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C and Cython: fixed and improved the associated columns system

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This commit is contained in:
Celine Mercier
2020-07-26 17:39:29 +02:00
parent e6feac93fe
commit e28507639a
4 changed files with 118 additions and 25 deletions
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47
python/obitools3/dms/column/column.pyx
View File

@ -40,7 +40,8 @@ from obitools3.utils cimport tobytes, \
from obitools3.dms.column import typed_column
from libc.stdlib cimport free
from libc.string cimport strcpy
import importlib
import inspect
import pkgutil
@ -97,6 +98,7 @@ cdef class Column(OBIWrapper) :
object alias=b""):
# TODO indexer_name?
cdef Column column
cdef bytes column_name_b = tobytes(column_name)
cdef bytes alias_b = tobytes(alias)
cdef bytes comments_b = str2bytes(json.dumps(bytes2str_object(comments)))
@ -132,13 +134,14 @@ cdef class Column(OBIWrapper) :
raise RuntimeError("Cannot create column %s in view %s: trying to create quality column but no NUC_SEQ column to associate it with in the view" % (bytes2str(column_name_b),
bytes2str(view.name)))
associated_column_name_b = NUC_SEQUENCE_COLUMN
associated_column_version = view[NUC_SEQUENCE_COLUMN].version
associated_column_version = view[NUC_SEQUENCE_COLUMN].version
elif column_name == REVERSE_QUALITY_COLUMN:
if REVERSE_SEQUENCE_COLUMN not in view:
raise RuntimeError("Cannot create column %s in view %s: trying to create reverse quality column but no REVERSE_SEQUENCE column to associate it with in the view" % (bytes2str(column_name_b),
bytes2str(view.name)))
associated_column_name_b = REVERSE_SEQUENCE_COLUMN
associated_column_version = view[REVERSE_SEQUENCE_COLUMN].version
if (obi_view_add_column(view = view.pointer(),
column_name = column_name_b,
@ -158,8 +161,19 @@ cdef class Column(OBIWrapper) :
create = True)<0):
raise RuntimeError("Cannot create column %s in view %s" % (bytes2str(column_name_b),
bytes2str(view.name)))
return Column.open(view, alias_b)
column = Column.open(view, alias_b)
# Automatically associate nuc sequence column to quality column if necessary
if data_type == OBI_QUAL:
if column_name == QUALITY_COLUMN:
view[NUC_SEQUENCE_COLUMN].associated_column_name = column.name
view[NUC_SEQUENCE_COLUMN].associated_column_version = column.version
elif column_name == REVERSE_QUALITY_COLUMN:
view[REVERSE_SEQUENCE_COLUMN].associated_column_name = column.name
view[REVERSE_SEQUENCE_COLUMN].associated_column_version = column.version
return column
@staticmethod
@ -407,6 +421,31 @@ cdef class Column(OBIWrapper) :
raise OBIDeactivatedInstanceError()
return obi_format_date(self.pointer().header.creation_date)
# associated_column name property getter and setter
@property
def associated_column_name(self):
if not self.active() :
raise OBIDeactivatedInstanceError()
return self.pointer().header.associated_column.column_name
@associated_column_name.setter
def associated_column_name(self, object new_name):
strcpy(self.pointer().header.associated_column.column_name, tobytes(new_name))
# associated_column version property getter and setter
@property
def associated_column_version(self):
if not self.active() :
raise OBIDeactivatedInstanceError()
return self.pointer().header.associated_column.version
@associated_column_version.setter
def associated_column_version(self, int new_version):
self.pointer().header.associated_column.version = new_version
# comments property getter
@property
def comments(self):

14
src/obidmscolumn.c
View File

@ -1312,19 +1312,10 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
return NULL;
}
// Store the associated column reference if needed // TODO discuss cases
if (data_type == OBI_QUAL)
// Store the associated column reference if needed
if ((associated_column_name != NULL) && (*associated_column_name != '\0'))
{
if ((associated_column_name == NULL) || (*associated_column_name == '\0'))
{
obidebug(1, "\nError: The name of the associated column when creating a new column is NULL");
munmap(new_column->header, header_size);
close(column_file_descriptor);
free(new_column);
return NULL;
}
strcpy((header->associated_column).column_name, associated_column_name);
if (associated_column_version == -1)
{
obidebug(1, "\nError: The version of the associated column when creating a new column is not defined");
@ -1336,6 +1327,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
(header->associated_column).version = associated_column_version;
}
// If the data type is OBI_STR, OBI_SEQ or OBI_QUAL, the associated obi_indexer is opened or created
if ((returned_data_type == OBI_STR) || (returned_data_type == OBI_SEQ) || (returned_data_type == OBI_QUAL) || tuples)
{

78
src/obiview.c
View File

@ -254,11 +254,15 @@ static int update_lines(Obiview_p view, index_t line_count);
/**
* @brief Internal function to clone a column in the context of a view.
*
* Used to edit a closed column.
*
* 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.
* @param clone_associated Whether to clone the associated column
* (should always be true except when calling from the function itself to avoid infinite recursion).
*
* @returns A pointer on the new column.
* @retval NULL if an error occurred.
@ -266,7 +270,7 @@ static int update_lines(Obiview_p view, index_t line_count);
* @since February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
static OBIDMS_column_p clone_column_in_view(Obiview_p view, const char* column_name);
static OBIDMS_column_p clone_column_in_view(Obiview_p view, const char* column_name, bool clone_associated);
/**
@ -845,7 +849,7 @@ static int update_lines(Obiview_p view, index_t line_count)
// Clone the column first if needed
if (!(column->writable))
{
column = clone_column_in_view(view, (((view->infos)->column_references)[i]).alias);
column = clone_column_in_view(view, (((view->infos)->column_references)[i]).alias, true);
if (column == NULL)
{
obidebug(1, "\nError cloning a column in a view when updating its line count");
@ -870,12 +874,14 @@ static int update_lines(Obiview_p view, index_t line_count)
}
static OBIDMS_column_p clone_column_in_view(Obiview_p view, const char* column_name)
static OBIDMS_column_p clone_column_in_view(Obiview_p view, const char* column_name, bool clone_associated)
{
int i;
int i, j;
OBIDMS_column_p column = NULL;
OBIDMS_column_p new_column = NULL;
OBIDMS_column_p column_buffer;
OBIDMS_column_p associated_cloned_column = NULL;
char* associated_column_alias = NULL;
// Check that the view is not read-only
if (view->read_only)
@ -916,11 +922,62 @@ static OBIDMS_column_p clone_column_in_view(Obiview_p view, const char* column_n
return NULL;
}
// Look for associated column to clone and reassociate
if ((column_buffer->header->associated_column).column_name[0] != '\0')
{
// Get the associated column alias
j=0;
while (((strcmp((((view->infos)->column_references)[j]).column_refs.column_name, (column_buffer->header->associated_column).column_name)) ||
((((view->infos)->column_references)[j]).column_refs.version != (column_buffer->header->associated_column).version)) &&
j<(view->infos)->column_count) // TODO function for that
j++;
if (j == (view->infos)->column_count) // not found
{
obi_set_errno(OBIVIEW_ERROR);
obidebug(1, "\nCould not find associated column when cloning a column for editing");
return NULL;
}
// No line selection: only this column is cloned, clone and reassociate the associated column
if ((view->line_selection == NULL) && clone_associated)
{
associated_column_alias = (((view->infos)->column_references)[j]).alias;
// Clone the associated column
associated_cloned_column = clone_column_in_view(view, associated_column_alias, false);
// Reassociate both ways
strcpy((associated_cloned_column->header->associated_column).column_name, column->header->name);
(associated_cloned_column->header->associated_column).version = column->header->version;
strcpy((column->header->associated_column).column_name, associated_cloned_column->header->name);
(column->header->associated_column).version = associated_cloned_column->header->version;
}
else
{
// Line selection: all columns are cloned, check if associated column has been cloned previously (it precedes this one in the list) to reassociate
if (j < i)
{
// Get pointer to associated column
associated_cloned_column = *((OBIDMS_column_p*)ll_get(view->columns, j));
if (associated_cloned_column == NULL)
{
obi_set_errno(OBIVIEW_ERROR);
obidebug(1, "\nError getting a column to clone from the linked list of column pointers of a view");
return NULL;
}
// Reassociate both ways
strcpy((associated_cloned_column->header->associated_column).column_name, column->header->name);
(associated_cloned_column->header->associated_column).version = column->header->version;
strcpy((column->header->associated_column).column_name, associated_cloned_column->header->name);
(column->header->associated_column).version = associated_cloned_column->header->version;
}
}
}
// Close old cloned column
obi_close_column(column_buffer);
if (!strcmp((((view->infos)->column_references)[i]).alias, column_name))
// Found the column to return
// Get the column to return
new_column = column;
}
}
@ -1193,7 +1250,7 @@ static int prepare_to_set_value_in_column(Obiview_p view, OBIDMS_column_p* colum
return -1;
}
(*column_pp) = clone_column_in_view(view, column_name);
(*column_pp) = clone_column_in_view(view, column_name, true);
if ((*column_pp) == NULL)
{
obidebug(1, "\nError trying to clone a column to modify it");
@ -1844,6 +1901,7 @@ Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p v
{
Obiview_p view;
OBIDMS_column_p associated_nuc_column;
OBIDMS_column_p associated_qual_column;
int nb_predicates;
if (view_to_clone != NULL)
@ -1896,6 +1954,10 @@ Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p v
obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
return NULL;
}
// Associating both ways: associating nuc sequences column to quality column
associated_qual_column = obi_view_get_column(view, QUALITY_COLUMN);
strcpy((associated_nuc_column->header->associated_column).column_name, associated_qual_column->header->name);
(associated_nuc_column->header->associated_column).version = associated_qual_column->header->version;
}
}
@ -1922,7 +1984,7 @@ Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p v
(view->predicate_functions)[(view->nb_predicates)] = view_has_nuc_sequence_column;
(view->predicate_functions)[(view->nb_predicates) + 1] = view_has_id_column;
(view->predicate_functions)[(view->nb_predicates) + 2] = view_has_definition_column;
// if (quality_column) # TODO discuss. Commented bc for example with obi annotate, clone view so clone predicate, then modify seq, so quality is deleted, and predicate boom
// if (quality_column) # TODO fix by triggering predicate deleting if quality deleting. Commented bc for example with obi annotate, clone view so clone predicate, then modify seq, so quality is deleted, and predicate boom
// (view->predicate_functions)[(view->nb_predicates) + 3] = view_has_quality_column;
view->nb_predicates = nb_predicates;
@ -2212,7 +2274,7 @@ Obiview_p obi_open_view(OBIDMS_p dms, const char* view_name)
// TODO return a pointer on the column?
int obi_view_add_column(Obiview_p view,
char* column_name,
char* column_name,
obiversion_t version_number,
const char* alias,
OBIType_t data_type,

4
src/obiview.h
View File

@ -406,7 +406,7 @@ Obiview_p obi_open_view(OBIDMS_p dms, const char* view_name);
* @param associated_column_name The name of the associated column if there is one (otherwise NULL or ""), if the column is created.
* @param associated_column_version The version of the associated column if there is one (otherwise -1), if the column is created.
* @param comments Optional comments associated with the column if it is created (NULL or "" if no comments associated).
* @param create Whether the column should be created (create == true) or opened (create == false).
* @param create Whether the column should be created (create == true) or already exists (create == false).
*
* @returns A value indicating the success of the operation.
* @retval 0 if the operation was successfully completed.
@ -416,7 +416,7 @@ Obiview_p obi_open_view(OBIDMS_p dms, const char* view_name);
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_view_add_column(Obiview_p view,
char* column_name,
char* column_name,
obiversion_t version_number,
const char* alias,
OBIType_t data_type,