def create_mapper(barcoded_location_tbl, rack_barcoded_location_tbl):
"Mapper factory."
bl = barcoded_location_tbl
rbl = rack_barcoded_location_tbl.alias()
m = mapper(BarcodedLocation, barcoded_location_tbl,
id_attribute='barcoded_location_id',
slug_expression=lambda cls: as_slug_expression(cls.name),
properties=dict(
label=column_property(
barcoded_location_tbl.c.label,
comparator_factory=CaseInsensitiveComparator
),
device=relationship(Device, uselist=False,
back_populates='locations'),
location_rack=relationship(BarcodedLocationRack,
uselist=False,
back_populates='location',
# lazy='joined',
cascade='all,delete,delete-orphan',
single_parent=True
),
empty=
column_property(~exists(# the symbol "~" negates the clause
select([rbl.c.barcoded_location_id],
bl.c.barcoded_location_id == rbl.c.barcoded_location_id
)),
deferred=True
),
)
)
return m
def create_mapper(experiment_metadata_tbl,
experiment_metadata_iso_request_tbl):
"Mapper factory."
m = mapper(
ExperimentMetadata,
experiment_metadata_tbl,
id_attribute='experiment_metadata_id',
slug_expression=lambda cls: as_slug_expression(cls.label),
properties=dict(
label=column_property(
experiment_metadata_tbl.c.label,
comparator_factory=CaseInsensitiveComparator),
experiment_design=relationship(
ExperimentDesign,
uselist=False,
cascade='all,delete,delete-orphan',
back_populates='experiment_metadata'),
subproject=relationship(Subproject, uselist=False),
lab_iso_request=relationship(
LabIsoRequest,
uselist=False,
secondary=experiment_metadata_iso_request_tbl,
back_populates='experiment_metadata',
cascade='all,delete,delete-orphan',
single_parent=True),
experiment_metadata_type=relationship(ExperimentMetadataType,
uselist=False),
),
)
return m
def create_mapper(experiment_metadata_tbl,
experiment_metadata_iso_request_tbl):
"Mapper factory."
m = mapper(
ExperimentMetadata, experiment_metadata_tbl,
id_attribute='experiment_metadata_id',
slug_expression=lambda cls: as_slug_expression(cls.label),
properties=
dict(label=column_property(
experiment_metadata_tbl.c.label,
comparator_factory=CaseInsensitiveComparator
),
experiment_design=relationship(ExperimentDesign,
uselist=False,
cascade='all,delete,delete-orphan',
back_populates='experiment_metadata'),
subproject=relationship(Subproject, uselist=False),
lab_iso_request=relationship(LabIsoRequest, uselist=False,
secondary=experiment_metadata_iso_request_tbl,
back_populates='experiment_metadata',
cascade='all,delete,delete-orphan',
single_parent=True),
experiment_metadata_type=relationship(ExperimentMetadataType,
uselist=False),
),
)
return m
def create_mapper(item_status_tbl):
"Mapper factory."
m = mapper(ItemStatus,
item_status_tbl,
id_attribute='item_status_id',
slug_expression=lambda cls: as_slug_expression(cls.name))
return m
def create_mapper(barcoded_location_tbl, rack_barcoded_location_tbl):
"Mapper factory."
bl = barcoded_location_tbl
rbl = rack_barcoded_location_tbl.alias()
m = mapper(
BarcodedLocation,
barcoded_location_tbl,
id_attribute='barcoded_location_id',
slug_expression=lambda cls: as_slug_expression(cls.name),
properties=dict(
label=column_property(
barcoded_location_tbl.c.label,
comparator_factory=CaseInsensitiveComparator),
device=relationship(Device,
uselist=False,
back_populates='locations'),
location_rack=relationship(
BarcodedLocationRack,
uselist=False,
back_populates='location',
# lazy='joined',
cascade='all,delete,delete-orphan',
single_parent=True),
empty=column_property(
~exists( # the symbol "~" negates the clause
select([rbl.c.barcoded_location_id],
bl.c.barcoded_location_id
== rbl.c.barcoded_location_id)),
deferred=True),
))
return m
def create_mapper(rack_specs_tbl):
"Mapper factory."
rs = rack_specs_tbl
polymorphic_select = select([
rs,
(case([(rs.c.has_movable_subitems,
literal(RACK_SPECS_TYPES.TUBE_RACK_SPECS))],
else_=literal(
RACK_SPECS_TYPES.PLATE_SPECS))).label('rackspecs_type')
], ).alias('rackspecs')
m = mapper(
RackSpecs,
polymorphic_select,
id_attribute='rack_specs_id',
slug_expression=lambda cls: as_slug_expression(cls.name),
properties=dict(
manufacturer=relationship(Organization),
shape=relationship(RackShape,
uselist=False,
back_populates='specs'),
rack_specs_type=column_property(
polymorphic_select.c.rackspecs_type),
),
polymorphic_on=polymorphic_select.c.rackspecs_type,
polymorphic_identity=RACK_SPECS_TYPES.RACK_SPECS,
)
RackSpecs.has_tubes = synonym('has_movable_subitems')
return m
def create_mapper(rack_tbl, rack_barcoded_location_tbl):
"Mapper factory."
rbl = rack_barcoded_location_tbl
m = mapper(Rack, rack_tbl,
id_attribute='rack_id',
slug_expression=lambda cls: as_slug_expression(cls.barcode),
properties=dict(
label=column_property(
rack_tbl.c.label,
comparator_factory=CaseInsensitiveComparator
),
specs=relationship(RackSpecs,
innerjoin=True, uselist=False),
status=relationship(ItemStatus,
innerjoin=True, uselist=False),
location_rack=relationship(BarcodedLocationRack,
uselist=False,
back_populates='rack',
cascade='all,delete,delete-orphan'),
_location=relationship(BarcodedLocation, viewonly=True,
uselist=False,
secondary=rbl,
foreign_keys=(rbl.c.rack_id, rbl.c.barcoded_location_id),
),
),
polymorphic_on=rack_tbl.c.rack_type,
polymorphic_identity=RACK_TYPES.RACK,
)
return m
def create_mapper(tag_tbl, tag_domain_tbl, tag_predicate_tbl, tag_value_tbl,
tagging_tbl):
"Mapper factory."
m = mapper(Tag,
tag_tbl,
id_attribute='tag_id',
slug_expression=lambda cls: as_slug_expression(
func.concatenate(cls.domain, ':',
cls.predicate, '=',
cls.value)),
extension=TagMapperExtension(tag_domain_tbl,
tag_predicate_tbl, tag_value_tbl),
properties=
dict(tagged=relationship(Tagged,
secondary=tagging_tbl,
back_populates='tags'),
domain=column_property(
select([tag_domain_tbl.c.domain]) \
.where(tag_tbl.c.tag_domain_id ==
tag_domain_tbl.c.tag_domain_id)
),
predicate=column_property(
select([tag_predicate_tbl.c.predicate]) \
.where(tag_tbl.c.tag_predicate_id ==
tag_predicate_tbl.c.tag_predicate_id)
),
value=column_property(
select([tag_value_tbl.c.value]) \
.where(tag_tbl.c.tag_value_id ==
tag_value_tbl.c.tag_value_id)
),
)
)
return m
def create_mapper(rack_specs_tbl):
"Mapper factory."
rs = rack_specs_tbl
polymorphic_select = select([
rs,
(case([(rs.c.has_movable_subitems,
literal(RACK_SPECS_TYPES.TUBE_RACK_SPECS))],
else_=literal(RACK_SPECS_TYPES.PLATE_SPECS))).label(
'rackspecs_type')
],
).alias('rackspecs')
m = mapper(RackSpecs, polymorphic_select,
id_attribute='rack_specs_id',
slug_expression=lambda cls: as_slug_expression(cls.name),
properties=dict(
manufacturer=relationship(Organization),
shape=relationship(RackShape, uselist=False,
back_populates='specs'),
rack_specs_type=
column_property(polymorphic_select.c.rackspecs_type),
),
polymorphic_on=polymorphic_select.c.rackspecs_type,
polymorphic_identity=RACK_SPECS_TYPES.RACK_SPECS,
)
RackSpecs.has_tubes = synonym('has_movable_subitems')
return m
def create_mapper(tag_tbl, tag_domain_tbl, tag_predicate_tbl, tag_value_tbl,
tagging_tbl):
"Mapper factory."
m = mapper(Tag,
tag_tbl,
id_attribute='tag_id',
slug_expression=lambda cls: as_slug_expression(
func.concatenate(cls.domain, ':',
cls.predicate, '=',
cls.value)),
extension=TagMapperExtension(tag_domain_tbl,
tag_predicate_tbl, tag_value_tbl),
properties=
dict(tagged=relationship(Tagged,
secondary=tagging_tbl,
back_populates='tags'),
domain=column_property(
select([tag_domain_tbl.c.domain]) \
.where(tag_tbl.c.tag_domain_id ==
tag_domain_tbl.c.tag_domain_id)
),
predicate=column_property(
select([tag_predicate_tbl.c.predicate]) \
.where(tag_tbl.c.tag_predicate_id ==
tag_predicate_tbl.c.tag_predicate_id)
),
value=column_property(
select([tag_value_tbl.c.value]) \
.where(tag_tbl.c.tag_value_id ==
tag_value_tbl.c.tag_value_id)
),
)
)
return m
def test_mapper(self):
class MyDerivedEntity(MyEntity):
pass
@implementer(IEntity)
class MyEntityWithCustomId(object):
def __init__(self, id=None): # redefining id pylint: disable=W0622
self.__id = id
self.__slug = str(id)
@property
def id(self):
return str(self.__id)
@property
def slug(self):
return str(self.__id)
class MyPolymorphicEntity1(MyEntityWithCustomId):
pass
class MyPolymorphicEntity2(MyEntityWithCustomId):
pass
t1 = self._make_table(True)
with self.assert_raises(ValueError) as cm:
mpr = mapper(MyDerivedEntity, t1, id_attribute='my_id')
msg_str = 'Attempting to overwrite the mapped'
self.assert_true(str(cm.exception).startswith(msg_str))
t2 = self._make_table(False)
with self.assert_raises(ValueError) as cm:
mpr = mapper(MyEntityWithCustomId, t2, id_attribute='my_id')
msg_str = 'Attempting to overwrite the custom data'
self.assert_true(str(cm.exception).startswith(msg_str))
#
slug_expr = lambda cls: as_slug_expression(cast(cls.id, String))
mpr = mapper(MyDerivedEntity, t2,
id_attribute='my_id', slug_expression=slug_expr)
self.assert_true(MyDerivedEntity.__dict__['slug'].expr
is slug_expr)
self.assert_true(isinstance(MyDerivedEntity.slug, Function))
mpr.dispose()
# Test mapping polymorphic class with custom slug in the base class.
base_mpr = mapper(MyEntityWithCustomId, t2,
polymorphic_on='my_type',
polymorphic_identity='base')
poly_mpr1 = mapper(MyPolymorphicEntity1, inherits=base_mpr,
polymorphic_identity='derived')
self.assert_true(isinstance(MyPolymorphicEntity1.__dict__['slug'],
hybrid_descriptor))
# We should not override the slug expression if we are inheriting
# a hybrid descriptor from the base class.
self.assert_raises(ValueError,
mapper, MyPolymorphicEntity2, inherits=base_mpr,
polymorphic_identity='derived',
slug_expression=slug_expr)
base_mpr.dispose()
poly_mpr1.dispose()
def create_mapper(device_type_tbl):
"Mapper factory."
m = mapper(DeviceType, device_type_tbl,
id_attribute='device_type_id',
slug_expression=lambda cls: as_slug_expression(cls.name),
properties=dict(
devices=relationship(Device, back_populates='type'),
),
)
return m
def _get_entity_from_aggregate(cls, entity_identifier):
"""
Retrieves the entity for the given identifier from the aggregate.
"""
cls._initialize_aggregate()
if cls._CONVERT_TO_SLUG:
slug = as_slug_expression(entity_identifier)
else:
slug = entity_identifier
return cls._aggregate.get_by_slug(slug)
def create_mapper(species_tbl):
"Mapper factory."
m = mapper(
Species,
species_tbl,
id_attribute='species_id',
slug_expression=lambda cls: as_slug_expression(cls.common_name),
properties=dict(genes=relationship(Gene, back_populates='species'), ),
)
return m
def create_mapper(barcoded_location_tbl):
"Mapper factory."
bl = barcoded_location_tbl.alias('bl')
location_select = select([bl.c.type.label('name')]
).distinct().alias('loctypes')
m = mapper(BarcodedLocationType, location_select,
slug_expression=lambda cls: as_slug_expression(cls.name),
primary_key=[location_select.c.name],
)
return m
def create_mapper(rack_shape_tbl):
"Mapper factory."
m = mapper(RackShape, rack_shape_tbl,
id_attribute='rack_shape_name',
slug_expression=lambda cls: as_slug_expression(cls.rack_shape_name),
properties=dict(
specs=relationship(RackSpecs, back_populates='shape'),
),
)
RackShape.name = synonym('rack_shape_name')
return m
def test_mapper(self):
class MyDerivedEntity(MyEntity):
pass
class MyEntityWithCustomId(object):
implements(IEntity)
def __init__(self, id=None): # redefining id pylint: disable=W0622
self.__id = id
self.__slug = str(id)
@property
def id(self):
return str(self.__id)
@property
def slug(self):
return str(self.__id)
class MyPolymorphicEntity(MyEntityWithCustomId):
pass
t1 = self._make_table(True)
with self.assert_raises(ValueError) as cm:
mpr = mapper(MyDerivedEntity, t1, id_attribute='my_id')
msg_str = 'Attempting to overwrite the mapped'
self.assert_true(cm.exception.message.startswith(msg_str))
t2 = self._make_table(False)
with self.assert_raises(ValueError) as cm:
mpr = mapper(MyEntityWithCustomId, t2, id_attribute='my_id')
msg_str = 'Attempting to overwrite the custom data'
self.assert_true(cm.exception.message.startswith(msg_str))
#
slug_expr = lambda cls: as_slug_expression(cast(cls.id, String))
mpr = mapper(MyDerivedEntity,
t2,
id_attribute='my_id',
slug_expression=slug_expr)
self.assert_true(MyDerivedEntity.__dict__['slug'].expr is slug_expr)
self.assert_true(isinstance(MyDerivedEntity.slug, Function))
mpr.dispose()
# Test mapping polymorphic class with custom slug in the base class.
base_mpr = mapper(MyEntityWithCustomId,
t2,
polymorphic_on='my_type',
polymorphic_identity='base')
mpr = mapper(MyPolymorphicEntity,
inherits=base_mpr,
polymorphic_identity='derived')
self.assert_true(
isinstance(MyPolymorphicEntity.__dict__['slug'],
hybrid_descriptor))
base_mpr.dispose()
mpr.dispose()
def create_mapper(species_tbl):
"Mapper factory."
m = mapper(Species, species_tbl,
id_attribute='species_id',
slug_expression=lambda cls: as_slug_expression(cls.common_name),
properties=dict(
genes=relationship(Gene,
back_populates='species'),
),
)
return m
def create_mapper(rack_shape_tbl):
"Mapper factory."
m = mapper(
RackShape,
rack_shape_tbl,
id_attribute='rack_shape_name',
slug_expression=lambda cls: as_slug_expression(cls.rack_shape_name),
properties=dict(specs=relationship(RackSpecs,
back_populates='shape'), ),
)
RackShape.name = synonym('rack_shape_name')
return m
def create_mapper(device_tbl):
"Mapper factory."
m = mapper(Device, device_tbl,
id_attribute='device_id',
slug_expression=lambda cls: as_slug_expression(cls.name),
properties=dict(
type=relationship(DeviceType),
locations=relationship(BarcodedLocation, back_populates='device'),
manufacturer=relationship(Organization, uselist=False),
),
)
return m
def create_mapper(barcoded_location_tbl):
"Mapper factory."
bl = barcoded_location_tbl.alias('bl')
location_select = select([bl.c.type.label('name')
]).distinct().alias('loctypes')
m = mapper(
BarcodedLocationType,
location_select,
slug_expression=lambda cls: as_slug_expression(cls.name),
primary_key=[location_select.c.name],
)
return m
def create_mapper(organization_tbl):
"Mapper factory."
m = mapper(
Organization,
organization_tbl,
id_attribute='organization_id',
slug_expression=lambda cls: as_slug_expression(cls.name),
properties=dict(name=column_property(
organization_tbl.c.name,
comparator_factory=CaseInsensitiveComparator), ),
)
return m
def create_mapper(organization_tbl):
"Mapper factory."
m = mapper(Organization, organization_tbl,
id_attribute='organization_id',
slug_expression=lambda cls: as_slug_expression(cls.name),
properties=dict(
name=column_property(
organization_tbl.c.name,
comparator_factory=CaseInsensitiveComparator
),
),
)
return m
def create_mapper(refseq_gene_tbl, molecule_design_gene_tbl,
molecule_design_set_gene_tbl,
molecule_design_tbl,
molecule_design_pool_tbl):
"Mapper factory."
rsg = refseq_gene_tbl
mdg = molecule_design_gene_tbl
mdsg = molecule_design_set_gene_tbl
md = molecule_design_tbl
mdp = molecule_design_pool_tbl
m = mapper(Gene, rsg,
id_attribute='gene_id',
slug_expression=lambda cls: as_slug_expression(cls.accession),
properties=dict(
accession=column_property(
rsg.c.accession,
comparator_factory=CaseInsensitiveComparator
),
locus_name=column_property(
rsg.c.locus_name,
comparator_factory=CaseInsensitiveComparator
),
molecule_designs=
relationship(
MoleculeDesign, viewonly=True,
secondary=mdg,
primaryjoin=(mdg.c.gene_id == rsg.c.gene_id),
secondaryjoin=(md.c.molecule_design_id ==
mdg.c.molecule_design_id),
foreign_keys=(mdg.c.molecule_design_id,
mdg.c.gene_id),
back_populates='genes',
),
molecule_design_pools=
relationship(
MoleculeDesignPool, viewonly=True,
secondary=mdsg,
primaryjoin=(mdsg.c.gene_id == rsg.c.gene_id),
secondaryjoin=(mdsg.c.molecule_design_set_id ==
mdp.c.molecule_design_set_id),
foreign_keys=(mdsg.c.molecule_design_set_id,
mdsg.c.gene_id),
),
species=relationship(Species, uselist=False,
back_populates='genes',
# lazy='joined'
),
),
)
Gene.name = synonym('locus_name')
return m
def create_mapper(planned_liquid_transfer_tbl):
"Mapper factory."
m = mapper(
PlannedLiquidTransfer,
planned_liquid_transfer_tbl,
id_attribute='planned_liquid_transfer_id',
properties=dict(
_transfer_type=planned_liquid_transfer_tbl.c.transfer_type,
_volume=planned_liquid_transfer_tbl.c.volume,
_hash_value=planned_liquid_transfer_tbl.c.hash_value),
slug_expression=lambda cls: as_slug_expression(cls._hash_value), # pylint: disable=W0212
polymorphic_on=planned_liquid_transfer_tbl.c.transfer_type,
polymorphic_identity=TRANSFER_TYPES.LIQUID_TRANSFER)
return m
def create_mapper(planned_liquid_transfer_tbl):
"Mapper factory."
m = mapper(PlannedLiquidTransfer, planned_liquid_transfer_tbl,
id_attribute='planned_liquid_transfer_id',
properties=dict(
_transfer_type=planned_liquid_transfer_tbl.c.transfer_type,
_volume=planned_liquid_transfer_tbl.c.volume,
_hash_value=planned_liquid_transfer_tbl.c.hash_value
),
slug_expression=lambda cls: as_slug_expression(cls._hash_value), # pylint: disable=W0212
polymorphic_on=planned_liquid_transfer_tbl.c.transfer_type,
polymorphic_identity=TRANSFER_TYPES.LIQUID_TRANSFER
)
return m
def create_mapper(device_tbl):
"Mapper factory."
m = mapper(
Device,
device_tbl,
id_attribute='device_id',
slug_expression=lambda cls: as_slug_expression(cls.name),
properties=dict(
type=relationship(DeviceType),
locations=relationship(BarcodedLocation, back_populates='device'),
manufacturer=relationship(Organization, uselist=False),
),
)
return m
def create_mapper(project_tbl):
"Mapper factory."
m = mapper(Project, project_tbl,
id_attribute='project_id',
slug_expression=lambda cls: as_slug_expression(cls.label),
properties=dict(
customer=relationship(Organization, uselist=False),
subprojects=relationship(Subproject,
back_populates='project',
cascade='all, delete-orphan'
),
leader=relationship(User, uselist=False),
),
)
return m
def create_mapper(pipetting_specs_tbl):
"Mapper factory."
tbl = pipetting_specs_tbl
m = mapper(
PipettingSpecs,
pipetting_specs_tbl,
id_attribute='pipetting_specs_id',
slug_expression=lambda cls: as_slug_expression(cls._name), # pylint: disable=W0212
properties=dict(_name=tbl.c.name,
_min_transfer_volume=tbl.c.min_transfer_volume,
_max_transfer_volume=tbl.c.max_transfer_volume,
_max_dilution_factor=tbl.c.max_dilution_factor,
_has_dynamic_dead_volume=tbl.c.has_dynamic_dead_volume,
_is_sector_bound=tbl.c.is_sector_bound))
return m
def create_mapper(pipetting_specs_tbl):
"Mapper factory."
tbl = pipetting_specs_tbl
m = mapper(PipettingSpecs, pipetting_specs_tbl,
id_attribute='pipetting_specs_id',
slug_expression=lambda cls: as_slug_expression(cls._name), # pylint: disable=W0212
properties=dict(
_name=tbl.c.name,
_min_transfer_volume=tbl.c.min_transfer_volume,
_max_transfer_volume=tbl.c.max_transfer_volume,
_max_dilution_factor=tbl.c.max_dilution_factor,
_has_dynamic_dead_volume=tbl.c.has_dynamic_dead_volume,
_is_sector_bound=tbl.c.is_sector_bound)
)
return m
def create_mapper(project_tbl):
"Mapper factory."
m = mapper(
Project,
project_tbl,
id_attribute='project_id',
slug_expression=lambda cls: as_slug_expression(cls.label),
properties=dict(
customer=relationship(Organization, uselist=False),
subprojects=relationship(Subproject,
back_populates='project',
cascade='all, delete-orphan'),
leader=relationship(User, uselist=False),
),
)
return m
def create_mapper(rack_barcoded_location_tbl):
"Mapper factory."
# FIXME: The table should be renamed to barcoded_location_rack.
m = mapper(BarcodedLocationRack, rack_barcoded_location_tbl,
id_attribute='barcoded_location_id',
slug_expression=lambda cls: as_slug_expression(cls.name),
properties=dict(
rack=relationship(Rack,
uselist=False,
# lazy='joined'
),
location=relationship(BarcodedLocation,
uselist=False)
),
)
return m
def create_mapper(reservoir_specs_tbl):
"Mapper factory."
tbl = reservoir_specs_tbl
m = mapper(ReservoirSpecs, reservoir_specs_tbl,
id_attribute='reservoir_specs_id',
slug_expression=lambda cls: as_slug_expression(cls._name), # pylint: disable=W0212
properties=dict(
_rack_shape=relationship(RackShape, uselist=False,
# lazy='joined'
),
_name=tbl.c.name,
_description=tbl.c.description,
_max_volume=tbl.c.max_volume,
_min_dead_volume=tbl.c.min_dead_volume,
_max_dead_volume=tbl.c.max_dead_volume)
)
return m
def create_mapper(dbuser_tbl):
"Mapper factory."
m = mapper(
User,
dbuser_tbl,
id_attribute='db_user_id',
slug_expression=lambda cls: as_slug_expression(cls.directory_user_id),
properties=dict(
username=column_property(
dbuser_tbl.c.username,
comparator_factory=CaseInsensitiveComparator),
user_preferenceses=relationship(UserPreferences,
back_populates='user',
cascade='all, delete-orphan'),
),
)
return m
def create_mapper(iso_tbl, job_tbl, iso_job_member_tbl, iso_pool_set_tbl):
"Mapper factory."
j = job_tbl
ijm = iso_job_member_tbl
m = mapper(
Iso,
iso_tbl,
id_attribute='iso_id',
slug_expression=lambda cls: as_slug_expression(cls.label),
properties=dict(
iso_request=relationship(IsoRequest,
uselist=False,
back_populates='isos'),
molecule_design_pool_set=relationship(MoleculeDesignPoolSet,
uselist=False,
secondary=iso_pool_set_tbl),
rack_layout=relationship(RackLayout,
uselist=False,
cascade='all,delete,delete-orphan',
single_parent=True),
iso_stock_racks=relationship(IsoStockRack,
back_populates='iso',
cascade='all,delete,delete-orphan'),
iso_sector_stock_racks=relationship(
IsoSectorStockRack,
back_populates='iso',
cascade='all,delete,delete-orphan'),
iso_aliquot_plates=relationship(IsoAliquotPlate,
back_populates='iso',
cascade='all,delete-orphan'),
iso_preparation_plates=relationship(IsoPreparationPlate,
back_populates='iso'),
iso_job=relationship(
IsoJob,
uselist=False,
primaryjoin=(iso_tbl.c.iso_id == ijm.c.iso_id),
secondaryjoin=(ijm.c.job_id == j.c.job_id),
secondary=ijm,
back_populates='isos',
cascade='all'),
),
polymorphic_on=iso_tbl.c.iso_type,
polymorphic_identity=ISO_TYPES.BASE,
)
return m
def create_mapper(dbuser_tbl):
"Mapper factory."
m = mapper(User, dbuser_tbl,
id_attribute='db_user_id',
slug_expression=
lambda cls: as_slug_expression(cls.directory_user_id),
properties=dict(
username=column_property(
dbuser_tbl.c.username,
comparator_factory=CaseInsensitiveComparator
),
user_preferenceses=relationship(UserPreferences,
back_populates='user',
cascade='all, delete-orphan'
),
),
)
return m
def create_mapper(container_specs_tbl):
"Mapper factory."
cs = container_specs_tbl.alias('cs')
polymorphic_select = select([
cs,
(case([(cs.c.has_barcode, literal(CONTAINER_SPECS_TYPES.TUBE))],
else_=literal(CONTAINER_SPECS_TYPES.WELL))).label(
'containerspecs_type')
],
).alias('containerspecs')
m = mapper(ContainerSpecs, polymorphic_select,
id_attribute='container_specs_id',
slug_expression=lambda cls: as_slug_expression(cls.name),
properties=dict(manufacturer=relationship(Organization),
),
polymorphic_on=polymorphic_select.c.containerspecs_type,
polymorphic_identity=CONTAINER_SPECS_TYPES.CONTAINER,
)
return m
def create_mapper(molecule_type_tbl, molecule_type_modification_vw,
chemical_structure_tbl):
"Mapper factory."
mt = molecule_type_tbl
mtmv = molecule_type_modification_vw
cs = chemical_structure_tbl
m = mapper(
MoleculeType,
mt,
id_attribute='molecule_type_id',
slug_expression=lambda cls: as_slug_expression(cls.name),
properties=dict(modifications=relationship(
ChemicalStructure,
secondary=mtmv,
primaryjoin=mtmv.c.molecule_type_id == mt.c.molecule_type_id,
secondaryjoin=cs.c.chemical_structure_id ==
mtmv.c.chemical_structure_id,
viewonly=True), ),
)
return m
def create_mapper(reservoir_specs_tbl):
"Mapper factory."
tbl = reservoir_specs_tbl
m = mapper(
ReservoirSpecs,
reservoir_specs_tbl,
id_attribute='reservoir_specs_id',
slug_expression=lambda cls: as_slug_expression(cls._name), # pylint: disable=W0212
properties=dict(
_rack_shape=relationship(
RackShape,
uselist=False,
# lazy='joined'
),
_name=tbl.c.name,
_description=tbl.c.description,
_max_volume=tbl.c.max_volume,
_min_dead_volume=tbl.c.min_dead_volume,
_max_dead_volume=tbl.c.max_dead_volume))
return m
def create_mapper(molecule_type_tbl, molecule_type_modification_vw, chemical_structure_tbl):
"Mapper factory."
mt = molecule_type_tbl
mtmv = molecule_type_modification_vw
cs = chemical_structure_tbl
m = mapper(
MoleculeType,
mt,
id_attribute="molecule_type_id",
slug_expression=lambda cls: as_slug_expression(cls.name),
properties=dict(
modifications=relationship(
ChemicalStructure,
secondary=mtmv,
primaryjoin=mtmv.c.molecule_type_id == mt.c.molecule_type_id,
secondaryjoin=cs.c.chemical_structure_id == mtmv.c.chemical_structure_id,
viewonly=True,
)
),
)
return m
def create_mapper(iso_tbl, job_tbl, iso_job_member_tbl, iso_pool_set_tbl):
"Mapper factory."
j = job_tbl
ijm = iso_job_member_tbl
m = mapper(Iso, iso_tbl,
id_attribute='iso_id',
slug_expression=lambda cls: as_slug_expression(cls.label),
properties=
dict(iso_request=relationship(IsoRequest,
uselist=False,
back_populates='isos'),
molecule_design_pool_set=
relationship(MoleculeDesignPoolSet,
uselist=False,
secondary=iso_pool_set_tbl),
rack_layout=relationship(RackLayout, uselist=False,
cascade='all,delete,delete-orphan',
single_parent=True),
iso_stock_racks=relationship(IsoStockRack,
back_populates='iso',
cascade='all,delete,delete-orphan'),
iso_sector_stock_racks=relationship(IsoSectorStockRack,
back_populates='iso',
cascade='all,delete,delete-orphan'),
iso_aliquot_plates=relationship(IsoAliquotPlate,
back_populates='iso',
cascade='all,delete-orphan'),
iso_preparation_plates=relationship(IsoPreparationPlate,
back_populates='iso'),
iso_job=relationship(IsoJob, uselist=False,
primaryjoin=(iso_tbl.c.iso_id == ijm.c.iso_id),
secondaryjoin=(ijm.c.job_id == j.c.job_id),
secondary=ijm,
back_populates='isos',
cascade='all'),
),
polymorphic_on=iso_tbl.c.iso_type,
polymorphic_identity=ISO_TYPES.BASE,
)
return m
def create_mapper(stock_info_vw, molecule_design_set_tbl,
molecule_design_set_gene_tbl, refseq_gene_tbl):
"Mapper factory."
siv = stock_info_vw
mds = molecule_design_set_tbl
mdsg = molecule_design_set_gene_tbl
rsg = refseq_gene_tbl
m = mapper(StockInfo, stock_info_vw,
id_attribute='stock_info_id',
slug_expression=lambda cls: as_slug_expression(cls.stock_info_id),
primary_key=[stock_info_vw.c.molecule_design_set_id,
stock_info_vw.c.concentration],
properties=dict(
molecule_design_pool=
relationship(MoleculeDesignPool,
primaryjoin=(mds.c.molecule_design_set_id ==
siv.c.molecule_design_set_id),
foreign_keys=[siv.c.molecule_design_set_id],
uselist=False,
# lazy='joined'
),
molecule_type=relationship(MoleculeType,
uselist=False,
# lazy='joined'
),
genes=relationship(Gene, viewonly=True,
primaryjoin=(mdsg.c.molecule_design_set_id ==
siv.c.molecule_design_set_id),
secondaryjoin=(rsg.c.gene_id == mdsg.c.gene_id),
foreign_keys=(mdsg.c.molecule_design_set_id,
mdsg.c.gene_id),
secondary=molecule_design_set_gene_tbl,
# lazy='joined'
),
),
)
return m
def create_mapper(molecule_design_library_tbl,
stock_sample_creation_iso_request_tbl,
molecule_design_library_creation_iso_request_tbl):
"Mapper factory."
mdl = molecule_design_library_tbl
sscir = stock_sample_creation_iso_request_tbl
mdlcir = molecule_design_library_creation_iso_request_tbl
m = mapper(MoleculeDesignLibrary, molecule_design_library_tbl,
id_attribute='molecule_design_library_id',
slug_expression=lambda cls: as_slug_expression(cls.label),
properties=dict(
molecule_design_pool_set=
relationship(MoleculeDesignPoolSet,
uselist=False,
cascade='all,delete-orphan',
single_parent=True),
rack_layout=relationship(RackLayout, uselist=False,
cascade='all,delete,delete-orphan',
single_parent=True),
creation_iso_request=relationship(
StockSampleCreationIsoRequest,
uselist=False,
back_populates='molecule_design_library',
primaryjoin=(mdl.c.molecule_design_library_id == \
mdlcir.c.molecule_design_library_id),
secondaryjoin=(mdlcir.c.iso_request_id == \
sscir.c.iso_request_id),
secondary=mdlcir,
cascade='all,delete-orphan',
single_parent=True),
library_plates=relationship(LibraryPlate,
back_populates='molecule_design_library',
cascade='all,delete-orphan')
)
)
return m
def create_mapper(molecule_design_library_tbl,
stock_sample_creation_iso_request_tbl,
molecule_design_library_creation_iso_request_tbl):
"Mapper factory."
mdl = molecule_design_library_tbl
sscir = stock_sample_creation_iso_request_tbl
mdlcir = molecule_design_library_creation_iso_request_tbl
m = mapper(MoleculeDesignLibrary, molecule_design_library_tbl,
id_attribute='molecule_design_library_id',
slug_expression=lambda cls: as_slug_expression(cls.label),
properties=dict(
molecule_design_pool_set=
relationship(MoleculeDesignPoolSet,
uselist=False,
cascade='all,delete-orphan',
single_parent=True),
rack_layout=relationship(RackLayout, uselist=False,
cascade='all,delete,delete-orphan',
single_parent=True),
creation_iso_request=relationship(
StockSampleCreationIsoRequest,
uselist=False,
back_populates='molecule_design_library',
primaryjoin=(mdl.c.molecule_design_library_id == \
mdlcir.c.molecule_design_library_id),
secondaryjoin=(mdlcir.c.iso_request_id == \
sscir.c.iso_request_id),
secondary=mdlcir,
cascade='all,delete-orphan',
single_parent=True),
library_plates=relationship(LibraryPlate,
back_populates='molecule_design_library',
cascade='all,delete-orphan')
)
)
return m
def create_mapper(item_status_tbl):
"Mapper factory."
m = mapper(ItemStatus, item_status_tbl,
id_attribute='item_status_id',
slug_expression=lambda cls: as_slug_expression(cls.name))
return m
def customer_slug(cls):
return as_slug_expression(cls.last_name + literal('-') + cls.first_name)
def project_slug(cls):
return as_slug_expression(cls.name)
def species_slug(cls):
return as_slug_expression(cls.genus_name + literal('-') +
cls.species_name + literal('-') +
cls.cultivar + literal('-') +
cls.author)
def site_slug(cls):
return as_slug_expression(cls.name)
