def __init__(self, sample, volume, time_stamp=None, **kw):
Entity.__init__(self, **kw)
self.sample = sample
self.volume = volume
if time_stamp is None:
time_stamp = get_utc_time()
self.time_stamp = time_stamp
def __init__(self, sample, volume, time_stamp=None, **kw):
Entity.__init__(self, **kw)
self.sample = sample
self.volume = volume
if time_stamp is None:
time_stamp = get_utc_time()
self.time_stamp = time_stamp
def check_out(self):
"""
Checks this sample out of the freezer it is currently in.
:raises RuntimeError: If the `checkout_date` attribute is not `None`.
"""
if not self.checkout_date is None:
raise RuntimeError("Trying to check out a sample that has not " "been checked in.")
self.checkout_date = get_utc_time()
def __init__(self, product_id, supplier, time_stamp=None, is_current=False, is_deleted=False, **kw):
Entity.__init__(self, **kw)
self.product_id = product_id
self.supplier = supplier
if time_stamp is None:
time_stamp = get_utc_time()
self.time_stamp = time_stamp
self.is_current = is_current
self.is_deleted = is_deleted
def __init__(self, user, tube_transfers=None, timestamp=None, **kw):
Entity.__init__(self, **kw)
self.user = user
if timestamp is None:
timestamp = get_utc_time()
self.timestamp = timestamp
if tube_transfers is None:
tube_transfers = []
self.tube_transfers = tube_transfers
def __init__(self, user, tube_transfers=None, timestamp=None, **kw):
Entity.__init__(self, **kw)
self.user = user
if timestamp is None:
timestamp = get_utc_time()
self.timestamp = timestamp
if tube_transfers is None:
tube_transfers = []
self.tube_transfers = tube_transfers
def __init__(self, label,
creation_date=None, active=False, project=None, **kw):
Entity.__init__(self, **kw)
self.label = label
if creation_date is None:
creation_date = get_utc_time()
self.creation_date = creation_date
self.active = active
if project is not None:
self.project = project
def check_out(self):
"""
Checks this sample out of the freezer it is currently in.
:raises RuntimeError: If the `checkout_date` attribute is not `None`.
"""
if not self.checkout_date is None:
raise RuntimeError('Trying to check out a sample that has not '
'been checked in.')
self.checkout_date = get_utc_time()
def __init__(self, label, leader,
customer=None, creation_date=None, subprojects=None, **kw):
Entity.__init__(self, **kw)
self.label = label
self.title = label
self.customer = customer
self.leader = leader
if creation_date is None:
creation_date = get_utc_time()
self.creation_date = creation_date
if subprojects is None:
subprojects = []
self.subprojects = subprojects
def __init__(self, label, specs, status, comment='',
creation_date=None, barcode=None, **kw):
Entity.__init__(self, **kw)
if self.__class__ is Rack:
raise NotImplementedError('Abstract class')
self.label = label
self.specs = specs
self.status = status
self.comment = comment
if creation_date is None:
creation_date = get_utc_time()
self.creation_date = creation_date
self.barcode = barcode
self.containers = []
self._location = None
def __init__(self, label, user, creation_time=None, job_type=None, **kw):
"""
Constructor
"""
if self.__class__ is Job:
raise NotImplementedError('Abstract class')
Entity.__init__(self, **kw)
if job_type is None:
job_type = JOB_TYPES.BASE
self.job_type = job_type
self.label = label
self.user = user
if creation_time is None:
creation_time = get_utc_time()
self.creation_time = creation_time
def __init__(self, label, user, creation_time=None, job_type=None, **kw):
"""
Constructor
"""
if self.__class__ is Job:
raise NotImplementedError('Abstract class')
Entity.__init__(self, **kw)
if job_type is None:
job_type = JOB_TYPES.BASE
self.job_type = job_type
self.label = label
self.user = user
if creation_time is None:
creation_time = get_utc_time()
self.creation_time = creation_time
def run(self):
self.reset()
self.add_info('Start tube transfer execution ...')
self.__check_input()
if not self.has_errors():
self.__scan_racks()
if not self.has_errors():
self.__check_transfers()
if not self.has_errors():
self.__update_tube_locations()
if not self.has_errors():
self.return_value = TubeTransferWorklist(user=self.user,
tube_transfers=self.tube_transfers,
timestamp=get_utc_time())
self.add_info('Tube transfer executor run completed.')
def __init__(self,
product_id,
supplier,
time_stamp=None,
is_current=False,
is_deleted=False,
**kw):
Entity.__init__(self, **kw)
self.product_id = product_id
self.supplier = supplier
if time_stamp is None:
time_stamp = get_utc_time()
self.time_stamp = time_stamp
self.is_current = is_current
self.is_deleted = is_deleted
def __init__(self, label, subproject, number_replicates,
experiment_metadata_type, experiment_design=None,
ticket_number=None, lab_iso_request=None, creation_date=None,
**kw):
Entity.__init__(self, **kw)
self.label = label
self.subproject = subproject
self.experiment_design = experiment_design
self.lab_iso_request = lab_iso_request
self.number_replicates = number_replicates
self.ticket_number = ticket_number
if creation_date is None:
creation_date = get_utc_time()
self.creation_date = creation_date
self.experiment_metadata_type = experiment_metadata_type
def run(self):
self.reset()
self.add_info('Start tube transfer execution ...')
self.__check_input()
if not self.has_errors():
self.__scan_racks()
if not self.has_errors():
self.__check_transfers()
if not self.has_errors():
self.__update_tube_locations()
if not self.has_errors():
self.return_value = TubeTransferWorklist(
user=self.user,
tube_transfers=self.tube_transfers,
timestamp=get_utc_time())
self.add_info('Tube transfer executor run completed.')
def __init__(self,
label,
leader,
customer=None,
creation_date=None,
subprojects=None,
**kw):
Entity.__init__(self, **kw)
self.label = label
self.title = label
self.customer = customer
self.leader = leader
if creation_date is None:
creation_date = get_utc_time()
self.creation_date = creation_date
if subprojects is None:
subprojects = []
self.subprojects = subprojects
def __init__(self, planned_liquid_transfer, user, timestamp=None,
transfer_type=None, **kw): # pylint: disable=W0622
if self.__class__ is ExecutedLiquidTransfer:
raise NotImplementedError('Abstract class')
Entity.__init__(self, **kw)
if transfer_type is None:
transfer_type = TRANSFER_TYPES.LIQUID_TRANSFER
self.transfer_type = transfer_type
if not planned_liquid_transfer.transfer_type == transfer_type:
msg = 'Invalid planned liquid transfer type "%s" for executed ' \
'transfer class %s.' \
% (planned_liquid_transfer.transfer_type,
self.__class__.__name__)
raise ValueError(msg)
self.planned_liquid_transfer = planned_liquid_transfer
self.user = user
if timestamp is None:
timestamp = get_utc_time()
self.timestamp = timestamp
def __init__(self,
label,
subproject,
number_replicates,
experiment_metadata_type,
experiment_design=None,
ticket_number=None,
lab_iso_request=None,
creation_date=None,
**kw):
Entity.__init__(self, **kw)
self.label = label
self.subproject = subproject
self.experiment_design = experiment_design
self.lab_iso_request = lab_iso_request
self.number_replicates = number_replicates
self.ticket_number = ticket_number
if creation_date is None:
creation_date = get_utc_time()
self.creation_date = creation_date
self.experiment_metadata_type = experiment_metadata_type
def __init__(self,
label,
specs,
status,
comment='',
creation_date=None,
barcode=None,
**kw):
Entity.__init__(self, **kw)
if self.__class__ is Rack:
raise NotImplementedError('Abstract class')
self.label = label
self.specs = specs
self.status = status
self.comment = comment
if creation_date is None:
creation_date = get_utc_time()
self.creation_date = creation_date
self.barcode = barcode
self.containers = []
self._location = None
def check_in(self):
"""
Checks this sample into a freezer.
Requires the `checkout_date` attribute to be set so that we can
determine if a freeze/thaw cycle increment is in order.
:raises RuntimeError: If the `checkout_date` attribute is `None`.
"""
checkout_date = self.checkout_date
if checkout_date is None:
raise RuntimeError("Trying to check in a sample that has not " "been checked out.")
if checkout_date.tzinfo is None:
checkout_date = as_utc_time(self.checkout_date)
checkout_secs = abs(get_utc_time() - checkout_date).seconds
if checkout_secs > self.thaw_time:
if self.freeze_thaw_cycles is None:
self.freeze_thaw_cycles = 1
else:
self.freeze_thaw_cycles += 1
self.checkout_date = None
def check_in(self):
"""
Checks this sample into a freezer.
Requires the `checkout_date` attribute to be set so that we can
determine if a freeze/thaw cycle increment is in order.
:raises RuntimeError: If the `checkout_date` attribute is `None`.
"""
checkout_date = self.checkout_date
if checkout_date is None:
raise RuntimeError('Trying to check in a sample that has not '
'been checked out.')
if checkout_date.tzinfo is None:
checkout_date = as_utc_time(self.checkout_date)
checkout_secs = abs(get_utc_time() - checkout_date).seconds
if checkout_secs > self.thaw_time:
if self.freeze_thaw_cycles is None:
self.freeze_thaw_cycles = 1
else:
self.freeze_thaw_cycles += 1
self.checkout_date = None
def __parse_scanning_files(self):
# Parses the scanning file(s). The result are stored in
# :attr:`__file_layouts`.
self.add_debug('Parse scanning files ...')
self.__max_age = timedelta(days=self.MAX_FILE_AGE)
self.__now = get_utc_time()
file_map = self.__get_files_from_directory()
if file_map is None and not self.has_errors():
file_map = read_zip_archive(zip_stream=self.rack_scanning_files)
if not file_map is None:
for fn, stream in file_map.iteritems():
self.__parse_rack_scanning_file(stream, fn)
elif not self.has_errors():
if isinstance(self.rack_scanning_files, StringIO):
stream = self.rack_scanning_files
else:
try:
stream = open(self.rack_scanning_files, 'r')
except IOError:
stream = self.rack_scanning_files
except TypeError:
stream = self.rack_scanning_files
self.__parse_rack_scanning_file(stream)
def __parse_scanning_files(self):
# Parses the scanning file(s). The result are stored in
# :attr:`__file_layouts`.
self.add_debug('Parse scanning files ...')
self.__max_age = timedelta(days=self.MAX_FILE_AGE)
self.__now = get_utc_time()
file_map = self.__get_files_from_directory()
if file_map is None and not self.has_errors():
file_map = read_zip_archive(zip_stream=self.rack_scanning_files)
if not file_map is None:
for fn, stream in file_map.iteritems():
self.__parse_rack_scanning_file(stream, fn)
elif not self.has_errors():
if isinstance(self.rack_scanning_files, StringIO):
stream = self.rack_scanning_files
else:
try:
stream = open(self.rack_scanning_files, 'r')
except IOError:
stream = self.rack_scanning_files
except TypeError:
stream = self.rack_scanning_files
self.__parse_rack_scanning_file(stream)
def from_rack(cls, tube_rack):
"""
Creates a :class:`RackScanningLayout` using the data of a the passed
rack.
:param tube_rack: The tube rack to create the layout for.
:type tube_rack: :class:`thelma.entities.rack.TubeRack`
:raises TypeError: If the tube rack is the wrong type (incl. other
rack types).
:return: :class:`RackScanningLayout`
"""
if not isinstance(tube_rack, TubeRack):
msg = 'The tube rack must be a %s type (obtained: %s).' \
% (TubeRack.__class__.__name__, tube_rack.__class__.__name__)
raise TypeError(msg)
rsl = RackScanningLayout(rack_barcode=tube_rack.barcode,
timestamp=get_utc_time())
# for tube in tube_rack.containers:
# rack_pos = tube.position
# rsl.add_position(rack_pos, tube.barcode)
for pos, tube in iteritems_(tube_rack.container_positions):
rsl.add_position(pos, tube.barcode)
return rsl
def __init__(self,
planned_liquid_transfer,
user,
timestamp=None,
transfer_type=None,
**kw): # pylint: disable=W0622
if self.__class__ is ExecutedLiquidTransfer:
raise NotImplementedError('Abstract class')
Entity.__init__(self, **kw)
if transfer_type is None:
transfer_type = TRANSFER_TYPES.LIQUID_TRANSFER
self.transfer_type = transfer_type
if not planned_liquid_transfer.transfer_type == transfer_type:
msg = 'Invalid planned liquid transfer type "%s" for executed ' \
'transfer class %s.' \
% (planned_liquid_transfer.transfer_type,
self.__class__.__name__)
raise ValueError(msg)
self.planned_liquid_transfer = planned_liquid_transfer
self.user = user
if timestamp is None:
timestamp = get_utc_time()
self.timestamp = timestamp
def __init__(self, molecule_design, supplier, **kw):
Entity.__init__(self, **kw)
self.molecule_design = molecule_design
self.supplier = supplier
self.insert_date = get_utc_time()
self.samples = []
def __init__(self, molecule_design, supplier, **kw):
Entity.__init__(self, **kw)
self.molecule_design = molecule_design
self.supplier = supplier
self.insert_date = get_utc_time()
self.samples = []
