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OBITools3
Commit 5d967f5b authored by Celine Mercier's avatar Celine Mercier
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fixed typos and other minor things

parent 9b6de9c4
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Showing with 171 additions and 141 deletions
src/obidms.c
View file @ 5d967f5b
......@@ -8,17 +8,17 @@
#include <obidms.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 directory name from a OBIDMS name.
* Internal function building the directory name from an OBIDMS name.
*
* The function build the directory name corresponding to a OBIDMS.
* The function builds the directory name corresponding to an OBIDMS.
* It checks also that the name is not too long.
*
* @warning The returned pointer has to be freed by the caller.
......@@ -30,7 +30,7 @@
* @retvalue NULL if an error occurs
*
* ###Error values
* - OBIDMS_MEMORY_ERROR : something wrong occurs during memory allocation.
* - OBIDMS_MEMORY_ERROR : something wrong occured during memory allocation.
* - OBIDMS_LONG_NAME_ERROR : the database name exceeds the limit.
*
* @since May 2015
......@@ -58,6 +58,7 @@ static char *build_directory_name(const char *name) {
return dirdbname;
}
/***********************************************************************
*
* 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
......@@ -111,6 +112,7 @@ OBIDMS_p obi_create_dms(const char *name) {
return obi_open_dms(name);
}
OBIDMS_p obi_open_dms(const char *name) {
OBIDMS_p dms=NULL;
char *dirdbname;
......@@ -162,6 +164,7 @@ OBIDMS_p obi_open_dms(const char *name) {
return dms;
}
OBIDMS_p obi_dms(const char *name) {
int exist = obi_dms_exists(name);
......
src/obidms.h
View file @ 5d967f5b
......@@ -35,43 +35,18 @@ typedef struct OBIDMS {
*/
} OBIDMS_t, *OBIDMS_p;
/**
* @defgroup OBIDMSErrors OBIDMS related error codes
*
* Error codes set in errno following an error related
* to the manipulation of an OBIDMS.
*
* @{
*/
#define OBIDMS_EXIST_ERROR (1) /**< Try to create an OBIDMS with a name
* that corresponds to an existing OBIDMS
*/
#define OBIDMS_NOT_EXIST_ERROR (2) /**< Try to open a non-existing OBIDMS
*/
#define OBIDMS_LONG_NAME_ERROR (3) /**< The specified OBIDMS name is too long
*/
#define OBIDMS_MEMORY_ERROR (4) /**< A memory error occurred during allocation
*/
#define OBIDMS_UNKNOWN_ERROR (5) /**< Not determined error
*/
#define OBIDMS_ACCESS_ERROR (6) /**< Permission error for accessing to the database
*/
#define OBIDMS_BAD_ENDIAN_ERROR (7) /**< The opened data structure does not corresponds
* to the endianess of the platform.
*/
/**@}*/
/*@
* @brief Check if a OBIDMS exist
* @brief Checks if an OBIDMS exists
*
* @param name a pointer to a C string containing the name of the database
* the actual directory name used to store the DMS will be
* `<name>.obidms`
* @param name a pointer to a C string containing the name of the database.
* The actual directory name used to store the DMS will be
* `<name>.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 occurs
* @retvalue -1 an error occured
*
* @see obi_close_dms()
* @since May 2015
......@@ -79,15 +54,16 @@ typedef struct OBIDMS {
*/
int obi_dms_exists(const char* name);
/**
* @brief Create a new OBITools Data Management instance (OBIDMS).
* @brief Creates a new OBITools Data Management instance (OBIDMS).
*
* A `DMS` is implemented as a directory. This function takes care
* to check if a directory with this name does not already exist
* before creating the new database
* A `DMS` is implemented as a directory. This function checks
* if a directory with this name does not already exist
* before creating the new database.
*
* @param name a pointer to a C string containing the name of the database
* the actual directory name used to store the DMS will be
* @param name a pointer to a C string containing the name of the database.
* The actual directory name used to store the DMS will be
* `<name>.obidms`
*
* @return a pointer to an OBIDMS structure describing the newly created DMS
......@@ -96,7 +72,7 @@ int obi_dms_exists(const char* 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 occurs during memory allocation.
* - OBIDMS_MEMORY_ERROR : something wrong occured during memory allocation.
*
* @see obi_close_dms()
* @since May 2015
......@@ -104,11 +80,12 @@ int obi_dms_exists(const char* name);
*/
OBIDMS_p obi_create_dms(const char *name);
/**
* @brief Open an existing OBITools Data Management instance (OBIDMS).
* @brief Opens an existing OBITools Data Management instance (OBIDMS).
*
* @param name a pointer to a C string containing the name of the database
* the actual directory name used to store the DMS will be
* @param name a pointer to a C string containing the name of the database.
* The actual directory name used to store the DMS will be
* `<name>.obidms`
*
* @return a pointer to an OBIDMS structure describing the newly created DMS
......@@ -117,7 +94,7 @@ OBIDMS_p obi_create_dms(const char *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 occurs during memory allocation.
* - OBIDMS_MEMORY_ERROR : something wrong occured during memory allocation.
*
* @see obi_close_dms()
* @since May 2015
......@@ -125,14 +102,15 @@ OBIDMS_p obi_create_dms(const char *name);
*/
OBIDMS_p obi_open_dms(const char *name);
/**
* @brief Create a new OBIDMS instance.
* @brief Creates a new OBIDMS instance.
*
* If the database already exist this function open it, otherwise it
* creates a new databse.
* If the database already exists, this function opens it, otherwise it
* creates a new database.
*
* @param name a pointer to a C string containing the name of the database
* the actual directory name used to store the DMS is
* @param name a pointer to a C string containing the name of the database.
* The actual directory name used to store the DMS is
* `<name>.obidms`
*
* @return a pointer to an OBIDMS structure describing the newly created DMS
......@@ -140,7 +118,7 @@ OBIDMS_p obi_open_dms(const char *name);
*
* ###Error values
* - OBIDMS_LONG_NAME_ERROR : the database name exceeds the limit.
* - OBIDMS_MEMORY_ERROR : something wrong occurs during memory allocation.
* - OBIDMS_MEMORY_ERROR : something wrong occured during memory allocation.
*
* @see obi_close_dms()
* @since May 2015
......@@ -148,8 +126,9 @@ OBIDMS_p obi_open_dms(const char *name);
*/
OBIDMS_p obi_dms(const char *name);
/**
* @brief Close an opened OBITools Data Management instance (OBIDMS).
* @brief Closes an opened OBITools Data Management instance (OBIDMS).
*
* @param dms a pointer as returned by obi_create_dms() or obi_open_dms()
*
......@@ -165,4 +144,5 @@ OBIDMS_p obi_dms(const char *name);
*/
int obi_close_dms(OBIDMS_p dms);
#endif /* OBIDMS_H_ */
src/obidmscolumn.c
View file @ 5d967f5b
/****************************************************************************
* OBIDMSColumn functions *
* OBIDMS_column functions *
****************************************************************************/
/**
* @file obidmscolumn.h
* @file OBIDMS_column.h
* @author Celine Mercier
* @date 22 May 2015
* @brief Functions for the shared elements of all the OBIColumn structures.
......@@ -16,17 +16,17 @@
#include <sys/mman.h> /* mmap() is defined in this header */
/***********************************************************************
/*************************************************************************
*
* 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
*
***********************************************************************/
*************************************************************************/
/**
* @brief Internal function building the file name for a column.
*
* The function build the file name corresponding to a column of an OBIDMS.
* The function builds the file name corresponding to a column of an OBIDMS.
*
* @warning The returned pointer has to be freed by the caller.
*
......@@ -36,12 +36,13 @@
* @retvalue NULL if an error occurs
*
* ###Error values
* - OBIDMS_MEMORY_ERROR : something wrong occurs during memory allocation.
* - OBIDMS_MEMORY_ERROR : something wrong occured during memory allocation.
*
* @since May 2015
* @author Eric Coissac (eric.coissac@metabarcoding.org)
*/
static char *build_column_name(const char *name,obiversion_t version);
static char *build_column_name(const char *name, obiversion_t version);
/**
* @brief Internal function building the file name for a version column file.
......@@ -64,6 +65,7 @@ static char *build_column_name(const char *name,obiversion_t version);
*/
static char *build_version_name(const char *name);
/**
* @brief Internal function returning a new column version number
* in the `dms` database
......@@ -82,6 +84,7 @@ static char *build_version_name(const char *name);
*/
static obiversion_t obi_new_version(OBIDMS_p dms,char *name, bool block);
/**
* @brief Internal function creating a new column version file
* in the `dms` database
......@@ -99,11 +102,12 @@ static obiversion_t obi_new_version(OBIDMS_p dms,char *name, bool block);
*/
static int create_version(OBIDMS_p dms,char *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_column_name(const char *name,obiversion_t version) {
......@@ -134,6 +138,7 @@ static char *build_version_name(const char *name) {
return filename;
}
static obiversion_t obi_new_version(OBIDMS_p dms,char *name, bool block) {
off_t locsize=sizeof(bool) + sizeof(obiversion_t);
......@@ -164,13 +169,16 @@ static obiversion_t obi_new_version(OBIDMS_p dms,char *name, bool block) {
}
//open the version file
versionfd = openat(directoryfd,versionfile,O_RDWR);
//versionfd = openat(directoryfd, versionfile, O_RDWR);
versionfd = open(versionfile, O_RDWR);
if (versionfd < 0) {
free(versionfile);
if (errno == ENOENT)
{
return create_version(dms,name);
return create_version(dms, name);
}
else
{
......@@ -180,7 +188,7 @@ static obiversion_t obi_new_version(OBIDMS_p dms,char *name, bool block) {
}
// Test if the version file size is ok
if (lseek(versionfd,SEEK_END,0) < locsize)
if (lseek(versionfd, SEEK_END, 0) < locsize)
{
close(versionfd);
obi_set_errno(OBIDMS_UNKNOWN_ERROR);
......@@ -189,7 +197,7 @@ static obiversion_t obi_new_version(OBIDMS_p dms,char *name, bool block) {
}
// prepare the file for locking
if (lseek(versionfd,SEEK_SET,0) != 0)
if (lseek(versionfd, SEEK_SET, 0) != 0)
{
close(versionfd);
obi_set_errno(OBIDMS_UNKNOWN_ERROR);
......@@ -216,7 +224,7 @@ static obiversion_t obi_new_version(OBIDMS_p dms,char *name, bool block) {
}
// check if endianess is correct
if (little != obi_is_little_end())
if (little != obi_is_little_endian())
{
close(versionfd);
obi_set_errno(OBIDMS_BAD_ENDIAN_ERROR);
......@@ -275,6 +283,7 @@ static obiversion_t obi_new_version(OBIDMS_p dms,char *name, bool block) {
return newversion;
}
static int create_version(OBIDMS_p dms,char *name) {
off_t locsize=sizeof(bool) + sizeof(obiversion_t);
obiversion_t version=0;
......@@ -295,10 +304,15 @@ static int create_version(OBIDMS_p dms,char *name) {
return -1;
}
versionfd = openat(directoryfd,
versionfile,
O_RDWR|O_CREAT|O_EXCL,
666);
//versionfd = openat(directoryfd,
// versionfile,
// O_RDWR|O_CREAT|O_EXCL,
// 666);
versionfd = open(versionfile,
O_RDWR|O_CREAT|O_EXCL,
666);
if (versionfd < 0) {
obi_set_errno(OBIDMS_UNKNOWN_ERROR);
......@@ -331,7 +345,7 @@ static int create_version(OBIDMS_p dms,char *name) {
return -1;
}
little = obi_is_little_end();
little = obi_is_little_endian();
if (write(versionfd, &little, sizeof(bool)) < sizeof(bool))
{
......@@ -372,6 +386,7 @@ static int create_version(OBIDMS_p dms,char *name) {
return version;
}
/***********************************************************************
*
* 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
......@@ -397,7 +412,9 @@ obiversion_t obi_latest_version(OBIDMS_p dms,char *name) {
return -1;
}
versionfd = openat(directoryfd,versionfile,O_RDWR);
//versionfd = openat(directoryfd,versionfile,O_RDWR);
versionfd = open(versionfile,O_RDWR);
if (versionfd < 0) {
obi_set_errno(OBIDMS_UNKNOWN_ERROR);
free(versionfile);
......@@ -428,7 +445,7 @@ obiversion_t obi_latest_version(OBIDMS_p dms,char *name) {
return -1;
}
if (little != obi_is_little_end())
if (little != obi_is_little_endian())
{
close(versionfd);
obi_set_errno(OBIDMS_BAD_ENDIAN_ERROR);
......@@ -450,20 +467,20 @@ obiversion_t obi_latest_version(OBIDMS_p dms,char *name) {
return version;
}
size_t obi_get_platform_header_size()
{
return getpagesize() * 1;
}
OBIDMSColumn_p obi_create_column(OBIDMS_p dms,
OBIDMS_column_p obi_create_column(OBIDMS_p dms,
char *name,
OBIType_t type,
size_t nbelement)
size_t nbelements)
{
OBIDMSColumn_p newcolumn=NULL;
OBIDMSColumnHeader_p header;
OBIDMS_column_p newcolumn=NULL;
OBIDMS_column_header_p header;
size_t filesize;
obiversion_t version;
char * columnfile;
......@@ -480,7 +497,7 @@ OBIDMSColumn_p obi_create_column(OBIDMS_p dms,
}
hsize = obi_get_platform_header_size();
dsize = obi_array_sizeof(type,nbelement);
dsize = obi_array_sizeof(type,nbelements);
filesize = hsize + dsize;
......@@ -494,10 +511,14 @@ OBIDMSColumn_p obi_create_column(OBIDMS_p dms,
columnfile = build_column_name(name,version);
columnfd = openat(directoryfd,
columnfile,
O_RDWR|O_CREAT|O_EXCL,
666);
//columnfd = openat(directoryfd,
// columnfile,
// O_RDWR|O_CREAT|O_EXCL,
// 666);
columnfd = open(columnfile,
O_RDWR|O_CREAT|O_EXCL,
666);
if (ftruncate(columnfd,filesize) < 0)
{
......@@ -507,7 +528,7 @@ OBIDMSColumn_p obi_create_column(OBIDMS_p dms,
return NULL;
}
newcolumn = (OBIDMSColumn_p) malloc(sizeof(OBIDMSColumn_t));
newcolumn = (OBIDMS_column_p) malloc(sizeof(OBIDMS_column_t));
if (newcolumn)
{
......@@ -556,9 +577,9 @@ OBIDMSColumn_p obi_create_column(OBIDMS_p dms,
newcolumn->writable= true;
header = newcolumn->header;
header->little_endian = obi_is_little_end();
header->little_endian = obi_is_little_endian();
header->header_size = hsize;
header->line_count = nbelement;
header->line_count = nbelements;
header->line_used = 0;
header->data_type = type;
header->creation_date = time(NULL);
......@@ -571,7 +592,6 @@ OBIDMSColumn_p obi_create_column(OBIDMS_p dms,
}
// if( access( fname, F_OK ) != -1 ) {
// // file exists
// } else {
......
src/obidmscolumn.h
View file @ 5d967f5b
/****************************************************************************
* OBIDMSColumn header file *
* OBIDMS_column header file *
****************************************************************************/
/**
* @file obidmscolumn.h
* @author Celine Mercier
* @date 12 May 2015
* @brief Header file for the shared elements of all the OBIColumn structures.
* @brief Header file for the shared elements of all the OBIDMS column structures.
*/
#ifndef OBIDMSCOLUMN_H_
......@@ -34,10 +34,10 @@ typedef int32_t obiversion_t; /**< Used to store the column version number
* @brief OBIColumnHeader structure.
*/
typedef struct OBIDMSColumnHeader {
typedef struct OBIDMS_column_header {
bool little_endian; /**< endianess of the column:
- `true` on little endian platform
- `false` on big endian platform
- `true` on little endian platforms
- `false` on big endian platforms
@see obi_is_little_end()
*/
......@@ -52,41 +52,42 @@ typedef struct OBIDMSColumnHeader {
*/
char comments[1]; /**< comments stored as a classical
zero end C string. T
The size of the comment is just limited
The size of the comment is only limited
by the header size
*/
} OBIDMSColumnHeader_t, *OBIDMSColumnHeader_p;
} OBIDMS_column_header_t, *OBIDMS_column_header_p;
/**
* @brief Structure describing a Column of the OBITools DMS
*
* A data structure of this type is returned by the functions
* creating, opening or cloning an OBIDMSColumn.
* creating, opening or cloning an OBIDMS_column.
*/
typedef struct OBIDMSColumn {
typedef struct OBIDMS_column {
OBIDMS_p dms ; /**< A pointer to a DMS instance
*/
OBIDMSColumnHeader_p header; /**< A pointer to the header of the column
OBIDMS_column_header_p header; /**< A pointer to the header of the column
*/
void* data; /**< A `void` pointer to the beginning of the
* data.
*
* @attention never use this member directly
* outside of the code of the
* low level functions
* of the OBITools DMS
* @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 he closes it.
* until it closes it.
*/
} OBIDMSColumn_t, *OBIDMSColumn_p;
} OBIDMS_column_t, *OBIDMS_column_p;
/**
* @brief Return the header size in bytes of a column on this platform.
* @brief Returns the header size in bytes of a column on this platform.
*
* Header size is defined as a multiple of the memory page size.
* Up to now the header size is defined as one time the page size
......@@ -99,27 +100,25 @@ typedef struct OBIDMSColumn {
size_t obi_get_platform_header_size();
/**
* @brief Create a column.
* @brief Creates a column.
*
* @param dms a pointer as returned by obi_create_dms() or obi_open_dms()
* @param name the name of the new column
* @param type the OBIType code used to create the column
* @param nbelement the number of element to be stored
* @param nbelements the number of elements to be stored
*
* @since May 2015
* @author Eric Coissac (eric.coissac@metabarcoding.org)
*/
OBIDMSColumn_p obi_create_column(OBIDMS_p dms,
OBIDMS_column_p obi_create_column(OBIDMS_p dms,
char* name,
OBIType_t type,
size_t nbelement);
size_t nbelements);
/**
* @brief Return the latest column version in the `dms` database
* @brief Returns the latest column version in the `dms` database
*
* @param dms a pointer as returned by obi_create_dms() or obi_open_dms()
* @param name the name of the column
......@@ -130,5 +129,4 @@ OBIDMSColumn_p obi_create_column(OBIDMS_p dms,
obiversion_t obi_latest_version(OBIDMS_p dms,char *name);
#endif /* OBIDMSCOLUMN_H_ */
src/obierrno.h
View file @ 5d967f5b
......@@ -11,26 +11,54 @@
/**
* @brief The declaration of the external variable `obi_errno`.
*
* `obi_errno` is an equivalent of `errno` for the system level error
* but for for error generated by the C layer of the OBITools framework.
* `obi_errno` is an equivalent of `errno` for the system level error,
* but for errors generated by the C layer of the OBITools framework.
*
* @todo We have to look for defining this variable as thread specific.
* @todo We have to look into defining this variable as thread specific.
*/
extern int obi_errno;
/**
* @brief set the global `obi_errno` variable with
* @brief Sets the global `obi_errno` variable with
* the specified `err` code
*
* This function is defined as a macro to reduce the risk
* to increase the problem generating the error by calling
* of increasing the problem generating the error by calling
* a new function.
*
* @param err the error code as an integer value
* @param err The error code as an integer value.
*
* @since May 2015
* @author Eric Coissac (eric.coissac@metabarcoding.org)
*/
#define obi_set_errno(err) (obi_errno = (err))
/**
* @defgroup OBIDMSErrors OBIDMS related error codes
*
* Error codes set in errno following an error related
* to the manipulation of an OBIDMS.
*
* @{
*/
#define OBIDMS_EXIST_ERROR (1) /**< Trying to create an OBIDMS with a name
* that corresponds to an existing OBIDMS
*/
#define OBIDMS_NOT_EXIST_ERROR (2) /**< Trying to open a non-existing OBIDMS
*/
#define OBIDMS_LONG_NAME_ERROR (3) /**< The specified OBIDMS name is too long
*/
#define OBIDMS_MEMORY_ERROR (4) /**< A memory error occurred during allocation
*/
#define OBIDMS_UNKNOWN_ERROR (5) /**< Undetermined error
*/
#define OBIDMS_ACCESS_ERROR (6) /**< Permission error trying to access the database
*/
#define OBIDMS_BAD_ENDIAN_ERROR (7) /**< The opened data structure does not corresponds
* to the endianess of the platform.
*/
/**@}*/
#endif /* OBIERRNO_H_ */