); close(version_file_descriptor); - obi_set_errno(OBIDMS_UNKNOWN_ERROR); + close(column_dir_file_descriptor); free(version_file_name); return -1; } // Lock the file - if (lockf(version_file_descriptor, lock_mode, loc_size) < -1) + if (lockf(version_file_descriptor, lock_mode, loc_size) < 0) { + obi_set_errno(OBICOL_UNKNOWN_ERROR); close(version_file_descriptor); - obi_set_errno(OBIDMS_UNKNOWN_ERROR); + close(column_dir_file_descriptor); free(version_file_name); return -1; } - // read the endianess of the file + // Read the endianness of the file if (read(version_file_descriptor, &little_endian, sizeof(bool)) < sizeof(bool)) { + obi_set_errno(OBICOL_UNKNOWN_ERROR); close(version_file_descriptor); - obi_set_errno(OBIDMS_UNKNOWN_ERROR); + close(column_dir_file_descriptor); free(version_file_name); return -1; } - // check if endianess is correct + // Check if endianness is correct if (little_endian != obi_is_little_endian()) { + obi_set_errno(OBICOL_BAD_ENDIAN_ERROR); close(version_file_descriptor); - obi_set_errno(OBIDMS_BAD_ENDIAN_ERROR); + close(column_dir_file_descriptor); free(version_file_name); return -1; } - // read the current version number + // Read the current version number if (read(version_file_descriptor, &new_version_number, sizeof(obiversion_t)) < sizeof(obiversion_t)) { + obi_set_errno(OBICOL_UNKNOWN_ERROR); close(version_file_descriptor); - obi_set_errno(OBIDMS_UNKNOWN_ERROR); + close(column_dir_file_descriptor); free(version_file_name); return -1; } new_version_number++; - // write the new version number + // Write the new version number if (lseek(version_file_descriptor, sizeof(bool), SEEK_SET) != sizeof(bool)) { + obi_set_errno(OBICOL_UNKNOWN_ERROR); close(version_file_descriptor); - obi_set_errno(OBIDMS_UNKNOWN_ERROR); + close(column_dir_file_descriptor); free(version_file_name); return -1; } if (write(version_file_descriptor, &new_version_number, sizeof(obiversion_t)) < sizeof(obiversion_t)) { + obi_set_errno(OBICOL_UNKNOWN_ERROR); close(version_file_descriptor); - obi_set_errno(OBIDMS_UNKNOWN_ERROR); + close(column_dir_file_descriptor); free(version_file_name); return -1; } - // prepare for the unlocking + // Prepare for unlocking if (lseek(version_file_descriptor, 0, SEEK_SET) != 0) { + obi_set_errno(OBICOL_UNKNOWN_ERROR); close(version_file_descriptor); - obi_set_errno(OBIDMS_UNKNOWN_ERROR); + close(column_dir_file_descriptor); free(version_file_name); return -1; } - // unlock the file - if (lockf(version_file_descriptor, F_ULOCK, loc_size) < -1) + // Unlock the file + if (lockf(version_file_descriptor, F_ULOCK, loc_size) < 0) { + obi_set_errno(OBICOL_UNKNOWN_ERROR); close(version_file_descriptor); - obi_set_errno(OBIDMS_UNKNOWN_ERROR); + close(column_dir_file_descriptor); free(version_file_name); return -1; } - close(version_file_descriptor); + //close(version_file_descriptor); + //close(column_dir_file_descriptor); free(version_file_name); + return new_version_number; } -static int create_version_file(OBIDMS_p dms, char *column_name) +static int create_version_file(OBIDMS_column_group_p column_group) { off_t loc_size; obiversion_t version_number; char* version_file_name; - int directory_file_descriptor; + int column_dir_file_descriptor; int version_file_descriptor; bool little_endian; loc_size = sizeof(bool) + sizeof(obiversion_t); version_number = 0; - version_file_name = build_version_file_name(column_name); - + version_file_name = build_version_file_name(column_group->column_name); if (version_file_name == NULL) return -1; - directory_file_descriptor = dirfd(dms->directory); - if (directory_file_descriptor < 0) + // Get the file descriptor associated to the column group directory + column_dir_file_descriptor = dirfd(column_group->directory); + if (column_dir_file_descriptor < 0) { - obi_set_errno(OBIDMS_UNKNOWN_ERROR); + obi_set_errno(OBICOL_UNKNOWN_ERROR); free(version_file_name); return -1; } - version_file_descriptor = private_openat(directory_file_descriptor, - version_file_name, - O_RDWR | O_CREAT); - + // Get the file descriptor associated to the version file + version_file_descriptor = private_openat(column_dir_file_descriptor, version_file_name, O_RDWR | O_CREAT); if (version_file_descriptor < 0) { - obi_set_errno(OBIDMS_UNKNOWN_ERROR); + obi_set_errno(OBICOL_UNKNOWN_ERROR); free(version_file_name); + close(column_dir_file_descriptor); return -1; } // Lock the file - if (lockf(version_file_descriptor, F_LOCK, loc_size) < -1) + if (lockf(version_file_descriptor, F_LOCK, loc_size) < 0) { - close(version_file_descriptor); - obi_set_errno(OBIDMS_UNKNOWN_ERROR); + obi_set_errno(OBICOL_UNKNOWN_ERROR); free(version_file_name); + close(version_file_descriptor); + close(column_dir_file_descriptor); return -1; } + // Truncate the version file to the right size if (ftruncate(version_file_descriptor, loc_size) < 0) { - close(version_file_descriptor); - obi_set_errno(OBIDMS_UNKNOWN_ERROR); + obi_set_errno(OBICOL_UNKNOWN_ERROR); free(version_file_name); + close(version_file_descriptor); + close(column_dir_file_descriptor); return -1; } + // Position offset to 0 to prepare for writing if (lseek(version_file_descriptor, 0, SEEK_SET) != 0) { - close(version_file_descriptor); - obi_set_errno(OBIDMS_UNKNOWN_ERROR); + obi_set_errno(OBICOL_UNKNOWN_ERROR); free(version_file_name); + close(version_file_descriptor); + close(column_dir_file_descriptor); return -1; } little_endian = obi_is_little_endian(); + // Write endianness if (write(version_file_descriptor, &little_endian, sizeof(bool)) < sizeof(bool)) { - close(version_file_descriptor); - obi_set_errno(OBIDMS_UNKNOWN_ERROR); + obi_set_errno(OBICOL_UNKNOWN_ERROR); free(version_file_name); + close(version_file_descriptor); + close(column_dir_file_descriptor); return -1; } + // Write version number if (write(version_file_descriptor, &version_number, sizeof(obiversion_t)) < sizeof(obiversion_t)) { - close(version_file_descriptor); - obi_set_errno(OBIDMS_UNKNOWN_ERROR); + obi_set_errno(OBICOL_UNKNOWN_ERROR); free(version_file_name); + close(version_file_descriptor); + close(column_dir_file_descriptor); return -1; } - // prepare for the unlocking + // Prepare for unlocking if (lseek(version_file_descriptor, 0, SEEK_SET) != 0) { - close(version_file_descriptor); - obi_set_errno(OBIDMS_UNKNOWN_ERROR); + obi_set_errno(OBICOL_UNKNOWN_ERROR); free(version_file_name); + close(version_file_descriptor); + close(column_dir_file_descriptor); return -1; } - // unlock the file - if (lockf(version_file_descriptor, F_ULOCK, loc_size) < -1) + // Unlock the file + if (lockf(version_file_descriptor, F_ULOCK, loc_size) < 0) { - close(version_file_descriptor); - obi_set_errno(OBIDMS_UNKNOWN_ERROR); + obi_set_errno(OBICOL_UNKNOWN_ERROR); free(version_file_name); + close(version_file_descriptor); + close(column_dir_file_descriptor); return -1; } - close(version_file_descriptor); + //close(version_file_descriptor); + //close(column_dir_file_descriptor); free(version_file_name); + return version_number; } @@ -404,80 +428,95 @@ static int create_version_file(OBIDMS_p dms, char *column_name) * **********************************************************************/ -obiversion_t obi_get_latest_version_number(OBIDMS_p dms, char *column_name) +obiversion_t obi_get_latest_version_number(OBIDMS_column_group_p column_group) { off_t loc_size; obiversion_t latest_version_number; char * version_file_name; - int directory_file_descriptor; + int column_dir_file_descriptor; int version_file_descriptor; bool little_endian; loc_size = sizeof(bool) + sizeof(obiversion_t); latest_version_number = 0; - version_file_name = build_version_file_name(column_name); + version_file_name = build_version_file_name(column_group->column_name); if (version_file_name==NULL) return -1; - directory_file_descriptor = dirfd(dms->directory); - if (directory_file_descriptor < 0) { - obi_set_errno(OBIDMS_UNKNOWN_ERROR); + // Get the file descriptor associated to the column group directory + column_dir_file_descriptor = dirfd(column_group->directory); + if (column_dir_file_descriptor < 0) + { + obi_set_errno(OBICOL_UNKNOWN_ERROR); free(version_file_name); return -1; } - version_file_descriptor = private_openat(directory_file_descriptor, version_file_name, O_RDONLY); - - if (version_file_descriptor < 0) { - obi_set_errno(OBIDMS_UNKNOWN_ERROR); + // Get the file descriptor associated to the version file + version_file_descriptor = private_openat(column_dir_file_descriptor, version_file_name, O_RDONLY); + if (version_file_descriptor < 0) + { + obi_set_errno(OBICOL_UNKNOWN_ERROR); free(version_file_name); + close(column_dir_file_descriptor); return -1; } + // Check that the version file size is ok if (lseek(version_file_descriptor, 0, SEEK_END) < loc_size) { - close(version_file_descriptor); - obi_set_errno(OBIDMS_UNKNOWN_ERROR); + obi_set_errno(OBICOL_UNKNOWN_ERROR); free(version_file_name); + close(version_file_descriptor); + close(column_dir_file_descriptor); return -1; } + // Set the offset to 0 in the version file if (lseek(version_file_descriptor, 0, SEEK_SET) != 0) { - close(version_file_descriptor); - obi_set_errno(OBIDMS_UNKNOWN_ERROR); + obi_set_errno(OBICOL_UNKNOWN_ERROR); free(version_file_name); + close(version_file_descriptor); + close(column_dir_file_descriptor); return -1; } + // Read the endianness if (read(version_file_descriptor, &little_endian, sizeof(bool)) < sizeof(bool)) { - close(version_file_descriptor); - obi_set_errno(OBIDMS_UNKNOWN_ERROR); + obi_set_errno(OBICOL_UNKNOWN_ERROR); free(version_file_name); + close(version_file_descriptor); + close(column_dir_file_descriptor); return -1; } + // Verify the endianness if (little_endian != obi_is_little_endian()) { - close(version_file_descriptor); - obi_set_errno(OBIDMS_BAD_ENDIAN_ERROR); + obi_set_errno(OBICOL_BAD_ENDIAN_ERROR); free(version_file_name); + close(version_file_descriptor); + close(column_dir_file_descriptor); return -1; } + // Read the latest version number if (read(version_file_descriptor, &latest_version_number, sizeof(obiversion_t)) < sizeof(obiversion_t)) { - close(version_file_descriptor); - obi_set_errno(OBIDMS_UNKNOWN_ERROR); + obi_set_errno(OBICOL_UNKNOWN_ERROR); free(version_file_name); + close(version_file_descriptor); + close(column_dir_file_descriptor); return -1; } - - close(version_file_descriptor); free(version_file_name); + //close(version_file_descriptor); + //close(column_dir_file_descriptor); + return latest_version_number; } @@ -489,104 +528,139 @@ size_t obi_get_platform_header_size() OBIDMS_column_p obi_create_column(OBIDMS_p dms, - char *column_name, - OBIType_t type, - size_t nb_elements) + const char *column_name, + OBIType_t type, + size_t nb_elements) { OBIDMS_column_p new_column; + OBIDMS_column_group_p column_group; OBIDMS_column_header_p header; size_t file_size; obiversion_t version_number; char* column_file_name; int column_file_descriptor; - int directory_file_descriptor; + int column_dir_file_descriptor; size_t header_size; size_t data_size; new_column = NULL; - directory_file_descriptor = dirfd(dms->directory); - if (directory_file_descriptor < 0) { - obi_set_errno(OBIDMS_UNKNOWN_ERROR); + // Get the column group structure associated to the column + column_group = obi_column_group(dms, column_name); + if (column_group == NULL) + return NULL; + + // Get the file descriptor associated to the column group directory + column_dir_file_descriptor = dirfd(column_group->directory); + if (column_dir_file_descriptor < 0) + { + obi_set_errno(OBICOLDIR_UNKNOWN_ERROR); + obi_close_column_group(column_group); return NULL; } + // Calculate the size needed header_size = obi_get_platform_header_size(); data_size = obi_array_sizeof(type, nb_elements); - file_size = header_size + data_size; - version_number = obi_get_new_version_number(dms, column_name, true); - + // Get the latest version number + version_number = obi_get_new_version_number(column_group, true); if (version_number < 0) { - obi_set_errno(OBIDMS_UNKNOWN_ERROR); + obi_close_column_group(column_group); + close(column_dir_file_descriptor); return NULL; } + // Get the column file name column_file_name = build_column_file_name(column_name, version_number); + if (column_file_name == NULL) + { + obi_close_column_group(column_group); + close(column_dir_file_descriptor); + return NULL; + } - column_file_descriptor = private_openat(directory_file_descriptor, - column_file_name, - O_RDWR | O_CREAT); + // Open the column file + column_file_descriptor = private_openat(column_dir_file_descriptor, column_file_name, O_RDWR | O_CREAT); + if (column_file_descriptor < 0) + { + obi_set_errno(OBICOL_UNKNOWN_ERROR); + obi_close_column_group(column_group); + close(column_dir_file_descriptor); + free(column_file_name); + return NULL; + } + // Truncate the column file to the right size if (ftruncate(column_file_descriptor, file_size) < 0) { + obi_set_errno(OBICOL_UNKNOWN_ERROR); + obi_close_column_group(column_group); + close(column_dir_file_descriptor); close(column_file_descriptor); - obi_set_errno(OBIDMS_UNKNOWN_ERROR); free(column_file_name); return NULL; } + // Allocate the memory for the column structure new_column = (OBIDMS_column_p) malloc(sizeof(OBIDMS_column_t)); - - if (new_column) + if (new_column == NULL) { + obi_set_errno(OBICOL_UNKNOWN_ERROR); + obi_close_column_group(column_group); + close(column_dir_file_descriptor); close(column_file_descriptor); - obi_set_errno(OBIDMS_MEMORY_ERROR); free(column_file_name); return NULL; } - new_column->dms = dms; - new_column->header = mmap(NULL, - header_size, - PROT_READ | PROT_WRITE, - MAP_SHARED, - column_file_descriptor, - 0 - ); + // Fill the column structure + new_column->dms = dms; + new_column->column_group = column_group; + new_column->header = mmap(NULL, + header_size, + PROT_READ | PROT_WRITE, + MAP_SHARED, + column_file_descriptor, + 0 + ); if (new_column->header == MAP_FAILED) { + obi_set_errno(OBICOL_UNKNOWN_ERROR); + obi_close_column_group(column_group); + close(column_dir_file_descriptor); close(column_file_descriptor); - obi_set_errno(OBIDMS_MEMORY_ERROR); free(column_file_name); free(new_column); return NULL; } - new_column->data = mmap(NULL, - data_size, - PROT_READ | PROT_WRITE, - MAP_SHARED, - column_file_descriptor, - header_size - ); + new_column->data = mmap(NULL, + data_size, + PROT_READ | PROT_WRITE, + MAP_SHARED, + column_file_descriptor, + header_size + ); if (new_column->data == MAP_FAILED) { munmap(new_column->header, header_size); + obi_set_errno(OBICOL_UNKNOWN_ERROR); + obi_close_column_group(column_group); + close(column_dir_file_descriptor); close(column_file_descriptor); - obi_set_errno(OBIDMS_MEMORY_ERROR); free(column_file_name); free(new_column); return NULL; } - new_column->writable= true; + new_column->writable = true; - header = new_column->header; + header = new_column->header; header->little_endian = obi_is_little_endian(); header->header_size = header_size; header->line_count = nb_elements; @@ -598,14 +672,9 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms, strncpy(header->name, column_name, OBIDMS_MAX_COLNAME); free(column_file_name); + //obi_close_column_group(column_group); + //close(column_dir_file_descriptor); + //close(column_file_descriptor); + return new_column; } - - -// if( access( fname, F_OK ) != -1 ) { -// // file exists -// } else { -// // file doesn't exist -// } - - diff --git a/src/obidmscolumn.h b/src/obidmscolumn.h index ad2d3b4..a190175 100644 --- a/src/obidmscolumn.h +++ b/src/obidmscolumn.h @@ -22,11 +22,9 @@ #include "obitypes.h" #include "obierrno.h" #include "obilittlebigman.h" +#include "obidmscolumngroup.h" -#define OBIDMS_MAX_COLNAME (128) /**< The maximum length of an OBIDMS column name - */ - typedef int32_t obiversion_t; /**< Used to store the column version number */ @@ -35,7 +33,7 @@ typedef int32_t obiversion_t; /**< Used to store the column version number */ typedef struct OBIDMS_column_header { - bool little_endian; /**< endianess of the column: + bool little_endian; /**< endianness of the column: - `true` on little endian platforms - `false` on big endian platforms @@ -57,6 +55,7 @@ typedef struct OBIDMS_column_header { */ } OBIDMS_column_header_t, *OBIDMS_column_header_p; + /** * @brief Structure describing a Column of the OBITools DMS * @@ -64,25 +63,27 @@ typedef struct OBIDMS_column_header { * creating, opening or cloning an OBIDMS_column. */ typedef struct OBIDMS_column { - OBIDMS_p dms ; /**< A pointer to a DMS instance - */ - OBIDMS_column_header_p header; /**< A pointer to the header of the column - */ - void* data; /**< A `void` pointer to the beginning of the - * data. - * - * @warning never use this member directly - * outside of the code of the - * low level functions - * of the OBITools DMS - */ - bool writable;/**< Indicates if the column is writable or not. - * - `true` the column is writable - * - `false` the column is read-only - * - * A column is writable only by its creator - * until it closes it. - */ + OBIDMS_p dms; /**< A pointer to a DMS instance + */ + OBIDMS_column_group_p column_group; /**< A pointer to an OBIDMS column group instance + */ + OBIDMS_column_header_p header; /**< A pointer to the header of the column + */ + void* data; /**< A `void` pointer to the beginning of the + * data. + * + * @warning never use this member directly + * outside of the code of the + * low level functions + * of the OBITools DMS + */ + bool writable; /**< Indicates if the column is writable or not. + * - `true` the column is writable + * - `false` the column is read-only + * + * A column is writable only by its creator + * until it closes it. + */ } OBIDMS_column_t, *OBIDMS_column_p; @@ -103,7 +104,7 @@ size_t obi_get_platform_header_size(); /** * @brief Creates a column. * - * @param dms a pointer as returned by obi_create_dms() or obi_open_dms() + * @param dms a pointer on an OBIDMS column * @param column_name the name of the new column * @param type the OBIType code used to create the column * @param nb_elements the number of elements to be stored @@ -112,9 +113,9 @@ size_t obi_get_platform_header_size(); * @author Eric Coissac (eric.coissac@metabarcoding.org) */ OBIDMS_column_p obi_create_column(OBIDMS_p dms, - char* column_name, - OBIType_t type, - size_t nb_elements); + const char* column_name, + OBIType_t type, + size_t nb_elements); /** @@ -126,7 +127,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms, * @return the bigger version number used for this column * @return -1 if the column does not exist */ -obiversion_t obi_get_latest_version_number(OBIDMS_p dms, char *column_name); +obiversion_t obi_get_latest_version_number(OBIDMS_column_group_p column_group); #endif /* OBIDMSCOLUMN_H_ */ diff --git a/src/obidmscolumngroup.c b/src/obidmscolumngroup.c new file mode 100644 index 0000000..cf8a28f --- /dev/null +++ b/src/obidmscolumngroup.c @@ -0,0 +1,283 @@ +/**************************************************************************** + * OBIDMS column groups functions * + ****************************************************************************/ + +/** + * @file obidmscolumngroup.c + * @author Celine Mercier + * @date 18 June 2015 + * @brief Functions for OBIDMS column groups. + */ + + +#include +#include +#include +#include +#include +#include + +#include "obidmscolumngroup.h" +#include "obidms.h" +#include "private_at_functions.h" +#include "obierrno.h" + + +/************************************************************************** + * + * 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 group directory name from an OBIDMS column name. + * + * The function builds the directory name corresponding to an OBIDMS column group. + * It checks also that the name is not too long. + * + * @warning The returned pointer has to be freed by the caller. + * + * @param column_name the name of the OBIDMS column + * + * @return a pointer to the OBIDMS column directory name + * @retvalue if everything is ok + * @retvalue NULL if an error occurs + * + * ###Error values + * - OBIDMS_MEMORY_ERROR : something wrong occurred during memory allocation. + * - OBIDMS_LONG_NAME_ERROR : the database name exceeds the limit. + * + * @since June 2015 + * @author Celine Mercier (celine.mercier@metabarcoding.org) + */ +static char* build_column_directory_name(const char* column_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_column_directory_name(const char* column_name) +{ + char* column_directory_name; + + // Build the database directory name + if (asprintf(&column_directory_name, "%s.obicol", column_name) < 0) + { + obi_set_errno(OBICOLDIR_MEMORY_ERROR); + return NULL; + } + + // Test if the database name is not too long + if (strlen(column_directory_name) >= OBIDMS_COLUMN_DIR_MAX_NAME) + { + obi_set_errno(OBICOLDIR_LONG_NAME_ERROR); + free(column_directory_name); + return NULL; + } + + return column_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_column_group_exists(OBIDMS_p dms, const char* column_name) +{ + struct stat buffer; + char* column_directory_name; + char* full_path; + int check_dir; + int dms_file_descriptor; + + // Build and check the directory name + column_directory_name = build_column_directory_name(column_name); + if (column_directory_name == NULL) + { + obi_set_errno(OBICOLDIR_UNKNOWN_ERROR); + return -1; + } + + // Get the file descriptor for the dms + dms_file_descriptor = dirfd(dms->directory); + if (dms_file_descriptor < 0) + { + obi_set_errno(OBIDMS_UNKNOWN_ERROR); + free(column_directory_name); + return -1; + } + + // Get the full path for the column directory + full_path = get_full_path(dms_file_descriptor, column_directory_name); + if (full_path == NULL) + { + obi_set_errno(OBICOLDIR_UNKNOWN_ERROR); + free(column_directory_name); + return -1; + } + + check_dir = stat(full_path, &buffer); + + free(column_directory_name); + free(full_path); + //close(dms_file_descriptor); + + if(check_dir == 0) + return 1; + else + return 0; +} + + +OBIDMS_column_group_p obi_create_column_group(OBIDMS_p dms, const char* column_name) +{ + char* column_directory_name; + int dms_file_descriptor; + + // Build and check the directory name + column_directory_name = build_column_directory_name(column_name); + if (column_directory_name == NULL) + { + obi_set_errno(OBICOLDIR_UNKNOWN_ERROR); + return NULL; + } + + // Get the file descriptor for the dms + dms_file_descriptor = dirfd(dms->directory); + if (dms_file_descriptor < 0) + { + obi_set_errno(OBIDMS_UNKNOWN_ERROR); + free(column_directory_name); + return NULL; + } + + // Try to create the directory + if (private_mkdirat(dms_file_descriptor, column_directory_name, 0x777) < 0) + { + if (errno == EEXIST) + obi_set_errno(OBICOLDIR_EXIST_ERROR); + else + obi_set_errno(OBICOLDIR_UNKNOWN_ERROR); + free(column_directory_name); + close(dms_file_descriptor); + return NULL; + } + + free(column_directory_name); + //close(dms_file_descriptor); + + return obi_open_column_group(dms, column_name); +} + + +OBIDMS_column_group_p obi_open_column_group(OBIDMS_p dms, const char* column_name) +{ + OBIDMS_column_group_p column_group; + char* column_directory_name; + DIR* directory; + int dms_file_descriptor; + + column_group = NULL; + + // Build and check the directory name + column_directory_name = build_column_directory_name(column_name); + if (column_directory_name == NULL) + return NULL; + + // Get the file descriptor for the dms + dms_file_descriptor = dirfd(dms->directory); + if (dms_file_descriptor < 0) + { + obi_set_errno(OBIDMS_UNKNOWN_ERROR); + free(column_directory_name); + return NULL; + } + + // Try to open the column directory + directory = private_opendirat(dms_file_descriptor, column_directory_name); + if (directory == NULL) { + switch (errno) + { + case ENOENT: + obi_set_errno(OBICOLDIR_NOT_EXIST_ERROR); + break; + + case EACCES: + obi_set_errno(OBICOLDIR_ACCESS_ERROR); + break; + + case ENOMEM: + obi_set_errno(OBICOLDIR_MEMORY_ERROR); + break; + + default: + obi_set_errno(OBICOLDIR_UNKNOWN_ERROR); + } + free(column_directory_name); + close(dms_file_descriptor); + return NULL; + } + + // Allocate the column dir structure + column_group = (OBIDMS_column_group_p) malloc(sizeof(OBIDMS_column_group_t)); + if (column_group == NULL) + { + obi_set_errno(OBICOLDIR_MEMORY_ERROR); + free(column_directory_name); + close(dms_file_descriptor); + return NULL; + } + + // Initialize the data structure + strcpy(column_group->directory_name, column_directory_name); + strcpy(column_group->column_name, column_name); + column_group->directory = directory; + + free(column_directory_name); + //close(dms_file_descriptor); + + return column_group; +} + + +OBIDMS_column_group_p obi_column_group(OBIDMS_p dms, const char* column_name) +{ + int exists; + exists = obi_column_group_exists(dms, column_name); + + switch (exists) + { + case 0: + return obi_create_column_group(dms, column_name); + case 1: + return obi_open_column_group(dms, column_name); + }; + + return NULL; +} + + +int obi_close_column_group(OBIDMS_column_group_p column_group) +{ + if (column_group != NULL) + { + // Close the column directory + if (closedir(column_group->directory) < 0) + { + obi_set_errno(OBICOLDIR_MEMORY_ERROR); + free(column_group); + return -1; + } + free(column_group); + } + + return 0; +} + diff --git a/src/obidmscolumngroup.h b/src/obidmscolumngroup.h new file mode 100644 index 0000000..3176ceb --- /dev/null +++ b/src/obidmscolumngroup.h @@ -0,0 +1,158 @@ +/**************************************************************************** + * OBIDMS column directories header file * + ****************************************************************************/ + +/** + * @file obidmscolumngroup.h + * @author Celine Mercier + * @date 18 June 2015 + * @brief Header file for OBIDMS column groups. + */ + +#ifndef OBIDMSCOLUMNGROUP_H_ +#define OBIDMSCOLUMNGROUP_H_ + +#include +#include +#include + +#include "obidms.h" + +#define OBIDMS_MAX_COLNAME (128) /**< The maximum length of an OBIDMS column name + */ + +#define OBIDMS_COLUMN_DIR_MAX_NAME (2048) /**< The maximum length of an OBIDMS column directory name + */ + +/** @brief A structure describing an OBIDMS column group instance + * + * A pointer to this structure is returned on creation + * and opening of an OBIDMS column group. + */ + +typedef struct OBIDMS_column_group { + OBIDMS_p dms; /**< A pointer to a DMS instance. + */ + char column_name[OBIDMS_MAX_COLNAME+1]; /**< The name of the column group + * contained in the directory. + */ + char directory_name[OBIDMS_COLUMN_DIR_MAX_NAME+1]; /**< The name of the directory + * containing the column group. + */ + DIR* directory; /**< A directory entry usable to + * refer and scan the database directory. + */ +} OBIDMS_column_group_t, *OBIDMS_column_group_p; + + +/*@ + * @brief Checks if an OBIDMS column group exists + * + * @param dms a pointer to an OBIDMS as returned by obi_create_dms() or obi_open_dms() + * @param column_name a pointer to a C string containing the name of the column. + * The actual directory name used to store the column is + * `.obicol`. + * + * @return an integer value indicating the status of the column group + * @retvalue 1 the group exist + * @retvalue 0 the group does not exist + * @retvalue -1 an error occurred + * + * @see obi_close_column_group() + * @since June 2015 + * @author Celine Mercier (celine.mercier@metabarcoding.org) + */ +int obi_column_group_exists(OBIDMS_p dms, const char* column_name); + + +/** + * @brief Creates a new OBIDMS column group instance. + * + * A new OBIDMS column group is created. This function checks + * if a directory with this name does not already exist + * before creating the new column group. + * + * @param dms a pointer to an OBIDMS as returned by obi_create_dms() or obi_open_dms() + * @param column_name a pointer to a C string containing the name of the column. + * The actual directory name used to store the column will be + * `.obicol`. + * + * @return a pointer to an OBIDMS column group structure describing the newly created + * group + * @retval NULL on error and the `obi_errno` variable is set. + * + * ###Error values + * - OBIDMS_COL_DIR_EXIST_ERROR : xxxxx a database with the same name already exists. + * + * @see obi_close_column_group() + * @since June 2015 + * @author Celine Mercier (celine.mercier@metabarcoding.org) + */ +OBIDMS_column_group_p obi_create_column_group(OBIDMS_p dms, const char* column_name); + + +/** + * @brief Opens an existing OBIDMS column group instance. + * + * @param dms a pointer to an OBIDMS as returned by obi_create_dms() or obi_open_dms() + * @param column_name a pointer to a C string containing the name of the column. + * The actual directory name used to store the column is + * `.obicol`. + * + * @return a pointer to the OBIDMS column group structure describing the group + * @retval NULL on error and the `obi_errno`variable is set. + * + * ###Error values + * - OBIDMS_COL_DIR_ERROR : xxxxx a database with the same name already exists. + * + * @see obi_close_column_group() + * @since June 2015 + * @author Celine Mercier (celine.mercier@metabarcoding.org) + */ +OBIDMS_column_group_p obi_open_column_group(OBIDMS_p dms, const char* column_name); + + +/** + * @brief Opens or creates a new OBIDMS column group instance. + * + * If the group already exists, this function opens it, otherwise it + * creates a new column group. + * + * @param dms a pointer to an OBIDMS as returned by obi_create_dms() or obi_open_dms() + * @param column_name a pointer to a C string containing the name of the column. + * The actual directory name used to store the column is + * `.obicol`. + * + * @return a pointer to the OBIDMS column group structure describing the group + * @retval NULL on error and the `obi_errno`variable is set. + * + * ###Error values + * - OBIDMS_LONG_NAME_ERROR : the database name exceeds the limit. + * - OBIDMS_MEMORY_ERROR : something wrong occurred during memory allocation. + * + * @since June 2015 + * @author Celine Mercier (celine.mercier@metabarcoding.org) + */ +OBIDMS_column_group_p obi_column_group(OBIDMS_p dms, const char* column_name); + + +/** + * @brief Closes an opened OBIDMS column group instance. + * + * @param column_group a pointer to an OBIDMS column group as returned by + * obi_create_column_group() or obi_open_column_group() + * + * @return an integer value indicating the success of the operation. Even on + * error, the `OBIDMS_column_group` structure is freed + * @retvalue 0 on success + * @retvalue -1 on failure and the `obi_errno` variable is set. + * + * @see obi_create_column_group() + * @see obi_open_column_group() + * @since June 2015 + * @author Celine Mercier (celine.mercier@metabarcoding.org) + */ +int obi_close_column_group(OBIDMS_column_group_p column_group); + + +#endif /* OBIDMSCOLUMNDIR_H_ */ diff --git a/src/obitypes.c b/src/obitypes.c index 2a8507f..ee6d8b1 100644 --- a/src/obitypes.c +++ b/src/obitypes.c @@ -8,7 +8,8 @@ #include -size_t obi_sizeof(OBIType_t type) { +size_t obi_sizeof(OBIType_t type) +{ size_t size=0; switch (type) { @@ -34,15 +35,16 @@ size_t obi_sizeof(OBIType_t type) { } -size_t obi_array_sizeof(OBIType_t type, size_t nbelements) { +size_t obi_array_sizeof(OBIType_t type, size_t nbelements) +{ size_t size; size_t rsize; size_t psize; size = obi_sizeof(type) * nbelements; - psize= getpagesize(); - rsize= size % psize; + psize = getpagesize(); + rsize = size % psize; // Round at a size multiple of pagesize if (rsize)