class BarcodePrintJobMember(Member):
relation = "%s/barcode" % RELATION_BASE_URL
title = attribute_alias('labels')
barcodes = terminal_attribute(str, 'barcodes')
labels = terminal_attribute(str, 'labels')
printer = terminal_attribute(str, 'printer')
type = terminal_attribute(str, 'type')
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 RackSpecsMember(Member):
relation = "%s/rack-specs" % RELATION_BASE_URL
title = attribute_alias('label')
label = terminal_attribute(str, 'label')
shape = member_attribute(IRackShape, 'shape')
manufacturer = member_attribute(IOrganization, 'manufacturer')
has_tubes = terminal_attribute(bool, 'has_tubes')
class SpeciesMember(Member):
relation = 'http://plantscribe.org/relations/species'
title = attribute_alias('species_name')
species_name = terminal_attribute(str, 'species_name')
genus_name = terminal_attribute(str, 'genus_name')
cultivar = terminal_attribute(str, 'cultivar')
author = terminal_attribute(str, 'author')
class SpeciesMember(Member):
relation = "%s/species" % RELATION_BASE_URL
title = attribute_alias('common_name')
genus_name = terminal_attribute(str, 'genus_name')
species_name = terminal_attribute(str, 'species_name')
common_name = terminal_attribute(str, 'common_name')
acronym = terminal_attribute(str, 'acronym')
ncbi_tax_id = terminal_attribute(int, 'ncbi_tax_id')
class RackShapeMember(Member):
relation = "%s/rack-shape" % RELATION_BASE_URL
id = terminal_attribute(str, 'id') # rack shape IDs are *strings*.
name = terminal_attribute(str, 'name')
label = terminal_attribute(str, 'label')
number_rows = terminal_attribute(int, 'number_rows')
number_columns = terminal_attribute(int, 'number_columns')
title = attribute_alias('label')
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 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 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 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 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 MyEntityParentMember(Member):
relation = 'http://test.org/myentity-parent'
# String terminal.
text = terminal_attribute(str, 'text')
# String terminal with different name in entity.
text_rc = terminal_attribute(str, 'text_ent')
#
text_alias = attribute_alias('text')
class ContainerSpecsMember(Member):
relation = "%s/container-specs" % RELATION_BASE_URL
title = attribute_alias('label')
label = terminal_attribute(str, 'label')
description = terminal_attribute(str, 'description')
max_volume = terminal_attribute(float, 'max_volume')
dead_volume = terminal_attribute(float, 'dead_volume')
manufacturer = member_attribute(IOrganization, 'manufacturer')
class MyEntityGrandchildMember(Member):
relation = 'http://test.org/myentity-grandchild'
# String terminal.
text = terminal_attribute(str, 'text')
# String terminal with different name in entity.
text_rc = terminal_attribute(str, 'text_ent')
# Member.
parent = member_attribute(IMyEntityChild, 'parent', backref='children')
class SampleRegistrationItemMember(Member):
relation = "%s/sample-registration-item" % RELATION_BASE_URL
supplier = member_attribute(IOrganization, 'supplier')
concentration = terminal_attribute(float, 'concentration')
volume = terminal_attribute(float, 'volume')
tube_barcode = terminal_attribute(str, 'tube_barcode')
rack_barcode = terminal_attribute(str, 'rack_barcode')
rack_position = member_attribute(IRackPosition, 'rack_position')
molecule_design_pool = member_attribute(IMoleculeDesignPool,
'molecule_design_pool')
class JobMember(Member):
relation = '%s/job' % RELATION_BASE_URL
job_type = terminal_attribute(str, 'job_type')
label = terminal_attribute(str, 'label')
user = member_attribute(IUser, 'user')
creation_time = terminal_attribute(datetime, 'creation_time')
@property
def title(self):
entity = self.get_entity()
return '%s: %s' % (entity.job_type, entity.label)
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 StockSampleCreationIsoRequestMember(IsoRequestMember):
relation = "%s/stock-sample-creation-iso-request" % RELATION_BASE_URL
stock_volume = terminal_attribute(float, 'stock_volume')
stock_concentration = terminal_attribute(float, 'stock_concentration')
number_designs = terminal_attribute(int, 'number_designs')
molecule_design_library = member_attribute(IMoleculeDesignLibrary,
'molecule_design_library')
@property
def title(self):
return 'Stock Sample Generation ISO Request'
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 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 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 SupplierSampleRegistrationItemMember(SampleRegistrationItemMember):
relation = "%s/supplier-sample-registration-item" % RELATION_BASE_URL
supplier = member_attribute(IOrganization, 'supplier')
product_id = terminal_attribute(str, 'product_id')
concentration = terminal_attribute(float, 'concentration')
volume = terminal_attribute(float, 'volume')
tube_barcode = terminal_attribute(str, 'tube_barcode')
rack_barcode = terminal_attribute(str, 'rack_barcode')
rack_position = member_attribute(IRackPosition, 'rack_position')
molecule_type = member_attribute(IMoleculeType, 'molecule_type')
molecule_design_pool_registration_item = \
member_attribute(IMoleculeDesignPoolRegistrationItem,
'molecule_design_pool_registration_item')
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 TubeMember(ContainerMember):
relation = "%s/tube" % RELATION_BASE_URL
position = member_attribute(IRackPosition, 'location.position')
location = member_attribute(ILocation, 'location.rack.location')
rack = member_attribute(IRack, 'location.rack')
rack_specs = member_attribute(IRackSpecs, 'location.rack.specs')
# None in containers that do not hold stock samples.
sample_product_id = terminal_attribute(str, 'sample.product_id')
sample_supplier = member_attribute(IOrganization, 'sample.supplier')
barcode = terminal_attribute(str, 'barcode')
@property
def title(self):
entity = self.get_entity()
return '%s @ %s' % (entity.barcode or 'NO BARCODE', entity.location)
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 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 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 SubprojectMember(Member):
relation = "%s/subproject" % RELATION_BASE_URL
label = terminal_attribute(str, 'label')
project = member_attribute(IProject, 'project')
creation_date = terminal_attribute(datetime, 'creation_date')
active = terminal_attribute(bool, 'active')
@property
def title(self):
# The title is formed from the project's and the subproject's label
# and does not need to be persisted or exposed.
return self.get_entity().title
def update(self, member):
super(SubprojectMember, self).update(member)
self.label = member.label
self.active = member.active
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')
def test_state_data(self):
data = dict(text='FOO',
number=-1,
parent=MyEntityParent(),
children=[MyEntityChild()])
entity = MyEntity(**data)
# We don't want to test the required unit of work here.
uow = MagicMock()
self.assert_raises(ValueError, EntityState.get_state, entity)
entity.__everest__ = EntityState(entity, uow)
state_data = EntityState.get_state(entity).data
for attr, value in state_data.items():
if attr.resource_attr == 'number':
number_attr = attr
elif attr.resource_attr == 'parent':
parent_attr = attr
elif attr.resource_attr == 'parent_text':
parent_text_attr = attr
if attr.resource_attr in data:
self.assert_equal(value, data[attr.resource_attr])
new_number = -2
state_data[number_attr] = new_number
EntityState.get_state(entity).data = state_data
self.assert_equal(entity.number, new_number)
new_entity = MyEntity()
self.assert_not_equal(new_entity.number, new_number)
new_entity.__everest__ = EntityState(new_entity, uow)
EntityState.transfer_state_data(entity, new_entity)
self.assert_equal(new_entity.number, new_number)
# Make setting invalid attribute fail.
invalid_number_attr = terminal_attribute(str, 'grmbl')
del state_data[number_attr]
state_data[invalid_number_attr] = -2
with self.assert_raises(ValueError) as cm:
EntityState.get_state(entity).data = state_data
self.assert_true(cm.exception.args[0].startswith('Can not set'))
# Make set nested attribute fail.
entity.parent = None
del state_data[invalid_number_attr]
del state_data[parent_attr]
state_data[parent_text_attr] = 'FOO PARENT'
state = EntityState.get_state(entity)
self.assert_raises(AttributeError, setattr, state, 'data', state_data)
def test_invalid_kind(self):
attr = terminal_attribute(str, 'foo')
attr.kind = 'INVALID'
mp_attr = MappedAttribute(attr, options={IGNORE_OPTION:None})
key = MappedAttributeKey(())
self.assert_raises(ValueError, mp_attr.should_ignore, key)
def test_is_terminal_attribute(self, attr_name):
mb_attr = member_attribute(Member, attr_name)
assert is_terminal_attribute(mb_attr) is False
t_attr = terminal_attribute(int, attr_name)
assert is_terminal_attribute(t_attr) is True
def test_get_attribute_cardinality(self, attr_name):
mb_attr = member_attribute(Member, attr_name)
assert get_attribute_cardinality(mb_attr) == CARDINALITY_CONSTANTS.ONE
t_attr = terminal_attribute(int, attr_name)
with pytest.raises(ValueError):
get_attribute_cardinality(t_attr)
def set_up(self):
self.member_attr = member_attribute(Member, 'attr')
self.terminal_attr = terminal_attribute(int, 'attr')