class IsoJobMember(JobMember):
relation = "%s/iso_job" % RELATION_BASE_URL
isos = collection_attribute(IIso, 'isos')
number_stock_racks = terminal_attribute(int, 'number_stock_racks')
stock_racks = collection_attribute(IStockRack, 'iso_job_stock_racks')
preparation_plates = collection_attribute(IPlate, 'preparation_plates')
status = terminal_attribute(str, 'status')
class ExperimentDesignMember(Member):
relation = "%s/experiment-design" % RELATION_BASE_URL
title = terminal_attribute(str, 'slug')
rack_shape = member_attribute(IRackShape, 'rack_shape')
experiment_design_racks = collection_attribute(IExperimentDesignRack,
'experiment_design_racks')
experiments = collection_attribute(IExperiment, 'experiments')
experiment_metadata = member_attribute(IExperimentMetadata,
'experiment_metadata')
class MoleculeDesignPoolMember(MoleculeDesignSetMember):
"""
"""
relation = "%s/molecule-design-pool" % RELATION_BASE_URL
molecule_type = member_attribute(IMoleculeType, 'molecule_type')
# stock_samples = collection_attribute(IStockSample, 'stock_samples')
# member_hash = terminal_attribute(str, 'member_hash')
number_designs = terminal_attribute(int, 'number_designs')
genes = collection_attribute(IGene, 'genes')
supplier_molecule_designs = \
collection_attribute(ISupplierMoleculeDesign,
'supplier_molecule_designs')
class MoleculeDesignMember(Member):
relation = "%s/molecule-design" % RELATION_BASE_URL
@property
def title(self):
return str(self.id)
molecule_type = member_attribute(IMoleculeType, 'molecule_type')
chemical_structures = collection_attribute(IChemicalStructure,
'chemical_structures')
genes = collection_attribute(IGene, 'genes',
cardinality=CARDINALITIES.MANYTOMANY)
supplier_molecule_designs = \
collection_attribute(ISupplierMoleculeDesign,
'supplier_molecule_designs')
class MoleculeTypeMember(Member):
relation = "%s/molecule-type" % RELATION_BASE_URL
title = attribute_alias('name')
name = terminal_attribute(str, 'name')
description = terminal_attribute(str, 'description')
thaw_time = terminal_attribute(float, 'thaw_time')
modifications = collection_attribute(IChemicalStructure, 'modifications')
class ExperimentDesignRackMember(Member):
relation = "%s/experiment-design-rack" % RELATION_BASE_URL
title = attribute_alias('label')
label = terminal_attribute(str, 'label')
rack_shape = member_attribute(IRackShape, 'rack_layout.shape')
rack_layout = member_attribute(IRackLayout, 'rack_layout')
tags = collection_attribute(ITag, 'tags')
class GeneMember(Member):
relation = "%s/gene" % RELATION_BASE_URL
title = attribute_alias('locus_name')
accession = terminal_attribute(str, 'accession')
locus_name = terminal_attribute(str, 'locus_name')
# nice_name = terminal_attribute('nice_name')
species = member_attribute(ISpecies, 'species')
molecule_designs = \
collection_attribute(IMoleculeDesign,
'molecule_designs',
cardinality=CARDINALITIES.MANYTOMANY)
molecule_design_pools = \
collection_attribute(IMoleculeDesignPool,
'molecule_design_pools',
cardinality=CARDINALITIES.MANYTOMANY)
class SiteMember(Member):
relation = 'http://plantscribe.org/relations/site'
title = attribute_alias('name')
name = terminal_attribute(str, 'name')
incidences = collection_attribute(IIncidence,
backref='site',
is_nested=True)
project = member_attribute(IProject, 'project')
class MoleculeMember(Member):
relation = "%s/molecule" % RELATION_BASE_URL
molecule_design = member_attribute(IMoleculeDesign, 'molecule_design')
molecule_design_id = terminal_attribute(int, 'molecule_design.id')
supplier = member_attribute(IOrganization, 'supplier')
product_id = terminal_attribute(str, 'supplier_molecule_design.product_id')
insert_date = terminal_attribute(datetime, 'insert_date')
samples = collection_attribute(ISample, 'samples')
class ProjectMember(Member):
relation = "%s/project" % RELATION_BASE_URL
title = attribute_alias('label')
label = terminal_attribute(str, 'label')
creation_date = terminal_attribute(datetime, 'creation_date')
leader = member_attribute(IUser, 'leader')
customer = member_attribute(IOrganization, 'customer')
subprojects = collection_attribute(ISubproject, 'subprojects')
class ChemicalStructureMember(Member):
relation = "%s/chemical-structure" % RELATION_BASE_URL
molecule_designs = collection_attribute(IMoleculeDesign,
'molecule_designs')
structure_type = member_attribute(IChemicalStructureType, 'structure_type')
representation = terminal_attribute(str, 'representation')
structure_type_id = terminal_attribute(str, 'structure_type_id')
title = attribute_alias('representation')
class UserMember(Member):
relation = "%s/user" % RELATION_BASE_URL
title = attribute_alias('username')
label = attribute_alias('username')
username = terminal_attribute(str, 'username')
user_preferenceses = collection_attribute(IUserPreferences,
'user_preferenceses')
directory_user_id = terminal_attribute(str, 'directory_user_id')
class SampleMember(Member):
relation = "%s/sample" % RELATION_BASE_URL
volume = terminal_attribute(float, 'volume')
container = member_attribute(IContainer, 'container')
sample_molecules = collection_attribute(ISampleMolecule,
'sample_molecules')
molecule_design_pool_id = terminal_attribute(int,
'molecule_design_pool_id')
class MoleculeDesignPoolSetMember(Member):
"""
"""
relation = "%s/molecule-design-pool-set" % RELATION_BASE_URL
molecule_type = member_attribute(IMoleculeType, 'molecule_type')
molecule_design_pools = collection_attribute(IMoleculeDesignPool,
'molecule_design_pools')
class TubeTransferWorklistMember(Member):
relation = '%s/tube-transfer-worklists' % RELATION_BASE_URL
user = member_attribute(IUser, 'user')
tube_transfers = collection_attribute(ITubeTransfer, 'tube_transfers')
@property
def title(self):
entity = self.get_entity()
return str(entity.id)
class LabIsoMember(IsoMember):
relation = "%s/lab-iso" % RELATION_BASE_URL
iso_request = member_attribute(ILabIsoRequest, 'iso_request')
library_plates = collection_attribute(ILibraryPlate,
'library_plates',
backref='lab_iso')
requested_library_plates = terminal_attribute(str,
'requested_library_plates')
class PlateMember(RackMember):
relation = "%s/plate" % RELATION_BASE_URL
containers = collection_attribute(IWell, 'containers', backref='rack')
def __getitem__(self, name):
if name == 'wells':
result = self.containers
else:
result = RackMember.__getitem__(self, name)
return result
class DeviceTypeMember(Member):
relation = "%s/device-type" % RELATION_BASE_URL
title = attribute_alias('label')
name = terminal_attribute(str, 'name')
label = terminal_attribute(str, 'label')
devices = collection_attribute(IDevice, 'devices', backref='type')
def update(self, member):
super(DeviceTypeMember, self).update(member)
self.get_entity().name = member.get_entity().name
self.label = member.label
class ContainerMember(Member):
relation = "%s/container" % RELATION_BASE_URL
specs = member_attribute(IContainerSpecs, 'specs')
sample_volume = terminal_attribute(float, 'sample.volume')
sample_molecules = collection_attribute(ISampleMolecule,
'sample.sample_molecules',
backref='sample.container')
status = member_attribute(IItemStatus, 'status')
sample_molecule_design_pool_id = \
terminal_attribute(str,
'sample.molecule_design_pool_id')
class IsoRequestMember(Member):
relation = "%s/iso-request" % RELATION_BASE_URL
iso_type = terminal_attribute(str, 'iso_type')
label = terminal_attribute(str, 'label')
owner = terminal_attribute(str, 'owner')
expected_number_isos = terminal_attribute(int, 'expected_number_isos')
number_aliquots = terminal_attribute(int, 'number_aliquots')
iso_jobs = collection_attribute(IIsoJob, 'iso_jobs')
@property
def title(self):
return 'Base ISO Request'
class MyEntityChildMember(Member):
relation = 'http://test.org/myentity-child'
# Member.
parent = member_attribute(IMyEntity, 'parent', backref='children')
# Collection accessed as entity attribute and represented as
# "parent equal to parent member" (backreferencing) specification.
children = collection_attribute(IMyEntityGrandchild,
entity_attr='children',
backref='parent')
# String terminal.
text = terminal_attribute(str, 'text')
# String terminal with different name in entity.
text_rc = terminal_attribute(str, 'text_ent')
class TubeRackMember(RackMember):
relation = "%s/tube-rack" % RELATION_BASE_URL
containers = collection_attribute(ITube,
'tube_locations.container',
backref='rack')
def __getitem__(self, name):
if name == 'tubes':
result = self.containers
elif name == 'shape':
result = self.specs.shape
else:
result = RackMember.__getitem__(self, name)
return result
class IsoMember(Member):
relation = "%s/iso" % RELATION_BASE_URL
title = attribute_alias('label')
iso_type = terminal_attribute(str, 'label')
label = terminal_attribute(str, 'label')
status = terminal_attribute(str, 'status')
rack_layout = member_attribute(IRackLayout, 'rack_layout')
iso_job = member_attribute(IIsoJob, 'iso_job')
number_stock_racks = terminal_attribute(int, 'number_stock_racks')
molecule_design_pool_set = member_attribute(IMoleculeDesignPoolSet,
'molecule_design_pool_set')
optimizer_excluded_racks = terminal_attribute(str,
'optimizer_excluded_racks')
optimizer_requested_tubes = terminal_attribute(
str, 'optimizer_requested_tubes')
preparation_plates = collection_attribute(IPlate, 'preparation_plates')
aliquot_plates = collection_attribute(IPlate, 'aliquot_plates')
stock_racks = collection_attribute(IStockRack, 'stock_racks')
def update(self, data):
if IDataElement.providedBy(data): # pylint: disable=E1101
raise SyntaxError('Should not get here.')
else:
Member.update(self, data)
class MoleculeDesignLibraryMember(Member):
relation = "%s/molecule-design-library" % RELATION_BASE_URL
molecule_design_pool_set = member_attribute(IMoleculeDesignPoolSet,
'molecule_design_pool_set')
label = terminal_attribute(str, 'label')
final_volume = terminal_attribute(float, 'final_volume')
final_concentration = terminal_attribute(float, 'final_concentration')
number_layouts = terminal_attribute(int, 'number_layouts')
rack_layout = member_attribute(IRackLayout, 'rack_layout')
library_plates = collection_attribute(ILibraryPlate, 'library_plates')
creation_iso_request = member_attribute(IIsoRequest,
'creation_iso_request')
@property
def title(self):
return self.label
class ExperimentMember(Member):
relation = '%s/experiment' % RELATION_BASE_URL
title = attribute_alias('label')
label = terminal_attribute(str, 'label')
source_rack = member_attribute(IRack, 'source_rack')
experiment_design = member_attribute(IExperimentDesign,
'experiment_design')
experiment_racks = collection_attribute(IExperimentRack,
'experiment_racks')
experiment_job = member_attribute(IExperimentJob, 'job')
experiment_metadata_type = \
member_attribute(IExperimentMetadataType,
'experiment_design.experiment_metadata.experiment_metadata_type')
def get_writer(self):
return get_writer(self.get_entity())
class StockInfoMember(Member):
relation = "%s/stock-info" % RELATION_BASE_URL
title = attribute_alias('id')
id = terminal_attribute(str, 'id') # stock info IDs are *strings*.
# FIXME: This should be called molecule_design_pool_id in the entity
molecule_design_pool_id = terminal_attribute(int,
'molecule_design_set_id')
total_tubes = terminal_attribute(int, 'total_tubes')
total_volume = terminal_attribute(float, 'total_volume')
maximum_volume = terminal_attribute(float, 'maximum_volume')
minimum_volume = terminal_attribute(float, 'minimum_volume')
concentration = terminal_attribute(float, 'concentration')
molecule_type = member_attribute(IMoleculeType, 'molecule_type')
molecule_design_pool = member_attribute(IMoleculeDesignPool,
'molecule_design_pool')
genes = collection_attribute(IGene, 'genes',
cardinality=CARDINALITIES.MANYTOMANY)
class MoleculeDesignSetMember(Member):
"""
"""
relation = "%s/molecule-design-set" % RELATION_BASE_URL
@property
def title(self):
return str(self.id)
molecule_designs = collection_attribute(IMoleculeDesign,
'molecule_designs')
set_type = terminal_attribute(str, 'set_type')
def update(self, data):
if IEntity.providedBy(data): # pylint: disable=E1101
self.get_entity().molecule_designs = data.molecule_designs
else:
Member.update(self, data)
class MyEntityMember(Member):
relation = 'http://test.org/myentity'
# Member.
parent = member_attribute(IMyEntityParent, 'parent')
# Nested member (i.e., URL built relative to parent).
nested_parent = member_attribute(IMyEntityParent, 'parent', is_nested=True)
# Collection.
children = collection_attribute(IMyEntityChild, 'children')
# String terminal.
text = terminal_attribute(str, 'text')
# String terminal with different name in entity.
text_rc = terminal_attribute(str, 'text_ent')
# Number terminal.
number = terminal_attribute(int, 'number')
# Date time terminal.
date_time = terminal_attribute(datetime.datetime, 'date_time')
# Nested attribute.
parent_text = terminal_attribute(str, 'parent.text_ent')
class MyEntityMember(Member):
relation = 'http://test.org/myentity'
# Member.
parent = member_attribute(IMyEntityParent, 'parent',
cardinality=CARDINALITIES.ONETOONE,
backref='child')
# Collection.
children = collection_attribute(IMyEntityChild, 'children',
backref='parent')
# String terminal.
text = terminal_attribute(str, 'text')
# String terminal with different name in entity.
text_rc = terminal_attribute(str, 'text_ent')
# Number terminal.
number = terminal_attribute(int, 'number')
# Date time terminal.
date_time = terminal_attribute(datetime.datetime, 'date_time')
# Dotted attribute.
parent_text = terminal_attribute(str, 'parent.text_ent')
class RackLayoutMember(Member):
relation = '%s/rack-layout' % RELATION_BASE_URL
@property
def title(self):
return str(self.id)
shape = member_attribute(IRackShape, 'shape')
tagged_rack_position_sets = \
collection_attribute(ITaggedRackPositionSet,
'tagged_rack_position_sets')
# @property
# def rack(self):
# tags = []
# for tp in self.tagged_rack_position_sets:
# tags.append(tp)
# return tags
def __getitem__(self, name):
if name == 'tagged-rack-position-sets':
return self.tagged_rack_position_sets
else:
raise KeyError(name)
def test_invalid_descriptors(self):
with self.assert_raises(ValueError) as cm:
collection_attribute(IMyEntity)
exc_msg = 'may be None, but not both.'
self.assert_true(cm.exception.message.endswith(exc_msg))
