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Updated the documentation for obidms functions

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This commit is contained in:
Celine Mercier
2016-04-22 11:28:09 +02:00
parent 4ead37ee48
commit 22e3c3eeed
2 changed files with 124 additions and 40 deletions
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16
src/obidms.c
View File

@ -420,7 +420,7 @@ OBIDMS_p obi_open_dms(const char* dms_name)
dms->opened_columns = (Opened_columns_list_p) malloc(sizeof(Opened_columns_list_t));
(dms->opened_columns)->nb_opened_columns = 0;
// Initialize the list of opened indexers // TODO should be handled somewhere else?
// Initialize the list of opened indexers
dms->opened_indexers = (Opened_indexers_list_p) malloc(sizeof(Opened_indexers_list_t));
(dms->opened_indexers)->nb_opened_indexers = 0;
@ -463,7 +463,7 @@ int obi_close_dms(OBIDMS_p dms)
free(dms);
return -1;
}
if (closedir(dms->indexer_directory) < 0) // TODO should be handled somewhere else?
if (closedir(dms->indexer_directory) < 0)
{
obi_set_errno(OBI_INDEXER_ERROR);
obidebug(1, "\nError closing an indexer directory");
@ -488,10 +488,10 @@ int obi_dms_is_column_name_in_list(OBIDMS_p dms, const char* column_name)
{
if (!strcmp(((*((columns_list->columns)+i))->header)->name, column_name))
{ // Found it
return 0;
return 1;
}
}
return 1;
return 0;
}
@ -512,7 +512,7 @@ OBIDMS_column_p obi_dms_get_column_from_list(OBIDMS_p dms, const char* column_na
}
void obi_dms_list_column(OBIDMS_p dms, OBIDMS_column_p column)
void obi_dms_list_column(OBIDMS_p dms, OBIDMS_column_p column) // TODO add check if column already in list?
{
*(((dms->opened_columns)->columns)+((dms->opened_columns)->nb_opened_columns)) = column;
((dms->opened_columns)->nb_opened_columns)++;
@ -551,7 +551,7 @@ Obi_indexer_p obi_dms_get_indexer_from_list(OBIDMS_p dms, const char* indexer_na
for (i=0; i < (indexers_list->nb_opened_indexers); i++)
{
if (!strcmp(((indexers_list->indexers)[i])->name, indexer_name)) // TODO it references something in AVL_group struct
if (!strcmp(((indexers_list->indexers)[i])->name, indexer_name)) // TODO get_name function indexer
{ // Found the indexer already opened, return it
return (indexers_list->indexers)[i];
}
@ -602,8 +602,8 @@ char* obi_dms_get_dms_path(OBIDMS_p dms)
return NULL;
}
if (getcwd(full_path, MAX_PATH_LEN) == NULL) // TODO not sure at all about this because the DMS must be in the working directory.
{ // Maybe better to store when opening, but opening function seems to assume that too.
if (getcwd(full_path, MAX_PATH_LEN) == NULL) // TODO store when opening
{
obi_set_errno(OBI_UTILS_ERROR);
obidebug(1, "\nError getting the path to a file or directory");
return NULL;

148
src/obidms.h
View File

@ -23,8 +23,7 @@
#include <stdbool.h>
#include "obierrno.h"
//#include "obidmscolumn.h"
//#include "obiblob_indexer.h"
#include "obitypes.h"
#define OBIDMS_MAX_NAME (2048) /**< The maximum length of an OBIDMS name.
@ -42,26 +41,33 @@
*/
typedef int32_t obiversion_t; /**< TODO put dans obitypes.h
*/
struct OBIDMS_column; /**< Declarations to avoid circular dependencies. */
typedef struct OBIDMS_column* OBIDMS_column_p; /**< Declarations to avoid circular dependencies. */
struct OBIDMS_column; // TODO
typedef struct OBIDMS_column* OBIDMS_column_p;
typedef struct Opened_columns_list { // TODO Handle the problem linked to columns with the same name + means only one version
int nb_opened_columns;
OBIDMS_column_p columns[MAX_NB_OPENED_COLUMNS];
/**
* @brief Structure listing the columns opened in a DMS, identified by their name and version number.
*/
typedef struct Opened_columns_list {
int nb_opened_columns; /**< Number of opened columns.
*/
OBIDMS_column_p columns[MAX_NB_OPENED_COLUMNS]; /**< Array of pointers on the opened columns.
*/
} Opened_columns_list_t, *Opened_columns_list_p;
struct OBIDMS_avl_group; // TODO
typedef struct OBIDMS_avl_group* OBIDMS_avl_group_p;
typedef OBIDMS_avl_group_p Obi_indexer_p;
// TODO Need to find a way to not refer to AVLs specifically
struct OBIDMS_avl_group; /**< Declarations to avoid circular dependencies. */
typedef struct OBIDMS_avl_group* OBIDMS_avl_group_p; /**< Declarations to avoid circular dependencies. */
typedef OBIDMS_avl_group_p Obi_indexer_p; /**< Declarations to avoid circular dependencies. */
/**
* @brief Structure listing the indexers opened in a DMS, identified by their name.
*/
typedef struct Opened_indexers_list {
int nb_opened_indexers;
Obi_indexer_p indexers[MAX_NB_OPENED_INDEXERS];
int nb_opened_indexers; /**< Number of opened indexers.
*/
Obi_indexer_p indexers[MAX_NB_OPENED_INDEXERS]; /**< Array of pointers on the opened indexers.
*/
} Opened_indexers_list_t, *Opened_indexers_list_p;
@ -81,10 +87,10 @@ typedef struct OBIDMS {
int dir_fd; /**< The file descriptor of the directory entry
* usable to refer and scan the database directory.
*/
DIR* indexer_directory; /**< A directory entry usable to
DIR* indexer_directory; /**< A directory entry usable to
* refer and scan the indexer directory.
*/
int indexer_dir_fd; /**< The file descriptor of the directory entry
int indexer_dir_fd; /**< The file descriptor of the directory entry
* usable to refer and scan the indexer directory.
*/
bool little_endian; /**< Endianness of the database.
@ -101,7 +107,7 @@ typedef struct OBIDMS {
*
* @param dms_name A pointer to a C string containing the name of the database.
*
* @returns An integer value indicating the status of the database
* @returns An integer value indicating the status of the database.
* @retval 1 if the database exists.
* @retval 0 if the database does not exist.
* @retval -1 if an error occurred.
@ -186,60 +192,138 @@ OBIDMS_p obi_dms(const char* dms_name);
int obi_close_dms(OBIDMS_p dms);
// TODO doc
/**
* @brief Checks if a column with a given name is in the list of opened columns.
*
* @warning: Checking only the name means that the column can be of any version.
*
* @param dms The OBIDMS.
* @param column_name The column name that should be looked for.
*
* @returns An integer value indicating whether there is at least one column with that name
* in the list of opened columns.
* @retval 0 if there is at least one column with that name in the list of opened columns.
* @retval 1 if there is no column with that name in the list of opened columns.
*
* @since April 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_dms_is_column_name_in_list(OBIDMS_p dms, const char* column_name);
/**
* @brief Returns a column identified by its name and its version number from the list of opened columns.
*
* @param dms The OBIDMS.
* @param column_name The column name that should be looked for.
* @param version The version number of the column that should be looked for.
*
* @returns A pointer on the column if it was found in the list of opened columns.
* @retval NULL if the column was not found in the list of opened columns.
*
* @since April 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
OBIDMS_column_p obi_dms_get_column_from_list(OBIDMS_p dms, const char* column_name, obiversion_t version);
/**
* @brief Adds a column identified by its name and its version number in the list of opened columns.
*
* @param dms The OBIDMS.
* @param column A pointer on the column that should be added in the list of opened columns.
*
* @since April 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
void obi_dms_list_column(OBIDMS_p dms, OBIDMS_column_p column);
/**
* @brief Removes a column identified by its name and its version number from the list of opened columns.
*
* @param dms The OBIDMS.
* @param column A pointer on the column that should be removed from the list of opened columns.
*
* @since April 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_dms_unlist_column(OBIDMS_p dms, OBIDMS_column_p column);
/**
* @brief Returns an indexer identified by its name from the list of opened indexers.
*
* @param dms The OBIDMS.
* @param indexer_name The indexer name that should be looked for.
*
* @returns A pointer on the indexer if it was found in the list of opened indexers.
* @retval NULL if the indexer was not found in the list of opened indexers.
*
* @since April 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
Obi_indexer_p obi_dms_get_indexer_from_list(OBIDMS_p dms, const char* indexer_name);
/**
* @brief Adds an indexer identified by its name in the list of opened indexers.
*
* @param dms The OBIDMS.
* @param indexer A pointer on the indexer that should be added in the list of opened indexers.
*
* @since April 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
void obi_dms_list_indexer(OBIDMS_p dms, Obi_indexer_p indexer);
/**
* @brief Removes an indexer identified by its name from the list of opened indexers.
*
* @param dms The OBIDMS.
* @param column A pointer on the indexer that should be removed from the list of opened indexers.
*
* @since April 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_dms_unlist_indexer(OBIDMS_p dms, Obi_indexer_p indexer);
/**
* Function meant to disappear soon
*/
char* obi_dms_get_path(OBIDMS_p dms);
/** TODO
* @brief Internal function getting the full path of a file or a directory from its
* path relative to a directory file descriptor.
/**
* @brief Gets the full path of a file or a directory from its
* path relative to the DMS.
*
* @warning The returned pointer has to be freed by the caller.
*
* @param directory_file_descriptor The file descriptor for the directory to which
* path_name is relative.
* @param path_name The path name for the file or directory, relative to directory_file_descriptor.
* @param dms The DMS to which path_name is relative.
* @param path_name The path name for the file or directory, relative to the DMS.
*
* @returns A pointer to the full path.
* @retval NULL if an error occurred.
*
* @since June 2015
* @since April 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
char* obi_dms_get_full_path(OBIDMS_p dms, const char* path_name);
/**
* @brief Replacement function for opendirat() : open a directory relative to a directory file descriptor.
* @brief Opens a directory relative to the DMS.
*
* @param directory_file_descriptor The file descriptor for the directory in which the directory should be opened.
* @param path_name The path name for the directory to be opened, relative to directory_file_descriptor.
* @param dms The DMS to which path_name is relative.
* @param path_name The path name for the directory to be opened, relative to the DMS.
*
* @returns The file descriptor of the opened directory.
* @returns The directory stream of the opened directory.
* @retval NULL if an error occurred.
*
* @since June 2015
* @since April 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
DIR* opendir_in_dms(OBIDMS_p dms, const char* path_name);