def __convert_one_to_many(self, rack_position, row_modifier=None,
col_modifier=None):
# Converts the given rack position of rack into to a rack position in
# a smaller (or equally sized) rack.
# :Note: Row and column modifier can be provided by the
# :func:`convert_many_to_many` method.
if row_modifier is None:
row_modifier = self.__row_modifier
if col_modifier is None:
col_modifier = self.__col_modifier
row_index = (float(rack_position.row_index - row_modifier) \
/ self.__row_count)
col_index = (float(rack_position.column_index - col_modifier) \
/ self.__col_count)
if not row_index.is_integer() or not col_index.is_integer():
msg = 'Invalid rack position for translation. Given rack ' \
'position: %s, resulting row index: %.1f, resulting column ' \
'index: %.1f, sector number: %i, row number: %i, column ' \
'number: %i, row modifier: %i, column modifier: %i, ' \
'translation type: %s.' \
% (rack_position, row_index, col_index, self.__number_sectors,
self.__row_count, self.__col_count, row_modifier,
col_modifier, self.behaviour)
raise ValueError(msg)
return get_rack_position_from_indices(int(row_index), int(col_index))
def _create_candidate_from_query_result(self, result_record):
"""
Converts a query result record into a candidate. By default all
column names are used as keyword.
If there \'row_index\' and \'column_index\' columns the two columns
are converted into a rack position value (keyword \'rack_position\').
"""
row_index = None
column_index = None
kw = dict()
for i in range(len(self.COLUMN_NAMES)):
col_name = self.COLUMN_NAMES[i]
if col_name in self.IGNORE_COLUMNS: continue
value = result_record[i]
if self.CONVERT_RACK_POSITION and col_name == 'row_index':
row_index = value
elif self.CONVERT_RACK_POSITION and col_name == 'column_index':
column_index = value
else:
kw[col_name] = value
if row_index is not None and column_index is not None:
rack_pos = get_rack_position_from_indices(row_index=row_index,
column_index=column_index)
kw['rack_position'] = rack_pos
return self.CANDIDATE_CLS(**kw) #pylint: disable=E1102
def _create_iso_candidates(self, tube_rack_fac, tube_rack_specs_matrix,
tube_fac, item_status_managed,
organization_cenix, stock_sample_fac):
ss_agg = get_root_aggregate(IStockSample)
rack_agg = get_root_aggregate(IRack)
tube_bc = 9000000000
vol = 1e-4
row_idx = 0
col_idx = 0
tube_rack = tube_rack_fac(label='test_iso_candidates',
specs=tube_rack_specs_matrix,
status=get_item_status_managed())
rack_agg.add(tube_rack)
mdp_agg = get_root_aggregate(IMoleculeDesignPool)
for mdp_id in [288282, 3349397, 3430173, 1139866, 199937]:
tube = tube_fac(barcode=str(tube_bc), status=item_status_managed)
col_idx += 1
tube_bc += 1
tube_rack.add_tube(
tube, get_rack_position_from_indices(row_idx, col_idx))
mdp = mdp_agg.get_by_id(mdp_id)
ss = stock_sample_fac(
volume=vol,
container=tube,
molecule_design_pool=mdp,
supplier=organization_cenix,
molecule_type=mdp.molecule_type,
concentration=mdp.default_stock_concentration)
ss_agg.add(ss)
def _create_candidate_from_query_result(self, result_record):
"""
Converts a query result record into a candidate. By default all
column names are used as keyword.
If there \'row_index\' and \'column_index\' columns the two columns
are converted into a rack position value (keyword \'rack_position\').
"""
row_index = None
column_index = None
kw = dict()
for i in range(len(self.COLUMN_NAMES)):
col_name = self.COLUMN_NAMES[i]
if col_name in self.IGNORE_COLUMNS: continue
value = result_record[i]
if self.CONVERT_RACK_POSITION and col_name == 'row_index':
row_index = value
elif self.CONVERT_RACK_POSITION and col_name == 'column_index':
column_index = value
else:
kw[col_name] = value
if row_index is not None and column_index is not None:
rack_pos = get_rack_position_from_indices(
row_index=row_index, column_index=column_index)
kw['rack_position'] = rack_pos
return self.CANDIDATE_CLS(**kw) #pylint: disable=E1102
def _create_iso_candidates(self, tube_rack_fac, tube_rack_specs_matrix,
tube_fac, item_status_managed,
organization_cenix, stock_sample_fac):
ss_agg = get_root_aggregate(IStockSample)
rack_agg = get_root_aggregate(IRack)
tube_bc = 9000000000
vol = 1e-4
row_idx = 0
col_idx = 0
tube_rack = tube_rack_fac(label='test_iso_candidates',
specs=tube_rack_specs_matrix,
status=get_item_status_managed())
rack_agg.add(tube_rack)
mdp_agg = get_root_aggregate(IMoleculeDesignPool)
for mdp_id in [288282, 3349397, 3430173, 1139866, 199937]:
tube = tube_fac(barcode=str(tube_bc),
status=item_status_managed)
col_idx += 1
tube_bc += 1
tube_rack.add_tube(
tube,
get_rack_position_from_indices(row_idx, col_idx))
mdp = mdp_agg.get_by_id(mdp_id)
ss = stock_sample_fac(
volume=vol,
container=tube,
molecule_design_pool=mdp,
supplier=organization_cenix,
molecule_type=mdp.molecule_type,
concentration=mdp.default_stock_concentration)
ss_agg.add(ss)
def __prepare_pool_stock_rack(self, empty_rack, sector_idx):
tube_specs_agg = get_root_aggregate(ITubeSpecs)
ts_matrix = tube_specs_agg.get_by_slug('matrix0500')
is_managed = get_item_status_managed()
pos_idxs_96 = zip([1, 1, 0, 0], [1, 1, 1, 1])
(row_idx, col_idx) = pos_idxs_96[sector_idx]
tube = Tube.create_from_data(
dict(barcode=str(9999999990 + tube_counter.next()),
status=is_managed,
specs=ts_matrix))
pos = get_rack_position_from_indices(row_idx, col_idx)
empty_rack.add_tube(tube, pos)
def __convert_many_to_one(self, rack_position, row_modifier=None,
col_modifier=None):
# Converts the given rack position of rack into to a rack position in
# a larger (or equally sized) rack.
# :Note: Row and column modifier can be provided by the
# :func:`convert_many_to_many` method.
if row_modifier is None:
row_modifier = self.__row_modifier
if col_modifier is None:
col_modifier = self.__col_modifier
row_index = (rack_position.row_index * self.__row_count) \
+ row_modifier
col_index = (rack_position.column_index * self.__col_count) \
+ col_modifier
return get_rack_position_from_indices(row_index, col_index)
def _store_result(self, result_record):
rack_barcode = result_record[self.RACK_BARCODE_INDEX]
scr = self.rack_map[rack_barcode]
rack_pos = get_rack_position_from_indices(
row_index=result_record[self.ROW_INDEX_INDEX],
column_index=result_record[self.COLUMN_INDEX_INDEX])
tube_barcode = result_record[self.TUBE_BARCODE_INDEX]
tube_status = result_record[self.TUBE_STATUS_INDEX]
if not tube_status == STOCK_ITEM_STATUS:
info = '%s (status: %s, rack: %s)' \
% (str(tube_barcode), tube_status, rack_barcode)
self.mismatching_tubes.append(info)
return None
tube_specs_name = result_record[self.TUBE_SPECS_NAME_INDEX]
if not tube_specs_name in STOCK_TUBE_SPECS:
info = '%s (tube specs: %s, rack: %s)' \
% (str(tube_barcode), tube_specs_name, rack_barcode)
self.mismatching_tubes.append(info)
return None
scr.add_tube(rack_pos, tube_barcode)
def _store_result(self, result_record):
rack_barcode = result_record[self.RACK_BARCODE_INDEX]
scr = self.rack_map[rack_barcode]
rack_pos = get_rack_position_from_indices(
row_index=result_record[self.ROW_INDEX_INDEX],
column_index=result_record[self.COLUMN_INDEX_INDEX])
tube_barcode = result_record[self.TUBE_BARCODE_INDEX]
tube_status = result_record[self.TUBE_STATUS_INDEX]
if not tube_status == STOCK_ITEM_STATUS:
info = '%s (status: %s, rack: %s)' \
% (str(tube_barcode), tube_status, rack_barcode)
self.mismatching_tubes.append(info)
return None
tube_specs_name = result_record[self.TUBE_SPECS_NAME_INDEX]
if not tube_specs_name in STOCK_TUBE_SPECS:
info = '%s (tube specs: %s, rack: %s)' \
% (str(tube_barcode), tube_specs_name, rack_barcode)
self.mismatching_tubes.append(info)
return None
scr.add_tube(rack_pos, tube_barcode)
def _convert_results_to_entity(self):
"""
Converts the parsing results into a :class:`LibraryBaseLayout`
(no entity class).
"""
self.add_info('Convert parser results ...')
if not self.has_errors():
self.__init_layout()
if not self.has_errors():
for rack_pos_container in self.parser.contained_wells:
rack_pos = get_rack_position_from_indices(
row_index=rack_pos_container.row_index,
column_index=rack_pos_container.column_index)
base_pos = LibraryBaseLayoutPosition(rack_pos)
self.__base_layout.add_position(base_pos)
if not self.has_errors() and len(self.__base_layout) < 1:
msg = 'The specified base layout is empty!'
self.add_error(msg)
if not self.has_errors():
self.__base_layout.close()
self.return_value = self.__base_layout
self.add_info('Conversion completed.')
def _convert_results_to_entity(self):
"""
Converts the parsing results into a :class:`LibraryBaseLayout`
(no entity class).
"""
self.add_info('Convert parser results ...')
if not self.has_errors():
self.__init_layout()
if not self.has_errors():
for rack_pos_container in self.parser.contained_wells:
rack_pos = get_rack_position_from_indices(
row_index=rack_pos_container.row_index,
column_index=rack_pos_container.column_index)
base_pos = LibraryBaseLayoutPosition(rack_pos)
self.__base_layout.add_position(base_pos)
if not self.has_errors() and len(self.__base_layout) < 1:
msg = 'The specified base layout is empty!'
self.add_error(msg)
if not self.has_errors():
self.__base_layout.close()
self.return_value = self.__base_layout
self.add_info('Conversion completed.')
def get_position(self):
"""
Returns a position which is then remove from the pool.
"""
row_index = self.free_row_indices.pop(0)
return get_rack_position_from_indices(row_index, self.column_index)
def _convert_to_rack_position(self, pos_container):
"""
Creates a rack position for a rack position container.
"""
return get_rack_position_from_indices(pos_container.row_index,
pos_container.column_index)
def _convert_to_rack_position(self, pos_container):
"""
Creates a rack position for a rack position container.
"""
return get_rack_position_from_indices(pos_container.row_index,
pos_container.column_index)
