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When retrieving the header of a column, the version number of the column

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wanted can now be provided.
This commit is contained in:
Celine Mercier
2015-11-10 13:30:10 +01:00
parent 8ce4f264aa
commit 410e2e02a0
4 changed files with 17 additions and 11 deletions
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4
python/obitools3/obidms/_obidms.pyx
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@ -95,7 +95,7 @@ cdef class OBIDMS :
column_name = entry.stem column_name = entry.stem
column_name_b = str2bytes(column_name) column_name_b = str2bytes(column_name)
dms[column_name] = {} dms[column_name] = {}
header = obi_column_get_header_from_name(self.pointer, column_name_b) header = obi_column_get_header_from_name(self.pointer, column_name_b, -1)
data_type = bytes2str(name_data_type(header.data_type)) data_type = bytes2str(name_data_type(header.data_type))
line_count = header.line_count line_count = header.line_count
creation_date = bytes2str(obi_column_format_date(header.creation_date)) creation_date = bytes2str(obi_column_format_date(header.creation_date))
@ -137,7 +137,7 @@ cdef class OBIDMS :
# Get the header of the latest version of the column if # Get the header of the latest version of the column if
# some needed informations are not provided # some needed informations are not provided
if ((not data_type or not nb_elements_per_line) and not create) : if ((not data_type or not nb_elements_per_line) and not create) :
header = obi_column_get_header_from_name(self.pointer, column_name_b) header = obi_column_get_header_from_name(self.pointer, column_name_b, version_number)
# Get the data type if not provided # Get the data type if not provided
if not data_type : if not data_type :

3
python/obitools3/obidms/capi/obidmscolumn.pxd
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@ -63,7 +63,8 @@ cdef extern from "obidmscolumn.h" nogil:
const_char_p column_name) const_char_p column_name)
OBIDMS_column_header_p obi_column_get_header_from_name(OBIDMS_p dms, OBIDMS_column_header_p obi_column_get_header_from_name(OBIDMS_p dms,
const_char_p column_name) const_char_p column_name,
obiversion_t version_number)
int obi_unmap_header(OBIDMS_column_header_p header) int obi_unmap_header(OBIDMS_column_header_p header)

8
src/obidmscolumn.c
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@ -1185,14 +1185,13 @@ void obi_ini_to_NA_values(OBIDMS_column_p column,
} }
OBIDMS_column_header_p obi_column_get_header_from_name(OBIDMS_p dms, const char* column_name) // TODO ADD VERSION ARGUMENT OBIDMS_column_header_p obi_column_get_header_from_name(OBIDMS_p dms, const char* column_name, obiversion_t version_number)
{ {
OBIDMS_column_header_p header; OBIDMS_column_header_p header;
OBIDMS_column_directory_p column_directory; OBIDMS_column_directory_p column_directory;
char* column_file_name; char* column_file_name;
int column_file_descriptor; int column_file_descriptor;
size_t header_size; size_t header_size;
obiversion_t version_number;
// Get the column directory structure associated to the column // Get the column directory structure associated to the column
column_directory = obi_open_column_directory(dms, column_name); column_directory = obi_open_column_directory(dms, column_name);
@ -1202,13 +1201,16 @@ OBIDMS_column_header_p obi_column_get_header_from_name(OBIDMS_p dms, const char*
return NULL; return NULL;
} }
// Get the latest version number // Get the latest version number if not provided
if (version_number < 0)
{
version_number = obi_get_latest_version_number(column_directory); version_number = obi_get_latest_version_number(column_directory);
if (version_number < 0) if (version_number < 0)
{ {
obidebug(1, "\nError getting the latest version number in a column directory"); obidebug(1, "\nError getting the latest version number in a column directory");
return NULL; return NULL;
} }
}
// Get the column file name // Get the column file name
column_file_name = build_column_file_name(column_name, version_number); column_file_name = build_column_file_name(column_name, version_number);

7
src/obidmscolumn.h
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@ -169,6 +169,7 @@ size_t obi_get_platform_header_size();
* @param nb_elements_per_line The number of elements per line. * @param nb_elements_per_line The number of elements per line.
* @param elements_names The names of the elements with ';' as separator. * @param elements_names The names of the elements with ';' as separator.
* @param array_name The name of the array if there is one associated with the column. * @param array_name The name of the array if there is one associated with the column.
* @param comments Optional comments associated with the column.
* *
* @returns A pointer on the newly created column structure. * @returns A pointer on the newly created column structure.
* @retval NULL if an error occurred. * @retval NULL if an error occurred.
@ -287,7 +288,7 @@ int obi_truncate_and_close_column(OBIDMS_column_p column);
* @since August 2015 * @since August 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org) * @author Celine Mercier (celine.mercier@metabarcoding.org)
*/ */
void obi_ini_to_NA_values(OBIDMS_column_p column, index_t first_line_nb, index_t nb_lines); // TO make private? void obi_ini_to_NA_values(OBIDMS_column_p column, index_t first_line_nb, index_t nb_lines); // TODO make private?
/** /**
@ -297,6 +298,8 @@ void obi_ini_to_NA_values(OBIDMS_column_p column, index_t first_line_nb, index_t
* *
* @param dms A pointer on an OBIDMS. * @param dms A pointer on an OBIDMS.
* @param column_name The name of an OBIDMS column. * @param column_name The name of an OBIDMS column.
* @param version_number The version of the column from which the header should be
* retrieved (-1: latest version).
* *
* @returns A pointer on the mmapped header of the column. * @returns A pointer on the mmapped header of the column.
* @retval NULL if an error occurred. * @retval NULL if an error occurred.
@ -304,7 +307,7 @@ void obi_ini_to_NA_values(OBIDMS_column_p column, index_t first_line_nb, index_t
* @since October 2015 * @since October 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org) * @author Celine Mercier (celine.mercier@metabarcoding.org)
*/ */
OBIDMS_column_header_p obi_column_get_header_from_name(OBIDMS_p dms, const char* column_name); OBIDMS_column_header_p obi_column_get_header_from_name(OBIDMS_p dms, const char* column_name, obiversion_t version_number);
/** /**