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fixed typos and other minor things

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This commit is contained in:
Celine Mercier
2015-06-10 15:19:02 +02:00
parent 9b6de9c411
commit 5d967f5b7b
9 changed files with 171 additions and 141 deletions
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94
src/obidmscolumn.c
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@ -1,9 +1,9 @@
/****************************************************************************
* 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 {