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Closes issue #47 by storing each view in a separate file named with the

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view's name and created upon view creation.
This commit is contained in:
Celine Mercier
2016-06-30 11:41:30 +02:00
parent ad2af0b512
commit 0869b9ba3f
7 changed files with 526 additions and 649 deletions
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43
src/obidms.c
View File

@ -252,7 +252,7 @@ OBIDMS_p obi_create_dms(const char* dms_path)
return NULL;
}
// Get file descriptor of DMS directory to create the indexer directory
// Get file descriptor of DMS directory to create other directories
dms_dir = opendir(directory_name);
if (dms_dir == NULL)
{
@ -280,6 +280,14 @@ OBIDMS_p obi_create_dms(const char* dms_path)
return NULL;
}
// Create the view directory
if (mkdirat(dms_file_descriptor, VIEW_DIR_NAME, 00777) < 0)
{
obi_set_errno(OBIVIEW_ERROR);
obidebug(1, "\nProblem creating a view directory");
return NULL;
}
// Isolate the dms name
j = 0;
for (i=0; i<strlen(dms_path); i++)
@ -447,6 +455,30 @@ OBIDMS_p obi_open_dms(const char* dms_path)
return NULL;
}
// Open the view directory
dms->view_directory = opendir_in_dms(dms, VIEW_DIR_NAME);
if (dms->view_directory == NULL)
{
obi_set_errno(OBIDMS_UNKNOWN_ERROR);
obidebug(1, "\nError opening the view directory");
closedir(dms->indexer_directory);
closedir(dms->directory);
free(dms);
return NULL;
}
// Store the view directory's file descriptor
dms->view_dir_fd = dirfd(dms->view_directory);
if (dms->view_dir_fd < 0)
{
obi_set_errno(OBIDMS_UNKNOWN_ERROR);
obidebug(1, "\nError getting the file descriptor of the view directory");
closedir(dms->view_directory);
closedir(dms->directory);
free(dms);
return NULL;
}
// Initialize the list of opened columns
dms->opened_columns = (Opened_columns_list_p) malloc(sizeof(Opened_columns_list_t));
(dms->opened_columns)->nb_opened_columns = 0;
@ -486,7 +518,7 @@ int obi_close_dms(OBIDMS_p dms)
while ((dms->opened_columns)->nb_opened_columns > 0)
obi_close_column(*((dms->opened_columns)->columns));
// Close dms and indexer directories
// Close dms, and view and indexer directories
if (closedir(dms->directory) < 0)
{
obi_set_errno(OBIDMS_MEMORY_ERROR);
@ -501,6 +533,13 @@ int obi_close_dms(OBIDMS_p dms)
free(dms);
return -1;
}
if (closedir(dms->view_directory) < 0)
{
obi_set_errno(OBIVIEW_ERROR);
obidebug(1, "\nError closing a view directory");
free(dms);
return -1;
}
free(dms);
}

8
src/obidms.h
View File

@ -30,6 +30,8 @@
*/
#define INDEXER_DIR_NAME "OBIBLOB_INDEXERS" /**< The name of the Obiblob indexer directory.
*/
#define VIEW_DIR_NAME "VIEWS" /**< The name of the view directory.
*/
#define TAXONOMY_DIR_NAME "TAXONOMY" /**< The name of the taxonomy directory.
*/
#define MAX_NB_OPENED_COLUMNS (100) /**< The maximum number of columns open at the same time.
@ -98,6 +100,12 @@ typedef struct OBIDMS {
int indexer_dir_fd; /**< The file descriptor of the directory entry
* usable to refer and scan the indexer directory.
*/
DIR* view_directory; /**< A directory entry usable to
* refer and scan the view directory.
*/
int view_dir_fd; /**< The file descriptor of the directory entry
* usable to refer and scan the view directory.
*/
bool little_endian; /**< Endianness of the database.
*/
Opened_columns_list_p opened_columns; /**< List of opened columns.

843
src/obiview.c
View File

File diff suppressed because it is too large Load Diff

98
src/obiview.h
View File

@ -34,8 +34,6 @@
*/
#define VIEW_TYPE_MAX_LENGTH (1024) /**< The maximum length of the type name of a view.
*/
#define OBIVIEW_FILE_NAME "obiviews" /**< The default name of a view file.
*/
#define LINES_COLUMN_NAME "LINES" /**< The name of the column containing the line selections
* in all views.
*/
@ -56,45 +54,6 @@
*/
/**
* @brief Structure for an opened view.
*/
typedef struct Obiview {
OBIDMS_p dms; /**< A pointer on the DMS to which the view belongs.
*/
char name[OBIVIEW_NAME_MAX_LENGTH+1]; /**< Name of the view.
*/
char created_from[OBIVIEW_NAME_MAX_LENGTH+1]; /**< Name of the view from which that view was cloned if the view was cloned.
*/
char view_type[VIEW_TYPE_MAX_LENGTH+1]; /**< Type of the view if there is one.
* Types existing: NUC_SEQS_VIEW.
*/
bool read_only; /**< Whether the view is read-only or can be modified.
*/
OBIDMS_column_p line_selection; /**< A pointer on the column containing the line selection
* associated with the view if there is one.
* This line selection is read-only, and when a line from the view is read,
* it is this line selection that is used.
*/
OBIDMS_column_p new_line_selection; /**< A pointer on the column containing the new line selection being built
* to associate with the view, if there is one.
* When a line is selected with obi_select_line() or obi_select_lines(),
* it is recorded in this line selection.
*/
index_t line_count; /**< The number of lines in the view. Refers to the number of lines in each
* column of the view if line_selection is NULL, or to the line count of
* line_selection if it is not NULL.
*/
int column_count; /**< The number of columns in the view.
*/
OBIDMS_column_p columns[MAX_NB_OPENED_COLUMNS]; /**< Array of pointers on all the columns of the view.
*/
char comments[OBIVIEW_COMMENTS_MAX_LENGTH+1]; /**< Comments, additional informations on the view.
*/
} Obiview_t, *Obiview_p;
/**
* @brief Structure referencing a column by its name and its version.
*/
@ -112,8 +71,6 @@ typedef struct Column_reference {
* Once a view has been written in the view file, it can not be modified and can only be read.
*/
typedef struct Obiview_infos {
int view_number; /**< Number of the view in the view file.
*/
time_t creation_date; /**< Time at which the view was written in the view file.
*/
char name[OBIVIEW_NAME_MAX_LENGTH+1]; /**< Name of the view, used to identify it.
@ -138,7 +95,29 @@ typedef struct Obiview_infos {
} Obiview_infos_t, *Obiview_infos_p;
// TODO : Combine the common elements of the Obiview_infos and Obiview structures in one structure used by both?
/**
* @brief Structure for an opened view.
*/
typedef struct Obiview {
Obiview_infos_p infos; /**< A pointer on the mapped view informations.
*/
OBIDMS_p dms; /**< A pointer on the DMS to which the view belongs.
*/
bool read_only; /**< Whether the view is read-only or can be modified.
*/
OBIDMS_column_p line_selection; /**< A pointer on the column containing the line selection
* associated with the view if there is one.
* This line selection is read-only, and when a line from the view is read,
* it is this line selection that is used.
*/
OBIDMS_column_p new_line_selection; /**< A pointer on the column containing the new line selection being built
* to associate with the view, if there is one.
* When a line is selected with obi_select_line() or obi_select_lines(),
* it is recorded in this line selection.
*/
OBIDMS_column_p columns[MAX_NB_OPENED_COLUMNS]; /**< Array of pointers on all the columns of the view.
*/
} Obiview_t, *Obiview_p;
/**
@ -269,6 +248,37 @@ Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p v
Obiview_p obi_new_view_nuc_seqs_cloned_from_name(OBIDMS_p dms, const char* view_name, const char* view_to_clone_name, index_t* line_selection, const char* comments);
/**
* @brief Maps a view file and returns the mapped structure stored in it.
*
* @param dms A pointer on the OBIDMS.
* @param view_name The unique name identifying the view.
*
* @returns A pointer on the mapped view infos structure.
* @retval NULL if an error occurred.
*
* @since June 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
Obiview_infos_p obi_view_map_file(OBIDMS_p dms, const char* view_name);
/**
* @brief Unmaps a view file.
*
* @param dms A pointer on the OBIDMS.
* @param view_infos A pointer on the mapped view infos structure.
*
* @returns A value indicating the success of the operation.
* @retval 0 if the operation was successfully completed.
* @retval -1 if an error occurred.
*
* @since June 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_view_unmap_file(OBIDMS_p dms, Obiview_infos_p view_infos);
/**
* @brief Opens a view identified by its name stored in the view file.
*