def update(self, data):
if IDataElement.providedBy(data): # pylint: disable=E1101
# FIXME: This really should be a PATCH operation.
prx = DataElementAttributeProxy(data)
self_entity = self.get_entity()
changed_num_reps = prx.number_replicates != self.number_replicates
emt_id = prx.experiment_metadata_type.get('id')
changed_em_type = emt_id != self.experiment_metadata_type.id
if changed_em_type or changed_num_reps:
if changed_num_reps:
self_entity.number_replicates = prx.number_replicates
if changed_em_type:
self_entity.experiment_metadata_type = \
get_experiment_metadata_type(emt_id)
if not self_entity.experiment_design is None:
# invalidate data to force a fresh upload of the XLS file
self_entity.experiment_design.experiment_design_racks = []
self_entity.experiment_design.worklist_series = None
if not self_entity.lab_iso_request is None:
shape = self_entity.lab_iso_request.rack_layout.shape
new_layout = RackLayout(shape=shape)
self_entity.lab_iso_request.rack_layout = new_layout
self_entity.lab_iso_request.owner = ''
changed_sp = self_entity.subproject.id != prx.subproject.get('id')
if changed_sp:
new_sp = \
url_to_resource(prx.subproject.get('href')).get_entity()
self_entity.subproject = new_sp
self_entity.label = prx.label
# Perform appropriate Trac updates.
if not self_entity.lab_iso_request is None:
if self.iso_request.owner == STOCKMANAGEMENT_USER:
ticket_activator = IsoRequestTicketActivator(
experiment_metadata=self_entity)
self.__run_trac_tool(ticket_activator,
'Could not update the ticket: %s.')
else:
if changed_em_type or changed_num_reps:
trac_updater = IsoRequestTicketDescriptionRemover(
experiment_metadata=self_entity,
changed_num_replicates=changed_num_reps,
changed_em_type=changed_em_type)
else:
url = 'http://thelma/public//LOUICe.html#' \
+ self.path
iso_url = 'http://thelma/public//LOUICe.html#' \
+ self.iso_request.path
trac_updater = IsoRequestTicketDescriptionUpdater(
experiment_metadata=self_entity,
experiment_metadata_link=url,
iso_request_link=iso_url)
self.__run_trac_tool(trac_updater,
'Could not update the ticket: %s.')
else:
Member.update(self, data)
def update(self, data):
if IDataElement.providedBy(data): # pylint: disable=E1101
# FIXME: This really should be a PATCH operation.
prx = DataElementAttributeProxy(data)
self_entity = self.get_entity()
changed_num_reps = prx.number_replicates != self.number_replicates
emt_id = prx.experiment_metadata_type.get('id')
changed_em_type = emt_id != self.experiment_metadata_type.id
if changed_em_type or changed_num_reps:
if changed_num_reps:
self_entity.number_replicates = prx.number_replicates
if changed_em_type:
self_entity.experiment_metadata_type = \
get_experiment_metadata_type(emt_id)
if not self_entity.experiment_design is None:
# invalidate data to force a fresh upload of the XLS file
self_entity.experiment_design.experiment_design_racks = []
self_entity.experiment_design.worklist_series = None
if not self_entity.lab_iso_request is None:
shape = self_entity.lab_iso_request.rack_layout.shape
new_layout = RackLayout(shape=shape)
self_entity.lab_iso_request.rack_layout = new_layout
self_entity.lab_iso_request.owner = ''
changed_sp = self_entity.subproject.id != prx.subproject.get('id')
if changed_sp:
new_sp = \
url_to_resource(prx.subproject.get('href')).get_entity()
self_entity.subproject = new_sp
self_entity.label = prx.label
# Perform appropriate Trac updates.
if not self_entity.lab_iso_request is None:
if self.iso_request.owner == STOCKMANAGEMENT_USER:
ticket_activator = IsoRequestTicketActivator(
experiment_metadata=self_entity)
self.__run_trac_tool(ticket_activator,
'Could not update the ticket: %s.')
else:
if changed_em_type or changed_num_reps:
trac_updater = IsoRequestTicketDescriptionRemover(
experiment_metadata=self_entity,
changed_num_replicates=changed_num_reps,
changed_em_type=changed_em_type)
else:
url = 'http://thelma/public//LOUICe.html#' \
+ self.path
iso_url = 'http://thelma/public//LOUICe.html#' \
+ self.iso_request.path
trac_updater = IsoRequestTicketDescriptionUpdater(
experiment_metadata=self_entity,
experiment_metadata_link=url,
iso_request_link=iso_url)
self.__run_trac_tool(trac_updater,
'Could not update the ticket: %s.')
else:
Member.update(self, data)
def update(self, data):
if IDataElement.providedBy(data): # pylint: disable=E1101
prx = DataElementAttributeProxy(data)
loc = self.get_entity()
try:
rack = prx.rack
except AttributeError:
loc.checkout_rack()
else:
loc.checkin_rack(rack.get_entity())
else:
Member.update(self, data)
def update(self, data):
if IDataElement.providedBy(data): # pylint: disable=E1101
prx = DataElementAttributeProxy(data)
loc = self.get_entity()
try:
rack = prx.rack
except AttributeError:
loc.checkout_rack()
else:
loc.checkin_rack(rack.get_entity())
else:
Member.update(self, data)
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 __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 update(self, data):
if IDataElement.providedBy(data): # pylint: disable=E1101
raise SyntaxError('Should not get here.')
else:
Member.update(self, data)
def update(self, data):
if IDataElement.providedBy(data): # pylint: disable=E1101
raise SyntaxError('Should not get here.')
else:
Member.update(self, data)
def update(self, data):
if IEntity.providedBy(data): # pylint: disable=E1101
self.get_entity().molecule_designs = data.molecule_designs
else:
Member.update(self, data)