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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
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@ -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):