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C Syntax error patches

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This commit is contained in:
Eric Coissac
2015-05-26 10:38:56 +02:00
parent 30ddb32dfe
commit 6248160eeb
6 changed files with 679 additions and 16 deletions
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5
src/obidms.c
View File

@ -51,7 +51,6 @@ static char *build_directory_name(const char *name) {
}
OBIDMS_p obi_create_dms(const char *name) {
OBIDMS_p dms=NULL;
char *dirdbname;
// Build and check the directory name
@ -61,7 +60,7 @@ OBIDMS_p obi_create_dms(const char *name) {
// Try to create the directory
if (mkdir(dirdbname,) < 0)
if (mkdir(dirdbname,0x777) < 0)
{
if (errno==EEXIST)
obi_set_errno(OBIDMS_EXIST_ERROR);
@ -111,7 +110,7 @@ OBIDMS_p obi_open_dms(const char *name) {
}
// Allocate the data structure
dms = <OBIDMS_p> malloc(sizeof(OBIDMS_t));
dms = (OBIDMS_p) malloc(sizeof(OBIDMS_t));
if (dms==NULL)
{

7
src/obidms.h
View File

@ -12,6 +12,8 @@
#include <sys/stat.h>
#include <errno.h>
#include <dirent.h>
#include <string.h>
#include <stdio.h>
#include <obierrno.h>
@ -28,7 +30,7 @@ typedef struct OBIDMS {
char dirname[OBIDMS_MAX_NAME+1]; /**< The name of the directory
* containing the DMS
*/
DIR *directory /**< A directory entry usable to
DIR *directory; /**< A directory entry usable to
* refer and scan the database directory
*/
} OBIDMS_t, *OBIDMS_p;
@ -54,6 +56,9 @@ typedef struct OBIDMS {
*/
#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.
*/
/**@}*/

570
src/obidmscolumn.c
View File

@ -10,11 +10,579 @@
*/
#include <stdio.h>
#include <obidmscolumn.h>
#include <stdlib.h>
#include <fcntl.h>
#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
*
***********************************************************************/
/**
* @brief Internal function building the file name for a column.
*
* The function build the file name corresponding to a column of an OBIDMS.
*
* @warning The returned pointer has to be freed by the caller.
*
* @param name the name of the column of the OBIDMS
*
* @return a pointer to the filename name
* @retvalue NULL if an error occurs
*
* ###Error values
* - OBIDMS_MEMORY_ERROR : something wrong occurs during memory allocation.
*
* @since May 2015
* @author Eric Coissac (eric.coissac@metabarcoding.org)
*/
static char *build_column_name(const char *name,obiversion_t version);
/**
* @brief Internal function building the file name for a version column file.
*
* The version column file indicate the latest version number for a column.
* This function returns the name of the file storing this information
*
* @warning The returned pointer has to be freed by the caller.
*
* @param name the name of the column of the OBIDMS
*
* @return a pointer to the filename name
* @retvalue NULL if an error occurs
*
* ###Error values
* - OBIDMS_MEMORY_ERROR : something wrong occurs during memory allocation.
*
* @since May 2015
* @author Eric Coissac (eric.coissac@metabarcoding.org)
*/
static char *build_version_name(const char *name);
/**
* @brief Internal function returning a new column version number
* 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
* @param block is the call is blocking or not
* - `true` the call is blocking
* - `false` the call is not blocking
*
* @return the bigger version number used for this column
* @retvalue -1 if the column does not exist
*
* @since May 2015
* @author Eric Coissac (eric.coissac@metabarcoding.org)
*/
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
*
* The new file is initialized with the minimum version number `0`.
*
* @param dms a pointer as returned by obi_create_dms() or obi_open_dms()
* @param name the name of the column
*
* @return the next usable version number for this comumn : `0`
* @retvalue -1 if the column does not exist
*
* @since May 2015
* @author Eric Coissac (eric.coissac@metabarcoding.org)
*/
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
*
***********************************************************************/
static char *build_column_name(const char *name,obiversion_t version) {
char *filename;
// Build the database directory name
if (asprintf(&filename,"%s@%d.odc",name,version) < 0)
{
obi_set_errno(OBIDMS_MEMORY_ERROR);
return NULL;
}
return filename;
}
static char *build_version_name(const char *name) {
char *filename;
// Build the database directory name
if (asprintf(&filename,"%s.odv",name) < 0)
{
obi_set_errno(OBIDMS_MEMORY_ERROR);
return NULL;
}
return filename;
}
static obiversion_t obi_new_version(OBIDMS_p dms,char *name, bool block) {
off_t locsize=sizeof(bool) + sizeof(obiversion_t);
obiversion_t newversion=0;
char * versionfile;
int directoryfd;
int versionfd;
bool little;
int lockmode;
// Select the correct lockf operation according to the blocking mode
if (block)
lockmode=F_LOCK;
else
lockmode=F_TLOCK;
// build the version file name
versionfile = build_version_name(name);
if (versionfile==NULL)
return -1;
// Get the file descriptior associated to the database directory
directoryfd = dirfd(dms->directory);
if (directoryfd < 0) {
obi_set_errno(OBIDMS_UNKNOWN_ERROR);
free(versionfile);
return -1;
}
//open the version file
versionfd = openat(directoryfd,versionfile,O_RDWR);
if (versionfd < 0) {
free(versionfile);
if (errno == ENOENT)
{
return create_version(dms,name);
}
else
{
obi_set_errno(OBIDMS_UNKNOWN_ERROR);
return -1;
}
}
// Test if the version file size is ok
if (lseek(versionfd,SEEK_END,0) < locsize)
{
close(versionfd);
obi_set_errno(OBIDMS_UNKNOWN_ERROR);
free(versionfile);
return -1;
}
// prepare the file for locking
if (lseek(versionfd,SEEK_SET,0) != 0)
{
close(versionfd);
obi_set_errno(OBIDMS_UNKNOWN_ERROR);
free(versionfile);
return -1;
}
// Lock the file
if (lockf(versionfd, lockmode, locsize) < -1)
{
close(versionfd);
obi_set_errno(OBIDMS_UNKNOWN_ERROR);
free(versionfile);
return -1;
}
// read the endianess of the file
if (read(versionfd, &little, sizeof(bool)) < sizeof(bool))
{
close(versionfd);
obi_set_errno(OBIDMS_UNKNOWN_ERROR);
free(versionfile);
return -1;
}
// check if endianess is correct
if (little != obi_is_little_end())
{
close(versionfd);
obi_set_errno(OBIDMS_BAD_ENDIAN_ERROR);
free(versionfile);
return -1;
}
// read the current version number
if (read(versionfd, &newversion, sizeof(obiversion_t)) < sizeof(obiversion_t))
{
close(versionfd);
obi_set_errno(OBIDMS_UNKNOWN_ERROR);
free(versionfile);
return -1;
}
newversion++;
// write the new version number
if (lseek(versionfd,SEEK_SET,sizeof(bool)) != sizeof(bool))
{
close(versionfd);
obi_set_errno(OBIDMS_UNKNOWN_ERROR);
free(versionfile);
return -1;
}
if (write(versionfd, &newversion, sizeof(obiversion_t)) < sizeof(obiversion_t))
{
close(versionfd);
obi_set_errno(OBIDMS_UNKNOWN_ERROR);
free(versionfile);
return -1;
}
// prepare for the unlocking
if (lseek(versionfd,SEEK_SET,0) != 0)
{
close(versionfd);
obi_set_errno(OBIDMS_UNKNOWN_ERROR);
free(versionfile);
return -1;
}
// unlock the file
if (lockf(versionfd, F_ULOCK, locsize) < -1)
{
close(versionfd);
obi_set_errno(OBIDMS_UNKNOWN_ERROR);
free(versionfile);
return -1;
}
close(versionfd);
free(versionfile);
return newversion;
}
static int create_version(OBIDMS_p dms,char *name) {
off_t locsize=sizeof(bool) + sizeof(obiversion_t);
obiversion_t version=0;
char * versionfile;
int directoryfd;
int versionfd;
bool little;
versionfile = build_version_name(name);
if (versionfile==NULL)
return -1;
directoryfd = dirfd(dms->directory);
if (directoryfd < 0) {
obi_set_errno(OBIDMS_UNKNOWN_ERROR);
free(versionfile);
return -1;
}
versionfd = openat(directoryfd,
versionfile,
O_RDWR|O_CREAT|O_EXCL,
666);
if (versionfd < 0) {
obi_set_errno(OBIDMS_UNKNOWN_ERROR);
free(versionfile);
return -1;
}
// Lock the file
if (lockf(versionfd, F_LOCK, locsize) < -1)
{
close(versionfd);
obi_set_errno(OBIDMS_UNKNOWN_ERROR);
free(versionfile);
return -1;
}
if (ftruncate(versionfd,locsize) < 0)
{
close(versionfd);
obi_set_errno(OBIDMS_UNKNOWN_ERROR);
free(versionfile);
return -1;
}
if (lseek(versionfd,SEEK_SET,0) != 0)
{
close(versionfd);
obi_set_errno(OBIDMS_UNKNOWN_ERROR);
free(versionfile);
return -1;
}
little = obi_is_little_end();
if (write(versionfd, &little, sizeof(bool)) < sizeof(bool))
{
close(versionfd);
obi_set_errno(OBIDMS_UNKNOWN_ERROR);
free(versionfile);
return -1;
}
if (write(versionfd, &version, sizeof(obiversion_t)) < sizeof(obiversion_t))
{
close(versionfd);
obi_set_errno(OBIDMS_UNKNOWN_ERROR);
free(versionfile);
return -1;
}
// prepare for the unlocking
if (lseek(versionfd,SEEK_SET,0) != 0)
{
close(versionfd);
obi_set_errno(OBIDMS_UNKNOWN_ERROR);
free(versionfile);
return -1;
}
// unlock the file
if (lockf(versionfd, F_ULOCK, locsize) < -1)
{
close(versionfd);
obi_set_errno(OBIDMS_UNKNOWN_ERROR);
free(versionfile);
return -1;
}
close(versionfd);
free(versionfile);
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
*
***********************************************************************/
obiversion_t obi_latest_version(OBIDMS_p dms,char *name) {
off_t locsize=sizeof(bool) + sizeof(obiversion_t);
obiversion_t version=0;
char * versionfile;
int directoryfd;
int versionfd;
bool little;
versionfile = build_version_name(name);
if (versionfile==NULL)
return -1;
directoryfd = dirfd(dms->directory);
if (directoryfd < 0) {
obi_set_errno(OBIDMS_UNKNOWN_ERROR);
free(versionfile);
return -1;
}
versionfd = openat(directoryfd,versionfile,O_RDWR);
if (versionfd < 0) {
obi_set_errno(OBIDMS_UNKNOWN_ERROR);
free(versionfile);
return -1;
}
if (lseek(versionfd,SEEK_END,0) < locsize)
{
close(versionfd);
obi_set_errno(OBIDMS_UNKNOWN_ERROR);
free(versionfile);
return -1;
}
if (lseek(versionfd,SEEK_SET,0) != 0)
{
close(versionfd);
obi_set_errno(OBIDMS_UNKNOWN_ERROR);
free(versionfile);
return -1;
}
if (read(versionfd, &little, sizeof(bool)) < sizeof(bool))
{
close(versionfd);
obi_set_errno(OBIDMS_UNKNOWN_ERROR);
free(versionfile);
return -1;
}
if (little != obi_is_little_end())
{
close(versionfd);
obi_set_errno(OBIDMS_BAD_ENDIAN_ERROR);
free(versionfile);
return -1;
}
if (read(versionfd, &version, sizeof(obiversion_t)) < sizeof(obiversion_t))
{
close(versionfd);
obi_set_errno(OBIDMS_UNKNOWN_ERROR);
free(versionfile);
return -1;
}
close(versionfd);
free(versionfile);
return version;
}
size_t obi_get_platform_header_size()
{
return getpagesize() * 1;
}
OBIDMSColumn_p obi_create_column(OBIDMS_p dms,
char *name,
OBIType_t type,
size_t nbelement)
{
OBIDMSColumn_p newcolumn=NULL;
OBIDMSColumnHeader_p header;
size_t filesize;
obiversion_t version;
char * columnfile;
int columnfd;
int directoryfd;
size_t hsize;
size_t dsize;
directoryfd = dirfd(dms->directory);
if (directoryfd < 0) {
obi_set_errno(OBIDMS_UNKNOWN_ERROR);
return NULL;
}
hsize = obi_get_platform_header_size();
dsize = obi_array_sizeof(type,nbelement);
filesize = hsize + dsize;
version = obi_new_version(dms,name,true);
if (version < 0)
{
obi_set_errno(OBIDMS_UNKNOWN_ERROR);
return NULL;
}
columnfile = build_column_name(name,version);
columnfd = openat(directoryfd,
columnfile,
O_RDWR|O_CREAT|O_EXCL,
666);
if (ftruncate(columnfd,filesize) < 0)
{
close(columnfd);
obi_set_errno(OBIDMS_UNKNOWN_ERROR);
free(columnfile);
return NULL;
}
newcolumn = (OBIDMSColumn_p) malloc(sizeof(OBIDMSColumn_t));
if (newcolumn)
{
close(columnfd);
obi_set_errno(OBIDMS_MEMORY_ERROR);
free(columnfile);
return NULL;
}
newcolumn->dms = dms;
newcolumn->header = mmap(NULL,
hsize,
PROT_READ | PROT_WRITE,
MAP_SHARED,
columnfd,
0
);
if (newcolumn->header == MAP_FAILED)
{
close(columnfd);
obi_set_errno(OBIDMS_MEMORY_ERROR);
free(columnfile);
free(newcolumn);
return NULL;
}
newcolumn->data = mmap(NULL,
dsize,
PROT_READ | PROT_WRITE,
MAP_SHARED,
columnfd,
hsize
);
if (newcolumn->data == MAP_FAILED)
{
munmap(newcolumn->header,hsize);
close(columnfd);
obi_set_errno(OBIDMS_MEMORY_ERROR);
free(columnfile);
free(newcolumn);
return NULL;
}
newcolumn->writable= true;
header = newcolumn->header;
header->little_endian = obi_is_little_end();
header->header_size = hsize;
header->line_count = nbelement;
header->line_used = 0;
header->data_type = type;
header->creation_date = time(NULL);
header->version = version;
header->comments[0] = 0x0;
strncpy(header->name,name,OBIDMS_MAX_COLNAME);
free(columnfile);
return newcolumn;
}
// if( access( fname, F_OK ) != -1 ) {
// // file exists
// } else {
// // file doesn't exist
// }
/************************************************************************
************************************************************************
************************************************************************/
/**
* @brief Reads a memory block from a file.
*

110
src/obidmscolumn.h
View File

@ -16,8 +16,12 @@
#include <sys/types.h>
#include <unistd.h>
#include <stdbool.h>
#include <time.h>
#include "obitypes.h"
#include <obidms.h>
#include <obitypes.h>
#include <obierrno.h>
#include <obilittlebigman.h>
/**
* @brief Value separator in OBIDMSColumn files.
@ -36,24 +40,110 @@ static const int HEADER_SIZE = 4096;
*/
static const int BUFFER_SIZE = 4;
#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
*/
/**
* @brief OBIColumnHeader structure.
*/
typedef struct OBIDMSColumnHeader {
bool endyan_byte_order; /**< endyan byte order */
int header_size_value; /**< size of the header: a multiple of PAGESIZE */
bool file_status; /**< file status : 0 is Open and 1 is Closed */
pid_t PID; /**< PID of the process that created the file and is
the only one allowed to modify it if it is open */
int line_count; /**< number of lines of data */
bool little_endian; /**< endianess of the column:
- `true` on little endian platform
- `false` on big endian platform
@see obi_is_little_end()
*/
int header_size; /**< size of the header in bytes */
size_t line_count; /**< number of lines of data */
size_t line_used; /**< number of lines of data used*/
OBIType_t data_type; /**< type of the data */
char* creation_date; /**< date of creation of the file */
int version; /**< version of the OBIColumn */
char* comments; /**< comments */
time_t creation_date; /**< date of creation of the file */
obiversion_t version; /**< version of the OBIColumn */
char name[OBIDMS_MAX_COLNAME]; /**< The column name as a NULL
* terminated string.
*/
char comments[1]; /**< comments stored as a classical
zero end C string. T
The size of the comment is just limited
by the header size
*/
} OBIDMSColumnHeader_t, *OBIDMSColumnHeader_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.
*/
typedef struct OBIDMSColumn {
OBIDMS_p dms ; /**< A pointer to a DMS instance
*/
OBIDMSColumnHeader_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
*/
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.
*/
} OBIDMSColumn_t, *OBIDMSColumn_p;
/**
* @brief Return 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
*
* @return a `size_t` value corresponding to the header size in bytes
*
* @since May 2015
* @author Eric Coissac (eric.coissac@metabarcoding.org)
*/
size_t obi_get_platform_header_size();
/**
* @brief Create 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
*
* @since May 2015
* @author Eric Coissac (eric.coissac@metabarcoding.org)
*/
OBIDMSColumn_p obi_create_column(OBIDMS_p dms,
char* name,
OBIType_t type,
size_t nbelement);
/**
* @brief Return 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
*
* @return the bigger version number used for this column
* @return -1 if the column does not exist
*/
obiversion_t obi_latest_version(OBIDMS_p dms,char *name);
char* obi_map_read_only(int file, int start, int size);

2
src/obitypes.c
View File

@ -8,7 +8,7 @@
#include <obitypes.h>
size_t obi_sizeof(OBIType_t type) {
size_t size=0
size_t size=0;
switch (type) {
case OBI_VOID: size = 1;

1
src/obitypes.h
View File

@ -10,6 +10,7 @@
#include <stdio.h>
#include <unistd.h>
#include <stdint.h>
#define OBIInt_NA (INT32_MIN)
#define OBIFloat_NA (NAN)