obitools3/src/obidmscolumn.c

/****************************************************************************
 * OBIDMS_column functions                                                   *
 ****************************************************************************/

/**
 * @file OBIDMS_column.h
 * @author Celine Mercier
 * @date 22 May 2015
 * @brief Functions for the shared elements of all the OBIColumn structures.
 */


#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 builds 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 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);


/**
 * @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);
	versionfd = open(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_endian())
	{
		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);

	versionfd = open(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_endian();

	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);
	versionfd = open(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_endian())
	{
		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;
}


OBIDMS_column_p obi_create_column(OBIDMS_p dms,
		                         char *name,
								 OBIType_t type,
								 size_t nbelements)
{
	OBIDMS_column_p newcolumn=NULL;
	OBIDMS_column_header_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,nbelements);

	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);

	columnfd =  open(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 = (OBIDMS_column_p) malloc(sizeof(OBIDMS_column_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_endian();
	header->header_size   = hsize;
	header->line_count    = nbelements;
	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
//	}