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Functions to truncate and/or close a column

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This commit is contained in:
Celine Mercier
2015-08-26 17:01:54 +02:00
parent fdc3b96beb
commit 48d10ea17c
9 changed files with 193 additions and 9 deletions
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1
python/obitools3/obidms/obidmscolumn/capidmscolumn.pxd
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@ -34,6 +34,7 @@ cdef extern from "obidmscolumn.h" nogil:
int obi_close_column(OBIDMS_column_p column)
OBIType_t obi_column_get_data_type_from_name(OBIDMS_p dms, const char* column_name)
OBIDMS_column_p obi_clone_column(OBIDMS_p dms, const char* column_name, obiversion_t version_number, bint clone_data)
int obi_truncate_and_close_column(OBIDMS_column_p column)
cdef class OBIDMS_column:

6
python/obitools3/obidms/obidmscolumn/capidmscolumn.pyx
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@ -65,11 +65,7 @@ cdef class OBIDMS_column:
def get_data_type(self):
return self.data_type
# def __del__(self):
# if obi_close_column(self.pointer) != 0 :
# raise Exception("Problem closing a column")
@staticmethod
def open(dms_name, column_name,
create=False, clone=False, clone_data=True,

11
python/obitools3/obidms/obidmscolumn/obidmscolumn_bool/capidmscolumn_bool.pyx
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@ -13,11 +13,20 @@ cdef class OBIDMS_column_bool_read(OBIDMS_column_bool) :
def set_item(self, line_nb, element_name, value):
raise Exception('Column is read-only')
def close(self):
if obi_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")
cdef class OBIDMS_column_bool_writable(OBIDMS_column_bool) :
def set_item(self, line_nb, element_name, value):
return obi_column_set_bool_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'), value)
def close(self):
if obi_truncate_and_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")

9
python/obitools3/obidms/obidmscolumn/obidmscolumn_char/capidmscolumn_char.pyx
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@ -8,16 +8,25 @@ cdef class OBIDMS_column_char(OBIDMS_column) :
def get_item(self, line_nb, element_name):
return (obi_column_get_char_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'))).decode(encoding='utf-8')[:1]
cdef class OBIDMS_column_char_read(OBIDMS_column_char) :
def set_item(self, line_nb, element_name, value):
raise Exception('Column is read-only')
def close(self):
if obi_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")
cdef class OBIDMS_column_char_writable(OBIDMS_column_char) :
def set_item(self, line_nb, element_name, value):
return obi_column_set_char_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'), value.encode('utf-8'))
def close(self):
if obi_truncate_and_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")

9
python/obitools3/obidms/obidmscolumn/obidmscolumn_float/capidmscolumn_float.pyx
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@ -8,15 +8,24 @@ cdef class OBIDMS_column_float(OBIDMS_column) :
def get_item(self, line_nb, element_name):
return obi_column_get_float_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'))
cdef class OBIDMS_column_float_read(OBIDMS_column_float) :
def set_item(self, line_nb, element_name, value):
raise Exception('Column is read-only')
def close(self):
if obi_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")
cdef class OBIDMS_column_float_writable(OBIDMS_column_float) :
def set_item(self, line_nb, element_name, value):
return obi_column_set_float_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'), value)
def close(self):
if obi_truncate_and_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")

9
python/obitools3/obidms/obidmscolumn/obidmscolumn_idx/capidmscolumn_idx.pyx
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@ -7,15 +7,24 @@ cdef class OBIDMS_column_idx(OBIDMS_column) :
def get_item(self, line_nb, element_name):
return obi_column_get_idx_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'))
cdef class OBIDMS_column_idx_read(OBIDMS_column_idx) :
def set_item(self, line_nb, element_name, value):
raise Exception('Column is read-only')
def close(self):
if obi_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")
cdef class OBIDMS_column_idx_writable(OBIDMS_column_idx) :
def set_item(self, line_nb, element_name, value):
return obi_column_set_idx_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'), value)
def close(self):
if obi_truncate_and_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")

10
python/obitools3/obidms/obidmscolumn/obidmscolumn_int/capidmscolumn_int.pyx
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@ -13,10 +13,18 @@ cdef class OBIDMS_column_int_read(OBIDMS_column_int) :
def set_item(self, line_nb, element_name, value):
raise Exception('Column is read-only')
def close(self):
if obi_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")
cdef class OBIDMS_column_int_writable(OBIDMS_column_int) :
def set_item(self, line_nb, element_name, value):
return obi_column_set_int_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'), value)
def close(self):
if obi_truncate_and_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")

119
src/obidmscolumn.c
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@ -948,15 +948,130 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p dms, const char* column_name, obiversi
(new_column->header)->lines_used = nb_lines;
}
// close column_to_clone TODO
return new_column;
}
int obi_close_column(OBIDMS_column_p column)
{
//munmap? TODO
//truncate to lines used TODO
size_t data_size;
// Munmap data
data_size = (column->header)->line_count * (column->header)->nb_elements_per_line * sizeof((column->header)->data_type);
if (munmap(column->data, data_size) < 0)
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError munmapping column data");
return -1;
}
// Munmap header
if (munmap(column->header, (column->header)->header_size) < 0)
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError munmapping a column header");
return -1;
}
free(column);
return 0;
}
int obi_truncate_column_to_lines_used(OBIDMS_column_p column)
{
size_t file_size;
size_t data_size;
int column_dir_file_descriptor;
int column_file_descriptor;
char* column_file_name;
// Get the file descriptor associated to the column directory
column_dir_file_descriptor = dirfd((column->column_directory)->directory);
if (column_dir_file_descriptor < 0)
{
obi_set_errno(OBICOLDIR_UNKNOWN_ERROR);
obidebug(1, "\nError getting the file descriptor for a column directory");
return -1;
}
// Get the column file name
column_file_name = build_column_file_name((column->header)->name, (column->header)->version);
if (column_file_name == NULL)
{
return -1;
}
// Open the column file
column_file_descriptor = openat(column_dir_file_descriptor, column_file_name, O_RDWR | O_CREAT);
if (column_file_descriptor < 0)
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
free(column_file_name);
return -1;
}
// Unmap the data before truncating the file
data_size = (column->header)->line_count * (column->header)->nb_elements_per_line * sizeof((column->header)->data_type);
if (munmap(column->data, data_size) < 0)
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError munmapping the data of a column before truncating");
free(column_file_name);
close(column_file_descriptor);
return -1;
}
// Truncate the column file at the number of lines used
data_size = (column->header)->lines_used * (column->header)->nb_elements_per_line * sizeof((column->header)->data_type);
file_size = (column->header)->header_size + data_size;
if (ftruncate(column_file_descriptor, file_size) < 0)
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError truncating a column file at the number of lines used");
free(column_file_name);
close(column_file_descriptor);
return -1;
}
// Remap the data
column->data = mmap(NULL,
data_size,
PROT_READ | PROT_WRITE,
MAP_SHARED,
column_file_descriptor,
(column->header)->header_size
);
if (column->data == MAP_FAILED)
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError re-mmapping the data of a column after truncating");
free(column_file_name);
close(column_file_descriptor);
return -1;
}
// Set line_count to lines_used
(column->header)->line_count = (column->header)->lines_used;
free(column_file_name);
close(column_file_descriptor);
return 0;
}
int obi_truncate_and_close_column(OBIDMS_column_p column)
{
if (obi_truncate_column_to_lines_used(column) < 0)
return -1;
if (obi_close_column(column) < 0)
return -1;
return 0;
}

28
src/obidmscolumn.h
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@ -191,6 +191,34 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p dms, const char* column_name, obiversi
int obi_close_column(OBIDMS_column_p column);
/**
* @brief Truncates a column file to the number of lines used.
*
* @param column a pointer on an OBIDMS column
*
* @return 0 if the operation was successfully completed
* @return -1 if an error occurred
*
* @since August 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_truncate_column_to_lines_used(OBIDMS_column_p column);
/**
* @brief Truncates a column file to the number of lines used and closes it.
*
* @param column a pointer on an OBIDMS column
*
* @return 0 if the operation was successfully completed
* @return -1 if an error occurred
*
* @since August 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_truncate_and_close_column(OBIDMS_column_p column);
/**
* @brief Sets the 'writable' header attribute of an OBIDMS column to False.
*