Commit 1bfb9602 by Celine Mercier

obi import: rewriting a column now deletes the old one to save disk

space
parent c67d6689
......@@ -102,7 +102,7 @@ cdef extern from "obiview.h" nogil:
const_char_p comments,
bint create)
int obi_view_delete_column(Obiview_p view, const_char_p column_name)
int obi_view_delete_column(Obiview_p view, const_char_p column_name, bint delete_file)
OBIDMS_column_p obi_view_get_column(Obiview_p view, const_char_p column_name)
......
......@@ -22,7 +22,8 @@ cdef class View(OBIWrapper):
cdef inline Obiview_p pointer(self)
cpdef delete_column(self,
object column_name)
object column_name,
bint delete_file=*)
cpdef rename_column(self,
object current_name,
......
......@@ -227,7 +227,8 @@ cdef class View(OBIWrapper) :
cpdef delete_column(self,
object column_name) :
object column_name,
bint delete_file=False) :
cdef bytes column_name_b = tobytes(column_name)
......@@ -239,7 +240,7 @@ cdef class View(OBIWrapper) :
col.close()
# Remove the column from the view which closes the C structure
if obi_view_delete_column(self.pointer(), column_name_b) < 0 :
if obi_view_delete_column(self.pointer(), column_name_b, delete_file) < 0 :
raise RollbackException("Problem deleting column %s from a view",
bytes2str(column_name_b), self)
......@@ -307,7 +308,7 @@ cdef class View(OBIWrapper) :
new_column[i] = old_column[i]
# Remove old column from view
self.delete_column(column_name_b)
self.delete_column(column_name_b, delete_file=True)
# Rename new
new_column.name = column_name_b
......
......@@ -2380,11 +2380,12 @@ int obi_view_add_column(Obiview_p view,
}
int obi_view_delete_column(Obiview_p view, const char* column_name)
int obi_view_delete_column(Obiview_p view, const char* column_name, bool delete_file)
{
int i;
bool found;
OBIDMS_column_p column;
char* col_to_delete_path;
// Check that the view is not read-only
if (view->read_only)
......@@ -2406,8 +2407,31 @@ int obi_view_delete_column(Obiview_p view, const char* column_name)
obidebug(1, "\nError getting a column from the linked list of column pointers of a view when deleting a column from a view");
return -1;
}
// Keep column path if need to delete the file
if (delete_file)
{
col_to_delete_path = obi_column_full_path(view->dms, column->header->name, column->header->version);
if (col_to_delete_path == NULL)
{
obidebug(1, "\nError getting a column file path when deleting a column");
return -1;
}
}
obi_close_column(column);
// Delete file if needed
if (delete_file)
{
if (remove(col_to_delete_path) < 0)
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError deleting a column file when deleting unfinished columns: file %s", col_to_delete_path);
return -1;
}
free(col_to_delete_path);
}
view->columns = ll_delete(view->columns, i);
// TODO how do we check for error? NULL can be empty list
found = true;
......@@ -3047,7 +3071,7 @@ int obi_create_auto_id_column(Obiview_p view, const char* prefix)
// Delete old ID column if it exists
if (obi_view_get_column(view, ID_COLUMN) != NULL)
{
if (obi_view_delete_column(view, ID_COLUMN) < 0)
if (obi_view_delete_column(view, ID_COLUMN, false) < 0)
{
obidebug(1, "Error deleting an ID column to replace it in a view");
return -1;
......
......@@ -440,6 +440,7 @@ int obi_view_add_column(Obiview_p view,
*
* @param view A pointer on the view.
* @param column_name The name of the column that should be deleted from the view.
* @param delete_file Whether the column file should be deleted. Use carefully re: dependencies.
*
* @returns A value indicating the success of the operation.
* @retval 0 if the operation was successfully completed.
......@@ -448,7 +449,7 @@ int obi_view_add_column(Obiview_p view,
* @since February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_view_delete_column(Obiview_p view, const char* column_name);
int obi_view_delete_column(Obiview_p view, const char* column_name, bool delete_file);
/**
......
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