Commit 767d9c78 authored by Celine Mercier's avatar Celine Mercier

Reordered view functions for better coherence

parent 2566377e
......@@ -307,53 +307,6 @@ int prepare_to_get_value_from_column(Obiview_p view, index_t* line_nb_p)
*
**********************************************************************/
Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p view_to_clone, index_t* line_selection, const char* comments)
{
Obiview_p view;
if (view_to_clone != NULL)
{ // Check that the view to clone is already a NUC_SEQS view (TODO discuss possibility of transforming type of a view)
if (strcmp(view_to_clone->view_type, VIEW_TYPE_NUC_SEQS))
{
obi_set_errno(OBIVIEW_ERROR);
obidebug(1, "Trying to clone a non-NUC SEQS view to create a NUC SEQS view");
return NULL;
}
}
view = obi_new_view(dms, view_name, view_to_clone, line_selection, comments);
if (view== NULL)
return NULL;
strcpy(view->view_type, VIEW_TYPE_NUC_SEQS);
if (view_to_clone == NULL)
{
// Adding sequence column
if (obi_view_add_column(view, NUC_SEQUENCE_COLUMN, -1, OBI_SEQ, 0, 1, NUC_SEQUENCE_COLUMN, NUC_SEQUENCE_INDEXER, "Nucleotide sequences", true) < 0)
{
obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
return NULL;
}
// Adding id column
if (obi_view_add_column(view, ID_COLUMN, -1, OBI_STR, 0, 1, ID_COLUMN, ID_INDEXER, "Ids", true) < 0)
{
obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
return NULL;
}
// Adding definition column
if (obi_view_add_column(view, DEFINITION_COLUMN, -1, OBI_STR, 0, 1, DEFINITION_COLUMN, DEFINITION_INDEXER, "Definitions", true) < 0)
{
obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
return NULL;
}
}
return view;
}
Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_clone, index_t* line_selection, const char* comments)
{
Obiview_p view;
......@@ -504,6 +457,52 @@ Obiview_p obi_new_view_cloned_from_name(OBIDMS_p dms, const char* view_name, con
}
Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p view_to_clone, index_t* line_selection, const char* comments)
{
Obiview_p view;
if (view_to_clone != NULL)
{ // Check that the view to clone is already a NUC_SEQS view (TODO discuss possibility of transforming type of a view)
if (strcmp(view_to_clone->view_type, VIEW_TYPE_NUC_SEQS))
{
obi_set_errno(OBIVIEW_ERROR);
obidebug(1, "Trying to clone a non-NUC SEQS view to create a NUC SEQS view");
return NULL;
}
}
view = obi_new_view(dms, view_name, view_to_clone, line_selection, comments);
if (view== NULL)
return NULL;
strcpy(view->view_type, VIEW_TYPE_NUC_SEQS);
if (view_to_clone == NULL)
{
// Adding sequence column
if (obi_view_add_column(view, NUC_SEQUENCE_COLUMN, -1, OBI_SEQ, 0, 1, NUC_SEQUENCE_COLUMN, NUC_SEQUENCE_INDEXER, "Nucleotide sequences", true) < 0)
{
obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
return NULL;
}
// Adding id column
if (obi_view_add_column(view, ID_COLUMN, -1, OBI_STR, 0, 1, ID_COLUMN, ID_INDEXER, "Ids", true) < 0)
{
obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
return NULL;
}
// Adding definition column
if (obi_view_add_column(view, DEFINITION_COLUMN, -1, OBI_STR, 0, 1, DEFINITION_COLUMN, DEFINITION_INDEXER, "Definitions", true) < 0)
{
obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
return NULL;
}
}
return view;
}
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)
{
Obiview_p view;
......@@ -683,113 +682,6 @@ Obiview_p obi_open_view(OBIDMS_p dms, const char* view_name)
}
Obiviews_infos_all_p obi_read_view_infos(OBIDMS_p dms)
{
char* view_file_name;
int obiview_file_descriptor;
size_t header_size;
Obiviews_header_p header;
Obiview_infos_p view_infos;
Obiviews_infos_all_p views;
view_file_name = build_obiview_file_name();
if (view_file_name == NULL)
return NULL;
// Open view file, read header size and map header and views
obiview_file_descriptor = openat(dms->dir_fd, view_file_name, O_RDWR, 0777);
if (obiview_file_descriptor < 0)
{ // No views yet
free(view_file_name);
return NULL;
}
free(view_file_name);
// Read the header size
if (read(obiview_file_descriptor, &header_size, sizeof(size_t)) < ((ssize_t) sizeof(size_t)))
{
obi_set_errno(OBIVIEW_ERROR);
obidebug(1, "\nError reading the header size of an obiview file (trying to open a view when there are none?)");
close(obiview_file_descriptor);
return NULL;
}
// Map the header
header = mmap(NULL,
header_size,
PROT_READ | PROT_WRITE,
MAP_SHARED,
obiview_file_descriptor,
0
);
if (header == MAP_FAILED)
{
obi_set_errno(OBIVIEW_ERROR);
obidebug(1, "\nError mmapping an obiview file header");
close(obiview_file_descriptor);
return NULL;
}
// Map the views
view_infos = mmap(NULL,
header->views_size,
PROT_READ | PROT_WRITE,
MAP_SHARED,
obiview_file_descriptor,
header_size
);
if (view_infos == MAP_FAILED)
{
obi_set_errno(OBIVIEW_ERROR);
obidebug(1, "\nError mmapping the views from an obiview file");
munmap(header, header_size);
close(obiview_file_descriptor);
return NULL;
}
views = (Obiviews_infos_all_p) malloc(sizeof(Obiviews_infos_all_t));
if (views == NULL)
{
obi_set_errno(OBIVIEW_ERROR);
obidebug(1, "\nError mmapping the views from an obiview file");
munmap(view_infos, header->views_size);
munmap(header, header_size);
close(obiview_file_descriptor);
return NULL;
}
views->header = header;
views->view_infos = view_infos;
close(obiview_file_descriptor);
return views;
}
int obi_close_view_infos(Obiviews_infos_all_p views)
{
if (munmap(views->view_infos, (views->header)->views_size) < 0)
{
obi_set_errno(OBIVIEW_ERROR);
obidebug(1, "\nError unmapping the views of an obiview file");
free(views);
return -1;
}
if (munmap(views->header, (views->header)->header_size) < 0)
{
obi_set_errno(OBIVIEW_ERROR);
obidebug(1, "\nError unmapping the header of an obiview file");
free(views);
return -1;
}
free(views);
return 0;
}
int obi_view_add_column(Obiview_p view,
const char* column_name,
obiversion_t version_number,
......@@ -946,6 +838,32 @@ int obi_view_delete_column(Obiview_p view, const char* column_name)
}
OBIDMS_column_p obi_view_get_column(Obiview_p view, const char* column_name)
{
int i;
for (i=0; i<(view->column_count); i++)
{
if (!(strcmp((((view->columns)[i])->header)->name, column_name)))
return (view->columns)[i];
}
return NULL;
}
OBIDMS_column_p* obi_view_get_pointer_on_column_in_view(Obiview_p view, const char* column_name)
{
int i;
for (i=0; i<(view->column_count); i++)
{
if (!(strcmp((((view->columns)[i])->header)->name, column_name)))
return ((view->columns)+i);
}
return NULL;
}
int obi_select_line(Obiview_p view, index_t line_nb)
{
// Check that the view is not read-only
......@@ -1038,32 +956,6 @@ int obi_view_update_lines(Obiview_p view, index_t line_count)
}
OBIDMS_column_p obi_view_get_column(Obiview_p view, const char* column_name)
{
int i;
for (i=0; i<(view->column_count); i++)
{
if (!(strcmp((((view->columns)[i])->header)->name, column_name)))
return (view->columns)[i];
}
return NULL;
}
OBIDMS_column_p* obi_view_get_pointer_on_column_in_view(Obiview_p view, const char* column_name)
{
int i;
for (i=0; i<(view->column_count); i++)
{
if (!(strcmp((((view->columns)[i])->header)->name, column_name)))
return ((view->columns)+i);
}
return NULL;
}
int obi_save_view(Obiview_p view)
{
int i;
......@@ -1257,6 +1149,113 @@ int obi_save_and_close_view(Obiview_p view)
}
Obiviews_infos_all_p obi_read_view_infos(OBIDMS_p dms)
{
char* view_file_name;
int obiview_file_descriptor;
size_t header_size;
Obiviews_header_p header;
Obiview_infos_p view_infos;
Obiviews_infos_all_p views;
view_file_name = build_obiview_file_name();
if (view_file_name == NULL)
return NULL;
// Open view file, read header size and map header and views
obiview_file_descriptor = openat(dms->dir_fd, view_file_name, O_RDWR, 0777);
if (obiview_file_descriptor < 0)
{ // No views yet
free(view_file_name);
return NULL;
}
free(view_file_name);
// Read the header size
if (read(obiview_file_descriptor, &header_size, sizeof(size_t)) < ((ssize_t) sizeof(size_t)))
{
obi_set_errno(OBIVIEW_ERROR);
obidebug(1, "\nError reading the header size of an obiview file (trying to open a view when there are none?)");
close(obiview_file_descriptor);
return NULL;
}
// Map the header
header = mmap(NULL,
header_size,
PROT_READ | PROT_WRITE,
MAP_SHARED,
obiview_file_descriptor,
0
);
if (header == MAP_FAILED)
{
obi_set_errno(OBIVIEW_ERROR);
obidebug(1, "\nError mmapping an obiview file header");
close(obiview_file_descriptor);
return NULL;
}
// Map the views
view_infos = mmap(NULL,
header->views_size,
PROT_READ | PROT_WRITE,
MAP_SHARED,
obiview_file_descriptor,
header_size
);
if (view_infos == MAP_FAILED)
{
obi_set_errno(OBIVIEW_ERROR);
obidebug(1, "\nError mmapping the views from an obiview file");
munmap(header, header_size);
close(obiview_file_descriptor);
return NULL;
}
views = (Obiviews_infos_all_p) malloc(sizeof(Obiviews_infos_all_t));
if (views == NULL)
{
obi_set_errno(OBIVIEW_ERROR);
obidebug(1, "\nError mmapping the views from an obiview file");
munmap(view_infos, header->views_size);
munmap(header, header_size);
close(obiview_file_descriptor);
return NULL;
}
views->header = header;
views->view_infos = view_infos;
close(obiview_file_descriptor);
return views;
}
int obi_close_view_infos(Obiviews_infos_all_p views)
{
if (munmap(views->view_infos, (views->header)->views_size) < 0)
{
obi_set_errno(OBIVIEW_ERROR);
obidebug(1, "\nError unmapping the views of an obiview file");
free(views);
return -1;
}
if (munmap(views->header, (views->header)->header_size) < 0)
{
obi_set_errno(OBIVIEW_ERROR);
obidebug(1, "\nError unmapping the header of an obiview file");
free(views);
return -1;
}
free(views);
return 0;
}
/*********** FOR BOOL COLUMNS ***********/
int obi_column_set_obibool_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, obibool_t value)
......
......@@ -291,35 +291,6 @@ Obiview_p obi_new_view_nuc_seqs_cloned_from_name(OBIDMS_p dms, const char* view_
Obiview_p obi_open_view(OBIDMS_p dms, const char* view_name);
/**
* @brief Opens the structure containing all the informations written in the view file.
*
* @param dms A pointer on the OBIDMS to which the view file belongs.
*
* @returns A pointer on the view informations structure.
* @retval NULL if an error occurred.
*
* @since February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
Obiviews_infos_all_p obi_read_view_infos(OBIDMS_p dms);
/**
* @brief Closes the structure containing all the informations written in the view file.
*
* @param views A pointer on the view informations 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 February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_close_view_infos(Obiviews_infos_all_p views);
/**
* @brief Adds a column to a view.
*
......@@ -355,6 +326,24 @@ int obi_view_add_column(Obiview_p view,
bool create);
/**
* @brief Clones a column in the context of a view.
*
* Clones with the right line selection and replaces the cloned columns with the new ones in the view.
* If there is a line selection, all columns have to be cloned, otherwise only the column of interest is cloned.
*
* @param view A pointer on the view.
* @param column_name The name of the column in the view that should be cloned.
*
* @returns A pointer on the new column.
* @retval NULL if an error occurred.
*
* @since February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
OBIDMS_column_p obi_view_clone_column(Obiview_p view, const char* column_name);
/**
* @brief Deletes a column from a view.
*
......@@ -373,6 +362,38 @@ int obi_view_add_column(Obiview_p view,
int obi_view_delete_column(Obiview_p view, const char* column_name);
/**
* @brief Gets the pointer on a column from its name in a view.
*
* @param view A pointer on the view.
* @param column_name The name of the column in the view.
*
* @returns A pointer on the column.
* @retval NULL if an error occurred.
*
* @since February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
OBIDMS_column_p obi_view_get_column(Obiview_p view, const char* column_name);
/**
* @brief Gets the pointer on the pointer on a column from its name in a view.
*
* Note: This is used to replace old cloned columns with new ones in views in layers above the C layer.
*
* @param view A pointer on the view.
* @param column_name The name of the column in the view.
*
* @returns A pointer on the pointer on the column.
* @retval NULL if an error occurred.
*
* @since February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
OBIDMS_column_p* obi_view_get_pointer_on_column_in_view(Obiview_p view, const char* column_name);
/**
* @brief Selects a line in the context of a view.
*
......@@ -439,61 +460,43 @@ int obi_view_update_lines(Obiview_p view, index_t line_count);
/**
* @brief Clones a column in the context of a view.
*
* Clones with the right line selection and replaces the cloned columns with the new ones in the view.
* If there is a line selection, all columns have to be cloned, otherwise only the column of interest is cloned.
*
* @param view A pointer on the view.
* @param column_name The name of the column in the view that should be cloned.
* @brief Saves a view, writing it in the view file.
*
* @returns A pointer on the new column.
* @retval NULL if an error occurred.
* The view is written at the end of the view file, following the latest written view.
*
* @since February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
OBIDMS_column_p obi_view_clone_column(Obiview_p view, const char* column_name);
/**
* @brief Gets the pointer on a column from its name in a view.
* @warning The view must be writable.
*
* @param view A pointer on the view.
* @param column_name The name of the column in the view.
*
* @returns A pointer on the column.
* @retval NULL if an error occurred.
* @returns A value indicating the success of the operation.
* @retval 0 if the operation was successfully completed.
* @retval -1 if an error occurred.
*
* @since February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
OBIDMS_column_p obi_view_get_column(Obiview_p view, const char* column_name);
int obi_save_view(Obiview_p view);
/**
* @brief Gets the pointer on the pointer on a column from its name in a view.
* @brief Closes an opened view.
*
* Note: This is used to replace old cloned columns with new ones in views in layers above the C layer.
* @warning Use obi_save_and_close_view() to automatically save the view if it's not already saved in the view file.
*
* @param view A pointer on the view.
* @param column_name The name of the column in the view.
*
* @returns A pointer on the pointer on the column.
* @retval NULL if an error occurred.
* @returns A value indicating the success of the operation.
* @retval 0 if the operation was successfully completed.
* @retval -1 if an error occurred.
*
* @since February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
OBIDMS_column_p* obi_view_get_pointer_on_column_in_view(Obiview_p view, const char* column_name);
int obi_close_view(Obiview_p view);
/**
* @brief Saves a view, writing it in the view file.
*
* The view is written at the end of the view file, following the latest written view.
*
* @warning The view must be writable.
* @brief Closes an opened view, and saves it if it is not read-only (meaning it is not already saved in the view file).
*
* @param view A pointer on the view.
*
......@@ -504,30 +507,27 @@ OBIDMS_column_p* obi_view_get_pointer_on_column_in_view(Obiview_p view, const ch
* @since February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_save_view(Obiview_p view);
int obi_save_and_close_view(Obiview_p view);
/**
* @brief Closes an opened view.
*
* @warning Use obi_save_and_close_view() to automatically save the view if it's not already saved in the view file.
* @brief Opens the structure containing all the informations written in the view file.
*
* @param view A pointer on the view.
* @param dms A pointer on the OBIDMS to which the view file belongs.
*
* @returns A value indicating the success of the operation.
* @retval 0 if the operation was successfully completed.
* @retval -1 if an error occurred.
* @returns A pointer on the view informations structure.
* @retval NULL if an error occurred.
*
* @since February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_close_view(Obiview_p view);
Obiviews_infos_all_p obi_read_view_infos(OBIDMS_p dms);
/**
* @brief Closes an opened view, and saves it if it is not read-only (meaning it is not already saved in the view file).
* @brief Closes the structure containing all the informations written in the view file.
*
* @param view A pointer on the view.
* @param views A pointer on the view informations structure.
*
* @returns A value indicating the success of the operation.
* @retval 0 if the operation was successfully completed.
......@@ -536,7 +536,7 @@ int obi_close_view(Obiview_p view);
* @since February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_save_and_close_view(Obiview_p view);
int obi_close_view_infos(Obiviews_infos_all_p views);
// TODO in following functions would it be better to use column names instead of column pointers?
......
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