def __fetch_tubes(self):
# Fetches tube (for location data), from the the DB. Uses the tube
# barcodes from the library layouts.
self.add_debug('Fetch tubes ...')
tube_barcodes = []
for lib_pos in self.__library_layout.working_positions():
for barcode in lib_pos.stock_tube_barcodes:
tube_barcodes.append(barcode)
tube_agg = get_root_aggregate(ITube)
tube_agg.filter = cntd(barcode=tube_barcodes)
iterator = tube_agg.iterator()
while True:
try:
tube = iterator.next()
except StopIteration:
break
else:
self.__tube_map[tube.barcode] = tube
if not len(tube_barcodes) == len(self.__tube_map):
missing_tubes = []
for tube_barcode in tube_barcodes:
if not self.__tube_map.has_key(tube_barcode):
missing_tubes.append(tube_barcode)
msg = 'Could not find tubes for the following tube barcodes: %s.' \
% (', '.join(sorted(missing_tubes)))
self.add_error(msg)
def __fetch_tubes(self):
# Fetches tube (for location data), from the the DB. Uses the tube
# barcodes from the library layouts.
self.add_debug('Fetch tubes ...')
tube_barcodes = []
for lib_pos in self.__library_layout.working_positions():
for barcode in lib_pos.stock_tube_barcodes:
tube_barcodes.append(barcode)
tube_agg = get_root_aggregate(ITube)
tube_agg.filter = cntd(barcode=tube_barcodes)
iterator = tube_agg.iterator()
while True:
try:
tube = iterator.next()
except StopIteration:
break
else:
self.__tube_map[tube.barcode] = tube
if not len(tube_barcodes) == len(self.__tube_map):
missing_tubes = []
for tube_barcode in tube_barcodes:
if not self.__tube_map.has_key(tube_barcode):
missing_tubes.append(tube_barcode)
msg = 'Could not find tubes for the following tube barcodes: %s.' \
% (', '.join(sorted(missing_tubes)))
self.add_error(msg)
def __get_tube_candidates_for_tubes(self, tube_barcodes, tube_type):
"""
As far as possible we use the tube aggregate to fetch tubes from the
DB. The tubes for the barcodes are converted into :class:`TubeCandidate`
objects and mapped onto pools.
Valid tubes must contain stock samples and be managed.
"""
self.__tube_agg.filter = cntd(barcode=tube_barcodes)
iterator = self.__tube_agg.iterator()
candidate_map = dict()
no_stock_sample = []
not_managed = []
while True:
try:
tube = iterator.next()
except StopIteration:
break
else:
if not tube.item_status == ITEM_STATUS_NAMES.MANAGED.upper():
not_managed.append(tube.barcode)
continue
sample = tube.sample
if not isinstance(sample, StockSample):
no_stock_sample.append(tube.barcode)
continue
pool = sample.molecule_design_pool
tc = TubeCandidate(pool_id=pool.id,
rack_barcode=tube.location.rack.barcode,
rack_position=tube.location.position,
tube_barcode=tube.barcode,
concentration=sample.concentration,
volume=sample.volume)
# we could store the pool itself to (instead of its ID), but
# for some reason the pool entities are not recognised as equal
add_list_map_element(candidate_map, pool.id, tc)
self.__tube_map[tube.barcode] = tube
if len(no_stock_sample) > 0:
msg = 'The following %s tubes do not contain stock ' \
'samples: %s! The referring tubes are replaced, if ' \
'possible.' % (tube_type,
self._get_joined_str(no_stock_sample))
self.add_warning(msg)
if len(not_managed) > 0:
msg = 'The following %s tubes are not managed: %s. They ' \
'are replaced, if possible.' \
% (tube_type, self._get_joined_str(not_managed))
self.add_warning(msg)
not_found = []
for tube_barcode in tube_barcodes:
if not self.__tube_map.has_key(tube_barcode):
not_found.append(tube_barcode)
if len(not_found) > 0:
msg = 'The following %s tubes have not been found in the DB: %s.' \
% (tube_type, self._get_joined_str(not_found))
self.add_warning(msg)
return candidate_map
def __get_tube_candidates_for_tubes(self, tube_barcodes, tube_type):
"""
As far as possible we use the tube aggregate to fetch tubes from the
DB. The tubes for the barcodes are converted into :class:`TubeCandidate`
objects and mapped onto pools.
Valid tubes must contain stock samples and be managed.
"""
self.__tube_agg.filter = cntd(barcode=tube_barcodes)
iterator = self.__tube_agg.iterator()
candidate_map = dict()
no_stock_sample = []
not_managed = []
while True:
try:
tube = iterator.next()
except StopIteration:
break
else:
if not tube.item_status == ITEM_STATUS_NAMES.MANAGED.upper():
not_managed.append(tube.barcode)
continue
sample = tube.sample
if not isinstance(sample, StockSample):
no_stock_sample.append(tube.barcode)
continue
pool = sample.molecule_design_pool
tc = TubeCandidate(pool_id=pool.id,
rack_barcode=tube.location.rack.barcode,
rack_position=tube.location.position,
tube_barcode=tube.barcode,
concentration=sample.concentration,
volume=sample.volume)
# we could store the pool itself to (instead of its ID), but
# for some reason the pool entities are not recognised as equal
add_list_map_element(candidate_map, pool.id, tc)
self.__tube_map[tube.barcode] = tube
if len(no_stock_sample) > 0:
msg = 'The following %s tubes do not contain stock ' \
'samples: %s! The referring tubes are replaced, if ' \
'possible.' % (tube_type,
self._get_joined_str(no_stock_sample))
self.add_warning(msg)
if len(not_managed) > 0:
msg = 'The following %s tubes are not managed: %s. They ' \
'are replaced, if possible.' \
% (tube_type, self._get_joined_str(not_managed))
self.add_warning(msg)
not_found = []
for tube_barcode in tube_barcodes:
if not self.__tube_map.has_key(tube_barcode):
not_found.append(tube_barcode)
if len(not_found) > 0:
msg = 'The following %s tubes have not been found in the DB: %s.' \
% (tube_type, self._get_joined_str(not_found))
self.add_warning(msg)
return candidate_map
def opt_callback(cls, value, options): # pylint: disable=W0613
agg = get_root_aggregate(option_type)
if not ',' in value:
val = agg.get_by_slug(value)
else:
agg.filter = cntd(slug=value.split(','))
val = [ent for ent in agg]
return val
def opt_callback(cls, value, options): # pylint: disable=W0613
agg = get_root_aggregate(option_type)
if not ',' in value:
val = agg.get_by_slug(value)
else:
agg.filter = cntd(slug=value.split(','))
val = [ent for ent in agg]
return val
def __get_tube_map_for_sector(self, layout):
# We fetch all tubes for the given sector layout in one go.
tube_agg = get_root_aggregate(ITube)
tube_agg.filter = \
cntd(barcode=reduce(add, [pos.stock_tube_barcodes
for pos in
layout.get_sorted_working_positions()])
)
return (dict([(t.barcode, t) for t in iter(tube_agg)]))
def __get_tube_map_for_sector(self, layout):
# We fetch all tubes for the given sector layout in one go.
tube_agg = get_root_aggregate(ITube)
tube_agg.filter = \
cntd(barcode=reduce(add, [pos.stock_tube_barcodes
for pos in
layout.get_sorted_working_positions()])
)
return (dict([(t.barcode, t) for t in iter(tube_agg)]))
def __get_molecule_design_pools(self):
"""
Returns the molecule design pool objects for the specified IDs.
"""
self.add_debug('Checks validity of the molecule design pool IDs ...')
ids = self.parser.molecule_design_pool_ids
agg = get_root_aggregate(IMoleculeDesignPool)
agg.filter = cntd(molecule_design_set_id=ids)
db_ids = set()
molecule_design_pools = set()
stock_concentrations = set()
iterator = agg.iterator()
while True:
try:
md_pool = iterator.next()
except StopIteration:
break
else:
if self.__molecule_type is None:
self.__molecule_type = md_pool.molecule_type
else:
if not self.__molecule_type == md_pool.molecule_type:
msg = 'There is more than one molecule type in the ' \
'the molecule design set ("%s" and "%s")!' \
% (self.__molecule_type.name,
md_pool.molecule_type.name)
self.add_error(msg)
return None
molecule_design_pools.add(md_pool)
db_ids.add(md_pool.id)
stock_conc = md_pool.default_stock_concentration \
* CONCENTRATION_CONVERSION_FACTOR
stock_concentrations.add(stock_conc)
if not len(molecule_design_pools) == len(ids):
unknown_molecule_design_pools = []
for pool_id in ids:
if not pool_id in db_ids:
unknown_molecule_design_pools.append(pool_id)
msg = 'The following molecule design pool IDs have not be found ' \
'in the DB: %s' % (unknown_molecule_design_pools)
self.add_error(msg)
if len(stock_concentrations) > 1:
conc = sorted(list(stock_concentrations))
msg = 'The pools in the set have different stock concentrations: ' \
'(shown in nM): %s.' % (', '.join([str(c) for c in conc]))
self.add_error(msg)
else:
self.__stock_concentration = list(stock_concentrations)[0]
return molecule_design_pools
def __get_molecule_design_pools(self):
"""
Returns the molecule design pool objects for the specified IDs.
"""
self.add_debug('Checks validity of the molecule design pool IDs ...')
ids = self.parser.molecule_design_pool_ids
agg = get_root_aggregate(IMoleculeDesignPool)
agg.filter = cntd(molecule_design_set_id=ids)
db_ids = set()
molecule_design_pools = set()
stock_concentrations = set()
iterator = agg.iterator()
while True:
try:
md_pool = iterator.next()
except StopIteration:
break
else:
if self.__molecule_type is None:
self.__molecule_type = md_pool.molecule_type
else:
if not self.__molecule_type == md_pool.molecule_type:
msg = 'There is more than one molecule type in the ' \
'the molecule design set ("%s" and "%s")!' \
% (self.__molecule_type.name,
md_pool.molecule_type.name)
self.add_error(msg)
return None
molecule_design_pools.add(md_pool)
db_ids.add(md_pool.id)
stock_conc = md_pool.default_stock_concentration \
* CONCENTRATION_CONVERSION_FACTOR
stock_concentrations.add(stock_conc)
if not len(molecule_design_pools) == len(ids):
unknown_molecule_design_pools = []
for pool_id in ids:
if not pool_id in db_ids:
unknown_molecule_design_pools.append(pool_id)
msg = 'The following molecule design pool IDs have not be found ' \
'in the DB: %s' % (unknown_molecule_design_pools)
self.add_error(msg)
if len(stock_concentrations) > 1:
conc = sorted(list(stock_concentrations))
msg = 'The pools in the set have different stock concentrations: ' \
'(shown in nM): %s.' % (', '.join([str(c) for c in conc]))
self.add_error(msg)
else:
self.__stock_concentration = list(stock_concentrations)[0]
return molecule_design_pools
def __get_tube_racks(self):
self.add_debug('Fetching tube racks.')
tube_rack_agg = get_root_aggregate(ITubeRack)
query_bcs = self.single_stock_racks
if not self.pool_stock_racks is None:
query_bcs.extend(self.pool_stock_racks)
tube_rack_agg.filter = cntd(barcode=query_bcs)
rack_map = dict([(tr.barcode, tr) for tr in tube_rack_agg])
bcs_not_found = set(rack_map.keys()).symmetric_difference(query_bcs)
if len(bcs_not_found) > 0:
msg = 'The following racks have not been found in the DB: %s!' \
% (', '.join(sorted(bcs_not_found)))
self.add_error(msg)
return rack_map
def __get_molecule_designs_and_pools(self):
# Fetches the molecule designs for all molecule design IDs and pools for
# all found pools.
self.add_debug('Fetch molecule designs and pools for IDs ...')
found_md_ids = set()
found_pool_ids = set()
i = 0
while True:
i += 1
md_ids, pool_id = self.__get_ids_for_row(i)
if md_ids is None and pool_id is None: break
if pool_id is not None: found_pool_ids.add(pool_id)
if md_ids is None: continue
for md_id in md_ids:
found_md_ids.add(md_id)
if len(found_md_ids) > 0:
md_filter = cntd(molecule_design_id=found_md_ids)
self.__fetch_entities(IMoleculeDesign, md_filter, found_md_ids,
'molecule design', self.__md_map)
if len(found_pool_ids) > 0:
pool_filter = cntd(molecule_design_set_id=found_pool_ids)
self.__fetch_entities(IMoleculeDesignPool, pool_filter,
found_pool_ids, 'pool', self.__pool_map)
def __get_tube_racks(self):
self.add_debug('Fetching tube racks.')
tube_rack_agg = get_root_aggregate(ITubeRack)
query_bcs = self.single_stock_racks
if not self.pool_stock_racks is None:
query_bcs.extend(self.pool_stock_racks)
tube_rack_agg.filter = cntd(barcode=query_bcs)
rack_map = dict([(tr.barcode, tr) for tr in tube_rack_agg])
bcs_not_found = set(rack_map.keys()).symmetric_difference(query_bcs)
if len(bcs_not_found) > 0:
msg = 'The following racks have not been found in the DB: %s!' \
% (', '.join(sorted(bcs_not_found)))
self.add_error(msg)
return rack_map
def __getitem__(self, name):
if name == 'completed-iso-plates' and self.iso_type == ISO_TYPES.LAB:
# These are the plates that can be used as input for experiment
# job scheduling.
iso_plate_bcs = []
for iso in self.isos:
if iso.status == ISO_STATUS.DONE:
for plt in self.__get_completed_iso_plates_for_iso(iso):
iso_plate_bcs.append(plt.barcode)
iso_plates = get_root_collection(IPlate)
iso_plates.filter = cntd(barcode=iso_plate_bcs)
result = iso_plates
else:
result = Member.__getitem__(self, name)
return result
def __getitem__(self, name):
if name == 'completed-iso-plates' and self.iso_type == ISO_TYPES.LAB:
# These are the plates that can be used as input for experiment
# job scheduling.
iso_plate_bcs = []
for iso in self.isos:
if iso.status == ISO_STATUS.DONE:
for plt in self.__get_completed_iso_plates_for_iso(iso):
iso_plate_bcs.append(plt.barcode)
iso_plates = get_root_collection(IPlate)
iso_plates.filter = cntd(barcode=iso_plate_bcs)
result = iso_plates
else:
result = Member.__getitem__(self, name)
return result
def __get_molecule_designs_and_pools(self):
# Fetches the molecule designs for all molecule design IDs and pools for
# all found pools.
self.add_debug("Fetch molecule designs and pools for IDs ...")
found_md_ids = set()
found_pool_ids = set()
i = 0
while True:
i += 1
md_ids, pool_id = self.__get_ids_for_row(i)
if md_ids is None and pool_id is None:
break
if pool_id is not None:
found_pool_ids.add(pool_id)
if md_ids is None:
continue
for md_id in md_ids:
found_md_ids.add(md_id)
if len(found_md_ids) > 0:
md_filter = cntd(molecule_design_id=found_md_ids)
self.__fetch_entities(IMoleculeDesign, md_filter, found_md_ids, "molecule design", self.__md_map)
if len(found_pool_ids) > 0:
pool_filter = cntd(molecule_design_set_id=found_pool_ids)
self.__fetch_entities(IMoleculeDesignPool, pool_filter, found_pool_ids, "pool", self.__pool_map)
def __getitem__(self, name):
if name == 'tags':
tags_dict = {}
design_racks = self.__get_design_racks()
for rack in design_racks:
for tp in rack.rack_layout.tagged_rack_position_sets:
for tag in tp.tags:
tags_dict[tag.get_entity().slug] = tag
tag_coll = get_root_collection(ITag)
tag_coll.filter = cntd(id=[tag.id for tag in tags_dict.values()])
result = tag_coll
elif name == 'experiment-design-racks':
result = self.__get_design_racks()
else:
result = Member.__getitem__(self, name)
return result
def __getitem__(self, name):
if name == 'tags':
tags_dict = {}
design_racks = self.__get_design_racks()
for rack in design_racks:
for tp in rack.rack_layout.tagged_rack_position_sets:
for tag in tp.tags:
tags_dict[tag.get_entity().slug] = tag
tag_coll = get_root_collection(ITag)
tag_coll.filter = cntd(id=[tag.id for tag in tags_dict.values()])
result = tag_coll
elif name == 'experiment-design-racks':
result = self.__get_design_racks()
else:
result = Member.__getitem__(self, name)
return result
def __get_molecule_design_pools(self):
self.add_debug("Fetch molecule design pools for IDs ...")
invalid_length = []
found_md_ids = set()
for md_ids in self.parser.molecule_design_lists:
if len(md_ids) != self.number_molecule_designs:
invalid_length.append("-".join([str(md_id) for md_id in md_ids]))
continue
for md_id in md_ids:
found_md_ids.add(md_id)
if len(invalid_length) > 0:
msg = (
"Some of the specified molecule design pools do not "
"have the expected number of molecule designs (%i): %s."
% (self.number_molecule_designs, ", ".join(invalid_length))
)
self.add_error(msg)
return
invalid_type = []
agg = get_root_aggregate(IMoleculeDesignPool)
agg.filter = cntd(molecule_design_id=found_md_ids)
iterator = agg.iterator()
while True:
try:
md = iterator.next()
except StopIteration:
break
else:
if md.molecule_type != self.molecule_type:
invalid_type.append(md.id)
self.__md_map[md.id] = md
# Search for missing molecule designs.
if len(found_md_ids) != len(self.__md_map):
diff = found_md_ids.symmetric_difference(self.__md_map.keys())
diff = sorted(list(diff))
msg = "The following molecule designs could not be found in " "the DB: %s." % (
", ".join([str(md_id) for md_id in diff])
)
self.add_error(msg)
if len(invalid_type) > 0:
msg = (
"The molecule designs in the list have different molecule "
"types. Expected: %s. Others (molecule designs): %s."
% (self.molecule_type, ", ".join([str(md_id) for md_id in sorted(invalid_type)]))
)
self.add_error(msg)
def __get_molecule_design_pools(self):
self.add_debug('Fetch molecule design pools for IDs ...')
invalid_length = []
found_md_ids = set()
for md_ids in self.parser.molecule_design_lists:
if len(md_ids) != self.number_molecule_designs:
invalid_length.append('-'.join(
[str(md_id) for md_id in md_ids]))
continue
for md_id in md_ids:
found_md_ids.add(md_id)
if len(invalid_length) > 0:
msg = 'Some of the specified molecule design pools do not ' \
'have the expected number of molecule designs (%i): %s.' \
% (self.number_molecule_designs, ', '.join(invalid_length))
self.add_error(msg)
return
invalid_type = []
agg = get_root_aggregate(IMoleculeDesignPool)
agg.filter = cntd(molecule_design_id=found_md_ids)
iterator = agg.iterator()
while True:
try:
md = iterator.next()
except StopIteration:
break
else:
if md.molecule_type != self.molecule_type:
invalid_type.append(md.id)
self.__md_map[md.id] = md
# Search for missing molecule designs.
if len(found_md_ids) != len(self.__md_map):
diff = found_md_ids.symmetric_difference(self.__md_map.keys())
diff = sorted(list(diff))
msg = 'The following molecule designs could not be found in ' \
'the DB: %s.' % (', '.join([str(md_id) for md_id in diff]))
self.add_error(msg)
if len(invalid_type) > 0:
msg = 'The molecule designs in the list have different molecule ' \
'types. Expected: %s. Others (molecule designs): %s.' \
% (self.molecule_type,
', '.join([str(md_id) for md_id in sorted(invalid_type)]))
self.add_error(msg)
def __check_new_molecule_designs(self):
self.add_debug('Checking for new molecule designs.')
md_agg = get_root_aggregate(IMoleculeDesign)
# Build a map design hash -> registration item for all molecule design
# registration items.
mdri_map = {}
for mdri in self.registration_items:
struc_hash = \
MoleculeDesign.make_structure_hash(mdri.chemical_structures)
mdri_map.setdefault(struc_hash, []).append(mdri)
# Build "contained" specification, filter all existing designs and
# build difference set of new designs.
md_agg.filter = cntd(structure_hash=mdri_map.keys())
existing_md_map = dict([(md.structure_hash, md)
for md in md_agg.iterator()])
# Update registration items with existing molecule designs and
# remove from hash map.
for struc_hash, md in existing_md_map.iteritems():
mdris = mdri_map.pop(struc_hash)
for mdri in mdris:
mdri.molecule_design = md
self.__new_mdris = list(mdri_map.values())
def __check_tubes(self):
tube_agg = get_root_aggregate(ITube)
bcs = [getattr(sri, 'tube_barcode')
for sri in self.registration_items]
self.add_debug('Checking tubes. Barcodes: %s' % bcs)
tube_agg.filter = cntd(barcode=bcs)
tube_map = dict([(tube.barcode, tube)
for tube in tube_agg.iterator()])
new_tubes = []
for sri in self.registration_items:
tube_bc = sri.tube_barcode
if not tube_bc in tube_map:
tube = self.__make_new_tube(sri)
tube_agg.add(tube)
new_tubes.append(tube)
else:
# FIXME: Do we need to apply location information here?
tube = tube_map[tube_bc]
if not self.__validate_tube(tube):
continue
sri.container = tube
self.return_value['tubes'] = new_tubes
def __check_racks(self):
rack_agg = get_root_aggregate(ITubeRack)
self.add_debug('Checking rack position information.')
pos_infos = [(getattr(sri, 'rack_barcode'),
getattr(sri, 'rack_position'))
for sri in self.registration_items
if not (getattr(sri, 'rack_barcode') is None
or getattr(sri, 'rack_position') is None)]
self.__has_location_info = len(pos_infos) > 0
if self.__has_location_info \
and len(pos_infos) != len(self.registration_items):
msg = 'Some sample registration items contain location ' \
'information (rack barcode and rack position), but ' \
'not all of them do.'
self.add_error(msg)
else:
new_racks = []
if self.__has_location_info:
rack_agg.filter = cntd(barcode=[pos_info[0]
for pos_info in pos_infos])
rack_map = dict([(rack.barcode, rack)
for rack in rack_agg.iterator()])
for sri in self.registration_items:
rack_bc = sri.rack_barcode
if not rack_bc in rack_map:
# Create new item and add.
rack = self.__make_new_rack(sri)
rack_agg.add(rack)
new_racks.append(rack)
rack_map[rack_bc] = rack
else:
rack = rack_map[rack_bc]
if not self.__validate_rack(rack):
continue
# Update sample registration item.
sri.rack = rack
self.return_value['racks'] = new_racks
def test_cntd_generator(self):
spec = cntd(text_attr=['attr'])
self.assert_true(spec.is_satisfied_by(self.candidate))
def get_ids_from_file(cls, file_name):
with open(file_name, 'rU') as input_file:
ids = [int(line.strip()) for line in input_file]
agg = get_root_aggregate(IMoleculeDesignPool)
agg.filter = cntd(id=ids)
return list(iter(agg))
def test_cntd_generator(self):
spec = cntd(text_attr=['attr'])
self.assert_true(spec.is_satisfied_by(self.candidate))
def __process_molecule_design_pools(self):
self.add_debug('Processing molecule design pools.')
md_pool_agg = get_root_aggregate(IMoleculeDesignPool)
mdpri_hash_map = {}
hash_func = MoleculeDesignPool.make_member_hash
new_mdpri_map = {}
new_mds = self.return_value['molecule_designs']
for mdpri in self.registration_items:
# By definition, any mdpri that contains one or more new designs
# must be new. We must treat this as a special case because
# building member hash values with the new designs does not work
# reliably since they may not have been flushed yet.
mds = [mdri.molecule_design
for mdri in mdpri.molecule_design_registration_items]
if any(md in new_mds for md in mds):
# We use the *structure* as key for the new pools map here
# as this is always available (unlike the design IDs, which
# may not have been generated at this point).
key = self.__make_new_mdpri_key(mdpri)
new_mdpri_map.setdefault(key, []).append(mdpri)
else:
# For pools that consist only of existing designs, we build
# a map with member hashes as keys so we can query with a
# single DB call.
hash_val = \
hash_func([mdri.molecule_design
for mdri in
mdpri.molecule_design_registration_items])
mdpri_hash_map.setdefault(hash_val, []).append(mdpri)
if len(mdpri_hash_map) > 0:
md_pool_agg.filter = cntd(member_hash=mdpri_hash_map.keys())
existing_mdp_map = dict([(mdp.member_hash, mdp)
for mdp in md_pool_agg.iterator()])
# Update existing molecule design pool registration items.
for hash_val, mdp in existing_mdp_map.iteritems():
mdpris = mdpri_hash_map[hash_val]
for mdpri in mdpris:
if not mdpri.molecule_design_pool is None \
and mdp.id != mdpri.molecule_design_pool.id:
msg = 'The molecule design pool ID (%s) specified ' \
'in the sample data does not match the ID ' \
'of the pool that retrieved for the design ' \
'structure information associated with it.'
self.add_error(msg)
continue
mdpri.molecule_design_pool = mdp
else:
existing_mdp_map = {}
# Determine non-existing molecule design pool registration items and
# build up a map (this makes sure the same design is registered at
# most once.
new_mdp_hashes = \
set(mdpri_hash_map.keys()).difference(existing_mdp_map.keys())
for new_mdp_hash in new_mdp_hashes:
mdpris = mdpri_hash_map[new_mdp_hash]
for mdpri in mdpris:
if not mdpri.molecule_design_pool is None:
# This is a case where we supplied both design pool ID *and*
# structure information in the data file and the two do not
# match (i.e., the structures were not found).
msg = 'The molecule design pool ID (%s) specified in the ' \
'sample data does not match the design structure ' \
'information associated with it.'
self.add_error(msg)
continue
key = self.__make_new_mdpri_key(mdpri)
new_mdpri_map.setdefault(key, []).append(mdpri)
if len(new_mdpri_map) > 0:
new_md_pools = []
for mdpris in new_mdpri_map.values():
# We use the first mdp registration item to create a
# new pool and update all with the latter.
md_pool = MoleculeDesignPool(
set([mdri.molecule_design
for mdri in
mdpris[0].molecule_design_registration_items]))
md_pool_agg.add(md_pool)
new_md_pools.append(md_pool)
for mdpri in mdpris:
mdpri.molecule_design_pool = md_pool
self.return_value['molecule_design_pools'] = new_md_pools
def __get_md_pool_map(self, pool_ids):
agg = get_root_aggregate(IMoleculeDesignPool)
agg.filter = cntd(id=pool_ids)
return dict([(md.id, md) for md in agg.iterator()])
def __get_tube_map(self, tube_barcodes):
tb_agg = get_root_aggregate(ITube)
tb_agg.filter = cntd(barcode=tube_barcodes)
return dict([(tb.barcode, tb) for tb in tb_agg.iterator()])
def get_ids_from_file(cls, file_name):
with open(file_name, 'rU') as input_file:
ids = [int(line.strip()) for line in input_file]
agg = get_root_aggregate(IMoleculeDesignPool)
agg.filter = cntd(id=ids)
return list(iter(agg))
def __get_molecule_types(self):
agg = get_root_aggregate(IMoleculeType)
agg.filter = cntd(id=self.molecule_type_ids)
return list(agg.iterator())