def __init__(self, name, label, devices=None, **kw):
Entity.__init__(self, **kw)
self.name = name
self.label = label
if devices is None:
devices = []
self.devices = devices
def __init__(self, species_name, genus_name,
cultivar=None, author=None, **kw):
Entity.__init__(self, **kw)
self.species_name = species_name
self.genus_name = genus_name
self.cultivar = cultivar
self.author = author
def __init__(self, specs, status, sample=None, **kw):
Entity.__init__(self, **kw)
if self.__class__ is Container:
raise NotImplementedError('Abstract class')
self.specs = specs
self.status = status
self.sample = sample
def __init__(self, specs, status, sample=None, **kw):
Entity.__init__(self, **kw)
if self.__class__ is Container:
raise NotImplementedError("Abstract class")
self.specs = specs
self.status = status
self.sample = sample
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 __init__(self, name, label, devices=None, **kw):
Entity.__init__(self, **kw)
self.name = name
self.label = label
if devices is None:
devices = []
self.devices = devices
def __init__(self, rack, location, checkin_date=None, **kw):
Entity.__init__(self, **kw)
self.rack = rack
self.location = location
if checkin_date is None:
checkin_date = datetime.datetime.now()
self.checkin_date = checkin_date
def __init__(self, username, directory_user_id, user_preferenceses=None,
**kw):
Entity.__init__(self, **kw)
self.username = username
self.directory_user_id = directory_user_id
if user_preferenceses is None:
user_preferenceses = []
self.user_preferenceses = user_preferenceses
def __init__(self, label, rack_layout, experiment_design=None,
worklist_series=None,
**kw):
Entity.__init__(self, **kw)
self.label = label
self.rack_layout = rack_layout
self.experiment_design = experiment_design
self.worklist_series = worklist_series
def __init__(self, tube, source_rack, source_position, target_rack,
target_position, **kw):
Entity.__init__(self, **kw)
self.tube = tube
self.source_rack = source_rack
self.source_position = source_position
self.target_rack = target_rack
self.target_position = target_position
def __init__(self, set_type, molecule_designs=None, **kw):
if self.__class__ is MoleculeDesignSetBase:
raise NotImplementedError('Abstract class.')
Entity.__init__(self, **kw)
if molecule_designs is None:
molecule_designs = set()
self.set_type = set_type
self.molecule_designs = molecule_designs
def __init__(self, text=None, text_ent=None, **kw):
Entity.__init__(self, **kw)
if text is None:
text = self.DEFAULT_TEXT
self.text = text
if text_ent is None:
text_ent = self.DEFAULT_TEXT
self.text_ent = text_ent
def __init__(self, molecule_design_library, rack, layout_number,
has_been_used=False, lab_iso=None, **kw):
Entity.__init__(self, **kw)
self.molecule_design_library = molecule_design_library
self.rack = rack
self.layout_number = layout_number
self.has_been_used = has_been_used
self.lab_iso = lab_iso
def __init__(self, tube, source_rack, source_position, target_rack,
target_position, **kw):
Entity.__init__(self, **kw)
self.tube = tube
self.source_rack = source_rack
self.source_position = source_position
self.target_rack = target_rack
self.target_position = target_position
def __init__(self, text=None, text_ent=None, **kw):
Entity.__init__(self, **kw)
if text is None:
text = self.DEFAULT_TEXT
self.text = text
if text_ent is None:
text_ent = self.DEFAULT_TEXT
self.text_ent = text_ent
def __init__(self, text, guid=None, time_stamp=None, **kw):
Entity.__init__(self, **kw)
if guid is None:
guid = str(uuid.uuid4())
if time_stamp is None:
time_stamp = datetime.now()
self.text = text
self.guid = guid
self.time_stamp = time_stamp
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, 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, iso, rack, iso_plate_type=None, **kw):
Entity.__init__(self, **kw)
if self.__class__ is IsoPlate:
raise NotImplementedError('Abstract class')
if iso_plate_type is None:
iso_plate_type = ISO_PLATE_TYPES.ISO_PLATE
self.iso_plate_type = iso_plate_type
self.iso = iso
self.rack = rack
def __init__(self, text, guid=None, time_stamp=None, **kw):
Entity.__init__(self, **kw)
if guid is None:
guid = str(uuid.uuid4())
if time_stamp is None:
time_stamp = datetime.now()
self.text = text
self.guid = guid
self.time_stamp = time_stamp
def __init__(self, name, description, rack_shape, max_volume,
min_dead_volume, max_dead_volume, **kw):
Entity.__init__(self, **kw)
self._name = name
self._description = description
self._rack_shape = rack_shape
self._max_volume = max_volume
self._min_dead_volume = min_dead_volume
self._max_dead_volume = max_dead_volume
def __init__(self, positions, hash_value, **kw):
"""
This construction should not be used. Use the factory method
:func:`from_positions` to load a potential existing rack position
set from DB instead of creating a new one.
"""
Entity.__init__(self, **kw)
self._positions = positions
self._hash_value = hash_value
def __init__(self, positions, hash_value, **kw):
"""
This construction should not be used. Use the factory method
:func:`from_positions` to load a potential existing rack position
set from DB instead of creating a new one.
"""
Entity.__init__(self, **kw)
self._positions = positions
self._hash_value = hash_value
def __init__(self, name, description, rack_shape, max_volume,
min_dead_volume, max_dead_volume, **kw):
Entity.__init__(self, **kw)
self._name = name
self._description = description
self._rack_shape = rack_shape
self._max_volume = max_volume
self._min_dead_volume = min_dead_volume
self._max_dead_volume = max_dead_volume
def __init__(self, iso, rack, iso_plate_type=None, **kw):
Entity.__init__(self, **kw)
if self.__class__ is IsoPlate:
raise NotImplementedError('Abstract class')
if iso_plate_type is None:
iso_plate_type = ISO_PLATE_TYPES.ISO_PLATE
self.iso_plate_type = iso_plate_type
self.iso = iso
self.rack = rack
def __init__(self, rack_shape=None, experiment_design_racks=None,
worklist_series=None, experiment_metadata=None, **kw):
Entity.__init__(self, **kw)
if experiment_design_racks is None:
experiment_design_racks = []
self.experiment_design_racks = experiment_design_racks
self.rack_shape = rack_shape
self.worklist_series = worklist_series
self.experiment_metadata = experiment_metadata
def __init__(self, name, min_transfer_volume, max_transfer_volume,
max_dilution_factor, has_dynamic_dead_volume, is_sector_bound,
**kw):
Entity.__init__(self, **kw)
self._name = name
self._min_transfer_volume = min_transfer_volume
self._max_transfer_volume = max_transfer_volume
self._max_dilution_factor = max_dilution_factor
self._has_dynamic_dead_volume = has_dynamic_dead_volume
self._is_sector_bound = is_sector_bound
def __init__(self, label, experiment_design,
source_rack=None, job=None, experiment_racks=None, **kw):
Entity.__init__(self, **kw)
self.label = label
self.source_rack = source_rack
self.experiment_design = experiment_design
self.job = job
if experiment_racks is None:
experiment_racks = []
self.experiment_racks = experiment_racks
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 __init__(self, row_index, column_index, label, **kw):
"""
This constructor should not be used. Load the rack positions from the
DB instead by means of one of fetcher methods (:func:`from_label`,
:func:`from_row_index_column_index` or :func:`from_row_column`).
"""
Entity.__init__(self, **kw)
self._label = label
self._row_index = row_index
self._column_index = column_index
def __init__(self, name, min_transfer_volume, max_transfer_volume,
max_dilution_factor, has_dynamic_dead_volume, is_sector_bound,
**kw):
Entity.__init__(self, **kw)
self._name = name
self._min_transfer_volume = min_transfer_volume
self._max_transfer_volume = max_transfer_volume
self._max_dilution_factor = max_dilution_factor
self._has_dynamic_dead_volume = has_dynamic_dead_volume
self._is_sector_bound = is_sector_bound
def __init__(self, row_index, column_index, label, **kw):
"""
This constructor should not be used. Load the rack positions from the
DB instead by means of one of fetcher methods (:func:`from_label`,
:func:`from_row_index_column_index` or :func:`from_row_column`).
"""
Entity.__init__(self, **kw)
self._label = label
self._row_index = row_index
self._column_index = column_index
def __init__(self, shape=None, tagged_rack_position_sets=None, **kw):
Entity.__init__(self, **kw)
self.shape = shape
if tagged_rack_position_sets is None:
tagged_rack_position_sets = []
self.tagged_rack_position_sets = tagged_rack_position_sets
self.__tag_to_positions_map = None
self.__position_to_tags_map = None
self.__all_tags = None
self.__all_positions = None
def __init__(self, genus_name, species_name, common_name, acronym,
ncbi_tax_id, genes=None, **kw):
Entity.__init__(self, **kw)
self.genus_name = genus_name
self.species_name = species_name
self.common_name = common_name
self.acronym = acronym
self.ncbi_tax_id = ncbi_tax_id
if genes is None:
genes = []
self.genes = genes
def __init__(self,
username,
directory_user_id,
user_preferenceses=None,
**kw):
Entity.__init__(self, **kw)
self.username = username
self.directory_user_id = directory_user_id
if user_preferenceses is None:
user_preferenceses = []
self.user_preferenceses = user_preferenceses
def __init__(self, name, default_stock_concentration,
description='', thaw_time=0, modifications=None, **kw):
if not 'id' in kw:
kw['id'] = name.lower()
Entity.__init__(self, **kw)
self.name = name
self.default_stock_concentration = default_stock_concentration
self.description = description
self.thaw_time = thaw_time
if modifications == None:
self.modifications = []
def __init__(self, structure_type_id, representation,
molecule_designs=None, **kw):
if self.__class__ is ChemicalStructure:
raise NotImplementedError('Abstract class.')
Entity.__init__(self, **kw)
self.structure_type_id = structure_type_id
self._validate_representation(representation)
self.representation = representation
if molecule_designs is None:
molecule_designs = []
self.molecule_designs = molecule_designs
def __init__(self, molecule_design_pool_set, label, final_volume,
final_concentration, number_layouts, rack_layout,
creation_iso_request=None, **kw):
Entity.__init__(self, **kw)
self.molecule_design_pool_set = molecule_design_pool_set
self.label = label
self.final_volume = final_volume
self.final_concentration = final_concentration
self.number_layouts = number_layouts
self.rack_layout = rack_layout
self.creation_iso_request = creation_iso_request
def __init__(self, name, label, command_definition, value_type,
description=None, parameter_options=None, **kw):
Entity.__init__(self, **kw)
self.name = name
self.label = label
self.command_definition = command_definition
self.value_type = value_type
self.description = description
if parameter_options is None:
parameter_options = []
self.parameter_options = parameter_options
def __init__(self,
barcodes='',
labels=None,
printer=None,
type=None,
**kw):
Entity.__init__(self, **kw)
self.barcodes = barcodes
self.labels = labels
self.printer = printer
self.type = type
def __init__(self,
label,
rack_layout,
experiment_design=None,
worklist_series=None,
**kw):
Entity.__init__(self, **kw)
self.label = label
self.rack_layout = rack_layout
self.experiment_design = experiment_design
self.worklist_series = worklist_series
def __init__(self, volume, hash_value=None, transfer_type=None, **kw):
"""
Constructor
"""
Entity.__init__(self, **kw)
if self.__class__ is PlannedLiquidTransfer:
raise NotImplementedError('Abstract class')
self._volume = volume
self._hash_value = hash_value
if transfer_type is None:
transfer_type = TRANSFER_TYPES.LIQUID_TRANSFER
self._transfer_type = transfer_type
def __init__(self, molecule_design_pool, molecule_type, concentration,
total_tubes, total_volume, minimum_volume, maximum_volume,
**kw):
Entity.__init__(self, **kw)
self.molecule_design_pool = molecule_design_pool
self.molecule_type = molecule_type
self.concentration = concentration
self.total_tubes = total_tubes
self.total_volume = total_volume
self.minimum_volume = minimum_volume
self.maximum_volume = maximum_volume
self.genes = []
def __init__(self, name, label, type, barcode, location_rack=None, # redef type pylint: disable=W0622
device=None, index=None, **kw):
Entity.__init__(self, **kw)
#FIXME: #pylint: disable=W0511
# this awaits proper handling of character ids on DB level
self.name = name
self.label = label
self.type = type
self.device = device
self.index = index
self.barcode = barcode
self.location_rack = location_rack
def __init__(self, volume, hash_value=None, transfer_type=None, **kw):
"""
Constructor
"""
Entity.__init__(self, **kw)
if self.__class__ is PlannedLiquidTransfer:
raise NotImplementedError('Abstract class')
self._volume = volume
self._hash_value = hash_value
if transfer_type is None:
transfer_type = TRANSFER_TYPES.LIQUID_TRANSFER
self._transfer_type = transfer_type
def __init__(self,
molecule_design_library,
rack,
layout_number,
has_been_used=False,
lab_iso=None,
**kw):
Entity.__init__(self, **kw)
self.molecule_design_library = molecule_design_library
self.rack = rack
self.layout_number = layout_number
self.has_been_used = has_been_used
self.lab_iso = lab_iso
def __init__(self,
rack_shape=None,
experiment_design_racks=None,
worklist_series=None,
experiment_metadata=None,
**kw):
Entity.__init__(self, **kw)
if experiment_design_racks is None:
experiment_design_racks = []
self.experiment_design_racks = experiment_design_racks
self.rack_shape = rack_shape
self.worklist_series = worklist_series
self.experiment_metadata = experiment_metadata
def __init__(self, tags, user):
"""
Constructor.
:param set tags: Set of :class:`Tag` instances associated to the rack
positions.
:param user: User who creates the tagged object.
:type user: class:`thelma.entities.user.User`
"""
Entity.__init__(self)
if len(tags) < 1:
raise ValueError('The tag list is empty!')
self.taggings = [Tagging(tag, self, user) for tag in tags]
self.tags = tags
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, tag, tagged, user, **kw):
"""
Constructor.
:param tag: tag for this tagging.
:type tag: :class:`Tag`.
:param tagged: object to tag.
:type tagged: :class:`Tagged`
:param user: User performing the tagging.
:type user: class:`thelma.entities.user.User`
"""
Entity.__init__(self, **kw)
self.tag = tag
self.tagged = tagged
self.user = user
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,
experiment_design,
source_rack=None,
job=None,
experiment_racks=None,
**kw):
Entity.__init__(self, **kw)
self.label = label
self.source_rack = source_rack
self.experiment_design = experiment_design
self.job = job
if experiment_racks is None:
experiment_racks = []
self.experiment_racks = experiment_racks